tag:blogger.com,1999:blog-76060984249485024602024-02-18T23:33:35.727-05:00Ethio Helix ኢትዮ:ሒሊክስA place to gather information on: Population genetics, Ethiopia, East Africa, Linguistics, News, History etc.....Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.comBlogger87125tag:blogger.com,1999:blog-7606098424948502460.post-18310912633649561292015-07-30T13:29:00.000-04:002015-07-30T13:29:21.314-04:00Ugandan mtDNA<span style="font-size: large;">Unfortunately I can not find the detailed breakdown of the mtDNA frequencies for the populations sampled in the supplemental materials for this paper, and hence can not build my sortable frequency charts. </span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6EGh0guJmWYdXT94ySXGdQuL6uEDjmpcLqjpDOezAFAjhjL0Juw38TUCvagIwhMqsAWgk1xHnqKVVwLePl28uwnlDP3OYWSU7e24g35yKp7BNVaL1DYAi79XvDGqCMNvx3OgfsUoH45Z_/s1600/uganda_mtdna.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="255" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6EGh0guJmWYdXT94ySXGdQuL6uEDjmpcLqjpDOezAFAjhjL0Juw38TUCvagIwhMqsAWgk1xHnqKVVwLePl28uwnlDP3OYWSU7e24g35yKp7BNVaL1DYAi79XvDGqCMNvx3OgfsUoH45Z_/s400/uganda_mtdna.png" width="400" /></a></div>
<span style="font-size: large;"><span style="color: blue;">Mosaic maternal ancestry in the Great Lakes region of East Africa <br /><br />Abstract<br /><br />The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.</span></span><br />
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<a href="http://www.ncbi.nlm.nih.gov/pubmed/26188410">Link</a>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com15tag:blogger.com,1999:blog-7606098424948502460.post-29194022739820268002015-06-24T21:31:00.000-04:002016-11-17T11:54:11.527-05:00Improved resolution of E-M215 (aka E3b / E1b1b)<span style="font-size: large;">A new paper has appeared with a a focus on Haplogroup E, and mostly focused on E-M215 and E-M35, with a moderate level of improvement in resolution from what <a href="http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html" target="_blank">we used to know</a>.</span><br />
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<span style="font-size: large;">Basically, at first glance, the major novelty with respect to E-M215 is that all E-Z830 (x M123) lineages are united under a new mutation dubbed V1515, and that the former solo lineages of E-M35, i.e. E-V92 and E-V6, now have a home and are included within this unification. In addition, the above named unifying mutation, V1515, apparently has a bifurcated structure itself, with one younger branch having the sole representation in the Southern parts of Ethiopia and further South, and the more diverse (hence ancient) branch being represented in the Northern parts of Ethiopia and further North. </span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">New basal haplogroup E mutations were also apparently found.</span><br />
<span style="font-size: large;"><br /><a href="http://gbe.oxfordjournals.org/content/early/2015/06/23/gbe.evv118.full.pdf+html" target="_blank">The paper is Open access</a> , and I will analyze it further in the coming days , but I just wanted to plot the Eastern African E-M215 variant frequencies for now.</span><br />
<span style="font-size: large;"> </span>
<script src="https://www.google.com/jsapi" type="text/javascript"></script>
<script src="https://ehelix.github.io/sorting_script/sort_stacked.js" type="text/javascript"></script>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbmSsOejDQYpQq6wxAkapPkyMWbmS0aVkJ5_GbLyLEFZ3s4dlJzv4iNZqEYJ9X053Sp7gaJZK34J6yugfhZW1LquOsPD_bGFnSSCvlQd529x1jCeTiuZVb6yPQdKvVB33WWSdIxI3wPwcr/s1600/phylogenym215.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="312" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbmSsOejDQYpQq6wxAkapPkyMWbmS0aVkJ5_GbLyLEFZ3s4dlJzv4iNZqEYJ9X053Sp7gaJZK34J6yugfhZW1LquOsPD_bGFnSSCvlQd529x1jCeTiuZVb6yPQdKvVB33WWSdIxI3wPwcr/s320/phylogenym215.png" width="320"></a></div>
<div id="EAM215" style="height: 1000px; width: 900px;">
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<b><span style="color: red;"><span style="font-size: large;">UPDATE (6/26/15) - Added NAfrica E-M215 frequencies
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<div id="EAM215_NA" style="height: 1000px; width: 900px;">
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<b><span style="color: red;"><span style="font-size: large;">UPDATE (6/26/15) - Added new mutation rate
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<span style="font-size: large;">The new fossil calibrated mutation rate has been added to the <a href="https://ehelix.pythonanywhere.com/init/default/index" target="_blank">TMRCA Calulator</a>, unfortunately 95% CI values have not been given (or at least I could not find where they have been given), in any event, central TMRCA estimates for this new mutation rate are a bit slower than mutation rates derived from the other ancient DNA calibrated sources, specifically, ~ 4% and 12% slower than Karmin (2015) and Fu (2014) respectively.</span><br />
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<div dir="ltr" id="docs-internal-guid-9cba78de-36c5-c73c-8811-ac7921d635f2" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b><span style="font-family: inherit;"><span style="color: red;"><span style="font-size: large;"><span style="background-color: transparent; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">UPDATE (6/27/15) - Comparison with YFull TMRCAs</span></span></span></span></b></div>
<span style="font-family: inherit;"><span style="font-size: large;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">I have created a table for the TMRCA of the major nodes in E-M215, in order to compare with <a href="http://www.yfull.com/tree/E1b1b/" target="_blank">YFull’s</a> estimates so that we can ‘fill in the gaps’ for the Nodes that have not been given estimates in Trombetta (2015). YFull uses a mutation rate that is almost exactly identical to Fu (2014)’s Ust-Ishim calibrated rates, so naturally some of the TMRCA’s would be closer to today than the Trombetta estimates, as pointed out above.</span></span></span><br />
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<span style="font-family: inherit;"><span style="font-size: large;"><span style="background-color: transparent; color: black; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;"><br id="docs-internal-guid-9cba78de-36c8-010b-82d7-8134012abb68" /></span></span></span>
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<table style="border-collapse: collapse; border: none;"><colgroup><col width="284"></col><col width="83"></col><col width="74"></col></colgroup><tbody>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">TMRCA (KYA)</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">Trombetta </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">YFull</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-M215</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">39</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">35</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-M35</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">25</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">24</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-V68</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">20</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">20</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-M78</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">15</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">13</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-Z827</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">?</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">24</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-V257</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">?</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">14</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-Z830</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">20</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">19</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-M34</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">?</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">15</span></div>
</td></tr>
<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-left: 144pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: bold; text-decoration: none; vertical-align: baseline;">E-V1515</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">12</span></div>
</td><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt; text-align: center;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: normal; text-decoration: none; vertical-align: baseline;">?</span></div>
</td></tr>
</tbody></table>
</div>
<br />Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com22tag:blogger.com,1999:blog-7606098424948502460.post-36341814927449599082015-06-16T01:04:00.000-04:002016-11-17T11:55:33.514-05:00Sudan MTDNA<span style="font-size: large;">Find below relative frequencies for Sudanese MTDNA from a thesis entitled "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan", the entire thesis can be downloaded from <a href="https://www.dropbox.com/s/1nmaqtc59wabowt/Genetic%20Patterns%20of%20Y-chromosome%20and%20Mitochondrial.pdf?dl=0" target="_blank">here</a>. The thesis also includes YDNA data, but those same results have been already covered in<a href="http://ethiohelix.blogspot.com/2013/02/sudan-ydna.html" target="_blank"> this blog post</a>. Additionally, some interesting ancient YDNA data is also included in the thesis.</span><br />
<br />
<span style="font-size: large;">Note, I wrote a small script that can enable sorting of the relative frequencies by clicking the haplogroups, you can find the script <complete id="goog_865268774">@ </complete><a href="https://jsfiddle.net/ehelix/tbksjw4y/1/" target="_blank">JSFiddle</a>, if you find the script useful and would like to use it for other relative frequency charts, please cite the JSFiddle link from above.</span><br />
<br />
<br />
<br />
<script src="https://www.google.com/jsapi" type="text/javascript"></script>
<script src="https://ehelix.github.io/sorting_script/sort_stacked.js" type="text/javascript"></script>
<br />
<div id="chart_div" style="height: 1000px; width: 900px;">
</div>
<script>
//Google charts sorting script, best works for stacked bars driven from google sheets, see sample sheet linked in query argument for input format.
// Created : Ethiohelix , http://ethiohelix.blogspot.com/
google.load('visualization', '1', {packages: ['corechart', 'bar']});
google.setOnLoadCallback( function () {
var Link = 'https://docs.google.com/spreadsheets/d/1_zdOzBGMSxc4UDWEM6yRdKWSoRLbm3yLT0kKARz8gG4/edit?usp=sharing&range=Sheet2!A1:BE16';
var my_div = "chart_div";
//set google visualization bar chart options here
//**********************************************************
var options = {
title: 'Sudan mtDNA - Mohammed (2009) Thesis',
chartArea: {
width: '55%',
height: '70%'
},
isStacked: true,
};
//***********************************************************
//pull data from spread sheet (Columns = Labels, Rows = pops)
// add sheet and range of data at the end like: &range=Sheet1!A1:H8
var query = new google.visualization.Query(Link);
query.send(handleQueryResponse);
function handleQueryResponse(response) {
var data = response.getDataTable();
process_data(data,my_div,options);
}
});
</script>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com5tag:blogger.com,1999:blog-7606098424948502460.post-53587577705856388062015-06-06T17:52:00.000-04:002015-06-07T15:40:23.532-04:00More Ethiopian Uniparental Data (More resolution.. less clarity)<div class="separator" style="clear: both; text-align: center;">
<a href="https://www.blogger.com/blogger.g?blogID=7606098424948502460" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"></a><a href="https://www.blogger.com/blogger.g?blogID=7606098424948502460" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"></a></div>
<span style="font-size: large;">A new paper attempting to decipher the out of Africa exit route by focusing on Ethiopian and Egyptian autosomal genetics was <a href="http://www.cell.com/ajhg/abstract/S0002-9297%2815%2900156-1" target="_blank">published </a>a couple of weeks ago. Putting aside the 'hocus pocus' autosomal analysis for a moment, I was quite intrigued by the more concrete uniparental relative frequency images published in the supplemental material, not a lot of clarity is attached with these images however as the actual numbers are not given.</span><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKt6TBwagtIi4PV7UhQWO8SIHdWkY2Xdpk8NSbCH2nNz74a7UzCxfsWFrCJNq7c4kPxGd8RPnRs4dSq6s5fNlz31Rnm4mObGZLG-2rzQSjlKiwNG93TY3o0Vk3b9pJ8dNDTwLNyX3Zj1wF/s1600/ETH_YDNA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="432" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKt6TBwagtIi4PV7UhQWO8SIHdWkY2Xdpk8NSbCH2nNz74a7UzCxfsWFrCJNq7c4kPxGd8RPnRs4dSq6s5fNlz31Rnm4mObGZLG-2rzQSjlKiwNG93TY3o0Vk3b9pJ8dNDTwLNyX3Zj1wF/s640/ETH_YDNA.png" width="640" /></a></div>
<br />
<span style="font-size: large;">Note that the phylogeny they reference for the results here, is from <a href="http://www.phylotree.org/Y/tree/index.htm" target="_blank">Phylotree Y.</a></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Below I have attempted to interpret some of the colors from the image into Numerical approximations, note these are only approximations and not a substitute for the real data, of which I am not privy to.</span><br />
<br />
<br />
<table border="2" bordercolor="#0033FF" cellpadding="3" cellspacing="3" style="background-color: white; width: 100%px;">
<tbody>
<tr>
<th></th>
<th>Amhara</th>
<th>Eth Somali</th>
<th>Gumuz</th>
<th>Oromo</th>
<th>Wolayta</th>
</tr>
<tr>
<td>A-M13</td>
<td>27%</td>
<td>0%</td>
<td>55%</td>
<td>19%</td>
<td>48%</td>
</tr>
<tr>
<td>B-M150</td>
<td>0%</td>
<td>0%</td>
<td>4%</td>
<td>0%</td>
<td>0%</td>
</tr>
<tr>
<td>B-M8495</td>
<td>0%</td>
<td>0%</td>
<td>35%</td>
<td>0%</td>
<td>0%</td>
</tr>
<tr>
<td>E-M96</td>
<td>3%</td>
<td>4%</td>
<td>0%</td>
<td>6%</td>
<td>12%</td>
</tr>
<tr>
<td>E-M215</td>
<td>3%</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
</tr>
<tr>
<td>E-V22</td>
<td>9%</td>
<td>0%</td>
<td>0%</td>
<td>5%</td>
<td>3%</td>
</tr>
<tr>
<td>E-Z1902</td>
<td>8%</td>
<td>80%</td>
<td>4%</td>
<td>20%</td>
<td>0%</td>
</tr>
<tr>
<td>E-Z830</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
<td>3%</td>
</tr>
<tr>
<td>E-M34</td>
<td>3%</td>
<td>0%</td>
<td>0%</td>
<td>5%</td>
<td>13%</td>
</tr>
<tr>
<td>EM4145</td>
<td>17%</td>
<td>0%</td>
<td>0%</td>
<td>25%</td>
<td>20%</td>
</tr>
<tr>
<td>J</td>
<td>25%</td>
<td>11%</td>
<td>0%</td>
<td>19%</td>
<td>0%</td>
</tr>
<tr>
<td>T</td>
<td>3%</td>
<td>4%</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
</tr>
</tbody></table>
<br />
<span style="font-size: large;"><u>A-M13</u> :</span><br />
<br />
<span style="font-size: large;">The prevalence of this haplogroup in Ethiopia has always been known to us, however the extremely high frequency in the Wolayta is quite a surprise, this could be due to the relatively small sample size however, as the much higher sample size of the Wolayta found in the <a href="http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html" target="_blank">Plaster thesis,</a> only showed 13% of A-M13.</span><br />
<br />
<span style="font-size: large;"><u>B-M150 and B-M8495 :</u></span><br />
<span style="font-size: large;"><u><br /></u></span>
<span style="font-size: large;">Only found in the Gumuz, we have known for a while that B is not prevalent at all in the wider Ethiopian population, rather it is a continuation of the much larger B frequencies found in Niloitic Sudan. Still, it is good to see a finer resolution of B, and that the majority of B clades in Ethiopia belong to the small B-M8495 branch.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>E-M96:</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">This could potentially be a wide variety of things, but my money would be on E-M329, sister clade to E-M2 and <u></u>child clade of E-V38, which in turn is a sister clade to E-M215, the most prevalent YDNA lineage in Ethiopia.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>E-M215</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">As this is showing only in Northern Ethiopia, I would think it maybe<a href="http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html" target="_blank"> E-V92</a>, it still could however be a basal "E3b" lineage.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>E-V22</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">A variant of E-M78, this lineage has always been found in low amounts in Ethiopia, with moderate amounts in <a href="http://ethiohelix.blogspot.com/2013/02/sudan-ydna.html" target="_blank">Sudan </a>and Egypt.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>E-Z1902</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">This is a lineage that is found downstream of E-M78, but unites E-V12 with E-V65, which means the results would include E-V32 , a sublineage of E-V12 and the most frequent YDNA lineage in Somalis, I would wager that all of the E-Z1902 is actually E-V32, since E-V65 has never been found in Ethiopia thus far. There is a chance that some E-V12* could be in the mix as well.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>E-Z830</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">This lineage has been <a href="http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html" target="_blank">discussed before</a>, it unites many lineages in Ethiopia, including E-M34,E-M293 and E-V42. It looks like they did not test for E-V42 from the image however, so it could be E-V42.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>E-M34</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The prevalence of this lineage in southern Ethiopia from the image above, could be further confirmation of the<a href="http://ethiohelix.blogspot.com/2014/02/ydna-e-m123-closer-look.html" target="_blank"> high frequency of E-M34 </a>found in the omotic speaking Maale from the plaster thesis.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>EM4145</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">This is a tricky one, I am not sure what it is , I have searched for SNPs named as such and came back empty handed, to complicate things further, it is shaded a similar color as E-M293, but I discounted that lineage based on the fact that the lineage they report here is found in relatively high frequency in Ethiopia, whereas previous data shows that E-M293 is only found in low to moderate frequencies in Ethiopia. My best guess for this SNP would be something equivalent to E-V6, if not that then E-P2(x E-M215), but with less confidence for the latter, as if that was the case, I would think they would have given it a more basal presence in the hierarchy of YDNA lineages from the image above.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>J and T</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">These F belonging lineages look both to be inline with what we already know in terms of frequency distribution throughout Ethiopia.</span><br />
<br />
<span style="font-size: large;">refs:</span><br />
<a href="http://ethiohelix.blogspot.com/2010_12_01_archive.html"><span style="font-size: large;">http://ethiohelix.blogspot.com/2010_12_01_archive.html</span></a><br />
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html">http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html</a> </span><br />
<a href="http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html"><span style="font-size: large;">http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html</span></a><br />
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2013/05/another-extensive-thesis-on-east.html">http://ethiohelix.blogspot.com/2013/05/another-extensive-thesis-on-east.html</a> </span><br />
<br />
<span style="color: red;"><span style="font-size: x-large;"><b>Update 06/07/2015 - MTDNA</b></span></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjob_W-nzChLNSZWelE_YIDiPVQAzZbhD2TTNQUi5nXZdSSXIqVPgot0yH6UPi-0RY7hFVnH5MriJ8-xFbweWrVwa6zhgXzPhZA51KiB0FEqQHpwFPMJPZS14PEiEFeKxHcuBhpCuGMhoBY/s1600/ETH_MTDNA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="189" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjob_W-nzChLNSZWelE_YIDiPVQAzZbhD2TTNQUi5nXZdSSXIqVPgot0yH6UPi-0RY7hFVnH5MriJ8-xFbweWrVwa6zhgXzPhZA51KiB0FEqQHpwFPMJPZS14PEiEFeKxHcuBhpCuGMhoBY/s320/ETH_MTDNA.png" width="320" /></a></div>
<br />
<a name='more'></a><br />
<br />
<span style="font-size: large;">Find below approximations for the frequencies of lineages found from the image above</span><br />
<br />
<br />
<br />
<table border="2" bordercolor="#0033FF" cellpadding="3" cellspacing="3" style="background-color: white; width: 100%px;">
<tbody>
<tr>
<th></th>
<th>Amhara</th>
<th>Eth Somali</th>
<th>Gumuz</th>
<th>Oromo</th>
<th>Wolayta</th>
</tr>
<tr>
<td>L0</td>
<td>8%</td>
<td>4%</td>
<td>11%</td>
<td>4%</td>
<td>17%</td>
</tr>
<tr>
<td>L1</td>
<td>7%</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
</tr>
<tr>
<td>L2</td>
<td>16%</td>
<td>27%</td>
<td>0%</td>
<td>4%</td>
<td>12%</td>
</tr>
<tr>
<td>L3(x M,N)</td>
<td>8%</td>
<td>41%</td>
<td>52%</td>
<td>32%</td>
<td>28%</td>
</tr>
<tr>
<td>L4</td>
<td>0%</td>
<td>0%</td>
<td>22%</td>
<td>0%</td>
<td>8%</td>
</tr>
<tr>
<td>L5</td>
<td>0%</td>
<td>0%</td>
<td>13%</td>
<td>4%</td>
<td>6%</td>
</tr>
<tr>
<td>L6</td>
<td>0%</td>
<td>0%</td>
<td>0%</td>
<td>4%</td>
<td>4%</td>
</tr>
<tr>
<td>M</td>
<td>24%</td>
<td>3%</td>
<td>0%</td>
<td>12%</td>
<td>4%</td>
</tr>
<tr>
<td>N(x H-X)</td>
<td>7%</td>
<td>20%</td>
<td>0%</td>
<td>4%</td>
<td>0%</td>
</tr>
<tr>
<td>R0</td>
<td>9%</td>
<td>3%</td>
<td>0%</td>
<td>18%</td>
<td>10%</td>
</tr>
<tr>
<td>U</td>
<td>4%</td>
<td>0%</td>
<td>0%</td>
<td>4%</td>
<td>0%</td>
</tr>
<tr>
<td>Other</td>
<td>15%</td>
<td>0%</td>
<td>0%</td>
<td>12%</td>
<td>9%</td>
</tr>
</tbody></table>
<br />
<br />
<span style="font-size: large;"><u>L0</u></span><br />
<span style="font-size: large;">L0 has been found readily in Ethiopia before, it is mostly of the L0a type, this finding is therefore inline with what was known before.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>L1</u></span><br />
<span style="font-size: large;">Low presence of L1 has also been found in Ethiopia, typically it has been of the L1b variety, here it was only found in 1 out of the 5 populations sampled from Ethiopia</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>L2</u></span><br />
<span style="font-size: large;">Significant frequencies of this lineage have been documented before, mostly of the L2a variety but to a lesser extent of the L2b variety as well.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>L3(x M,N)</u></span><br />
<span style="font-size: large;">L3 encompasses all maternal lineages outside Africa, and many inside Africa. The results shown here are L3 lineages that do not include the signature lineages of the out of Africa migration , i.e. M and N. These L3 lineages have an ample variety of sub-lineages found in Ethiopia, look <a href="http://ethiohelix.blogspot.com/2012/01/mother-of-mothers.html" target="_blank">here</a> for a more detailed accounting for this lineage.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>L4</u></span><br />
<span style="font-size: large;">This data shows L4 only being found in the Gumuz and Wolayta, but in fact it has been found throughout Ethiopia in moderate frequencies , albeit much higher frequencies have been found in hunter gatherers further south from Ethiopia (Hadza). </span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>L5</u></span><br />
<span style="font-size: large;">Similar to L4 , L5 has also been found throughout Ethiopia but in slightly lower frequencies.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>L6</u></span><br />
<span style="font-size: large;">This is quite a rare lineage outside of Ethiopia, and within it, has only been found in low frequencies.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>M</u></span><br />
<span style="font-size: large;">The first of L3's sub lineages found outside Africa, the frequencies shown here are consistent with previous findings. The origin of this lineage is obscure and has a TMRCA of 60 KYA, close to when the out of Africa migrations are thought to have occurred and only 10 KYA younger than its predecessor L3. Almost all lineages found in Ethiopia are of the M1a variety however, with an estimated TMRCA of 20-30 KYA.</span><br />
<br />
<span style="font-size: large;"><u>N(x H-X)</u></span><br />
<span style="font-size: large;">The other L3 sub lineage found outside of Africa, N encompasses all non-African maternal lineages that do not belong to M. It is also estimated to have a TMRCA of about 60 KYA. Most N designated lineages in Ethiopia are further categorized as N1a with a TMRCA of ~ 20 KYA.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>R0</u></span><br />
<span style="font-size: large;">A sub-lineage of N, that is found throughout East Africa but mostly in Ethiopia, the sginifcant varient of this lineage is R0a1. Note that in the image provided, it is hard to distinguish between R0a, T and K, all of which have been found in Ethiopia before, however, R0a with much larger frequencies.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>U</u></span><br />
<span style="font-size: large;">Another sub-lineage of N with an ancient presence in Ethiopia, it should mostly be of the U6a1 variety.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><u>Other</u></span><br />
<span style="font-size: large;">Other refers to lineages that belong to N, but not to R0 or U. These 'other' lineages are for the most part limited to HV, I and T.</span><br />
<br />
<span style="font-size: large;">Refs:</span><br />
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2012/01/mother-of-mothers.html#uds-search-results" target="_blank">http://ethiohelix.blogspot.com/2012/01/mother-of-mothers.html#uds-search-results</a></span><br />
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2012/04/copernican-reassessment-of-human.html" target="_blank">http://ethiohelix.blogspot.com/2012/04/copernican-reassessment-of-human.html</a></span><br />
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2013/01/east-african-mtdna-variation-has.html#uds-search-results" target="_blank">http://ethiohelix.blogspot.com/2013/01/east-african-mtdna-variation-has.html#uds-search-results</a> </span><br />
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2013/12/more-east-african-mtdna-charts.html#uds-search-results" target="_blank">http://ethiohelix.blogspot.com/2013/12/more-east-african-mtdna-charts.html#uds-search-results</a> </span>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com16tag:blogger.com,1999:blog-7606098424948502460.post-83543899782368595012015-04-03T18:04:00.001-04:002015-07-01T11:29:50.278-04:00Revised Timeline and Distribution of the Earliest Diverged Human Maternal Lineages in Southern Africa<h2>
<span style="font-size: large;"><span style="color: blue;">Abstract</span></span></h2>
<span style="font-size: large;"></span><span style="font-size: large;"><span style="color: blue;">The
oldest extant human maternal lineages include mitochondrial haplogroups
L0d and L0k found in the southern African click-speaking forager
peoples broadly classified as Khoesan. Profiling these early
mitochondrial lineages allows for better understanding of modern human
evolution. In this study, we profile 77 new early-diverged complete
mitochondrial genomes and sub-classify another 105 L0d/L0k individuals
from southern Africa. We use this data to refine basal phylogenetic
divergence, coalescence times and Khoesan prehistory. </span></span><br />
<div class="separator" style="clear: both; text-align: center;">
<span style="font-size: large;"><span style="color: blue;"><a href="http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0121223.g002" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0121223.g002" height="320" width="119" /></a></span></span></div>
<span style="font-size: large;"><span style="color: blue;">
Our results
confirm L0d as the earliest diverged lineage (~172 kya, 95%CI: 149–199
kya), followed by L0k (~159 kya, 95%CI: 136–183 kya) and a new lineage
we name L0g (~94 kya, 95%CI: 72–116 kya). We identify two new L0d1
subclades we name L0d1d and L0d1c4/L0d1e, and estimate L0d2 and L0d1
divergence at ~93 kya (95%CI:76–112 kya). We concur the earliest
emerging L0d1’2 sublineage L0d1b (~49 kya, 95%CI:37–58 kya) is widely
distributed across southern Africa. Concomitantly, we find the most
recent sublineage L0d2a (~17 kya, 95%CI:10–27 kya) to be equally common.
<span id="goog_1918002192"></span><span id="goog_1918002193"></span>While we agree that lineages L0d1c and L0k1a are restricted to
contemporary inland Khoesan populations, our observed predominance of
L0d2a and L0d1a in non-Khoesan populations suggests a once independent
coastal Khoesan prehistory. The distribution of early-diverged human
maternal lineages within contemporary southern Africans suggests a rich
history of human existence prior to any archaeological evidence of
migration into the region. For the first time, we provide a
genetic-based evidence for significant modern human evolution in
southern Africa at the time of the Last Glacial Maximum at between
~21–17 kya, coinciding with the emergence of major lineages L0d1a,
L0d2b, L0d2d and L0d2a.</span></span><span style="font-size: large;"><span style="color: blue;"></span></span><br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://journals.plos.org/plosone/article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0121223.g002" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><br /></a></div>
<span style="font-size: large;"><span style="color: blue;"><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121223" target="_blank">Link (Open Access) </a></span></span><br />
<br /><span style="font-size: large;"><span style="color: blue;"></span></span>
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Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-38970181354120199012015-03-17T23:46:00.000-04:002015-03-17T23:54:21.196-04:00New NGS study of the Y DNA<span style="font-size: large;">A new Y-DNA study has appeared using Next Generation Sequencing, where ~9 Mb of the Y Chromosome was sequenced for 456 samples (299 of which were new) some preliminary observations are outlined below:</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><b>(1) Mutation Rate:</b></span><br />
<br />
<span style="font-size: large;">This is the second published study to calibrate the substitution mutation rate for the YDNA based on fossil evidence, to do this, they used a combination of derived mutation rates from 2 separate fossils; the 12.6 KY old Anzick fossil from Montana belonging to haplogroup Q1b and the 4 KY old Saqqaq fossil from Greenland belonging to haplogroup Q2b. The first study, <a href="http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html" target="_blank">Fu (2014)</a> used the 45 KY old Ust-Ishim fossil from Siberia belonging to haplogroup K(xLT). Interestingly, despite the big difference in age of these fossils of ~ 36 KYA (on average), the derived mutation rates were quite close to each other, with the current study's central estimate only ~8% slower than the rates derived from the Ust-Ishim fossil. The 95% CI bounds for this study were however less tight than the 95% CI bounds of Fu (2014). I have </span><span style="font-size: large;"><span style="font-size: large;"> already </span>incorporated these new rates into the <a href="https://ehelix.pythonanywhere.com/init/default/index" target="_blank">TMRCA calculator</a> under Karmin (2015).</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><b>(2) Coalescence of Non-African YDNA chromosomes:</b></span><br />
<br />
<span style="font-size: large;">The authors report :</span><br />
<blockquote class="tr_bq">
<span style="font-size: large;"><span style="color: blue;">....... a cluster of major non-African founder haplogroups in a narrow
time
interval at 47–52 kya, consistent with a rapid
initial colonization model of Eurasia and Oceania after the
out-of-Africa bottleneck</span></span></blockquote>
<span style="font-size: large;">Which aligns almost perfectly with the recent <a href="http://ethiohelix.blogspot.com/2015/01/smoking-gun-found-for-out-of-africa.html" target="_blank">find in Manot, Israel</a> of the 49.2 - 60.2 KY old non-African AMH fossil believed of being closely related to the ancestors of all extant non-Africans, i.e. the first OOA migrants.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><b>(3) A "New" E1b1b (E-M215) topology:</b></span><br />
<br />
<span style="font-size: large;">The "new" topology of E-M215 they outline below is in-fact over 3 years old, actually, we knew more back then than what they show in this paper today (see <a href="http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html" target="_blank">here</a>)</span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg68JO_prVV6A48dly_LzWij88HIi4O1lS2AT4x4KBIOhZmcPepdcEOC-QZSzY3EqabFGmhs3PGv7q589PZu-0HKa7i2a9P_MBpyZKgNGt6r3L2lZWn9KPkCUaho_QfpJ4SnemI-GzZjaDn/s1600/EM215_Karmin.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg68JO_prVV6A48dly_LzWij88HIi4O1lS2AT4x4KBIOhZmcPepdcEOC-QZSzY3EqabFGmhs3PGv7q589PZu-0HKa7i2a9P_MBpyZKgNGt6r3L2lZWn9KPkCUaho_QfpJ4SnemI-GzZjaDn/s1600/EM215_Karmin.png" height="287" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">E-M215 Karmin (2015)</td></tr>
</tbody></table>
<span style="font-size: large;">Compared with what we knew 3 years ago (note: CTS8288 above is equivalent to E-Z830 below):</span><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKcMbKwlKBrGGn4KMBJvGT4vP5knh9GLPV9msFz5BapXSYmqrKj04lvBoZPbHj25gAYTtb4wpTqlWQN1WJBSy_XSV_ryUcO-NnU74U-THcm1UBW_xEYlIsNnNkFRfiRHP6FUuotLJVjXG1/s1600/EM35_Phylogeny.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKcMbKwlKBrGGn4KMBJvGT4vP5knh9GLPV9msFz5BapXSYmqrKj04lvBoZPbHj25gAYTtb4wpTqlWQN1WJBSy_XSV_ryUcO-NnU74U-THcm1UBW_xEYlIsNnNkFRfiRHP6FUuotLJVjXG1/s1600/EM35_Phylogeny.png" height="320" width="247" /></a></div>
<br />
<span style="font-size: large;">The unanswered questions with respect to the major topology of E-M215 remain:</span><br />
<ul>
<li><span style="font-size: large;">What is the relationship, if any, of E-V92 with respect to E-Z827, E-Z830 or E-V68</span></li>
<li><span style="font-size: large;">What is the relationship, if any, of E-V6 with respect to E-Z827, E-Z830 or E-V68</span></li>
</ul>
<br />
<span style="font-size: large;"><span style="color: blue;">A recent bottleneck of Y chromosome diversity coincides with a global change in culture<br /> </span></span><br />
<span style="font-size: large;"><span style="color: blue;">Abstract<br /><br />It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.</span></span><br />
<br />
<span style="font-size: large;"><a href="http://genome.cshlp.org/content/early/2015/03/13/gr.186684.114.abstract" target="_blank">Link (Closed Access)</a></span>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-76243898865366708292015-02-03T19:42:00.004-05:002015-02-09T15:56:01.682-05:00SNP based module added to the Y TMRCA calculator<span style="font-size: large;">The solely STR based Y TMRCA calculator now also can accept SNP based input to compute the TMRCA of a node. Instructions and methodology can be found within the app at the link below:</span><br />
<a href="https://ehelix.pythonanywhere.com/init/default/index" target="_blank"><span style="font-size: large;">https://ehelix.pythonanywhere.com/init/default/index</span></a><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">For now, it uses 7 separate mutation rates that all come from different publications, but not all necessarily using differing methods to derive the rates. I will look to expand these as more substitution mutation rates become available.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Below I have run some quick verifications for 3 separate mutation rate sources:</span><br />
<ul><span style="font-size: large;">
</span>
<li><span style="font-size: large;">Poznick (2013) rates via <a href="http://www.nature.com/ejhg/journal/v23/n1/full/ejhg201450a.html">Underhill (2014)</a></span></li>
<span style="font-size: large;">
</span>
<li><span style="font-size: large;">Xue (2009) rates via <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113241/">Cruciani (2013)</a></span></li>
<span style="font-size: large;">
</span>
<li><span style="font-size: large;"><a href="http://genome.cshlp.org/content/early/2014/01/06/gr.160788.113.abstract">Scozzari (2013)</a> rates for the same publication</span></li>
</ul>
<br />
<span style="font-size: large;"><u>Poznick (2013) rates via Underhill (2014)</u></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The following is stated in Underhill (2014):</span><br />
<blockquote class="tr_bq">
<span style="color: blue;"><span style="font-size: large;">A consensus has not yet been reached on the rate at which Y-chromosome SNPs accumulate within this 9.99Mb sequence. Recent estimates include one SNP per: ~100 years,⁵⁸ 122 years,⁴ 151 years⁵ (deep sequencing reanalysis rate), and 162 years.⁵⁹ Using a rate of one SNP per 122 years, and based on an average branch length of 206 SNPs from the common ancestor of the 13 sequences, we estimate the bifurcation of R1 into R1a and R1b to have occurred ~25,100 ago (95% CI: 21,300–29,000). Using the 8 R1a lineages, with an average length of 48 SNPs accumulated since the common ancestor, we estimate the splintering of R1a-M417 to have occurred rather recently, B5800 years ago (95% CI: 4800–6800). The slowest mutation rate estimate would inflate these time estimates by one third, and the fastest would deflate them by 17%.</span></span></blockquote>
<span style="font-size: large;">Putting in the variables for the R1 node from above into the calculator,</span><br />
<span style="font-size: large;">We get an output of:</span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><span style="font-size: large;"></span><br />
<span style="font-size: large;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLy-vILZjSwAcTQU4Re_fbFsc1UdOyzAcwabcf0IgCdkEBid6Kze6vXus2YJR7_cQyaKwKbuB_rS3PEXSzJ2tD2nqHdHWFkWCJoKA_2bFcJYKqHEzi0EsglLhaaU24H-9eabeVWvXeXuHz/s1600/fig1.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLy-vILZjSwAcTQU4Re_fbFsc1UdOyzAcwabcf0IgCdkEBid6Kze6vXus2YJR7_cQyaKwKbuB_rS3PEXSzJ2tD2nqHdHWFkWCJoKA_2bFcJYKqHEzi0EsglLhaaU24H-9eabeVWvXeXuHz/s1600/fig1.png" height="174" width="320" /></a></span></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: large;"> <span style="font-size: small;">R1 - Underhill (2014) </span></span></td></tr>
</tbody></table>
<span style="font-size: large;">which for the mutation rate they used , i.e. Poznick (2013), the calculator gives 25.15 KYA, close enough to their estimate of 25.1 KYA.<br />Similarliy for the R1a-M417 node , we get:</span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><span style="font-size: large;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigX6sQesO0ZGggJxNg0KVD231xfod1ehiN5qrZsPGL9yJ3McKXvuFVXAUOUxBuwFsMlyKvPrN2aR1-4ON-3OXWeuHvugPByhOBJBcUvhp1fDb9Z8z20w3pg4OoTyUcyCeRpaz_92MLoFv6/s1600/fig2.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigX6sQesO0ZGggJxNg0KVD231xfod1ehiN5qrZsPGL9yJ3McKXvuFVXAUOUxBuwFsMlyKvPrN2aR1-4ON-3OXWeuHvugPByhOBJBcUvhp1fDb9Z8z20w3pg4OoTyUcyCeRpaz_92MLoFv6/s1600/fig2.png" height="177" width="320" /></a></span></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">R1a-M417 - Underhill (2014)</span></td></tr>
</tbody></table>
<span style="font-size: large;">Again, looking @ the calculator's Poznick TMRCA of 5.86 KYA, we can see it is close enough to their estimate of 5.8 KYA.</span><br />
<br />
<a name='more'></a><br />
<span style="font-size: large;"><u>Xue (2009) rates via Cruciani (2013)</u><br />Here we need to look at Fig. 1 from the publication to estimate the average branch lengths,<br />For example, for the CT node, the average branch length (not counting the indels) is (10 +6) /2 = 8<br />For the BT node, the average branch length is (8 + 7 + 16) /2 = 15.5<br />For a total sequence length of 205.938 Kb (look @ the supplemental material) we get the following results from the calculator for the above nodes:<br />CT node: </span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><span style="font-size: large;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgm9NlK97dOpe9O3K92cF22zCSAD6yelWHvP0ktUTMPjKprNXu96XTzeSDJyhjrSZqsgDQQpwc7SHpAZheZlQkKbYWFWQdXtEuuZsD2CPYbAYN7Jw_1p5Yp2roGm6tndq6PswHUYM8iUum-/s1600/fig3.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgm9NlK97dOpe9O3K92cF22zCSAD6yelWHvP0ktUTMPjKprNXu96XTzeSDJyhjrSZqsgDQQpwc7SHpAZheZlQkKbYWFWQdXtEuuZsD2CPYbAYN7Jw_1p5Yp2roGm6tndq6PswHUYM8iUum-/s1600/fig3.png" height="184" width="320" /></a></span></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">CT Node - Cruciani (2013)</span></td></tr>
</tbody></table>
<span style="font-size: large;">Giving 38.85 KYA for Xue (2009), which compares well to the result of 38.8 KYA found in the publication.<br />Similarly for the BT node: </span><br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: 0px; margin-right: auto; text-align: left;"><tbody></tbody></table>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: 0px; margin-right: auto; text-align: left;"><tbody></tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><span style="font-size: large;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEpIfXc4lfwJ6zXdb_cLYNDTkr8OVq08WrW80vofZwlewxFWh4QFxxWs9uRgxDsXAHuFN-eaOm-u9frHDT4K4N7934_K8QGJFoVmFcdxkTkqiwAoIfS6FNZ7tAv1ECuCWUuS4VJ1y0hj1x/s1600/fig4.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEpIfXc4lfwJ6zXdb_cLYNDTkr8OVq08WrW80vofZwlewxFWh4QFxxWs9uRgxDsXAHuFN-eaOm-u9frHDT4K4N7934_K8QGJFoVmFcdxkTkqiwAoIfS6FNZ7tAv1ECuCWUuS4VJ1y0hj1x/s1600/fig4.png" height="176" width="320" /></a></span></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">BT Node - Cruciani (2013)</span></td></tr>
</tbody></table>
<br />
<div style="text-align: left;">
<span style="font-size: large;">Giving 75.27 KYA for Xue (2009) vs 74.5 KYA in the publication, here the calculator is off by 0.77KYA, I suspect the reason could be with the average branch length estimation.</span></div>
<div style="text-align: left;">
<span style="font-size: large;"><br /><u>Scozzari (2013) rates for same publication</u><br />Branch lengths for this publication are give in the phylogenetic figure at the bottom of the publication;</span></div>
<div style="text-align: left;">
<span style="font-size: large;">For example, for the node uniting S04 and S05 (within A1b) we get an average branch length of (10 +14) / 2 = 12 and for the node uniting S18, S19 and S17 (within B2b) we get an average branch length of (((62+43)/2) + 1) + 51)/2 = 52.25<br />Using a total sequence length of 1.495512 Mb, we get the following results for the above average lengths respectively:</span></div>
<div style="text-align: left;">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: 0px; margin-right: auto; text-align: left;"></table>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: 0px; margin-right: auto; text-align: left;"></table>
</div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><span style="font-size: large;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju0msHzb7rpFhfTpMy4Rr7raWOvftS27I9pokXSxC1d3QH2xTdKhxuV76Wn-sestLEaoxaAa1YIaB5PKlph0lQlUHT_uJ0jpdXJPleq8eM2d2keE6js_9ZwDa-ZWau4EApSDer4b5eZsvL/s1600/fig5.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju0msHzb7rpFhfTpMy4Rr7raWOvftS27I9pokXSxC1d3QH2xTdKhxuV76Wn-sestLEaoxaAa1YIaB5PKlph0lQlUHT_uJ0jpdXJPleq8eM2d2keE6js_9ZwDa-ZWau4EApSDer4b5eZsvL/s1600/fig5.png" height="190" width="320" /></a></span></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">S04 + S05 - Scozzari (2013)</span></td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><span style="font-size: large;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiT719qVrPu1B-mGZjUTTYEw9-OZSaWelTbd-kNkCEMRZ7WzKbWpRvuyVM9vn4LHifbPg1JfIIWngu5lnUW-p9X9NKX-p_4SjKbIlzP_V2pU7J2ZYkfPbbXlYs0-Hju16aqImXqzVk-5yrV/s1600/fig6.png" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiT719qVrPu1B-mGZjUTTYEw9-OZSaWelTbd-kNkCEMRZ7WzKbWpRvuyVM9vn4LHifbPg1JfIIWngu5lnUW-p9X9NKX-p_4SjKbIlzP_V2pU7J2ZYkfPbbXlYs0-Hju16aqImXqzVk-5yrV/s1600/fig6.png" height="184" width="320" /></a></span></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;">S18 + S19 + S17 - Scozzari (2013)</span></td></tr>
</tbody></table>
<span style="font-size: large;">As can be seen above, for the node within A1b, and for the Scozzari rates we get 12.54 KYA, which is in the range of their computation of 12.5 – 13.5 KYA. Similarly for the node within B2b, we get 54.59 KYA, which is again in the range they give of 51.5 – 55 KYA.<br /><br />So overall the calculator gives satisfactory results which are in-line with published material.</span><br />
<br />
<span style="font-size: large;"><b><span style="color: red;">UPDATE</span></b>: Incorporated Mendez' 95% CI Mutation rate bounds, Mendez et al. generated 95% CI bounds as a function of years/generation ranging from 20 - 40 years, which is different from the other publications that used a constant 30 years/generation, therefore to obtain 95% CI bounds in terms of </span><span style="font-size: medium;"><span style="font-size: large;"><i>per site per generation</i>, I multiplied Mendez' lower bound 95% CI by 20 and the upper bound by 40.</span></span><br />
<br />
<span style="font-size: medium;"><span style="font-size: large;"><span style="color: red;"><b>UPDATE2</b></span>: Taking advantage of the linear relationship of the formula, I have updated the calculator to also accept actual TMRCAs in KYA for a particular mutation rate source as an input, and output the corresponding TMRCAs for the remaining sources. </span></span><br />
<br />
see also:<br />
<a href="http://ethiohelix.blogspot.com/2014/12/snp-vs-str-ydna-tmrca-estimation.html">http://ethiohelix.blogspot.com/2014/12/snp-vs-str-ydna-tmrca-estimation.html</a><br />
<a href="http://ethiohelix.blogspot.com/2014/02/comprehensive-ethiopian-ydna-tmrca.html">http://ethiohelix.blogspot.com/2014/02/comprehensive-ethiopian-ydna-tmrca.html</a><br />
<a href="http://ethiohelix.blogspot.com/2014/01/y-tmrca-calculator-as-web-app.html">http://ethiohelix.blogspot.com/2014/01/y-tmrca-calculator-as-web-app.html </a><br />
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: 0px; margin-right: auto; text-align: left;"><tbody></tbody></table>
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Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com2tag:blogger.com,1999:blog-7606098424948502460.post-28754397479720870932015-01-28T16:37:00.001-05:002015-01-28T16:39:34.138-05:00'Smoking gun' found for the Out of Africa Theory<span style="font-size: large;">An Israeli anthropologist, Israel Hershkovitz, claims that he and his team have found the archaeological smoking gun for the Out of Africa theory, a theory which has been genetically reinforced for the past couple of decades,</span><br />
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">"This is the smoking gun that confirms what geneticists have been
predicting," he said. "We had finds from Africa and from Europe but we
were missing the connection between them; it's like finishing a puzzle
and finding that a piece is missing: it drives you crazy. This is the
missing connection between the older African populations and the later
European populations."
</span></blockquote>
<span style="font-size: large;">The evidence, a 55,000 year old partial skull found in a cave called Manot in Northern Israel, also disqualifies the popular Bab-el-mandeb route that modern humans may have took as they were leaving Africa, and strengthens a Nile valley route according to the same Anthropologist,</span><br />
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">Hershkovitz told Haaretz that the presence of modern humans at Manot also supports the idea that <i>Homo sapiens sapiens</i> left Africa through the Nile valley, Sinai and what is today known as Israel,</span></blockquote>
<blockquote class="tr_bq">
<span style="font-size: large;"><a href="http://www.haaretz.com/life/archaeology/1.639350">http://www.haaretz.com/life/archaeology/1.639350</a></span></blockquote>
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Obviously, a scenario of <a href="http://ethiohelix.blogspot.com/2014/04/genomic-and-cranial-phenotype-data.html">multiple exits out of Africa</a>, first via Bab-el-mandeb and then via the Nile valley, can not be necessarily discounted by this find.</span><br />
<br />
<h1 class="article-heading">
<span style="color: blue; font-size: large;">Levantine cranium from Manot Cave (Israel) foreshadows the first European modern humans</span></h1>
<h1 class="article-heading">
<span style="color: blue; font-size: large;"><span style="font-weight: normal;">A key event in human evolution is the expansion of modern humans of
African origin across Eurasia between 60 and 40 thousand years (kyr)
before present (<span class="scp">bp</span>), replacing all other forms of hominins<sup><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14134.html#ref1" id="ref-link-21" title="Hublin, J. J. The earliest modern human colonization of Europe. Proc. Natl Acad. Sci. USA 109, 13471-13472 (2012)">1</a></sup>.
Owing to the scarcity of human fossils from this period, these
ancestors of all present-day non-African modern populations remain
largely enigmatic. Here we describe a partial calvaria, recently
discovered at Manot Cave (Western Galilee, Israel) and dated to
54.7 ± 5.5 kyr <span class="scp">bp</span> (arithmetic mean ± 2 standard
deviations) by uranium–thorium dating, that sheds light on this crucial
event. The overall shape and discrete morphological features of the
Manot 1 calvaria demonstrate that this partial skull is unequivocally
modern. It is similar in shape to recent African skulls as well as to
European skulls from the Upper Palaeolithic period, but different from
most other early anatomically modern humans in the Levant. This suggests
that the Manot people could be closely related to the first modern
humans who later successfully colonized Europe. Thus, the anatomical
features used to support the ‘assimilation model’ in Europe might not
have been inherited from European Neanderthals, but rather from earlier
Levantine populations. Moreover, at present, Manot 1 is the only modern
human specimen to provide evidence that during the Middle to Upper
Palaeolithic interface, both modern humans and Neanderthals
contemporaneously inhabited the southern Levant, close in time to the
likely interbreeding event with Neanderthals<sup><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14134.html#ref2" id="ref-link-22" title="Sankararaman, S., Patterson, N., Li, H., Paabo, S. & Reich, D. The date of interbreeding between Neandertals and modern humans. PLoS Genet. 8, e1002947 (2012)">2</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14134.html#ref3" id="ref-link-23" title="Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710-722 (2010)">3</a></sup>.</span></span></h1>
<h1 class="article-heading">
<span style="font-size: large;">
</span><span style="font-size: small;"><span style="color: blue; font-size: large;"><span style="font-weight: normal;"><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14134.html">Link </a>( Closed Access) </span></span> </span></h1>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com18tag:blogger.com,1999:blog-7606098424948502460.post-72355125184488972182015-01-20T14:25:00.000-05:002015-01-20T14:25:56.364-05:00Genes & Language, Impact of Oldest Butchering Tools on Communication, Lalibela Archaeology<div class="section abstract" id="abstract-2">
<blockquote class="tr_bq">
<h2>
<span style="font-size: large;"><span style="color: blue;">A comparison of worldwide phonemic and genetic variation in human populations</span></span></h2>
<h2>
<span style="font-size: large;"><span style="color: blue;">Abstract</span></span></h2>
<div id="p-7">
<span style="font-size: large;"><span style="color: blue;">Worldwide patterns of genetic
variation are driven by human demographic history. Here, we test whether
this demographic history
has left similar signatures on
phonemes—sound units that distinguish meaning between words in
languages—to those it has left
on genes. We analyze, jointly and in
parallel, phoneme inventories from 2,082 worldwide languages and
microsatellite polymorphisms
from 246 worldwide populations. On a
global scale, both genetic distance and phonemic distance between
populations are significantly
correlated with geographic distance.
Geographically close language pairs share significantly more phonemes
than distant language
pairs, whether or not the languages are
closely related. The regional geographic axes of greatest phonemic
differentiation
correspond to axes of genetic
differentiation, suggesting that there is a relationship between human
dispersal and linguistic
variation. However, the geographic
distribution of phoneme inventory sizes does not follow the predictions
of a serial founder
effect during human expansion out of
Africa. Furthermore, although geographically isolated populations lose
genetic diversity
via genetic drift, phonemes are not
subject to drift in the same way: within a given geographic radius,
languages that are
relatively isolated exhibit more variance
in number of phonemes than languages with many neighbors. This finding
suggests
that relatively isolated languages are
more susceptible to phonemic change than languages with many neighbors.
Within a language
family, phoneme evolution along genetic,
geographic, or cognate-based linguistic trees predicts similar ancestral
phoneme
states to those predicted from ancient
sources. More genetic sampling could further elucidate the relative
roles of vertical
and horizontal transmission in phoneme
evolution. </span></span></div>
<div id="p-7">
<span style="font-size: large;"><span style="color: blue;"><br /></span></span></div>
<div id="p-7">
<span style="font-size: large;"><span style="color: blue;"><a href="http://www.pnas.org/content/early/2015/01/15/1424033112.abstract">Link (Closed Access)</a></span></span></div>
</blockquote>
<div id="p-7">
<br /></div>
<div id="p-7">
<span style="font-size: large;">See Also: </span></div>
<h3 class="post-title entry-title" itemprop="name">
<span style="font-size: large;"><a href="http://ethiohelix.blogspot.com/2012/05/novel-solution-for-dating-origin-of.html">A Novel Solution For Dating The Origin Of Language.</a> <a href="http://www.sciencemag.org/content/335/6069/657.5.full">Response to Comments on “Phonemic Diversity Supports a Serial Founder Effect Model of Language Expansion from Africa”</a></span></h3>
</div>
<hr />
<div class="section abstract" id="abstract-2">
<blockquote class="tr_bq">
<h1 class="article-heading">
<span style="color: blue;"><span style="font-family: inherit; font-size: large;">Experimental evidence for the co-evolution of hominin tool-making teaching and language</span></span></h1>
<h1 class="section-heading">
<span style="color: blue;"><span style="font-size: large;">Abstract</span></span></h1>
<span style="color: blue;"><span style="font-size: large;">Hominin reliance on Oldowan stone tools—which appear from
2.5 mya and are believed to have been socially transmitted—has been
hypothesized to have led to the evolution of teaching and language. Here
we present an experiment investigating the efficacy of transmission of
Oldowan tool-making skills along chains of adult human participants (<i>N</i>=184)
using five different transmission mechanisms. Across six measures,
transmission improves with teaching, and particularly with language, but
not with imitation or emulation. Our results support the hypothesis
that hominin reliance on stone tool-making generated selection for
teaching and language, and imply that (i) low-fidelity social
transmission, such as imitation/emulation, may have contributed to the
~700,000 year stasis of the Oldowan technocomplex, and (ii) teaching or
proto-language may have been pre-requisites for the appearance of
Acheulean technology. This work supports a gradual evolution of
language, with simple symbolic communication preceding behavioural
modernity by hundreds of thousands of years.</span></span><br />
<span style="color: blue;"><span style="font-size: large;"><br /></span></span>
<span style="color: blue;"><span style="font-size: large;"><a href="http://www.nature.com/ncomms/2015/150113/ncomms7029/full/ncomms7029.html">Link (Closed Access)</a></span></span></blockquote>
<br />
<hr />
<blockquote class="tr_bq">
<span style="color: blue;"><span style="font-family: inherit; font-size: large;"><b>The Lalibela Rock Hewn Site and its Landscape (Ethiopia): An Archaeological Analysis</b> </span></span><br />
<span style="color: blue;"><span style="font-size: large;"><br /></span></span>
<div id="p-7">
<span style="color: blue;"><span style="font-size: large;"><b>Abstract</b></span></span><br />
<span style="color: blue;"><span style="font-size: large;"><br /></span></span>
<span style="color: blue;"><span style="font-size: large;">This article presents the methods employed at the
site of Lalibela, Ethiopia during the 2009, 2010, 2011 and part of the
2012 campaigns, as well as the first results obtained. This site
consists of a group of rock-cut churches attributed to the sovereign of
the same name, King Lalibela, who we know to have reigned in the late
12th century and in the first third of the 13th century. Cut out of
solid rock, Lalibela is an exceptional archaeological site since most of
the traces of its early phases were eliminated in the process of its
transformation. The site thus presents a significant challenge for
historians and archaeologists. How is it possible to write its history
without excavation? Geomorphological observations of the region offer
new keys for understanding Lalibela; identification of the spoil heap,
in which we discovered a clear stratigraphy confirming the existence of
different cutting phases; the topographic and taphonomic analysis of the
remains, and investigations in the cemetery of Qedemt, revealed that
the site was formed in multiple phases, probably reflecting a long
occupation sequence spanning at least eleven centuries (from the 10th to
the 21st century).</span></span></div>
<div id="p-7">
<span style="color: blue;"><span style="font-size: large;"><br /></span></span></div>
<div id="p-7">
<span style="color: blue;"><span style="font-size: large;"> <a href="http://www.african-archaeology.de/index.php?page_id=154&journal_id=37&pdf_id=300">Link (Closed Access)</a></span></span></div>
</blockquote>
</div>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-89912420791857047392014-12-08T16:30:00.000-05:002014-12-09T14:54:53.661-05:00SNP vs. STR YDNA TMRCA Estimation<span style="font-size: large;">An interesting comparison of YDNA TMRCA estimates using the SNP counting method and STRs (with both pedigree and Zhivotovsky rates as well as rho and ASD methods) can be found in a recently published study.</span><br />
<span style="font-size: large;"><br /></span>
<br />
<blockquote class="tr_bq">
<i><span style="font-size: large;"><span style="color: blue;">The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades</span></span></i><br />
<span style="font-size: large;"><span style="color: blue;"><br /></span></span>
<span style="font-size: large;"><span style="color: blue;">Many studies of human populations have used the male-specific region of
the Y chromosome (MSY) as a marker, but MSY sequence
variants have traditionally been subject to
ascertainment bias. Also, dating of haplogroups has relied on Y-specific
short
tandem repeats (STRs), involving problems of
mutation rate choice, and possible long-term mutation saturation.
Next-generation
sequencing can ascertain single nucleotide
polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which
branch-lengths
are proportional to time, and allowing the
times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated
directly.
Here we describe the sequencing of 3.7 Mb of MSY in
each of 448 human males at a mean coverage of 51 ×, yielding 13,261
high-confidence
SNPs, 65.9% of which are previously unreported. The
resulting phylogeny covers the majority of the known clades, provides
date estimates of nodes, and constitutes a robust
evolutionary framework for analysing the history of other classes of
mutation.
Different clades within the tree show subtle but
significant differences in branch lengths to the root. <b>We also apply a
set
of 23 Y-STRs to the same samples, allowing SNP- and
STR-based diversity and TMRCA estimates to be systematically compared.
</b>Ongoing purifying selection is suggested by our
analysis of the phylogenetic distribution of non-synonymous variants in
15
MSY single-copy genes. </span></span><br />
<br />
<span style="font-size: large;"><span style="color: blue;">Link (<a href="http://mbe.oxfordjournals.org/content/early/2014/11/26/molbev.msu327.short?rss=1">Open Access</a>)</span></span><br />
<span style="font-size: large;"><span style="color: blue;"><br /></span></span>
<span style="font-size: large;"><span style="color: blue;">(iii) The evolutionary STR mutation rate consistently overestimates, and the pedigree rate underestimates, the TMRCAs of nodes (Figure 4a).As expected, the pedigree mutation rate performs better for young nodes (<10 KYA; Table S6 ), while the evolutionary rate performs better for older nodes.</span></span></blockquote>
<br />
<span style="font-size: large;">Off course "overestimation" and "underestimation"in this case are both relative to the particular mutation rate used by the authors for the SNP counting method in the first place, the authors used the <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748900/">Xue (2009)</a> mutation rate estimate of 1 X 10^-9/bp/year , therefore, a slower mutation rate choice (like from <a href="http://www.sciencemag.org/content/341/6145/562">Poznick (2013)</a> or <a href="http://www.sciencemag.org/content/341/6145/565.abstract">Francalacci (2013)</a> for instance ) would obviously reduce the "overestimation" of the evolutionary STR mutation rate performance and conversely, a faster mutation rate choice would reduce the "underestimation" of the pedigree mutation rate performance, also important to note is that there is quite a bit of variance within the pedigree rates themselves, the authors chose to use a mean pedigree rate from <a href="http://yhrd.org/pages/resources/mutation_rates">YHRD </a>(see the <a href="https://ehelix.pythonanywhere.com/">YTMRCA Calculator</a> to see how pedigree rates from different sources impact TMRCA estimation). All in all however this was an interesting exercise, I hope we can get to see more of these types of comparisons, especially with fossil calibrated mutation rate estimates used for the SNP counting method.</span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEn-sPYUf_jFzM_UMX8DlvetAN7zmzMMlvCcBQIyBCOpERNDbKNRI8a1ywB7tAxTZNnMOW20ypALNn_Rbz7kZxvhouNqEHeVjfeALWMvtYImf7NrlHA0oEHk6q2JfoUwSFOETJGVRYafgH/s1600/str_SNP.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEn-sPYUf_jFzM_UMX8DlvetAN7zmzMMlvCcBQIyBCOpERNDbKNRI8a1ywB7tAxTZNnMOW20ypALNn_Rbz7kZxvhouNqEHeVjfeALWMvtYImf7NrlHA0oEHk6q2JfoUwSFOETJGVRYafgH/s1600/str_SNP.png" height="327" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div style="text-align: center;">
Figure4: Relationship between SNP-and STR-based TMRCA estimates.SNP-based node estimates are plotted against STR-based estimates for (a) 21 STRs (b) 17 STRs and <b>(c) 13 STRs</b>, here using ASD with the ‘ancestral haplotype’ root specification. The black dashed linein each case indicates x=y.U nderlying data and correlation coefficients are given in Tables S6 and S7. </div>
</td></tr>
</tbody></table>
<br />
<span style="font-size: x-large;"><b><span style="color: red;">UPDATE:</span></b></span><br />
<span style="font-size: large;"><span style="color: red;"><span style="color: black;">For further insight in the current understanding of substitution rates used for the SNP counting method, I direct readers to the <a href="http://www.investigativegenetics.com/content/5/1/12">Wang (2014)</a></span></span></span><b><span style="font-size: large;"><span style="color: red;"> </span></span></b><span style="font-size: large;"><span style="color: red;"><span style="color: black;">article which enumerates on the 4 primary methods that have been used to calculate the substitution rate:</span></span></span><br />
<ol>
<li><span style="font-size: large;"><span style="color: red;"><span style="color: black;">Human - Chimp Comparisons : <a href="http://www.pnas.org/content/97/13/7360">Thompson (2000)</a> , <a href="http://www.nature.com/ng/journal/v38/n2/full/ng1729.html">Kuroki (2006)</a></span></span></span></li>
<li><span style="font-size: large;"><span style="color: red;"><span style="color: black;">Deep Rooting Pedigree: </span></span></span><span style="font-size: large;"><span style="color: red;"><span style="color: black;"><span style="font-size: large;"><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748900/">Xue (2009)</a></span></span></span></span></li>
<li><span style="font-size: large;"><span style="color: red;"><span style="color: black;"><span style="font-size: large;">Autosomal Mutation Rate Adjustment: <a href="http://www.ncbi.nlm.nih.gov/pubmed?Db=pubmed&Cmd=Retrieve&list_uids=23453668&dopt=abstractplus">Mendez (2013)</a></span></span></span></span></li>
<li><span style="font-size: large;"><span style="color: red;"><span style="color: black;"><span style="font-size: large;">Founding Migrations Based Inference: </span></span></span></span><span style="font-size: large;"><a href="http://www.sciencemag.org/content/341/6145/562">Poznick (2013)</a>, </span><span style="font-size: large;"><a href="http://www.sciencemag.org/content/341/6145/565.abstract">Francalacci (2013)</a> </span><span style="font-size: large;"></span></li>
</ol>
<span style="font-size: large;">In terms of inferences based on the Y Chromosome TMRCA and the Out Of Africa migrations the authors suggest that </span><span style="font-size: large;"><span style="color: red;"><span style="color: black;"><span style="font-size: large;"><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748900/">Xue (2009)</a> and </span></span></span></span><span style="font-size: large;"><a href="http://www.sciencemag.org/content/341/6145/562">Poznick (2013)</a> give the most reasonable estimates. </span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.investigativegenetics.com/content/figures/2041-2223-5-12-1-l.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.investigativegenetics.com/content/figures/2041-2223-5-12-1-l.jpg" height="400" width="382" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><strong>Comparison of different Y chromosomal substitution rates in time estimation using
Y chromosome dataset of 1000 Genome dataset.</strong> Time estimations are performed in BEAST. <strong>(a)</strong> TMRCA of 526 Y chromosomes (including haplogroup A1b1b2b-M219 to T). <strong>(b)</strong> Time of Out-of-Africa migration, the age of macro-haplogroup CT. HCR- Thomson and
HCR-Kuroki: Y chromosome base-substitution rate measured from human-chimpanzee comparison
by Thomson <em>et al. </em><a href="https://www.blogger.com/null" name="d2626e585"></a>[<a href="http://www.investigativegenetics.com/content/5/1/12#B6">6</a>] and Kuroki <em>et al. </em><a href="https://www.blogger.com/null" name="d2626e591"></a>[<a href="http://www.investigativegenetics.com/content/5/1/12#B7">7</a>], respectively. Pedigree rate: Y chromosome base-substitution rate measured in a deep-rooting
pedigree by Xue <em>et al. </em><a href="https://www.blogger.com/null" name="d2626e598"></a>[<a href="http://www.investigativegenetics.com/content/5/1/12#B8">8</a>]. Autosomal Rate Adjusted: Y chromosome substitution rate adjusted from autosomal
mutation rates by Mendez <em>et al. </em><a href="https://www.blogger.com/null" name="d2626e604"></a>[<a href="http://www.investigativegenetics.com/content/5/1/12#B9">9</a>]. AEFM-America and AEFM-Sardinian: Y chromosome base-substitution rate based on archaeological
evidence of founding migrations using initial peopling of Americas <a href="https://www.blogger.com/null" name="d2626e608"></a>[<a href="http://www.investigativegenetics.com/content/5/1/12#B10">10</a>] and initial Sardinian expansion <a href="https://www.blogger.com/null" name="d2626e612"></a>[<a href="http://www.investigativegenetics.com/content/5/1/12#B11">11</a>], respectively. Different reported mutation rates are given at the log scale. Confidence
intervals for some of the mutation rates are very wide, and time calculations here
use only the point estimate. The times would overlap more if all the uncertainties
were taken into account. Figure was drawn using boxplot in R 3.0.2.
</td></tr>
</tbody></table>
<br />
<span style="font-size: large;">However a fifth method , entirely sequencing Y chromosomes from verifiable ancient individuals , a method which is still at its infancy but gaining momentum, should refine the substitution rate to a level of precision that as of yet has not been available. It stands to be seen if it will corroborate the rates from the front runners (</span><span style="font-size: large;"><span style="color: red;"><span style="color: black;"><span style="font-size: large;"><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748900/">Xue (2009)</a>, </span></span></span></span><span style="font-size: large;"><a href="http://www.sciencemag.org/content/341/6145/562">Poznick (2013)</a> ) or maybe even yield unforeseen results.</span><br />
<br />Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-22119910106216464722014-11-13T17:10:00.000-05:002014-11-13T17:11:14.673-05:00Novel genomic signals of recent selection in an Ethiopian population<h2 id="atl">
</h2>
<span style="font-size: large;"><span style="color: blue;"><span class="vcard"><span class="author fn">Fasil Tekola-Ayele</span></span>, <span class="vcard"><span class="author fn">Adebowale Adeyemo</span></span>, <span class="vcard"><span class="author fn">Guanjie Chen</span></span>, <span class="vcard"><span class="author fn">Elena Hailu</span></span>, <span class="vcard"><span class="author fn">Abraham Aseffa</span></span>, <span class="vcard"><span class="author fn">Gail Davey</span></span>, <span class="vcard"><span class="author fn">Melanie J Newport</span></span> and <span class="vcard"><span class="author fn">Charles N Rotimi</span></span></span></span><br />
<span style="font-size: large;"><span style="color: blue;">
</span></span>
<div class="entry-summary" id="abs">
<h3 class="hidden">
<span style="font-size: large;"><span style="color: blue;">Abstract</span></span></h3>
<div class="lead">
<span style="font-size: large;"><span style="color: blue;">The
recent feasibility of genome-wide studies of adaptation in human
populations has provided novel insights into biological pathways that
have been affected by adaptive pressures. However, only a few African
populations have been investigated using these genome-wide approaches.
Here, we performed a genome-wide analysis for evidence of recent
positive selection in a sample of 120 individuals of Wolaita ethnicity
belonging to Omotic-speaking people who have inhabited the mid- and
high-land areas of southern Ethiopia for millennia. Using the 11 HapMap
populations as the comparison group, we found Wolaita-specific signals
of recent positive selection in several human leukocyte antigen (HLA)
loci. Notably, the selected loci overlapped with HLA regions that we
previously reported to be associated with podoconiosis–a geochemical
lymphedema of the lower legs common in the Wolaita area. We found
selection signals in PPARA, a gene involved in energy metabolism during
prolonged food deficiency. This finding is consistent with the dietary
use of enset, a crop with high-carbohydrate and low-fat and -protein
contents domesticated in Ethiopia subsequent to food deprivation 10<span class="mb"><span class="mb"> </span></span>000
years ago, and with metabolic adaptation to high-altitude hypoxia. We
observed novel selection signals in CDKAL1 and NEGR1, well-known
diabetes and obesity susceptibility genes. Finally, the SLC24A5 gene
locus known to be associated with skin pigmentation was in the top
selection signals in the Wolaita, and the alleles of single-nucleotide
polymorphisms rs1426654 and rs1834640 (SLC24A5) associated with light
skin pigmentation in Eurasian populations were of high frequency (47.9<span class="mb">%</span>) in this Omotic-speaking indigenous Ethiopian population.</span></span></div>
<div class="lead">
<br /></div>
<div class="lead">
<span style="font-size: large;"><span style="color: blue;">Link (<a href="http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2014233a.html">Closed Access</a>) </span></span></div>
</div>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com1tag:blogger.com,1999:blog-7606098424948502460.post-49261458672574844432014-10-08T17:20:00.000-04:002014-10-08T17:20:08.861-04:00Assumptions on the genesis of artistic expression in humans shattered by Indonesian find.<span style="font-size: large;">Hand stencils and paintings of pigs found in Indonesian caves are cause for experts to rethink the genesis of artistic expression in humans according to a new publication in nature.</span><br />
<span style="font-size: large;"><br /></span>
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">Archaeologists have long been puzzled by the appearance in Europe ~40–35
thousand years (kyr) ago of a rich corpus of sophisticated artworks,
including parietal art (that is, paintings, drawings and engravings on
immobile rock surfaces)<sup><a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref1" id="ref-link-2" title="Lewis-Williams, D. J. The Mind in the Cave: Consciousness and the Origins Of Art (Thames & Hudson, 2002)">1</a>, <a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref2" id="ref-link-3" title="White, R. et al. Context and dating of Aurignacian vulvar representations from Abri Castanet, France. Proc. Natl Acad. Sci. USA 109, 8450-8455 (2012)">2</a></sup> and portable art (for example, carved figurines)<sup><a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref3" id="ref-link-4" title="Conard, N. J. Palaeolithic ivory sculptures from southwestern Germany and the origins of figurative art. Nature 426, 830-832 (2003)">3</a>, <a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref4" id="ref-link-5" title="Dowson, T. A. & Porr, M. in The Archaeology of Shamanism (ed. Price, N.) 165-177 (Routledge, 2001)">4</a></sup>,
and the absence or scarcity of equivalent, well-dated evidence
elsewhere, especially along early human migration routes in South Asia
and the Far East, including Wallacea and Australia<sup><a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref5" id="ref-link-6" title="Aubert, M. A review of rock art dating in the Kimberley, Western Australia. J. Archaeol. Sci. 39, 573-577 (2012)">5</a>, <a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref6" id="ref-link-7" title="Brumm, A. & Moore, M. W. Symbolic revolutions and the Australian archaeological record. Camb. Archaeol. J. 15, 157-175 (2005)">6</a>, <a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref7" id="ref-link-8" title="Langley, M. C., Clarkson, C. & Ulm, S. From small holes to grand narratives: the impact of taphonomy and sample size on the modernity debate in Australia and New Guinea. J. Hum. Evol. 61, 197-208 (2011)">7</a>, <a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref8" id="ref-link-9" title="Mellars, P. Going east: new genetic and archaeological perspectives on the modern human colonization of Eurasia. Science 313, 796-800 (2006)">8</a></sup>, where modern humans (<i>Homo sapiens</i>) were established by 50 kyr ago<sup><a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref9" id="ref-link-10" title="Roberts, R. G., Jones, R. & Smith, M. Thermoluminescence dating of a 50,000-year-old human occupation site in northern Australia. Nature 345, 153-156 (1990)">9</a>, <a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref10" id="ref-link-11" title="Roberts, R. G. et al. The human colonisation of Australia: optical dates of 53,000 and 60,000 years bracket human arrival at Deaf Adder Gorge, Northern Territory. Quat. Sci. Rev. 13, 575-583 (1994)">10</a></sup>.
Here, using uranium-series dating of coralloid speleothems directly
associated with 12 human hand stencils and two figurative animal
depictions from seven cave sites in the Maros karsts of Sulawesi, we
show that rock art traditions on this Indonesian island are at least
compatible in age with the oldest European art<sup><a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#ref11" id="ref-link-12" title="Pike, A. W. G. et al. U-series dating of Paleolithic art in 11 caves in Spain. Science 336, 1409-1413 (2012)">11</a></sup>.
The earliest dated image from Maros, with a minimum age of 39.9 kyr, is
now the oldest known hand stencil in the world. In addition, a painting
of a babirusa (‘pig-deer’) made at least 35.4 kyr ago is among the
earliest dated figurative depictions worldwide, if not the earliest one.
Among the implications, it can now be demonstrated that humans were
producing rock art by ~40 kyr ago at opposite ends of the Pleistocene
Eurasian world.</span></blockquote>
<span style="font-size: large;"><a href="http://www.nature.com/nature/journal/v514/n7521/full/nature13422.html#access">Link (Closed Access) </a></span><br />
<br />
<span style="font-size: large;">Watch Video:</span><br />
<br />
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<br />
<span style="font-size: large;">From the Press (<a href="http://www.bbc.com/news/science-environment-29415716">BBC</a>):</span><br />
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">But the discovery of paintings of a similar age in Indonesia shatters
this view, according to Prof Chris Stringer of the Natural History
Museum in London.</span><br />
<span style="color: blue; font-size: large;">"It is a really important find; it enables us to get away
from this Euro-centric view of a creative explosion that was special to
Europe and did not develop in other parts of the world until much
later," he said. </span><br />
<div id="story_continues_6">
<span style="color: blue; font-size: large;">The discovery of 40,000-year-old cave
paintings at opposite ends of the globe suggests that the ability to
create representational art had its origins further back in time in
Africa, before modern humans spread across the rest of the world.</span></div>
<span style="color: blue; font-size: large;">"That's kind of my gut feeling," says Prof Stringer. "The
basis for this art was there 60,000 years ago; it may even have been
there in Africa before 60,000 years ago and it spread with modern
humans". </span></blockquote>
<br />
<br />Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com1tag:blogger.com,1999:blog-7606098424948502460.post-39367131539879362382014-10-02T18:24:00.002-04:002014-10-02T18:30:40.351-04:00Statisitics on African born immigrants in the U.S.<span style="font-size: large;">I stumbled upon an <a href="http://www.washingtonpost.com/local/african-immigrant-population-doubling-each-decade-washington-area-among-highest/2014/10/01/efbada70-498f-11e4-891d-713f052086a0_story.html">interesting article</a> in the WP that led me to a <a href="http://www.census.gov/newsroom/press-releases/2014/cb14-184.html">recently released brief</a> by the US Census Bureau outlining some interesting stats on the growing demography of Africans in America.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The article can be freely accessed <a href="http://www.census.gov/content/dam/Census/library/publications/2014/acs/acsbr12-16.pdf">here</a>.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Some figures and highlights I found interesting follows:</span><br />
<span style="font-size: large;"><br /></span>
<br />
<blockquote class="tr_bq">
<span style="font-size: large;"><span style="color: blue;">According to the 2008–2012 American Community Survey (ACS), 39.8 million foreign-born people resided in the United States, including 1.6 million from Africa, or about 4 percent of the total foreign-born population. In 1970, there were about 80,000 African foreign born, representing less than 1 percent of the total foreign-born population (Figure 1). During the following four decades, the number of foreign born from Africa grew rapidly, roughly doubling each decade.<br />About three-fourths of the foreign-born population from Africa came to live in the United States after 1990. The timing of this movement was driven in part by historical changes. Outmigration from Africa increased rapidly after World War II, as migrants responded to.....</span></span></blockquote>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-ujW2Hj5SKO5Trt6qrnf9zMMGApkC04ciXBPw9ShLAAgA7nVrOnDauKihsagHKvcRo7dP59pL0e3FCiWjE51z0EylvQPIXykiP2x519JilnoaQbf9u1OhPdON9VANimOneVifs_OC50Ha/s1600/Fig1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg-ujW2Hj5SKO5Trt6qrnf9zMMGApkC04ciXBPw9ShLAAgA7nVrOnDauKihsagHKvcRo7dP59pL0e3FCiWjE51z0EylvQPIXykiP2x519JilnoaQbf9u1OhPdON9VANimOneVifs_OC50Ha/s1600/Fig1.png" height="400" width="273" /></a></div>
<br />
<blockquote class="tr_bq">
<span style="font-size: large;"><span style="color: blue;">Of the 1.6 million foreign born from Africa in the United States, 36 percent were from Western Africa, 29 percent were from Eastern Africa, and 17 percent were from Northern Africa, followed by Southern Africa (5 percent), Middle Africa (5 percent), and other Africa (7 percent)</span></span></blockquote>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpTeFs-B0kV8h4u8XeWG1IEl74peP1ygasoHfjZSLNEn4MLFsa8lVf0HzmDAspjixU2abDdz71u_fX92FxIc4MLWxJpJfbTxS6vBwQ6QnmODVZfJ839dqx3YDri-OXnJIoEpGmLhuZVKDL/s1600/Fig2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjpTeFs-B0kV8h4u8XeWG1IEl74peP1ygasoHfjZSLNEn4MLFsa8lVf0HzmDAspjixU2abDdz71u_fX92FxIc4MLWxJpJfbTxS6vBwQ6QnmODVZfJ839dqx3YDri-OXnJIoEpGmLhuZVKDL/s1600/Fig2.png" height="400" width="328" /></a></div>
<br />
<blockquote class="tr_bq">
<span style="font-size: large;"><span style="color: blue;">...Of these seven, the four largest were Nigeria (221,000 or 14 percent of the African-born population), Ethiopia (164,000 or 10 percent), Egypt (143,000 or 9 percent), and Ghana (121,000 or 8 percent), together constituting 41 percent of the African-born total....</span></span></blockquote>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNm9_6EBuWuplSJn5lfT2hl7mhGArOGwiDRboI2buRtsP09lNVLDpRLWvm0hwitcrn_QJO-PK7hSlLjYf1obneuPel99QVgdQeazxOkUuUhop_-4p-okUBirePxypnOw8ZUTTOlwB3qExm/s1600/Fig3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNm9_6EBuWuplSJn5lfT2hl7mhGArOGwiDRboI2buRtsP09lNVLDpRLWvm0hwitcrn_QJO-PK7hSlLjYf1obneuPel99QVgdQeazxOkUuUhop_-4p-okUBirePxypnOw8ZUTTOlwB3qExm/s1600/Fig3.png" height="275" width="400" /></a></div>
<br />
<blockquote class="tr_bq">
<span style="font-size: large;"><span style="color: blue;">.....Forty-one percent of the African-born population had a bachelor’s degree or higher in 2008–2012, compared with 28 percent of the overall foreign born. Egypt (64 percent) and Nigeria (61 percent) were among the African countries of birth with the highest proportion of bachelor’s and higher degrees. </span></span></blockquote>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi3IpQnQCtsbbeemrhY7GUEsoakcAisuIUl7Gm69rEgPwgLmQ_YYiYFmgpIgyQTrRiYilNkuVEdlkQoPjCYNC6ZOnwKCaqTJe8X6BmEifHfUMdu6iAIWfVacIIouS-PGgbxPuIe6egF5uew/s1600/Fig4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi3IpQnQCtsbbeemrhY7GUEsoakcAisuIUl7Gm69rEgPwgLmQ_YYiYFmgpIgyQTrRiYilNkuVEdlkQoPjCYNC6ZOnwKCaqTJe8X6BmEifHfUMdu6iAIWfVacIIouS-PGgbxPuIe6egF5uew/s1600/Fig4.png" height="296" width="400" /></a></div>
<br />
<span style="font-size: large;"><span style="color: blue;"> <span style="color: black;">^ I was surprised (and slightly disappointed) by the relatively lower attainment of Bachelor's degrees by Ethiopians in the US. According to the report, 26% of Ethiopians attained a Bachelor's degree or higher, which is lower than both the foreign born (28%) and the <a href="http://www.census.gov/newsroom/releases/archives/education/cb12-33.html">National </a>(30%) attainment levels.</span></span></span><br />
<br />
<span style="font-size: large;"><span style="color: blue;"><span style="color: black;">The article attempts at explaining the disparity in educational attainment levels by stating:</span></span></span><br />
<br />
<blockquote class="tr_bq">
<span style="font-size: large;"><span style="color: blue;"><span style="color: black;"><span style="color: blue;">The difference in educational attainment among the populations from different African countries in part reflects how they immigrated to the United States. A relatively high proportion of immigrants from Africa entered the United States on diversity visas (24 percent as compared with 5 percent of the overall foreign born), which require a high school diploma or equivalent work experience.The foreign born from Somalia, who mostly entered the United States as refugees or asylees (82 percent in 2010), not as diversity migrants (1 percent in 2010), were an exception to this overall pattern. Forty percent of the Somali born had less than a high school education.</span></span></span></span></blockquote>
<br />
<span style="color: blue;"><span style="color: black;"><span style="font-size: large;"><span style="color: blue;"><span style="color: black;">On the bright side, Nigerians and Egyptians have attained Bachelor's degrees (or higher) at a level 2 times than that of the whole nation, which is impressive.</span></span></span> </span></span><br />
<br />
<br />Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com1tag:blogger.com,1999:blog-7606098424948502460.post-34954057742692741142014-08-19T21:30:00.000-04:002014-08-19T21:30:58.275-04:00East African Climate on Hominin Evolution , Archaelogical evidence for African Homo Sapiens Substructure (pre-OOA)<h1 class="svTitle" id="title0010">
<span style="color: blue;">East African climate pulses and early human evolution</span></h1>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://ars.els-cdn.com/content/image/1-s2.0-S0277379114002418-gr1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://ars.els-cdn.com/content/image/1-s2.0-S0277379114002418-gr1.jpg" /></a><span style="color: blue;"> </span></div>
<div class="abstract svAbstract " data-etype="ab">
<h2 class="secHeading" id="authorabs00101">
<span style="font-size: large;"><span style="color: blue;">Abstract</span></span></h2>
<div id="abspara0010">
<span style="font-size: large;"><span style="color: blue;">Current
evidence suggests that all of the major events in hominin evolution
have occurred in East Africa. Over the last two decades, there has been
intensive work undertaken to understand African palaeoclimate and
tectonics in order to put together a coherent picture of how the
environment of East Africa has varied in the past. The landscape of East
Africa has altered dramatically over the last 10 million years. It has
changed from a relatively flat, homogenous region covered with mixed
tropical forest, to a varied and heterogeneous environment, with
mountains over 4 km high and vegetation ranging from desert to cloud
forest. The progressive rifting of East Africa has also generated
numerous lake basins, which are highly sensitive to changes in the local
precipitation-evaporation regime. There is now evidence that the
presence of precession-driven, ephemeral deep-water lakes in East Africa
were concurrent with major events in hominin evolution. It seems the
unusual geology and climate of East Africa created periods of highly
variable local climate, which, it has been suggested could have driven
hominin speciation, encephalisation and dispersal out of Africa. One
example is the significant hominin speciation and brain expansion event
at ∼1.8 Ma that seems to have been coeval with the occurrence of highly
variable, extensive, deep-water lakes. This complex, climatically very
variable setting inspired first the <em>variability selection hypothesis</em>, which was then the basis for the <em>pulsed climate variability hypothesis</em>.
The newer of the two suggests that the long-term drying trend in East
Africa was punctuated by episodes of short, alternating periods of
extreme humidity and aridity. Both hypotheses, together with other key
theories of climate-evolution linkages, are discussed in this paper.
Though useful the actual evolution mechanisms, which led to early
hominins are still unclear and continue to be debated. However, it is
clear that an understanding of East African lakes and their
palaeoclimate history is required to understand the context within which
humans evolved and eventually left East Africa.</span></span></div>
<div id="abspara0010">
<br /></div>
<div id="abspara0010">
<span style="font-size: large;"><span style="color: blue;"><a href="http://www.sciencedirect.com/science/article/pii/S0277379114002418">Link</a> (Open Access) </span></span></div>
<div id="abspara0010">
<br /></div>
<h1 class="svTitle" id="title0010">
<span style="color: blue;">Earliest evidence for the structure of <em>Homo sapiens</em> populations in Africa</span></h1>
<div class="abstract svAbstract " data-etype="ab">
<h2 class="secHeading" id="authorabs00101">
<span style="font-size: large;"><span style="color: blue;">Abstract</span></span></h2>
<div id="abspara0010">
<span style="font-size: large;"><span style="color: blue;">Understanding the structure and variation of <em>Homo sapiens</em>
populations in Africa is critical for interpreting multiproxy evidence
of their subsequent dispersals into Eurasia. However, there is no
consensus on early <em>H. sapiens</em> demographic structure, or its
effects on intra-African dispersals. Here, we show how a patchwork of
ecological corridors and bottlenecks triggered a successive budding of
populations across the Sahara. Using a temporally and spatially explicit
palaeoenvironmental model, we found that the Sahara was not uniformly
ameliorated between ∼130 and 75 thousand years ago (ka), as has been
stated. Model integration with multivariate analyses of corresponding
stone tools then revealed several spatially defined technological
clusters which correlated with distinct palaeobiomes. Similarities
between technological clusters were such that they decreased with
distance except where connected by palaeohydrological networks. These
results indicate that populations at the Eurasian gateway were strongly
structured, which has implications for refining the demographic
parameters of dispersals out of Africa.</span></span></div>
<div id="abspara0010">
<br /></div>
<div id="abspara0010">
<span style="font-size: large;"><span style="color: blue;"><a href="http://www.sciencedirect.com/science/article/pii/S0277379114003023">Link</a> (Closed Access) </span></span></div>
</div>
</div>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com5tag:blogger.com,1999:blog-7606098424948502460.post-88937022349018918952014-06-09T16:59:00.001-04:002014-06-09T16:59:11.545-04:00Mutation rate of the nuclear genome is getting a fossil calibration<span style="font-size: large;">The <a href="http://smbe.org/annual/2014/">SMBE 2014 conference</a> is showcasing a presentation where a 45,000 year old genome is being fully sequenced by Fu et al. and where the sequence will be used to calibrate, to my knowledge for the first time, the mutation rate of the nuclear genome.</span><br />
<br />
<span style="font-size: large;">Previously, <a href="https://www.eva.mpg.de/fileadmin/content_files/staff/paabo/pdf/Fu_Revised_CurrentBiology_2013.pdf">Fu et al. (2013)</a> had calibrated the Mitochondrial genome's mutation rate by using some 10 non-African fossils as a reference, with results by and large in compliance with previously established mutation rate estimates.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The rate of accumulation of SNPs on the YDNA, will thus be the last remaining thing to get a fossil calibration. Once we get that, temporal based analysis using these calibrated mutation rates should gain a much more solid basis.</span><br />
<span style="font-size: large;"><br /></span>
<div style="margin-bottom: 10pt; margin-top: 0pt;">
<span style="font-size: large;"><span style="color: blue;"><strong>O-15</strong>
</span></span></div>
<span style="font-size: large;"><span style="color: blue;">
</span></span><div style="margin-bottom: 10pt; margin-top: 0pt;">
<span style="font-size: large;"><span style="color: blue;"><strong>The complete genome sequence of a 45,000-year-oldmodern human from Eurasia</strong></span></span>
</div>
<span style="font-size: large;"><span style="color: blue;">
</span></span><div style="margin-bottom: 10pt; margin-top: 0pt;">
<span style="font-size: large;"><span style="color: blue;"><u>Qiaomei Fu</u>
<sup>1
,2</sup>, Bence Viola<sup>1
,3</sup>, Heng Li<sup>5
,6</sup>, Priya Moorjani<sup>6</sup>, Flora Jay<sup>4</sup>, Aximu Ayinuer-Petri<sup>1</sup>, Susan Keates<sup>8</sup>, Yaroslav V. Kuzmin<sup>7</sup>, Montgomery Slatkin<sup>4</sup>, David Reich<sup>5
,6</sup>, Janet Kelso<sup>1</sup>, Svante Pääbo<sup>1</sup>
</span></span>
<span style="font-size: large;"><span style="color: blue;"><em>
<sup> </sup></em></span></span></div>
<div style="margin-bottom: 10pt; margin-top: 0pt;">
<span style="font-size: large;"><span style="color: blue;"><em><sup>1</sup>Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,<sup> 2</sup>Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Beijing, China,<sup> 3</sup>Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,<sup> 4</sup>Department of Integrative Biology, University of California, Berkeley, USA,<sup> 5</sup>Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,<sup> 6</sup>Department of Genetics,Harvard Medical School, Boston, USA,<sup> 7</sup>Institute of Geology & Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia,<sup> 8</sup>University Village, Columbia, USA</em></span></span>
</div>
<br />
<span style="font-size: large;"><span style="color: blue;">We have sequenced to high coverage the genome of a femur
recently discovered near Ust-Ishim in Siberia. The bone was directly
carbon-dated to 45,000 years before present. Analyses of the
relationship of the Ust-Ishim individual to present-day humans show that
he is closely related to the ancestral population shared between
present-day Europeans and present-day Asians. The over-all amount of
genomic admixture from Neandertals is similar to that in present-day
non-Africans and there is no evidence for admixture from Denisovans.
However, the size of the genomic segments of Neandertal ancestry in the
Ust-Ishim individual is substantially larger than in present-day
individuals. From the size distribution of these segments we estimated
that this individual lived about 200-400 generations after the admixture
with Neandertals occurred.<b> The age of this genome allows us to directly
assess the mutation rate in the different compartments of the human
genome. These results will be presented and discussed.</b></span></span><br />
<br />
<span style="color: blue;"><b><span style="font-size: large;"><a href="https://mcidublin.conference-services.net/reports/template/onetextabstract.xml?xsl=template/onetextabstract.xsl&conferenceID=3958&abstractID=811773">Link </a></span></b></span>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-55793225113243689902014-04-21T23:50:00.003-04:002014-04-21T23:51:21.167-04:00Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia <div class="executive-summary significance-box">
<h2>
<span style="font-size: large;"><span style="color: blue;">Significance</span></span></h2>
<span style="font-size: large;"><span style="color: blue;">
</span></span><br />
<div id="p-3">
<span style="font-size: large;"><span style="color: blue;">Current consensus indicates that modern humans originated from an ancestral <span class="search-term-highlight">Africa</span>n
population between ∼100–200 ka. The ensuing dispersal pattern is
controversial, yet has important implications for the demographic
history and genetic/phenotypic structure
of extant human populations. We test for the first time to our knowledge
the spatiotemporal
dimensions of competing out-of-<span class="search-term-highlight">Africa</span>
dispersal models, analyzing in parallel genomic and craniometric data.
<b>Our results support an initial dispersal into Asia
by a southern route beginning as early as
∼130 ka and a later dispersal into northern Eurasia by ∼50 ka. Our
findings indicate
that <span class="search-term-highlight">Africa</span>n Pleistocene population structure may account for observed plesiomorphic genetic/phenotypic patterns in extant Australians
and Melanesians. They point to an earlier out-of-<span class="search-term-highlight">Africa</span> dispersal than previously hypothesized. </b></span></span></div>
<div id="p-3">
<br /></div>
<div class="section abstract" id="abstract-2">
<h2>
<span style="color: blue;"><span style="font-size: large;">Abstract</span></span></h2>
<span style="color: blue;"><span style="font-size: large;">
</span></span><br />
<div id="p-4">
<span style="color: blue;"><span style="font-size: large;">Despite broad consensus on <span class="search-term-highlight">Africa</span>
as the main place of origin for anatomically modern humans, their
dispersal pattern out of the continent continues to be
intensely debated. In extant human
populations, the observation of decreasing genetic and phenotypic
diversity at increasing
distances from sub-Saharan <span class="search-term-highlight">Africa</span>
has been interpreted as evidence for a single dispersal, accompanied by
a series of founder effects. In such a scenario,
modern human genetic and phenotypic
variation was primarily generated through successive population
bottlenecks and drift
during a rapid worldwide expansion out of <span class="search-term-highlight">Africa</span>
in the Late Pleistocene. However, recent genetic studies, as well as
accumulating archaeological and paleoanthropological
evidence, challenge this parsimonious
model. They suggest instead a “southern route” dispersal into Asia as
early as the late
Middle Pleistocene, followed by a separate
dispersal into northern Eurasia. Here we test these competing out-of-<span class="search-term-highlight">Africa</span>
scenarios by modeling hypothetical geographical migration routes and
assessing their correlation with neutral population
differentiation, as measured by genetic
polymorphisms and cranial shape variables of modern human populations
from <span class="search-term-highlight">Africa</span> and Asia. <b>We show
that both lines of evidence support a multiple-dispersals model in
which Australo-Melanesian populations
are relatively isolated descendants of an
early dispersal, whereas other Asian populations are descended from, or
highly admixed
with, members of a subsequent migration
event. </b></span></span></div>
<div id="p-4">
<br /></div>
<div id="p-4">
<span style="color: blue;"><span style="font-size: large;"><b><a href="http://www.pnas.org/content/early/2014/04/16/1323666111.abstract?sid=962fa76c-14cf-4f5d-a432-54e891c0b5f1">Link</a> (Closed Access) </b></span></span></div>
</div>
<div id="p-3">
<span style="font-size: large;"><span style="color: blue;"> </span></span> </div>
</div>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com1tag:blogger.com,1999:blog-7606098424948502460.post-28966676173817422532014-04-04T19:35:00.001-04:002014-05-01T13:44:52.541-04:00Median Joining Networks<span style="font-size: large;">This post will be dedicated to YSTR median joining networks I will be creating using the <a href="http://www.fluxus-engineering.com/sharenet.htm">Fluxus Network Software<sup>©</sup></a></span><br />
<br />
<span style="font-size: large;"><sup>The Y TMRCA calculator now also has the capability to create the input file necessary to create median joining networks using the Fluxus Network Software, see <a href="https://ehelix.pythonanywhere.com/init/default/instructions#Fluxus">here</a> for more details.</sup></span><br />
<br />
<span style="font-size: large;"><sup>This blog-post will be updated routinely with network diagrams as I make more of them, since I do not have access to the </sup><sup><a href="http://www.fluxus-engineering.com/nwpub.htm"><u>Network Publisher </u></a>add-on, it takes a considerable amount of time to properly format the diagrams.</sup></span><br />
<br />
<span style="font-size: large;"><sup>I will start with Ethiopian E-M34 data from the Plaster thesis, see also the following post for more detail on Ethiopian E-M34: <a href="http://ethiohelix.blogspot.com/2014/02/ydna-e-m123-closer-look.html">YDNA E-M123; A closer look </a></sup></span><br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_CLMNl-PCwvoKmrhXSQdN84QttL3SV81EubXnu31jepn4cSQSmXnSFKDECIzQh_BuNN6Rw0NBqYabvHUkmNrZNIBIhrT4wsZxVyFoNKEnEs2OI1hNiSpeLjDB2Aym_2Cylsp7OEXxqVSC/s1600/EM34_Ethiopia_EM123_FTDNA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_CLMNl-PCwvoKmrhXSQdN84QttL3SV81EubXnu31jepn4cSQSmXnSFKDECIzQh_BuNN6Rw0NBqYabvHUkmNrZNIBIhrT4wsZxVyFoNKEnEs2OI1hNiSpeLjDB2Aym_2Cylsp7OEXxqVSC/s1600/EM34_Ethiopia_EM123_FTDNA.png" height="400" width="308" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWiFYyXiXI6EwVMvuEafvjFyofF6wG0oQdj54p2Sr71EsAUhJw9vhNNq3pQuWKpl4NG39xLVmZ4pDOvpeZ7RbFbtq8oJjdizuuz6j7R7cLqJD4Ulq94LJxRR0LY4Qy-W7_KURkMfP_MkKi/s1600/EM34_Ethiopia.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWiFYyXiXI6EwVMvuEafvjFyofF6wG0oQdj54p2Sr71EsAUhJw9vhNNq3pQuWKpl4NG39xLVmZ4pDOvpeZ7RbFbtq8oJjdizuuz6j7R7cLqJD4Ulq94LJxRR0LY4Qy-W7_KURkMfP_MkKi/s1600/EM34_Ethiopia.png" height="400" width="308" /></a></div>
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<span style="font-size: large;"></span></div>
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<a name='more'></a><br />
<span style="font-size: large;">14-Marker J-M267 haplotypes from the Plaster Thesis, see this post for TMRCA results : <a href="http://ethiohelix.blogspot.com/2014/02/ethiopian-ydna-j-str-analysis-addendum.html">http://ethiohelix.blogspot.com/2014/02/ethiopian-ydna-j-str-analysis-addendum.html</a> </span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgN1mw0hPg1xX_t7g5ZJh7K0P8DZPkGhwxED0vY9zH7lW-QR8da3tz8UrAG8cuKduRWzd9FI_P0eS5tAX5avokaD_Z1PrHKD1otyog4smE1pgWNLnuyvYrhbqYxKAIruouBQ8xsBpPw7pZX/s1600/JM267_Ethiopia.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgN1mw0hPg1xX_t7g5ZJh7K0P8DZPkGhwxED0vY9zH7lW-QR8da3tz8UrAG8cuKduRWzd9FI_P0eS5tAX5avokaD_Z1PrHKD1otyog4smE1pgWNLnuyvYrhbqYxKAIruouBQ8xsBpPw7pZX/s1600/JM267_Ethiopia.png" height="400" width="308" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDe9EQmNqpafVN_4VE1SNfhwFLt13rLio0IyMegCGcmghOvtgR7nsaIAqjOBY9FCdwaIUjBIeMEZ8CGeZ238j1T8gcHdbtIKXACFdq1IbhmdIVLSejtkRUvWYDg3xSLZBdSYfKDm9jiB7N/s1600/JM267_Ethiopia_JM267_FTDNA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDe9EQmNqpafVN_4VE1SNfhwFLt13rLio0IyMegCGcmghOvtgR7nsaIAqjOBY9FCdwaIUjBIeMEZ8CGeZ238j1T8gcHdbtIKXACFdq1IbhmdIVLSejtkRUvWYDg3xSLZBdSYfKDm9jiB7N/s1600/JM267_Ethiopia_JM267_FTDNA.png" height="400" width="308" /></a></div>
<hr />
E-Z830* Clusters from Haplozone site<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDPKSEQAhC5B8QYsiVEyFakP3PBnCNAO6sEp-m-J6jJMZea1zSwvmwa9ENig7ivTXNHbp6w95oQWUdWHs3kQy_ogR_0LaQNuOOy2DwRxMZGu_nLtnymfjc7WejtCmDTQdVCIcfTRRgy93W/s1600/EZ830_Haplozone.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDPKSEQAhC5B8QYsiVEyFakP3PBnCNAO6sEp-m-J6jJMZea1zSwvmwa9ENig7ivTXNHbp6w95oQWUdWHs3kQy_ogR_0LaQNuOOy2DwRxMZGu_nLtnymfjc7WejtCmDTQdVCIcfTRRgy93W/s1600/EZ830_Haplozone.png" height="400" width="308" /></a></div>
<hr />
E_V32 from Plaster (14 markers)<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgRsZSxWkU7LXDyDfKObBHp-GbvMsZ85di99wS1nh8SQ4prAaR6YT0BQYgX-0KaYXM31QDYHtLThdxHbIrjTOZigX46wN1vWn2X_DjjnFVzlzyT6jx_ICkoP1xHZC11qwALdBXcz7gvNIo/s1600/EV32_Ethiopia.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgRsZSxWkU7LXDyDfKObBHp-GbvMsZ85di99wS1nh8SQ4prAaR6YT0BQYgX-0KaYXM31QDYHtLThdxHbIrjTOZigX46wN1vWn2X_DjjnFVzlzyT6jx_ICkoP1xHZC11qwALdBXcz7gvNIo/s1600/EV32_Ethiopia.png" height="400" width="308" /></a></div>
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<hr />
A3b2 from Plaster (14 markers)<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQL-riXs9-cFWI9VLrIpUzaGkGEjYyaMM5MlHnFEsTthvXisZdZKe4fgQ094_FIREyXxz4pv1d1KHrBtb__pTxNfkykLEIntG1-d4m-YSDC9QsdUPBkuuG92Gv6JX2r2lGUQ3y4DxfNwge/s1600/A3b2_Ethiopia.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQL-riXs9-cFWI9VLrIpUzaGkGEjYyaMM5MlHnFEsTthvXisZdZKe4fgQ094_FIREyXxz4pv1d1KHrBtb__pTxNfkykLEIntG1-d4m-YSDC9QsdUPBkuuG92Gv6JX2r2lGUQ3y4DxfNwge/s1600/A3b2_Ethiopia.png" height="400" width="308" /></a></div>
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<hr />
E-M2 Haplotypes from FTDNA Project page<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8YEv2vxzW6pV8pi1HMPIzqlGsyx3IprxJEmptRvFswHQz-uR6UzkIpKDmHMzzxNDasxg0FShxF8_gEM8qsPPPPEhT1vq-rwFEbosxh2-2h4Np_q09vxrpe9yu4dMuDwlWP0_1wZH_DXI4/s1600/FTDNA_EM2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8YEv2vxzW6pV8pi1HMPIzqlGsyx3IprxJEmptRvFswHQz-uR6UzkIpKDmHMzzxNDasxg0FShxF8_gEM8qsPPPPEhT1vq-rwFEbosxh2-2h4Np_q09vxrpe9yu4dMuDwlWP0_1wZH_DXI4/s1600/FTDNA_EM2.png" height="400" width="308" /></a></div>
<br />Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-74286049542135693162014-03-24T19:57:00.000-04:002014-03-24T19:57:06.049-04:00Modeling 3D Facial Shape from DNA <span style="font-size: large;">While still at its infancy, this technology is quite fascinating</span><br />
<br />
<h2>
Abstract</h2>
<a href="https://www.blogger.com/null" id="article1.front1.article-meta1.abstract1.p1" name="article1.front1.article-meta1.abstract1.p1"></a><span style="color: blue;">Human
facial diversity is substantial, complex, and largely scientifically
unexplained. We used spatially dense quasi-landmarks to measure face
shape in population samples with mixed West African and European
ancestry from three locations (United States, Brazil, and Cape Verde).
Using bootstrapped response-based imputation modeling (BRIM), we uncover
the relationships between facial variation and the effects of sex,
genomic ancestry, and a subset of craniofacial candidate genes. The
facial effects of these variables are summarized as response-based
imputed predictor (RIP) variables, which are validated using
self-reported sex, genomic ancestry, and observer-based facial ratings
(femininity and proportional ancestry) and judgments (sex and population
group). By jointly modeling sex, genomic ancestry, and genotype, the
independent effects of particular alleles on facial features can be
uncovered. Results on a set of 20 genes showing significant effects on
facial features provide support for this approach as a novel means to
identify genes affecting normal-range facial features and for
approximating the appearance of a face from genetic markers.</span><br />
<br />
<span style="color: blue;"><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004224">Link (Open Access)</a> </span><br />
<span style="color: blue;"><br /></span>
<br /><span style="color: blue;">......Since both categorical and continuous variables can be modeled using
BRIM, this approach might be used to test for relationships between
facial features and other factors, <em>e.g.</em>, age, adiposity, and
temperament. The methods illustrated here also provide for the
development of diagnostic tools by modeling validated cases of overt
craniofacial dysmorphology. Most directly, our methods provide the means
of identifying the genes that affect facial shape and for modeling the
effects of these genes to generate a predicted face. Although much more
work is needed before we can know how many genes will be required to
estimate the shape of a face in some useful way and many more
populations need to be studied before we can know how generalizable the
results are, these results provide both the impetus and analytical
framework for these studies.....</span><br />
<span style="color: blue;"><br /></span>
<span style="font-size: large;">Some interesting figures:</span><br />
<span style="color: blue;"><br /></span>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004224.g001&representation=PNG_M" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004224.g001&representation=PNG_M" height="292" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div class="title">
<b>Figure 1:</b> Workflow for 3D face scan processing.</div>
<div class="desc">
A)
original surface, B) trimmed to exclude non-face parts, C) reflected to
make mirror image, D) anthropometric mask of quasi-landmarks, E)
remapped, F) reflected remapped, G) symmetrized, H) reconstructed.<br />
</div>
</td></tr>
</tbody></table>
<div class="separator" style="clear: both; text-align: center;">
</div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004224.g003&representation=PNG_M" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004224.g003&representation=PNG_M" height="320" width="157" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div class="title">
<b>Figure 3:</b> Transformations and heat maps showing how face shape is affected by (A) RIP-A and (B) RIP-S.</div>
<div class="desc">
The
top row of each panel shows the shape transformations three standard
deviations below and above the mean of the RIPs in this sample. The
second row shows the R<sup>2</sup> (proportion of the total variation in
each quasi-landmark) and the three primary facial shape change
parameters: area ratio, curvature difference, and normal displacement.
The bottom row shows in yellow the regions of the face that are
statistically significantly different (<em>p</em><0.001) between the two transformations. The max R<sup>2</sup> values for RIP-A and RIP-S are 40.83% and 38.21%, respectively. </div>
</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004224.g004&representation=PNG_L" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004224.g004&representation=PNG_L" height="320" width="183" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div class="title">
<b>Figure 4:</b> Relationships between the ancestry and sex RIP variables and their initial predictor variables.</div>
<div class="desc">
(A)
RIP-A with genomic ancestry; genomic ancestry is calculated using the
core panel of 68 AIMs and RIP-A is calculated using this ancestry
estimate on the set of three populations combined (N = 592). Populations
are indicated as shown in the legend with United States participants
shown with black circles, Brazilians with red circles, and Cape Verdeans
with blue circles. (B) Histograms of RIP-S by self-reported sex.</div>
</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghM5udX4Z5oPMXLEgFkIZeFB8xYjG9O-ggfH1SCrAzAkPLzVqKFnJmMVbt5xdJ-s4z3nLvHrYwucYyUiGA7zegCI2Zt8ofanCWJnhyphenhyphen_K5amn_xjT_Te_VNGABQUDuLVUiwpPYmt5w3y5EF/s1600/journal.pgen.1004224.g006.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghM5udX4Z5oPMXLEgFkIZeFB8xYjG9O-ggfH1SCrAzAkPLzVqKFnJmMVbt5xdJ-s4z3nLvHrYwucYyUiGA7zegCI2Zt8ofanCWJnhyphenhyphen_K5amn_xjT_Te_VNGABQUDuLVUiwpPYmt5w3y5EF/s1600/journal.pgen.1004224.g006.png" height="320" width="139" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div class="title">
<b>Figure 6:</b> Transformations and heat maps showing how face shape is affected by three particular RIP-G variables.</div>
<div class="desc">
The initial predictor variables are SNPs in the genes (A) <em>SLC35D1</em> (B) <em>FGFR1</em>, and (C) <em>LRP6</em>.
The top row of each panel shows the shape transformations near the
extreme values of the particular RIP-G shown. The second row shows the R<sup>2</sup>
(proportion of the facial total variation), the three primary facial
shape change parameters: area ratio, curvature difference, and normal
displacement. The max R<sup>2</sup> values for A, B, and C are 11.68%, 15.16% and 10.10%, respectively.</div>
</td></tr>
</tbody></table>
<span style="color: blue;"><br /></span>
<span style="color: blue;"><br /></span>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-28540674424814197142014-03-23T12:25:00.004-04:002014-03-23T12:25:48.253-04:00The $1,000 genome<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.nature.com/polopoly_fs/7.16222.1395137244!/image/falling-fast-nature.png_gen/derivatives/landscape_630/falling-fast-nature.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://www.nature.com/polopoly_fs/7.16222.1395137244!/image/falling-fast-nature.png_gen/derivatives/landscape_630/falling-fast-nature.png" height="335" width="400" /></a></div>
<br />
<br />
<br />
<span style="color: blue;">.................The price of sequencing an average human genome has plummeted from about
US$10 million to a few thousand dollars in just six years (see <a href="http://www.nature.com/news/technology-the-1-000-genome-1.14901#falling">‘Falling fast’</a>).
That does not just outpace Moore's law — it makes the once-powerful
predictor of unbridled progress look downright sedate. And just as the
easy availability of personal computers changed the world, the breakneck
pace of genome-technology development has revolutionized bioscience
research. It is also set to cause seismic shifts in medicine...........</span><br />
<br />
Read More Here: <a href="http://www.nature.com/news/technology-the-1-000-genome-1.14901">http://www.nature.com/news/technology-the-1-000-genome-1.14901 </a>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-51675063460189444842014-02-26T12:36:00.000-05:002014-02-26T12:41:16.914-05:00Was skin cancer a selective force for black pigmentation in early hominin evolution?<div class="tr_bq">
<span style="font-size: large;"><br /></span></div>
<div class="tr_bq">
<span style="font-size: large;">Some excerpts from a very interesting read, I suggest reading the whole article here:</span></div>
<br />
<a href="http://rspb.royalsocietypublishing.org/content/281/1781/20132955.full">http://rspb.royalsocietypublishing.org/content/281/1781/20132955.full</a><br />
<br />
<blockquote>
<span style="color: blue;">Dark or black skin lowers the risk of ultraviolet radiation (UVR)-induced skin cancer by several orders of magnitude and, while this might be considered an incidental benefit, here I make a case for lethal skin cancer—in reproductive, young, early humans, as a potent selective force underlying the emergence of black skin as the ancestral pigmentation state.</span></blockquote>
<br />
<blockquote>
<span style="color: blue;">Were it not for the efficacy of DNA repair of UV-induced DNA damage, those with white skin would all have cancer, and at a very young age, as evidenced by the impact of the inherited disorder of nucleotide excision DNA repair, xeroderma pigmentosum (XP) [25,26]. Black- or dark-skinned ethnic groups are substantially less at risk but when they do have a diagnosis of skin cancer, it is often on soles and palms—less pigmented regions of the body [27,28].</span></blockquote>
<br />
<blockquote>
<span style="color: blue;">In black-skinned individuals, melanocytes synthesize brown/black eumelanin which is then packaged into peri-nuclear distributed, ellipsoid melanosomes of keratinocytes (figure 1). This appears to be a near optimal arrangement for UV filtration and DNA protection. In white skin, melanocytes synthesize a higher proportion of yellow and/or red pheomelanin and this is then assembled into clustered small, circular melanosomes in keratinocytes. The compound effect is minimal UV filtration.</span></blockquote>
<br />
<blockquote>
<span style="color: blue;">Whatever the evolutionary logic, the acquisition of pale skin has become a liability. But only so because pale-skinned Europeans have been subject to either voluntary or enforced migration to much sunnier climes (e.g. Queensland, Australia, and other subtropical zones) and, more recently, have availed themselves of youthful opportunities for intermittent high level sun exposure via inexpensive air travel and recreational holidays in the sun. In this context, skin cancer arises as the consequence of a mismatch between the ancestral environmental conditions that shaped our genetics and skin properties and our current behavioural and social activities [3]. This narrative is reasonably well established. What I address here is another and, in a sense, reciprocal evolutionary aspect of skin coloration and cancer risk.</span></blockquote>
<br />
<blockquote>
<span style="color: blue;">Early hominin evolution in East Africa at some 2–3 Ma was associated with a dramatic loss of the body hair development that is retained by our primate cousins [68,69]. Hair growth was retained on the head—the most UVR-exposed part of the body of a bipedal hominin. Some exotic explanations have been entertained for this dramatic phenotypic shift, including avoidance of fur parasites or of catching fire, a response to wearing clothes or an adaptation to an aquatic way of life [68–72]. But the most likely major adaptive advantage would have been for thermoregulation or facilitation of sweating and heat loss for physically active, hunter–gatherers in the savannah [69,73,74]. But what colour was the exposed skin of the first hairless hominins? Not black it would seem. The skin of our nearest primate relative, the chimpanzee, is, under the fur, essentially pale or white with melanocytes restricted to hair follicles [67]. The exposed and relatively hairless face and hands are also white in infant chimpanzees of three Pan subspecies (but black in Pan paniscus) and they become facultatively pigmented with age [75]. It has therefore been considered very likely, albeit not unambiguously so [76], that the first African hominins to discard hirsutism were also white- or pale-skinned [7,43,50].</span></blockquote>
<br />
<blockquote>
<span style="color: blue;">There are no population-based databases that provide for accurate age incidence rates of skin cancer in African albinos. However, multiple clinical reports testify to the fact that the prevalence of skin cancer in African albinos, though variable according to geographical region, is exceptionally high in low-latitude (5–10°) regions with high year-round UVB exposures, including Tanzania [97,109–111], Cameroon [112] and Nigeria [93,113,114]. In South Africa, skin cancer rates in albinos vary with latitude and altitude, being relatively high in Soweto and the Transvaal and lower in the Transkei [107,115]. The risk of developing skin cancer in Soweto albinos was estimated to be some 1000 times that of pigmented blacks [116]. Erythema and burns occur in infant albinos and focal skin lesions develop as early as 5 years of age [97]. By the age of 20 years, most albino individuals in low-latitude regions have multiple actinic keratoses (figure 3) [97], the precursor lesions for SCC [117,118]. Many of these regress spontaneously but most, if not all albinos, have overt skin cancer in their twenties or thirties [97,115,119,120], with occasional presentation even in childhood [97]. </span></blockquote>
<br />
<blockquote>
<span style="color: blue;">8. Concluding remarks<br />Extrapolation from the current risk of skin cancer in OCA2 albinos to that of early hominins in equatorial Africa is clearly speculative but if early humans were indeed pale-skinned, they would most probably have similarly suffered substantial affliction during reproductively active years from non-melanoma skin cancers. That skin cancer in African albinos might be germane to considerations of the adaptive significance of dark skin has been noted before [7,11,138,139], but never explored.</span></blockquote>
<br />
<blockquote>
<span style="color: blue;">The age-related incidence and mortality from skin cancer, both historically and in contemporary albinos, have been modulated by many factors, including lifestyle, occupation and varying degrees of awareness, preventive measures and medical intervention [91]. In these cultural respects, the lethal impact of skin cancer would have been more severe in naked, pale-skinned and outdoor living hominins, dwelling in a habitat with the highest levels of year-round UVB radiation—in open and arid equatorial savannah. It is difficult to imagine a more potent prescription for cancer: maximum, sustained, whole-body carcinogenic exposure (UVB) coupled with minimal attenuation capacity (via melanin). Young hunter–gatherer males might have suffered the greatest UV exposure and risk of cancer. Death would have ensued at a young age from either metastases or localized invasion, ulceration, bleeding and infection. The detrimental impact on reproductive fitness would then have been severe, providing potent pressure for both the selective sweep of the highly stable African MC1R variant, promoting eumelanin synthesis and black skin and its subsequent stable maintenance for more than a million years. This critical gene clearly did diversify in sequence and function in the descendents of most of those migrants that left Africa to populate the rest of the world. In those, the selective pressures via UVR were both relaxed and different.</span></blockquote>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com2tag:blogger.com,1999:blog-7606098424948502460.post-84702623686448514122014-02-25T00:11:00.001-05:002014-02-25T00:11:21.847-05:00mtDNA from Southern Africa<span style="font-size: large;">Reference mtDNA from Southern Africa from the pre-print "<a href="http://biorxiv.org/content/early/2014/02/18/002808">Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa</a>" (Thanks to Maju for the referral)</span><br />
<script src="//ajax.googleapis.com/ajax/static/modules/gviz/1.0/chart.js" type="text/javascript"> {"dataSourceUrl":"//docs.google.com/spreadsheet/tq?key=0AnED03mcS8t5dGtYdXBSQVBoOVpZVWxwVnQ0VzZPcWc&transpose=0&headers=1&range=A1%3AT24&gid=0&pub=1","options":{"vAxes":[{"useFormatFromData":true,"minValue":null,"viewWindowMode":null,"textStyle":{"bold":true,"color":"#222","fontSize":"12"},"viewWindow":null,"maxValue":null},{"useFormatFromData":true}],"titleTextStyle":{"bold":true,"color":"#000","fontSize":16},"booleanRole":"certainty","title":"Southern African mtDNA","height":912,"animation":{"duration":500},"legend":"right","width":900,"hAxis":{"useFormatFromData":true,"minValue":0,"viewWindowMode":"explicit","logScale":false,"viewWindow":{"min":0,"max":1},"maxValue":1},"tooltip":{},"isStacked":true},"state":{},"view":{},"isDefaultVisualization":false,"chartType":"BarChart","chartName":"Chart 1"} </script>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com2tag:blogger.com,1999:blog-7606098424948502460.post-15113475483889866662014-02-21T20:48:00.001-05:002014-04-04T19:56:13.757-04:00YDNA E-M123; A closer look<span style="font-size: large;">E-M123 (as well as E-M34) was first discovered by <a href="http://www.ncbi.nlm.nih.gov/pubmed/11062480">Underhill(2000)</a> and is found with a low to medium frequency distribution in East Africa and the Middle East, while it has a low frequency distribution in North Africa and Europe.</span><br />
<span style="font-size: large;"><br /></span>
<b><span style="font-size: large;">Phylogeny:</span></b><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKcMbKwlKBrGGn4KMBJvGT4vP5knh9GLPV9msFz5BapXSYmqrKj04lvBoZPbHj25gAYTtb4wpTqlWQN1WJBSy_XSV_ryUcO-NnU74U-THcm1UBW_xEYlIsNnNkFRfiRHP6FUuotLJVjXG1/s1600/EM35_Phylogeny.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKcMbKwlKBrGGn4KMBJvGT4vP5knh9GLPV9msFz5BapXSYmqrKj04lvBoZPbHj25gAYTtb4wpTqlWQN1WJBSy_XSV_ryUcO-NnU74U-THcm1UBW_xEYlIsNnNkFRfiRHP6FUuotLJVjXG1/s1600/EM35_Phylogeny.png" height="320" width="247" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 1 - Current and previous E-M215 phylogenetic structure </td></tr>
</tbody></table>
<b><span style="font-size: large;"><br /></span></b>
<span style="font-size: large;">Figure 1 shows a comparison of the basic phylogeny of E-M215/M35 as was known before 2011 (a) and after (b), with a 'who and when' key for the Discovery of the UEPs. Notice the impact the rearrangement has on the phylogenetic placement of E-M123, specifically the fact that E-M123 is shown to have a more recent common ancestor with the East and Southern African variants of E-M35, i.e. E-V42 and E-M293, before it does with any of the other variants of E-M35.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><b>Previous publications:</b></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">While it is unfortunate that all of the research that has previously been published on E-M123 was done under the consideration of the older (and rather out of date) configuration of the basic structure of E-M35, it is still worth while to look at articles that have tried to untangle the origins and history of this lineage, of these, 3 come to mind:</span><br />
<span style="font-size: large;"></span><br />
<a name='more'></a><span style="font-size: large;"><br /></span>
<span style="font-size: large;">(1) </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181965/"><span style="font-size: large;">Semino et al.</span></a><span style="font-size: large;">, in which the following paragraph was said with respect to E-M123:</span><br />
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">"The very low frequency of E-M123 in Ethiopia does not allow any inferences about the origin of this clade. The network of E-M78 and that of E-M123 are in agreement with the hypothesis of their ancient presence in the Near East and their subsequent expansion into the southern Balkans. The divergence time (TD) (Zhivotovsky 2001) between the Near East and European lineages has been estimated to a range of 7–14 thousand years (ky) ago. Cinnioğlu et al. ( 2004) found a high degree of variance of E-M123 in Turkey, which has been interpreted as being due to multiple founders rather than a single early dispersal event that has remained geographically circumscribed."</span></blockquote>
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">(2) </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181964/"><span style="font-size: large;">Cruciani et al</span>.</a><span style="font-size: large;">, in which this was said about the lineage:</span><br />
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">"In our data set, all the E-M123 chromosomes also carry the M34 mutation (E-M34), with the exception of one E-M123* subject from Bulgaria. This paragroup has been previously reported only in one individual from Central Asia (Underhill et al. 2000). Although the frequency distribution of E-M34 could suggest that eastern Africa was the place in which the haplogroup arose, two observations point to a Near Eastern origin: (1)Within eastern Africa, the haplogroup appears to be restricted to Ethiopia, since it has not been observed in either neighboring Somalia or Kenya (present study) or Sudan (Underhill et al. 2000). By contrast, E-M34 chromosomes have been found in a large majority of the populations from the Near East so far analyzed </span><span style="color: blue; font-size: large;">(Underhill et al. 2000; Cinniog˘ lu et al. 2004; Semino et al. 2004 [in this issue]; present study). (2) E-M34 chromosomes from Ethiopia show lower variances than those from the Near East and appear closely related in the E-M34 network (fig. 2D). If our interpretation is correct, E-M34 chromosomes could have been introduced into Ethiopia from the Near East. The high frequency of E-M34 observed for some of the Ethiopian populations could be the consequence of subsequent genetic drift, which can also explain the lower frequencies (2.3% [Underhill et al. 2000] and 4.0% [Semino et al. 2002]) reported for two large independent samples of Ethiopians."</span></blockquote>
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">(3) The last comes from a thesis, commonly referred to in this blog as the '</span><a href="http://drum.lib.umd.edu/handle/1903/11443"><span style="font-size: large;">Hirbo thesis</span></a><span style="font-size: large;">' (2011), where it said:</span><br />
<span style="font-size: large;"></span>
<br />
<blockquote class="tr_bq">
<span style="color: blue; font-size: large;">"The E3b3 haplotype, defined by the M123 mutation, was previously suggested to have originated in the Middle East and is found at low frequencies both in the Middle Eastern and East African populations [153, 434] (Appendix 6a). This conclusion was based on the fact that the E3b3 haplotype was observed only in Ethiopian samples from among the nine East African populations analyzed in a previous study [153], and lower STR variances in the Ethiopian E3b3 samples than in the Middle East [153]. However, extensive analysis of East African populations in the current study shows that this haplotype is found in Kenyan and Tanzanian Cushitic speakers as well, albeit, at low frequency (Figure 3.3.2, Appendix 6a). Its frequency maximum is centered in northeastern Africa (Table A9.1.1, Figure A9.1.7). Considering that the highest frequency is observed among the Ethiopian Jews [164] (Appendix 6a) a population that has been shown to be paternally [505, 565] and maternally [219] distinct from other Jewish populations, and genetically most similar to Sub-Saharan Africans [219, 505, 565], and the highest variance is observed in African populations (Table A9.1.2), the origin of E3b3 will most probably be among Cushitic/Omotic speaking populations of Southwest and Central Ethiopia."</span></blockquote>
<br />
<span style="font-size: large;"><b>Frequency:</b></span><br />
<br />
<span style="font-size: large;">Below are some of the more significant (>5%) frequencies of E-M123 found in published papers. Note that almost all E-M123 haplotypes also belong to E-M34, but since some papers directly test for E-M34 and others test just for E-M123, I have noted all the UEPs as E-M123 for the sake of uniformity:</span><br />
<br />
<b><span style="font-size: large;">2002</span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/11719903">Semino et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Ethiopian Oromo<br />
<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/11910562">Cruciani et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>14% of E-M123 in the Beta Israel of Ethiopia<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<b><span style="font-size: large;">2003</span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/14586639">Cinnioglu et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5-9% of E-M123 in all regions of Turkey except regions 1,2 & 8<br />
<br />
<b><span style="font-size: large;">2004</span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181964/">Cruciani et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>24% of E-M123 in Ethiopian_Amhara<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>8% of E-M123 in Ethiopian_Wolayta<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>8% of E-M123 in Erzurum Turkish<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>8% of E-M123 in Ethiopian_Oromo<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>8% of E-M123 in Omanite<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>7% of E-M123 in Bedouins<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>7% of E-M123 in Sicilians<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Sephardi Turks<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Northern Egyptians<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181965/">Semino et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>13% of E-M123 in an Albanian community of the Cosenza province in Italy<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>12% of E-M123 in Ashkenazi Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Sephardi Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Tunisians<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Lebanese<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1216069/">Arredi et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Algerian Berbers<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>9% of E-M123 in Northern Egyptians<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>7% of E-M123 in Southern Egyptians<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/15300852">Shen et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>20% of E-M123 in Libyan Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>12% of E-M123 in Ethiopian Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Ashkenazi Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Yemeni Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/15503146">Moran et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>11% of E-M123 in Ethiopian Track and Field<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Ethiopian Marathon<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>6% of E-M123 in Ethiopian General Control<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Ethiopian Arsi Control<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<b><span style="font-size: large;">2005 </span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182266/#!po=25.0000">Luis et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Arabs from Oman<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Arabs from Egypt<br />
<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/16142507">Flores et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>31% of E-M123 in Jordainians from the Dead Sea<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<b><span style="font-size: large;">2006</span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/16626329">Beleza et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>12% of E-M123 in Beja, Portugal<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Coimbra, Portugal<br />
<br />
<b><span style="font-size: large;">2007 </span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/17928816">Cadenas et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>8% of E-M123 in Yemenis<br />
<br />
<b><span style="font-size: large;">2008 </span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001430">Contu et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Tempio, Sardinia<br />
<br />
<b><span style="font-size: large;">2009 </span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771134/">Hammer et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Israelite Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Cohanim Jews<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2985948/#!po=7.14286">Di Gaetano et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>11% of E-M123 in Mazara del Vallo, Sicilly<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>11% of E-M123 in Piazza Armerina, Sicilly<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Troina, Sicilly<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<b><span style="font-size: large;">2011</span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>The supplemental data of the <a href="http://discovery.ucl.ac.uk/1331901/">Plaster thesis</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>25% of E-M123 in Ethiopian_Maale<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>13% of E-M123 in Ethiopian_Amhara<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>10% of E-M123 in Ethiopian_Oromo<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>The <a href="http://drum.lib.umd.edu/handle/1903/11443">Hirbo thesis</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>9% of E-M123 in Ethiopian_Burji<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>8% of E-M123 in Kenyan_Yaku<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>5% of E-M123 in Kenyan_Boni<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><br />
<b><span style="font-size: large;">2013 </span></b><br />
<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056775">Bekada et al.</a> found:<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>11% of E-M123 in Sahara + Mauritania<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>7% of E-M123 in Egypt<br />
<span class="Apple-tab-span" style="white-space: pre;"> </span>6% of E-M123 in Turkey<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirbpKVRp9ip3j7M685a6-RKoiECWYlV0XoPCq7V8QMjMY6bDHCOhnn-eX1G2ZSpjzCe6qZ7bC-h49M617w1xYq5CDLnZGl7O1XsgaHWhhEo5MG3jn0Le6YeCIjMYqL8wDC-kQJkg8mxAvt/s1600/Hirbo_Frequency.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEirbpKVRp9ip3j7M685a6-RKoiECWYlV0XoPCq7V8QMjMY6bDHCOhnn-eX1G2ZSpjzCe6qZ7bC-h49M617w1xYq5CDLnZGl7O1XsgaHWhhEo5MG3jn0Le6YeCIjMYqL8wDC-kQJkg8mxAvt/s1600/Hirbo_Frequency.PNG" height="238" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 2 - E-M123 Contour Map from the Hirbo Thesis </td></tr>
</tbody></table>
<br />
<span style="font-size: large;">The contour map shown above is taken from Figure A9.1.7 of the </span><a href="http://drum.lib.umd.edu/handle/1903/11443"><span style="font-size: large;">Hirbo thesis</span></a><span style="font-size: large;"> and shows the general spatial frequency distribution of E-M123 in Africa, Near East and Southern Europe. While the map obviously does not include data from sources published after 2011, like Bekada (2013) for instance, also note that it does not include the E-M123 data found from the Plaster thesis as well.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><b>TMRCA/Variance:</b></span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181964/">Cruciani 2004</a> used Microsatelite networks (Figure 2D in the publication) to infer that Ethiopian E-M34 variance is lower than that found in the near east, since the Ethiopian M34 haplotypes appeared to be more closely related than the Near Eastern ones in the network. <a href="http://drum.lib.umd.edu/handle/1903/11443">Hirbo </a>on the other hand, inferred higher variance (Table A9.1.2) in Africa than outside of Africa.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Below, I have used the <a href="http://ehelix.pythonanywhere.com/init/default/calc_approach">ASD approach</a> to compute and compare TMRCAs of several E-M123/M34 datasets:</span><br />
<br />
<ol>
<li><span style="font-size: large;">The Plaster E-M34, N = 34 dataset, representing haplotypes from Ethiopia, filed under <a href="http://ehelix.pythonanywhere.com/init/default/Example_Files">Ethiopian_EM34.csv</a>.</span></li>
<li><span style="font-size: large;">The Plaster Ethiopian Amhara Dataset, N = 9, A subset of (1)</span></li>
<li><span style="font-size: large;">The Plaster Ethiopian Maale Datastet, N = 16, A subset of (1)</span></li>
<li><span style="font-size: large;">The global E-M123 dataset from publicly available FTDNA haplotypes, N = 129, note that a very vast majority of these are not of African origin, although a few could be, filed under <a href="http://ehelix.pythonanywhere.com/init/default/Example_Files">FTDNA_EM123.csv</a></span></li>
<li><span style="font-size: large;">The global E-M84 dataset from publicly available FTDNA haplotypes, N = 69, note that E-M84 is a variant of E-M34, filed under <a href="http://ehelix.pythonanywhere.com/init/default/Example_Files">FTDNA_EM84.csv</a></span></li>
</ol>
<br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The TMRCAs for these haplotypes were computed using the germline mutation (pedigree) rates and effective (Zhivotovsky) rates separately, see Figures 3-4 below. In addition, 2 different sets of markers were analyzed, the first set included all markers available in the calculator, intersected with all the markers available in the Plaster thesis, yielding 14 markers. The second set comes from an intersection of the markers from the thesis with the <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181912/">recommended Zhivotovsky markers</a>, yielding 9 markers.</span><br />
<span style="font-size: large;"><br /></span>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3zbmtL1BeJJwaQ0AGl0hc7DL_-sSH7bHo8PjZd047CEWdTmI2twDjh-ezvLxBhtyaoag7gNNUq1y3k9cZVYF1hnHGqNAojAOepz3MI5AS6YNNnQ3ao0Fk331jZQ3sJTGK_nALcNPnM-B4/s1600/Zhiv.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3zbmtL1BeJJwaQ0AGl0hc7DL_-sSH7bHo8PjZd047CEWdTmI2twDjh-ezvLxBhtyaoag7gNNUq1y3k9cZVYF1hnHGqNAojAOepz3MI5AS6YNNnQ3ao0Fk331jZQ3sJTGK_nALcNPnM-B4/s1600/Zhiv.PNG" height="204" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 3 - Zhivotovsky Central TMRCA Estimates</td></tr>
</tbody></table>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_KP1tkn0aNOoNjDVzglUH4ld6iPnplh_GqVnHl0YoTX62zDzWSCvBWsy-w9k-aiA5aaP2iPzLQtw-SNNbib_pdSQOYidNHKFk97GET5-xa0DY24lTII-TbTrKcT1NcDHl22FnAQn1XCy_/s1600/Pedigree_9.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_KP1tkn0aNOoNjDVzglUH4ld6iPnplh_GqVnHl0YoTX62zDzWSCvBWsy-w9k-aiA5aaP2iPzLQtw-SNNbib_pdSQOYidNHKFk97GET5-xa0DY24lTII-TbTrKcT1NcDHl22FnAQn1XCy_/s1600/Pedigree_9.PNG" height="209" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 4a - Pedigree Central TMRCA Estimate Ranges - 9 Markers</td></tr>
</tbody></table>
<span style="font-size: large;"><br /></span>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6u9qoOrroRDFofX8So4VB1MmJJcF90nXkWFOGUR7aOptqRpIAVsODBsW6mZJJcCY1hhL3zhjAjo7uqZF-7qx3LHIenwFVgEeLxQeGKUo7Iryz43vWiIJJK4-agEjgLWZrFkPm9BUybVsO/s1600/Pedigree_14.PNG" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg6u9qoOrroRDFofX8So4VB1MmJJcF90nXkWFOGUR7aOptqRpIAVsODBsW6mZJJcCY1hhL3zhjAjo7uqZF-7qx3LHIenwFVgEeLxQeGKUo7Iryz43vWiIJJK4-agEjgLWZrFkPm9BUybVsO/s1600/Pedigree_14.PNG" height="206" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 4b - Pedigree Central TMRCA Estimate Ranges - 14 Markers</td></tr>
</tbody></table>
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The results of the comparative TMRCA calculations are by no means unequivocal, but nevertheless allow for several observations to be made:</span><br />
<br />
<ul>
<li><span style="font-size: large;">The overall Ethiopian E-M34 haplotypes have comparable and greater central TMRCA estimates than the global E-M123 samples with the exception of the scenario of 14 markers with the use of pedigree mutation rates (Figure 4b)</span></li>
<li><span style="font-size: large;">The Ethiopian Maale dataset consistently shows the least central TMRCA estimate compared with the other datasets, conversely, the Ethiopian Amhara datastet consistently shows the highest central TMRCA estimate compared to all other datasets. </span></li>
<li><span style="font-size: large;">The remaining Ethiopian haplotypes, mostly belonging to the Oromo, have an intermediate TMRCA estimate between the Amhara and Maale samples, although a lot closer to the Amhara estimates.</span><span style="font-size: large;"> </span></li>
</ul>
<span style="font-size: large;"><br /></span>
<br />
<ul>
</ul>
<div>
<b style="font-size: x-large;">Conclusion:</b></div>
<div>
<ul>
<li><span style="font-size: large;">The current phylogenetic positioning of E-M123 (Figure 1b) reduces the probability of the lineage originating in the Near East (vs. Eastern Africa), relative to the independent positioning that the lineage used to have within E-M35 (Figure 1a). This is because the new position reveals that E-M123 shares a more recent common ancestor with lineages of E-M35 that are either East African (E-V42) or South/East African (E-M293) specific, rather than, either (a) showing a closer relationship to the main variant of E-M35 that is found outside of Africa, i.e. E-M78 or (b) maintaining its old independent position within E-M35.</span></li>
<li><span style="font-size: large;">Of the two arguments lending support to a Near Eastern origin of E-M123 brought forth by <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181964/">Cruciani (2004)</a>, the first, "restriction of the haplogroup within Ethiopia", has been invalidated by sampling that has been done since the report, namely</span><span style="font-size: large;"> (a) the finds of E-M123 in the Yaaku, Boni and Turkana of Kenya in the <a href="http://drum.lib.umd.edu/handle/1903/11443">Hirbo Thesis</a>, (b) one of the highest ever recorded frequencies of E-M123 found in southern most Ethiopia (Semien Omo Zone) among the Omotic speaking Maale in the <a href="http://discovery.ucl.ac.uk/1331901/">Plaster thesis</a> and (c) the E-M123 find in a Somali dataset in </span><a href="http://www.nature.com/ejhg/journal/v13/n7/fig_tab/5201390f1.html#figure-title"><span style="font-family: inherit; font-size: large;">Sanchez (2005)</span></a><span style="font-size: large;">, albeit at quite a low frequency. The second argument, "lower variance of E-M34 chromosomes in Ethiopia", proves to be at best inconclusive and at worst wrong, after carrying out further analysis on E-M34 haplotypes from Ethiopia relative to large global samples of publicly available E-M123 haplotypes, see Figures 3 - 4, in addition to the analysis carried out in the Hirbo thesis (</span><span style="font-size: large;">Table A9.1.2).</span></li>
<li><span style="font-size: large;">The previous understanding of a decreasing frequency of E-M34 haplotypes from Northern to Southern Ethiopia has been upset by the samples that appeared with the Plaster thesis, since the highest frequency of the lineage was found in the Omotic speaking Maale, however, while the frequency appears to be higher in the South and lower in the North, the diversity of the lineage appears to have an opposite pattern, i.e. higher in the North and lower in the South.</span></li>
</ul>
<span style="font-size: large;"><span style="color: red;"><b>UPDATE (04/04/2014)</b></span></span></div>
<div>
<span style="font-size: large;">Median Joining Networks (created using the Fluxus Network Software)</span></div>
<div>
<span style="font-size: large;"><span style="color: red;"><br /></span></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGlc-7AodR7gdWWkh3bxVLaRumKGB8Wr-y_tHN4UDpi946kub-W7rnXY80AmXIHE-LuHLJjVZFlzkJSBfxR1HyLpc-GLfw_8F7Cy2A5x7-2L0OHvPVaUcWyJQ3cZQ3QHnRYIi1RGd1Hgg0/s1600/EM34_Ethiopia.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGlc-7AodR7gdWWkh3bxVLaRumKGB8Wr-y_tHN4UDpi946kub-W7rnXY80AmXIHE-LuHLJjVZFlzkJSBfxR1HyLpc-GLfw_8F7Cy2A5x7-2L0OHvPVaUcWyJQ3cZQ3QHnRYIi1RGd1Hgg0/s1600/EM34_Ethiopia.png" height="200" width="154" /></a></div>
<div>
<span style="font-size: large;"><span style="color: red;"></span></span><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9M2CUKsUWxte4Bc_9AjA0KcVubx9WEwYVds3Ts_3uNcsF5tms81bV3elMW32Tac5MEhf7addBmzQNlPpc2Fgqhvuw1YqRS5VK5_VDauAI5cNen5eOSb2s9En2lakvBItLl6oT0LLjTw4b/s1600/EM34_Ethiopia_EM123_FTDNA.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi9M2CUKsUWxte4Bc_9AjA0KcVubx9WEwYVds3Ts_3uNcsF5tms81bV3elMW32Tac5MEhf7addBmzQNlPpc2Fgqhvuw1YqRS5VK5_VDauAI5cNen5eOSb2s9En2lakvBItLl6oT0LLjTw4b/s1600/EM34_Ethiopia_EM123_FTDNA.png" height="200" width="154" /></a></div>
<div>
<span style="font-size: large;"><span style="color: red;"><b> </b></span> </span><ul>
</ul>
</div>
Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com11tag:blogger.com,1999:blog-7606098424948502460.post-16056366172062575742014-02-14T16:41:00.001-05:002014-02-21T20:49:51.721-05:00Comprehensive Ethiopian YDNA TMRCA Estimates<span style="font-size: large;">Find below a comprehensive list for all central TMRCA estimates calculated from the Plaster thesis for 6 UEPs (look <a href="http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html">at this post under Interactive Chart of Figure 3.2</a> for the frequencies of the UEPs). </span><span style="font-size: large;">P*(x R1a) & Y*(x BT,A3b2) </span><span style="font-size: large;"> are not included due to their minimal frequency and very sporadic distribution. </span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">There were a total of 5,756 haplotypes reported with the paper for the markers <i>DYS19, DYS388, DYS390, DYS391, DYS392 and DYS393</i>.</span><span style="font-size: large;"> 30 of those haplotypes belonged to P*(x R1a) & Y*(x BT,A3b2), leaving a total of 5,726 haplotypes. These remaining haplotypes, were then categorized with the criteria of Cultural ID + Generic Language Group<span style="color: red;">*</span> + UEP, any group of haplotypes that conformed to this criteria with N >1 and with a coalescent not equal to 0 (meaning non-identical haplotypes) were processed for their TMRCA and reported, accounting for 5,668 or 98% of the total haplotypes reported for the paper.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">The tables are ordered according to the frequencies of the tested UEPs in Ethiopia, i.e. E*(x E1b1a), 3985 Haplotypes > J, 689</span><span style="font-size: large;"> Haplotypes</span><span style="font-size: large;"> </span><span style="font-size: large;"> > A3b2, 601</span><span style="font-size: large;"> Haplotypes</span><span style="font-size: large;"> </span><span style="font-size: large;"> > K*(xL,N1c,O2b,P) , 154</span><span style="font-size: large;"> Haplotypes</span><span style="font-size: large;"> </span><span style="font-size: large;">> BT*(xDE,JT), 193</span><span style="font-size: large;"> Haplotypes</span><span style="font-size: large;"> </span><span style="font-size: large;"> and E1b1a7, 46</span><span style="font-size: large;"> Haplotypes</span><span style="font-size: large;"> </span><span style="font-size: large;">.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Note that both the mean TMRCA's for Zhivotovsky (Z-TMRCA) and the pedigree rates (P-TMRCA), some times also known as germline rates, are in units of generations, the suitable length of a generation for the Z-TMRCA is 25 years, while for the P-TMRCA it may range from 28 to 33 years.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">If detail of the TMRCA analysis for any of the populations listed below maybe required, go to the <a href="https://ehelix.pythonanywhere.com/init/default/Example_Files">table here</a>, and upload the necessary file into the <a href="https://ehelix.pythonanywhere.com/init/default/index">Y TMRCA calculator</a> and filter for the specific population in question.</span><br />
<span style="font-size: large;"></span><br />
<a name='more'></a><span style="font-size: large;"><br /></span>
<span style="font-size: large;"><span style="color: red;">*Modification: </span>The initial blog post used First-Language-Group as the criteria, before changing it to the default language group of the Cultural ID, the reason for the change was because in the former case, too many groups of haplotypes with only 2 or 3 samples were generated, thus skewing the TMRCA results. However, keep in mind that some of the samples shown below do not speak a language in the 'Generic Language Group' as their first language. The original dataset which used the 'First-Language-Group' as a criteria can be downloaded <a href="https://dl.dropboxusercontent.com/u/42082352/Example_YSTR_FILES/Plaster_YDNA_first_lang.zip">from here</a>.</span>
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><br /></span><br />
<br />
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Mashile,Maale,Mejenger,Zayse,Anuak,Alaba,Amhara,Afar,Agew,Ari,Tigray,Tsemay,Sheko,Hadiya,Dasanach,Dirasha,Dawuro,Hamer,Dorze,Dizi,Yem,Sidama,Oromo,Shekecho,Somali,Kore,Konso,Kembata,Konta,Kefa,Gamo,Genta,Gobeze,Gedeo,Gofa,Ganjule,Gurage,Gewada,Nuer,Burji,Busa,Basketo,Wolayta,Bench,BenaAnonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-11311649946255676242014-02-11T21:08:00.000-05:002014-02-14T17:52:23.123-05:00Ethiopian YDNA J STR Analysis - An addendum<span style="font-size: large;">In the past, I had carried out a TMRCA (STR) analysis of <a href="http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-j-lineages-in-ethiopian.html" target="_blank">YDNA haplogroup J haplotypes</a> from Ethiopia using the primary dataset from the Plaster thesis that was <a href="http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html" target="_blank">discussed here</a>. While that particular dataset had a large number of haplotypes, it also had a low number of Markers (6). However there was supplementary data that had Y-STR Haplotypes from haplogroup J supplied with the paper. While it only had data for a select few of the populations found in the main paper, it however had better resolution typing at 14 markers. Below are the TMRCA results for those haplotypes. The Dataset can be found <a href="http://ehelix.pythonanywhere.com/init/default/Example_Files" target="_blank">in this table</a> in .csv format under "Ethiopian_JM267.csv".</span><br />
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<span style="font-size: large;">In total, 54 haplotypes were found in the supplementary dataset, nevertheless the total number of haplotypes among the population groups sum up to 53 above, the reason is because one haplotype that belonged to the Anuak dataset was not included.</span><br />
<br />
<span style="font-size: large;">The results are quite consistent with the results I got from the dataset with less resolution, even if the sample sizes are quite small. For instance, although the Afar had the J Haplogroup in excess of 25%, their haplotypes show the least amount of diversity, conversely the high diversity of Haplogroup J in the other populations is still maintained. </span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">While the Zhivotovsky TMRCA (Z-TMRCA) for all the 691 YDNA J haplotypes found in Ethiopia in the lower resolution dataset was previously calculated to 595 generations, the Z-TMRCA for the higher resolution dataset for all 54 haplotypes, as seen above, was calculated to 705 generations, if only the markers that were used in the lower resolution data set were used to compute the Z-TMRCA in these 54 haplotypes we would get a Z-TMRCA of 631 Generations. Furthermore, if we intersected the 14 markers from this dataset with the <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181912/">recommended Zhivotovsky markers</a>, the resulting markers of '19', '393', '392', '391', '390', '439', '388', '389-1' and '389-2' , would yield</span><span style="font-size: large;"> a Z-TMRCA of 920 generations, implicating an introduction of YDNA J-M267 in Ethiopia well into the </span><span style="font-size: large;">Upper Paleolithic.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"><b><span style="color: red;">Update</span></b>: With respect to the low resolution haplotypes from the plaster thesis; I have added 5,726 YDNA str haplotypes in *.csv format compatible with the calculator and tabulated according to the UEPs tested, in the Table at this link below as well: <a href="http://ehelix.pythonanywhere.com/init/default/Example_Files">http://ehelix.pythonanywhere.com/init/default/Example_Files</a></span>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0tag:blogger.com,1999:blog-7606098424948502460.post-1150972145614504932014-01-27T19:00:00.000-05:002014-03-25T21:49:45.398-04:00Y TMRCA Calculator as a Web App<span style="font-size: large;">The Y DNA (STR) TMRCA calculator can now be accessed as a web application with full functionality here:</span><br />
<br />
<a href="http://ehelix.pythonanywhere.com/">http://ehelix.pythonanywhere.com/</a><br />
<br />
<span style="font-size: large;">It is also embedded in this blog in a new page (above)</span><br />
<span style="font-size: large;"><br /></span>
<span style="color: red; font-size: large;"><b>UPDATE (02/11/2014)</b></span><br />
<span style="color: red; font-size: large;"><b><br /></b></span>
<span style="font-size: large;">Another series of updates for the calculator:</span><br />
<br />
<ul>
<li><span style="font-size: large;">User now able to utilize the previously idle first column in the csv file to group haplotypes together and thus compute the TMRCA for a specified group (see example below)</span></li>
<li><span style="font-size: large;">The application now also accepts Locus names in <a href="http://www.cstl.nist.gov/strbase/ystr_fact.htm" target="_blank">NIST </a>format as well.</span></li>
<li><span style="font-size: large;">It also now automatically deletes any haplotype with a non-integer value given for any locus in the *.csv file. (instead of producing an error for that scenario)</span></li>
</ul>
<br />
<a name='more'></a><br />
<br />
<span style="font-size: large;">To demonstrate the filtration utility, consider the YDNA E-V13 portion of the Bulgarian dataset from “Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry”, the *.csv file for this dataset can be downloaded from the link below as well : </span><br />
<span style="font-size: large;"><a href="http://ehelix.pythonanywhere.com/init/default/Example_Files">http://ehelix.pythonanywhere.com/init/default/Example_Files</a>.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">When the file is uploaded, the application gives the option to analyze any subset of haplotypes with N>1 that is available, i.e in this case: Bulgaria/Central, Bulgaria/East and Bulgaria/West, in addition to all of the Haplotypes.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Picking each of the above subsets from the “Choose a filter” listbox and running them separately produces the following results:</span><br />
<span style="font-size: large;"><br /></span>
****************************************************************************************************<br />
Active Y-str file: Bulgaria_EV13.csv<br />
Active Markers file: Full_marker_list.txt<br />
Dataset: Bulgaria_EV13<br />
Sample size: 49<br />
****************************************************************************************************<br />
*Marker Details*<br />
8 requested markers included in analysis (41 excluded):-<br />
<br />
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']<br />
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']<br />
****************************************************************************************************<br />
*Coalescent Details*<br />
Ballantyne--Generations(Median)--74.17 Generations(Modal)--74.17<br />
<br />
Burgarella_Navascues--Generations(Median)--89.57 Generations(Modal)--89.57<br />
<br />
Chandler--Generations(Median)--101.78 Generations(Modal)--101.78<br />
<br />
Stafford--Generations(Median)--87.07 Generations(Modal)--87.07<br />
<br />
Zhivotovsky--Generations(Median)--317.95 Generations(Modal)--317.95<br />
<br />
****************************************************************************************************<br />
*Pedigree/Familial Rates Summary*<br />
Years/Generation: 28 - 33<br />
<br />
TMRCA Range: 2076 - 3358<br />
<br />
Mean TMRCA: 2688<br />
<br />
Median TMRCA: 2678<br />
<br />
****************************************************************************************************<br />
Active Y-str file: Bulgaria_EV13.csv<br />
Active Markers file: Full_marker_list.txt<br />
Dataset: Bulgaria_EV13, <span style="background-color: yellow;">Filter = Bulgaria/Central</span><br />
Sample size: 17<br />
****************************************************************************************************<br />
*Marker Details*<br />
8 requested markers included in analysis (41 excluded):-<br />
<br />
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']<br />
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']<br />
****************************************************************************************************<br />
*Coalescent Details*<br />
Ballantyne--Generations(Median)--50.30 Generations(Modal)--50.30<br />
<br />
Burgarella_Navascues--Generations(Median)--61.98 Generations(Modal)--61.98<br />
<br />
Chandler--Generations(Median)--64.37 Generations(Modal)--64.37<br />
<br />
Stafford--Generations(Median)--53.36 Generations(Modal)--53.36<br />
<br />
<span style="background-color: yellow;">Zhivotovsky--Generations(Median)--245.10 Generations(Modal)--245.10</span><br />
<br />
****************************************************************************************************<br />
*Pedigree/Familial Rates Summary*<br />
Years/Generation: 28 - 33<br />
<br />
TMRCA Range: 1408 - 2124<br />
<br />
Mean TMRCA: 1753<br />
<br />
Median TMRCA: 1748<br />
<br />
****************************************************************************************************<br />
Active Y-str file: Bulgaria_EV13.csv<br />
Active Markers file: Full_marker_list.txt<br />
Dataset: Bulgaria_EV13, <span style="background-color: yellow;">Filter = Bulgaria/East</span><br />
Sample size: 16<br />
****************************************************************************************************<br />
*Marker Details*<br />
8 requested markers included in analysis (41 excluded):-<br />
<br />
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']<br />
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']<br />
****************************************************************************************************<br />
*Coalescent Details*<br />
Ballantyne--Generations(Median)--85.28 Generations(Modal)--85.28<br />
<br />
Burgarella_Navascues--Generations(Median)--100.69 Generations(Modal)--100.69<br />
<br />
Chandler--Generations(Median)--116.98 Generations(Modal)--116.98<br />
<br />
Stafford--Generations(Median)--102.94 Generations(Modal)--102.94<br />
<br />
<span style="background-color: yellow;">Zhivotovsky--Generations(Median)--339.67 Generations(Modal)--339.67</span><br />
<br />
****************************************************************************************************<br />
*Pedigree/Familial Rates Summary*<br />
Years/Generation: 28 - 33<br />
<br />
TMRCA Range: 2387 - 3860<br />
<br />
Mean TMRCA: 3094<br />
<br />
Median TMRCA: 3078<br />
<br />
****************************************************************************************************<br />
Active Y-str file: Bulgaria_EV13.csv<br />
Active Markers file: Full_marker_list.txt<br />
Dataset: Bulgaria_EV13, <span style="background-color: yellow;">Filter = Bulgaria/West</span><br />
Sample size: 16<br />
****************************************************************************************************<br />
*Marker Details*<br />
8 requested markers included in analysis (41 excluded):-<br />
<br />
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']<br />
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']<br />
****************************************************************************************************<br />
*Coalescent Details*<br />
Ballantyne--Generations(Median)--88.42 Generations(Modal)--88.42<br />
<br />
Burgarella_Navascues--Generations(Median)--107.76 Generations(Modal)--107.76<br />
<br />
Chandler--Generations(Median)--126.34 Generations(Modal)--126.34<br />
<br />
Stafford--Generations(Median)--107.00 Generations(Modal)--107.00<br />
<br />
<span style="background-color: yellow;">Zhivotovsky--Generations(Median)--373.64 Generations(Modal)--373.64</span><br />
<br />
****************************************************************************************************<br />
*Pedigree/Familial Rates Summary*<br />
Years/Generation: 28 - 33<br />
<br />
TMRCA Range: 2475 - 4169<br />
<br />
Mean TMRCA: 3275<br />
<br />
Median TMRCA: 3274<br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Notice that if a filter is chosen, the applied filter's name will be appended to the Dataset field of the results with “Filter =”, if all haplotypes are requested on the other hand, the Dataset field will just contain the Dataset's name as specified by the user.</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">To double check if the ASD computation has been carried out correctly for the central TMRCA estimates, we can cross-check the result of the publication itself for the 3 regions (Table S7 in the supporting information), against the Zhivotvsky results computed by the app. (highlighted above) multiplied by 25 (for 25years/generation according to Zhivotovsky).</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;"> (Publication) app. Zhivotovsky results</span><br />
<span style="font-size: large;">Bulgaria/Central 6,100YA<span class="Apple-tab-span" style="white-space: pre;"> </span> 6,127.5 YA<span class="Apple-tab-span" style="white-space: pre;"> </span></span><br />
<span style="font-size: large;">Bulgaria/East <span class="Apple-tab-span" style="white-space: pre;"> </span> 8,400YA<span class="Apple-tab-span" style="white-space: pre;"> </span>8,491.75 YA</span><br />
<span style="font-size: large;">Bulgaria/West<span class="Apple-tab-span" style="white-space: pre;"> </span> 9,300YA<span class="Apple-tab-span" style="white-space: pre;"> </span>9,341.00 YA</span><br />
<span style="font-size: large;"><br /></span>
<span style="font-size: large;">Close Enough!</span><br />
<span style="font-size: large;"></span><br />
<span style="font-size: large;"></span><br />
<span style="font-size: large;"></span><br />
<br />
<span style="color: red; font-size: large;"><b>UPDATE (03/16/2014)</b></span><br />
<span style="color: red; font-size: large;"><b> </b></span>
<br />
<div style="margin-bottom: 0in;">
<span style="font-size: large;">It is now possible to copy and paste
FTDNA-type haplotype repeats into the app, instead of only being able
to upload csv files.</span></div>
<br />
<span style="color: red; font-size: large;"><b>UPDATE (03/21/2014)</b></span><br />
<div style="margin-bottom: 0in;">
Added another 'mode' of analysis, the
'compare mode':</div>
<div style="margin-bottom: 0in;">
<br /></div>
<div style="margin-bottom: 0in;">
<span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;"><b>Compare
Mode</b></span></span></span><span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;">
- If there is more than one unique subset in the dataset, then TMRCA
computations will be carried out on each unique subset
simultaneously, summarized results will then be printed for each
subset in a tabular format. A "Sample Size Threshold" can
be assigned in this mode if the user wants to require a minimum
sample size from each subset to be analyzed , if nothing is assigned
in this field, then the application will use N = 2 as the minimum
sample size. </span></span></span><span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;"><b>Note:</b></span></span></span><span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;">
Slightly longer computation times will be required relative to
analysis carried out in single mode depending on sample size and the
total number of markers.</span></span></span>
</div>
<div style="margin-bottom: 0in;">
<br /></div>
<span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;">The
<b>Compare mode results</b> area below the submission form is divided
into two parts:</span></span></span><br />
<ol>
<li><span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;">The
first part establishes baseline information for the entire dataset
including the active STR and marker files, the sample size, DYS#'s
<br />used and the mean TMRCAs.</span></span></span><br />
</li>
<li><span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;">The
second part tabulates the results for each unique subset. The first
column of the table simply shows the name of the subset as <br />assigned
in the <a href="http://127.0.0.1:8000/TMRCA_V4a/default/instructions#filtering">filter
column</a> of the Y-STR file. The second column is for the sample
size of the subset. The third column shows the <br />ratio of the
number of haplotypes in the subset, relative to the total number of
haplotypes in the entire dataset. The fourth column,<br />Z-TMRCA,
shows the mean TMRCA in generations using the Zhivotovsky rates. The
last column, P-TMRCA, shows the mean TMRCA<br />in generations using
all the available pedigree rates. All of the columns are sortable in
ascending or descending order.</span></span></span><br />
</li>
<li><span style="color: #333333;"><span style="font-family: Georgia, serif;"><span style="font-size: medium;">A
link is given in the event that the user needs to open the results
of the compare mode analysis in a separate tab. This maybe useful<br />if
one wants to drill into a detailed analysis of any of the subsets
found in the table using the single mode analysis, with out closing
the <br />the results of the compare mode analysis for the active
dataset. </span></span></span>
<br />
</li>
</ol>
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To Demonstrate, with a total of N=1391
of 67 marker E1b1b haplotypes copied from the FTDNA public pages,
and using the 'Country' column as the filter.</div>
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For a threshold of N = 25 and the full marker list, sorted for descending Z-TMRCA: </div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhq43ukw14Q939SM1yfFEgSNTDi5RxUFQ-udJEiudbxWVnulrUj7zqRSnJPH57Y90doY5nt2PlTgf10abIspMBVjtFk4siASSMf9uyGoJJfkKgmoOlp9v3atJH6KviG71n9JwcLrqlDci9M/s1600/fullmarker.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhq43ukw14Q939SM1yfFEgSNTDi5RxUFQ-udJEiudbxWVnulrUj7zqRSnJPH57Y90doY5nt2PlTgf10abIspMBVjtFk4siASSMf9uyGoJJfkKgmoOlp9v3atJH6KviG71n9JwcLrqlDci9M/s1600/fullmarker.png" height="237" width="320" /></a></div>
<br />
<br />
<br />
For a threshold of N = 25 and the Zhivotovsky marker list, sorted for descending Z-TMRCA:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEja_m7t2ZCo0GkB6wsns1QaOTiP6Z2T5OBSZY97yO3qGemV39tTTQhGrNfQq81EH_TMOg7fK5SLjG7nNuNtjTiohBblYOWUH0bvxEcSRMET0KAmYhsqmuUlexRFgmDHdAvCcYPXPU6Sg-De/s1600/zhivmarker.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEja_m7t2ZCo0GkB6wsns1QaOTiP6Z2T5OBSZY97yO3qGemV39tTTQhGrNfQq81EH_TMOg7fK5SLjG7nNuNtjTiohBblYOWUH0bvxEcSRMET0KAmYhsqmuUlexRFgmDHdAvCcYPXPU6Sg-De/s1600/zhivmarker.png" height="231" width="320" /></a></div>
<span style="color: red; font-size: large;"><b>UPDATE (03/25/2014)</b></span><br />
<tt>Instead of using the 0.00069 rate for all the markers in the<br />
calculator that were not found in the Zhivotovsky publication, I have<br />
normalized the rates for the markers using an average of all the<br />
pedigree rates normalized with the effective rate's ratio , specific<br />
procedure I used to do this can be seen in the spreadsheet below.</tt><br />
<br />
<tt><a href="https://docs.google.com/spreadsheets/d/1D6FU4fpB6vwAnle2-oiEvCV7_50QQhdhk6irSSVQtDE/edit#gid=467401003"><tt>https://docs.google.com/spreadsheets/d/1D6FU4fpB6vwAnle2-oiEvCV7_50QQhdhk6irSSVQtDE/edit#gid=467401003</tt></a> </tt><br />
<br />
<span style="font-size: large;">See Also:</span><br />
<a href="http://ethiohelix.blogspot.com/2012/06/finding-tmrca-of-ethiopian-ydna.html">http://ethiohelix.blogspot.com/2012/06/finding-tmrca-of-ethiopian-ydna.html</a><br />
<a href="http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html">http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html</a><br />
<a href="http://ethiohelix.blogspot.com/2013/01/tmrca-calculations-from-plaster-nry.html">http://ethiohelix.blogspot.com/2013/01/tmrca-calculations-from-plaster-nry.html</a><br />
<a href="http://ethiohelix.blogspot.com/2013/02/the-zhivotovsky-multiplier.html">http://ethiohelix.blogspot.com/2013/02/the-zhivotovsky-multiplier.html</a><br />
<a href="http://ethiohelix.blogspot.com/2013/03/african-sahel-ydna.html">http://ethiohelix.blogspot.com/2013/03/african-sahel-ydna.html</a><br />
<a href="http://ethiohelix.blogspot.com/2013/04/source-code-for-asd-based-tmrca.html">http://ethiohelix.blogspot.com/2013/04/source-code-for-asd-based-tmrca.html</a><br />
<a href="http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-j-lineages-in-ethiopian.html">http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-j-lineages-in-ethiopian.html</a><br />
<a href="http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-m13-lineages-in.html">http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-m13-lineages-in.html</a>Anonymoushttp://www.blogger.com/profile/06247500186976801582noreply@blogger.com0