Ugandan mtDNA

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. 

Mosaic maternal ancestry in the Great Lakes region of East Africa

Abstract

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.

Link

Sudan MTDNA

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 here. The thesis also includes YDNA data, but those same results have been already covered in this blog post. Additionally, some interesting ancient YDNA data is also included in the thesis.

Note, I wrote a small script that can enable sorting of the relative frequencies by clicking the haplogroups, you can find the script @ JSFiddle, if you find the script useful and would like to use it for other relative frequency charts, please cite the JSFiddle link from above.

More Ethiopian Uniparental Data (More resolution.. less clarity)

A new paper attempting to decipher the out of Africa exit route by focusing on Ethiopian and Egyptian autosomal genetics was published 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.

Note that the phylogeny they reference for the results here, is from Phylotree Y.

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.

	Amhara	Eth Somali	Gumuz	Oromo	Wolayta
A-M13	27%	0%	55%	19%	48%
B-M150	0%	0%	4%	0%	0%
B-M8495	0%	0%	35%	0%	0%
E-M96	3%	4%	0%	6%	12%
E-M215	3%	0%	0%	0%	0%
E-V22	9%	0%	0%	5%	3%
E-Z1902	8%	80%	4%	20%	0%
E-Z830	0%	0%	0%	0%	3%
E-M34	3%	0%	0%	5%	13%
EM4145	17%	0%	0%	25%	20%
J	25%	11%	0%	19%	0%
T	3%	4%	0%	0%	0%

A-M13 :

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 Plaster thesis, only showed 13% of A-M13.

B-M150 and  B-M8495 :

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.

E-M96:

This could potentially be a wide variety of things, but my money would be on E-M329, sister clade to E-M2 and  child clade of E-V38, which in turn is a sister clade to E-M215, the most prevalent YDNA lineage in Ethiopia.

E-M215

As this is showing only in Northern Ethiopia, I would think it maybe E-V92, it still could however be a basal "E3b" lineage.

E-V22

A variant of E-M78, this lineage has always been found in low amounts in Ethiopia, with moderate amounts in Sudan and Egypt.

E-Z1902

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.

E-Z830

This lineage has been discussed before, 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.

E-M34

The prevalence of this lineage in southern Ethiopia from the image above, could be further confirmation of the high frequency of E-M34 found in the omotic speaking Maale from the plaster thesis.

EM4145

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.

J and T

These F belonging lineages look both to be inline with what we already know in terms of frequency distribution throughout Ethiopia.

refs:
http://ethiohelix.blogspot.com/2010_12_01_archive.html
http://ethiohelix.blogspot.com/2012/01/e1b1b-update.html 
http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html
http://ethiohelix.blogspot.com/2013/05/another-extensive-thesis-on-east.html

Update 06/07/2015 - MTDNA

Revised Timeline and Distribution of the Earliest Diverged Human Maternal Lineages in Southern Africa

Abstract

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.

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. 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.

Link (Open Access) 

mtDNA from Southern Africa

Reference mtDNA from Southern Africa from the pre-print "Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa" (Thanks to Maju for the referral)

More East African mtDNA Charts

Below are more East African mtDNA bar graphs from the Hirbo Thesis, the complementary YDNA charts can be seen in this post, along with the Boattini paper featured here, this gives us a more complete picture of East African mtDNA with a reasonable amount of detail.

Google Visualization API has been having problems for the past couple of months, so the tool tips as well as other functionalities of Google charts may not work, this post will be updated if they fix some of these issues.

With respect to some of the data points, the populations labeled with a * had their total number of samples adjusted in order for the percentages shown in Table 3.4.1 to make sense, that is, Orma has been adjusted from 20 to 21, Marakwet from 22 to 23, Pokot from 39 to 38, San from 11 to 12 and Bamoun from 18 to 20.

A summary of interesting recent genetics papers.

I'm taking a break from my Summer break to post a few interesting papers that have come out within the past couple of months.

(1) Inferring Demographic History from a Spectrum of Shared Haplotype Lengths (Open Access)

This paper supports such a notion of continuous gene-flow between Africans and non-Africans since the major Out of Africa event that was precursor to the populating of all continents outside of Africa.

To be sure, such a notion is not new but has been highlighted before by methods used by authors such as Li and Durbin (2011) for instance. Such a notion, is also sufficient to explain the intermediate genetic nature of West Eurasians, I.e between Africans and East Asian/Native Americans, that I have blogged about and demonstrated using ADMIXTURE in the past.

A few quotes from the paper:

"In this paper, we study the length distribution of tracts of identity by state (IBS), which are the gaps between pairwise differences in an alignment of two DNA sequences. These tract lengths contain information about the amount of genetic diversity that existed at various times in the history of a species and can therefore be used to estimate past population sizes. IBS tracts shared between DNA sequences from different populations also contain information about population divergence and past gene flow. By looking at IBS tracts shared within Africans and Europeans, as well as between the two groups, we infer that the two groups diverged in a complex way over more than 40,000 years, exchanging DNA as recently as 12,000 years ago." 

"To illustrate the power of our method, we use it to infer a joint history of Europeans and Africans from the high coverage 1000 Genomes trio parents. Previous analyses agree that Europeans experienced an out-of-Africa bottleneck and recent population growth, but other aspects of the divergence are contested [47]. In one analysis, Li and Durbin separately estimate population histories of Europeans, Asians, and Africans and observe that the African and non-African histories begin to look different from each other about 100,000–120,000 years ago; at the same time, they argue that substantial migration between Africa and Eurasia occurred as recently as 20,000 years ago and that the out-of-Africa bottleneck occurred near the end of the migration period, about 20,000–40,000 years ago. In contrast, Gronau, et al. use a likelihood analysis of many short loci to infer a Eurasian-African split that is recent enough (50 kya) to coincide with the start of the out of Africa bottleneck, detecting no evidence of recent gene flow between Africans and non-Africans [14]. The older Schaffner, et al. demographic model contains no recent European-African gene flow either [48], but Gutenkunst,et al. and Gravel, et al. use SFS data to infer divergence times and gene flow levels that are intermediate between these two extremes [22], [49]. We aim to contribute to this discourse by using IBS tract lengths to study the same class of complex demographic models employed by Gutenkunst, et al. and Gronau, et al., models that have only been previously used to study allele frequencies and short haplotypes that are assumed not to recombine. Our method is the first to use these models in conjunction with haplotype-sharing information similar to what is used by the PSMC and other coalescent HMMs, fitting complex, high-resolution demographic models to an equally high-resolution summary of genetic data."

"We estimate that the European-African divergence occurred 55 kya and that gene flow continued until 13 kya. About 5.8% of European genetic material is derived from a ghost population that diverged 420 kya from the ancestors of modern humans. The out-of-Africa bottleneck period, where the European effective population size is only 1,530, lasts until 5.9 kya."

"Our inferred human history mirrors several controversial features of the history inferred by Li and Durbin from whole genome sequence data: a post-divergence African population size reduction, a sustained period of gene flow between Europeans and Yorubans, and a “bump” period when the ancestral human population size increased and then decreased again. Unlike Li and Durbin, we do not infer that either population increased in size between 30 and 100 kya. Li and Durbin postulate that this size increase might reflect admixture between the two populations rather than a true increase in effective population size; since our method is able to model this gene flow directly, it makes sense that no size increase is necessary to fit the data. In contrast, it is possible that the size increase we infer between 240 kya and 480 kya is a signature of gene flow among ancestral hominids."

"Our estimated divergence time of 55 kya is very close to estimates published by Gravel, et al.and Gronau, et al., who use very different methods but similar estimated mutation rates to the  per site per generation that we use in this paper. However, recent studies of de novo mutation in trios have shown that the mutation rate may be closer to  per site per generation [51], [55], [56]. We would estimate older divergence and gene flow times (perhaps  times older) if we used the lower, more recently estimated mutation rate. This is because the lengths of the longest IBS tracts shared between populations should be approximately exponentially distributed with decay rate ."

(2) Genetic and archaeological perspectives on the initial modern human colonization of southern Asia (Closed Access)

This paper discusses some points, rather the lack of evidence, that makes a pre-toba migration of modern humans outside of Africa almost impossible to reconcile with currently available evidence.

A few quotes from the paper:

"There are currently two sharply conflicting models for the earliest modern human colonization of South Asia, with radically different implications for the interpretation of the associated genetic and archaeological evidence (Fig. 1). The first is that modern humans arrived ∼50–60 ka, as part of a generalized Eurasian dispersal of anatomically modern humans, which spread (initially as a very small group) from a region of eastern Africa across the mouth of the Red Sea and expanded rapidly around the coastlines of southern and Southeast Asia, to reach Australia by ∼45–50 ka (7–10, 14–18) (Fig. 2). The second, more recently proposed view, is that there was a much earlier dispersal of modern humans from Africa sometime before 74 ka (and conceivably as early as 120–130ka), reaching southern Asia before the time of the volcanic “supereruption” of Mount Toba in Sumatra (the largest volcanic eruption of the past 2 million y) at ∼74 ka (1–6)."

"We find no evidence, either genetic or archaeological, for a very early modern human colonization of South Asia, before the Toba eruption. All of the available evidence supports a much later colonization beginning ∼50–55 ka, carrying mitochondrial L3 and Y chromosome C, D, and F lineages from eastern Africa, along with the Howiesons Poort-like microlithic technologies (see above and Genetics and Archaeology). We see no reason to believe that the initial modern human colonization of South and Southeast Asia was distinct from the process that is now well documented for effectively all of the other regions of Eurasia from ∼60 ka onward, even if the technological associations of these expanding populations differed (most probably for environmental reasons) between the eastern and northwestern ranges of the geographical dispersal routes."

"The archaeological evidence initially advanced to support an earlier (pre-Toba) dispersal of African-derived populations to southern Asia has since been withdrawn by the author responsible for the original lithic analyses, who now suggests that they are most likely “the work of an unidentified population of archaic people” (ref. 11, p. 26). Meanwhile, the genetic evidence outlined earlier indicates that any populations dispersing from Africa before 74 ka would predate the emergence of the mtDNA L3 haplogroup, the source for all known, extant maternal lineages in Eurasia (8, 28) (Fig. 5). The size of the mtDNA database is very substantial: currently there are almost 13,000 complete non-African mtDNA genomes available, not one of which is pre-L3."

(3) An experimental computer-generated Y-chromosomal phylogeny, leveraging public Geno 2.0 results and the current ISOGG tree

This paper, written by a geneaolgoical community member, has made an impressive effort at creating and automating a comprehensive method to pylogenetically classify Geno 2.0 YDNA SNPs. Details of the algorithm are not available:

"To illustrate this, the author has used this Y-tree clade predictor (using the latest ISOGG tree as a basis for comparison) to classify over 1650 sets of publicly accessible Geno 2.0 Y-SNP calls. This information was then used as an input into another algorithm designed by the author – an algorithm developed to automate the construction of a phylogenetic Y-tree, while overcoming the challenges identified above. The technical details of this process will remain proprietary for the time being."

East African mtDNA variation has implications on the origin of Afroasiatic

The Dienekes' Anthropology Blog shows a new paper on East African mtDNA with implications for the origin of Afroasiatic, namely with the citing: "making the hypothesis of a Levantine origin of AA unlikely",  unfortunately I do not have access to the paper, I would greatly appreciate if anyone has access to it to please send me a copy here: ethiohelix@gmail.com.

Here is the abstract and the link:

Abstract

East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations—explored using spatial Principal Component Analysis and Model-based clustering—turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.

mtDNA variation in East Africa unravels the history of afro-asiatic groups

UPDATE: Ok, got it, this was a nice little article to read, however with respect to the implications of East African mtDNA variation on the origin of Afroasiatic, it did not offer nothing really substantially new, in terms of material evidence, that any reasonable person that has read up on this subject a little bit would not have known beforehand, namely:


Concerning the third point, i.e., the place of origin of AA (EA or the Levant), our results do not allow us to make conclusive statements. Indeed, coalescent simulations of different genetic parameters (Supporting Information Fig. 4) according to the two mentioned hypotheses show that—even assuming complete correlation between languages and mtDNA variability—their confidence intervals largely overlap. Thus, we limit ourselves to the following observations. First, EA shows the highest levels of nucleotide diversity among the studied populations with a decreasing cline towards NA and the Levant (Supporting Information Fig. 1 and Supporting Information Table 1). This is true not only for the Ethiopian cluster A, but also, and especially, for groups belonging to clusters B1 and B2. Second, EA hosts the two deepest clades of AA, Omotic and Cushitic. These families are found exclusively in EA, while the presence of Semitic in this area is much more recent. Third, cluster C – collecting Berber- and Semitic-speaking populations from NA and the Levant – shows only modest signals of admixture with clusters A and B (Fig. 2, Supporting Information Table 1). None of these points,
taken by itself, is conclusive, but undoubtedly the hypothesis of origin of AA in EA is the most parsimonious one, if compared to the Levant.

It did also have some very nicely made contour maps for EA, as well as detailed mtDNA haplogroup assignments for some 30 or so East African groups, which I will make an interactive chart for within the next couple of days.

UPDATE2 (01/08/2013): mtDNA haplogroups (46) in 31 groups.

A note on the sources for the samples listed above:

The Dinka Samples are from Krings etal. (1999)

The Sudan and Ethiopia Samples are from Soares et al. (2011)

The Tigrai, Amhara, Gurage, Oromo and Yemeni1 Samples are from Kivisild et al. (2004)

The Beta Israel Samples are from Beharet al. (2008)

The Ethiopian Jewish Samples are from Non et al. (2011)

The Somali Samples are from Soares et al. (2011) and Watson et al. (1997)

The Daasanach and Nyangatom Samples are from Poloni et al. (2009)

The Turkana2 Samples are from Poloni et al. (2009) and Watson et al. (1997)

The Nairobi Samples are from Brandstatter et al. (2004)

The Kikuyu Samples are from Watson et al. (1997)

The Hutu Samples are from Castrì etal. (2009)

The Iraqw Samples are from Knight etal. (2003)

The Burunge and Turu Samples are from Tishkoff et al. (2007)

The Datoga and Sukuma Samples are from Tishkoff et al. (2007) and Knight etal. (2003)

All the remaining samples: Dawro Konta, Ongota, Hamer, Rendille, Elmolo, Luo, Maasai, Samburu and Turkana are new and sampled along with this study.

Extensive Doctoral Thesis on Ethiopian Y and mtDNA

I was contacted earlier by Dr. Chris Plaster about a doctoral thesis on Ethiopian Y & mtDNA that was completed 2 years ago but had been embargoed to the public until only about two months ago. As this is the first time I am coming across of it, plus since it is 204 pages long I have not had a chance to go through it thoroughly, but suffice it to say that this is the most extensive work on Ethiopian NRY & mtDNA that I have seen to date, although the resolution leaves a lot to be desired, I will update this post more as I read it more thoroughly over the next few days/weeks...

Variation in Y chromosome, mitochondrial DNA and labels of identity on Ethiopia

Some numbers and figures that caught my attention at first glance:

The Discussion section also has some interesting things to say, especially with respects to haplogroups A3b2 and J, but also the remaining ones found in Ethiopia as well.

A ‘‘Copernican’’ Reassessment of the Human Mitochondrial DNA Tree from its Root

Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This ‘‘Copernican’’ reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.

Source (Open Access)

Some quotes and figures from the paper: 

"Supported by a consensus of many colleagues and after a few years of hesitation, we have reached the conclusion that on the verge of the deep-sequencing revolution (47,55) when perhaps tens of thousands of additional complete mtDNA sequences are expected to be generated over the next few years, the principal change we suggest cannot be postponed any longer: an ancestral rather than a ‘‘phylogenetically peripheral’’ and modern mitogenome from Europe should serve as the epicenter of the human mtDNA reference system."

"Interestingly, the ranges of substitution counts within haplogroups M and N, which are hallmarks of the relatively recent out-of-Africa exodus of humans, are also very large. For example, within M there are two mitogenomes with 43 substitutions (in M30a and M44) and two mitogenomes with as many as 71 substitutions (in M2b1b and M7b3a). This is especially striking because the path from the RSRS to the root of M already contains 39 substitutions. Hence, the difference between the M root and its M44 descendant is only four substitutions (two in the coding region and two in the control region) as compared to 32 substitutions in the M2b1b and M7b3a mitogenomes. These observations raise the possibility that the tree in general, and haplogroup M in particular, might not adhere uniformly to the assumed molecular clock, under which substitutions occur at a fixed rate on all branches of the tree over time."

Some inferred dates of interest (from the supplemental file):
L3 : 67,262 (SD 4,434)
        M : 49,590 (SD 1,824)
              M1'20'51 : 47,641 (SD 2,851)
                                 M1 : 23,680 (SD 4,378)
                                          M1a : 19,183 (SD 3,226)
                                                    M1a1 : 12,910 (SD 3,341)
        N : 58,860 (SD 2,352)
              N1'5 : 56,547 (SD 4,705)
                         N1 : 51,643 (SD 5,640)
                                 N1a : 18,118 (SD 5,247)


Others;
R0a1 :   20,766 (SD 5,754)
U6a1 : 20,133 (SD 4,941)
J1 : 26,935 (SD 5,273)
T : 25,149 (SD 4,668)
K : 26,682 (SD 4,339)


 

Updates on the Human Journey Project: Spencer Wells

Notes:

• Estimates YDNA TMRCA to 60 KYA, this is in conflict with Cruciani et. al (2011) :"A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa", where the root of the MSY was estimated to 142 KYA, although Dr. Wells may be talking about CT-M168, it is not clear enough from the video.
• So far the project has sampled over 1000 different populations around the world, with about 75,000 samples collected from 'indigenous' people, and an additional 415,000 samples from the public who purchased kits.
• Climate appearing to be a 'key motivator' of migrations.
• Europe colonized from the south at the end of the ice age from two different directions/sources that acted as a 'Refugium' during the ice age, a Franco-Cantabrian refugium in the southwest of Europe and another refugium in the Southeast (around the Balkans).
• 'Middle Easterners' from the 'northern area of the Fertile crescent' literally replaced Mesolithic Europeans during the Neolithic revolution, he points to ancient DNA evidence for this.

The Mother of Mothers !

It has been well known for about 20 years now that the mother of all Non-Africans, and indeed a lot of Africans, was an East African woman, in more recent nomenclature this woman has been called L3, so what do geneticists recently say about this woman, mother to greater than six and a half billion people on Earth, including many who still inhabit her original homeland?

The most recent study conducted to uncover the story behind L3 and her compatriots was one from the end of last year entitled “The Expansion of mtDNA Haplogroup L3 within and out of Africa”. 

This important study capped the timing of the out of Africa migrations, which all contemporary men and women outside of Africa are descended from, to no earlier than Seventy Thousand Years Ago.

The basis for this reasoning can be found in this paragraph from the text:

“The time window for the out-of-Africa migration on the basis of mtDNA lies between the emergence of haplogroup L3 in Eastern Africa and its derivative non-African haplogroups M and N, which most likely arose during the departure or outside Africa (Richards et al. 2006).”

Meaning, since all Non-Africans are descended from this woman, the timing of the out of Africa migration can not be any older than when she lived and can not be any younger than when here descendant daughters M and N lived, although there still remains a possibility that M and N emerged in Africa, albeit increasingly unlikely.

The expansion of L3 however has been linked in the past to not only the Out of Africa expansion but also Expansions within Africa, generally in association with two different episodes:

1. With the spread of Pastoralism in the Sahara of the early Holocene
2.  With the Bantu Expansion/s

To this end, the samples for this study were said to come from:

“We collected a total of 102 Sudanese, 77 Ethiopian (both emigrants in Dubai), and 148 Somali (refugees in Yemen) samples, belonging to unrelated individuals, who gave appropriate informed consent for their biological samples to be used for mtDNA characterization.”

Where a set of identified L3 lineages from above (plus other previous papers) were then selected for complete mtDNA sequencing:

“We selected for complete mtDNA sequencing a total of 21 Sudanese, 16 Ethiopian, and 20 Somali samples chosen from the sequences characterized in this work, and 11 from Chad and 2 from Soqotra belonging to haplogroup L3 from data sets published previously (Cerny´ et al. 2007; Cerny´, Pereira, et al. 2009).”

So what were the main results of the extensive statistical analysis done on this lineage?

A) Complete mtDNA phylogeny for Haplogroup L3:

 

Schematic tree of haplogroup L3. Age estimates are respectively rho estimates from the complete mtDNA genome (black font), rho estimates using the synonymous clock (gray font), and ML estimates using the complete mtDNA genome (black font underlined). Color scheme for each clade indicates the probable geographic origin. Haplogroups M and N are indicated and age estimates are according to Soares et al. (2009). MSA refers to Middle Stone Age and LSA to Late Stone Age.

B) Reaffirmation of what was known in the past with respect to the origins of L3:

“L3 most likely had an origin in Eastern Africa (Torroni et al. 2006). This is supported by the presence of all major branches, with L3a and L3h virtually specific to the region and L3eikx and the L3f haplogroups having a probable origin there as well, whereas for L3bcd, the region of origin is less clear and will be discussed in more detail below. The other two main branches of L3, M and N, exist only outside Africa, except for some back-migrations into Africa around 50–30 ka in the form of haplogroups U6 and M1 (Olivieri et al. 2006; Pereira et al. 2010) and some more recent intrusions (Cherni et al. 2009; Ottoni et al. 2010). Since there is strong evidence that the dispersal out of Africa was via the Horn, soon after L3 arose (Macaulay et al. 2005), the distribution of M and N also points to Eastern Africa as the center of gravity for L3.”

C) Temporal analysis of the sampled L3 lineages with origins bracketed within 60 – 70 thousand years ago:

 

"It seems likely that L3 dates somewhere between 60 and 70 ka, as the TMRCA estimates vary between 58.9 ka (using rho and the complete genome) and 70.2 (using ML), with the synonymous clock providing a value between the two (63.1 ka). We checked if the L3 tree rejected a strict molecular clock by running the ML analysis without stipulating a molecular clock and performing a likelihood ratio test that clearly did not reject the clock hypothesis (P 5 0.9899). These results led us to consider an age of 65 ka (varying between 60 and 70 ka in the 95% percentile) in the internal calibration of BEAST, as there was no other reliable calibration point we could use. The ages using the complete genome and the synonymous clock were 1.04 and 0.97 times the BEAST estimates, respectively, indicating that the BSPs were calculated using a similar rate to the other analyses, as we intended.”

D) Identification of 3 main episodes of population growth/expansion within Africa:

i) Approximately 40 thousand years ago corresponding with the emergence of the various intra-African subclades of L3.

ii) Around the Holocene, associated mainly with L3bd and L3e (Central Africa)

iii) The largest increase of the expansions detected around four thousand years ago and most pronounced in the Central African Bayesian Skyline Plots.

E) L3f and L3eikx both implied to have an origin in Eastern Africa. Where L3f was carried into the Sahel and Central Africa, with L3f3 specifically expanding into the Sahel 8 to 9 thousand years ago.

F) The most frequent clade of L3, i.e. L3e implied to have an origin in Central/Western Africa. With Eastern African L3e discounted as more recent introgression from there.

 

G) An ambiguous interpretation for the origin of L3bcd, a tentative east African origin is however suggested:

“L3bcd has three main subclades, with L3b and L3d tentatively united by a transition at control region position 16124 to form the putative subclade L3bd. The great age of L3bcd and its wide distribution across Africa makes phylogeographic inferences difficult. Furthermore, L3c is extremely rare: Only two samples have been detected so far, one in Eastern Africa and the other in the Near East. This might echo an early origin of L3bcd in Eastern Africa, before moving west, but its rarity makes this conclusion extremely tentative. In a scenario of an early origin of L3bcd in Eastern Africa, M and N would be the only subclades of L3 to have most likely originated outside of Eastern Africa (although an origin in Eastern Africa remains possible: Richards et al. 2006).

H) A virtual exclusion of a scenario in which the ancestors of contemporary people outside of Africa migrated out of Africa before the eruption of Toba.

I) And finally the most interesting part of this paper's conclusion, a unified demographic process that led to both the out-of-Africa and within Africa primary expansion of L3:

“Furthermore, since the age of the M and N Eurasian founders of ;50 to 65 ka (Soares et al. 2009) is close to the age of their ancestral L3 clade in Africa, the out of-Africa dispersal may have been of a piece with the initial diversification and expansion of L3, so that the L3 expansions in Eastern Africa and the exit of modern humans from Africa;60 ka were all part of a single demographic process.

It seems likely that the moister climate after;70 ka in Eastern Africa allowed dramatic human population growth (Scholz et al. 2007), perhaps associated with improved hunting, marine exploitation, exchange networks, and possibly even plant food management strategies as suggested by Mellars (2006). This generated the oldest major signal of expansion in the human mtDNA tree, the radiation of L3, leading rapidly to the spread of H. sapiens toward the rest of the world. It is worth stressing that this signal is not reflected in other mtDNA lineages at this time (Behar et al. 2008). Within Africa, the Pleistocene migrations detected in the L3 pool were responsible for the introduction of L3bd and L3e into Central Africa in the period between 60 and 35 ka (fig. 5A), but none reached Southern Africa at that time.”

Interestingly, the previous explanations that the Out of Africa expansion of modern humans being linked with behavioral modern thinking is largely dismissed by these authors for the sole explanation of Environmental factors, their main reasoning being that there is evidence for behavioral modernity of humans in Africa (Both in South and North Africa) long before their proposed timing of the OOA migrations.

“Thus, as suggested by Basell (2008), the demographic expansions that led to the first successful dispersal out of Africa seem better explained by the play of palaeoenvironmental forces than by recourse to the advantages of ‘‘modernity." 

More interesting figures from the paper:

“Frequency maps based on HVS-I data for haplogroups L3a, L3i, L3h, and L3x combined (A), L3f (B), L3e (C), L3b (D), and L3d (E).”

“Outline of the main dispersals detected in this work during the Pleistocene (A) and the Holocene (B).”

 ** Sketches on top of page depicting contemporary women that still live in the putative land of  L3's origin. Credit goes to Ethiopian Artist Adis Gebru and taken from this blog.