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

Improved resolution of E-M215 (aka E3b / E1b1b)

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 we used to know.

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.

New basal haplogroup E mutations were also apparently found.

The paper is Open access , 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.
 

UPDATE (6/26/15) - Added NAfrica E-M215 frequencies

UPDATE (6/26/15) - Added new mutation rate
The new fossil calibrated mutation rate has been added to the TMRCA Calulator, 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.

UPDATE (6/27/15) - Comparison with YFull TMRCAs

I have created a table for the TMRCA of the major nodes in E-M215, in order to compare with YFull’s 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.

	TMRCA (KYA)
	Trombetta	YFull
E-M215	39	35
E-M35	25	24
E-V68	20	20
E-M78	15	13
E-Z827	?	24
E-V257	?	14
E-Z830	20	19
E-M34	?	15
E-V1515	12	?

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) 

New NGS study of the Y DNA

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:

(1) Mutation Rate:

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, Fu (2014) 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 already incorporated these new rates into the TMRCA calculator under Karmin (2015).

(2) Coalescence of Non-African YDNA chromosomes:

The authors report :

....... 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

Which aligns almost perfectly with the recent find in Manot, Israel 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.

(3) A "New" E1b1b (E-M215) topology:

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 here)

E-M215 Karmin (2015)

Compared with what we knew 3 years ago (note: CTS8288 above is equivalent to E-Z830 below):

The unanswered questions with respect to the major topology of E-M215 remain:

• What is the relationship, if any,  of E-V92 with respect to E-Z827, E-Z830 or E-V68
• What is the relationship, if any, of E-V6 with respect to E-Z827, E-Z830 or E-V68

A recent bottleneck of Y chromosome diversity coincides with a global change in culture
 
Abstract

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.

Link (Closed Access)

SNP based module added to the Y TMRCA calculator

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:
https://ehelix.pythonanywhere.com/init/default/index

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.

Below I have run some quick verifications for 3 separate mutation rate sources:

• Poznick (2013) rates via Underhill (2014)
• Xue (2009) rates via Cruciani (2013)
• Scozzari (2013) rates for the same publication

Poznick (2013) rates via Underhill (2014)

The following is stated in Underhill (2014):

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%.

Putting in the variables for the R1 node from above into the calculator,
We get an output of:

 R1 - Underhill (2014)

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.
Similarliy for the R1a-M417 node , we get:

R1a-M417 - Underhill (2014)

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.

'Smoking gun' found for the Out of Africa Theory

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,

"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."

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,

Hershkovitz told Haaretz that the presence of modern humans at Manot also supports the idea that Homo sapiens sapiens left Africa through the Nile valley, Sinai and what is today known as Israel,

http://www.haaretz.com/life/archaeology/1.639350

Obviously, a scenario of multiple exits out of Africa, first via Bab-el-mandeb and then via the Nile valley, can not be necessarily discounted by this find.

Levantine cranium from Manot Cave (Israel) foreshadows the first European modern humans

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 (bp), replacing all other forms of hominins¹. 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 bp (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^{2, 3}.

Link ( Closed Access) 

Genes & Language, Impact of Oldest Butchering Tools on Communication, Lalibela Archaeology

A comparison of worldwide phonemic and genetic variation in human populations

Abstract

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. 

Link (Closed Access)

See Also: 

A Novel Solution For Dating The Origin Of Language. Response to Comments on “Phonemic Diversity Supports a Serial Founder Effect Model of Language Expansion from Africa”

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Experimental evidence for the co-evolution of hominin tool-making teaching and language

Abstract

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 (N=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.

Link (Closed Access)

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The Lalibela Rock Hewn Site and its Landscape (Ethiopia): An Archaeological Analysis

Abstract

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).

 Link (Closed Access)

SNP vs. STR YDNA TMRCA Estimation

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.

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

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. 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. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes. 

Link (Open Access)

(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.

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 Xue (2009) mutation rate estimate of 1 X 10^-9/bp/year , therefore, a slower mutation rate choice (like from Poznick (2013) or Francalacci (2013) 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 YHRD (see the YTMRCA Calculator 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.

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 (c) 13 STRs, 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.

UPDATE:
For further insight in the current understanding of substitution rates used for the SNP counting method, I direct readers to the Wang (2014) article which enumerates on the 4 primary methods that have been used to calculate the substitution rate:

1. Human - Chimp Comparisons : Thompson (2000) , Kuroki (2006)
2. Deep Rooting Pedigree: Xue (2009)
3. Autosomal Mutation Rate Adjustment: Mendez (2013)
4. Founding Migrations Based Inference:  Poznick (2013), Francalacci (2013)  

In terms of inferences based on the Y Chromosome TMRCA and the Out Of Africa migrations the authors suggest that Xue (2009) and Poznick (2013) give the most reasonable estimates. 

Comparison of different Y chromosomal substitution rates in time estimation using Y chromosome dataset of 1000 Genome dataset. Time estimations are performed in BEAST. (a) TMRCA of 526 Y chromosomes (including haplogroup A1b1b2b-M219 to T). (b) 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 et al. [6] and Kuroki et al. [7], respectively. Pedigree rate: Y chromosome base-substitution rate measured in a deep-rooting pedigree by Xue et al. [8]. Autosomal Rate Adjusted: Y chromosome substitution rate adjusted from autosomal mutation rates by Mendez et al. [9]. AEFM-America and AEFM-Sardinian: Y chromosome base-substitution rate based on archaeological evidence of founding migrations using initial peopling of Americas [10] and initial Sardinian expansion [11], 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.

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 (Xue (2009), Poznick (2013) ) or maybe even yield unforeseen results.

Novel genomic signals of recent selection in an Ethiopian population

Fasil Tekola-Ayele, Adebowale Adeyemo, Guanjie Chen, Elena Hailu, Abraham Aseffa, Gail Davey, Melanie J Newport and Charles N Rotimi

Abstract

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 10 000 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%) in this Omotic-speaking indigenous Ethiopian population.

Link (Closed Access)

Assumptions on the genesis of artistic expression in humans shattered by Indonesian find.

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.

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)^{1, 2} and portable art (for example, carved figurines)^{3, 4}, 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^{5, 6, 7, 8}, where modern humans (Homo sapiens) were established by 50 kyr ago^{9, 10}. 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 art¹¹. 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.

Link (Closed Access)

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From the Press (BBC):

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.
"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.

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.

"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".

Statisitics on African born immigrants in the U.S.

I stumbled upon an interesting article in the WP that led me to a recently released brief by the US Census Bureau outlining some interesting stats on the growing demography of Africans in America.

The article can be freely accessed here.

Some figures and highlights I found interesting follows:

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.
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.....

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)

...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....

.....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. 

 ^ 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 National (30%) attainment levels.

The article attempts at explaining the disparity in educational attainment levels by stating:

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.

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.

East African Climate on Hominin Evolution , Archaelogical evidence for African Homo Sapiens Substructure (pre-OOA)

East African climate pulses and early human evolution

Abstract

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 variability selection hypothesis, which was then the basis for the pulsed climate variability hypothesis. 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.

Link (Open Access)

Earliest evidence for the structure of Homo sapiens populations in Africa

Abstract

Understanding the structure and variation of Homo sapiens populations in Africa is critical for interpreting multiproxy evidence of their subsequent dispersals into Eurasia. However, there is no consensus on early H. sapiens 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.

Link (Closed Access)