The slow death of Out of Africa

The significance of the discovery of modern humans in Arabia >85kya is that it provides a second spot (other than Israel) were modern humans existed outside Africa long before the alleged 60kya blitz out of the continent. We now have modern humans outside Africa in roughly two locations (Israel and Arabia), and three time slices (~175-85kya) in Misliya, Shkul/Qafzeh, and Al Wusta-1. It is no longer tenable to claim that these modern humans "died out" to make way for the alleged 60kya OoA event.

An important implication of pre-60kya Eurasians not dying out is that in all likelihood mtDNA haplogroup L3 and Y-chromosome haplogroup E originated in Eurasia, not Africa, and represent major Eurasian admixture into Africa.

Out of Africa theory is not dead (yet), but it resembles Rocky Balboa taking punch after punch round after round over the last 10 years or so. Will it make a cinematic last round comeback and prove itself, or will it be dealt a knockout punch in the near future? 

Nature Ecology and Evolution (2018) doi:10.1038/s41559-018-0518-2

Homo sapiens in Arabia by 85,000 years ago

Understanding the timing and character of the expansion of Homo sapiens out of Africa is critical for inferring the colonization and admixture processes that underpin global population history. It has been argued that dispersal out of Africa had an early phase, particularly ~130–90 thousand years ago (ka), that reached only the East Mediterranean Levant, and a later phase, ~60–50 ka, that extended across the diverse environments of Eurasia to Sahul. However, recent findings from East Asia and Sahul challenge this model. Here we show that H. sapiens was in the Arabian Peninsula before 85 ka. We describe the Al Wusta-1 (AW-1) intermediate phalanx from the site of Al Wusta in the Nefud desert, Saudi Arabia. AW-1 is the oldest directly dated fossil of our species outside Africa and the Levant. The palaeoenvironmental context of Al Wusta demonstrates that H. sapiens using Middle Palaeolithic stone tools dispersed into Arabia during a phase of increased precipitation driven by orbital forcing, in association with a primarily African fauna. A Bayesian model incorporating independent chronometric age estimates indicates a chronology for Al Wusta of ~95–86 ka, which we correlate with a humid episode in the later part of Marine Isotope Stage 5 known from various regional records. Al Wusta shows that early dispersals were more spatially and temporally extensive than previously thought. Early H. sapiens dispersals out of Africa were not limited to winter rainfall-fed Levantine Mediterranean woodlands immediately adjacent to Africa, but extended deep into the semi-arid grasslands of Arabia, facilitated by periods of enhanced monsoonal rainfall.

Link

Human pigmentation mega-study

A great new study on the genetics of human (including African) pigmentation. I would love to see a future study that would reconstruct what ancestral modern humans looked like pigmentation-wise, as this trait is tightly correlated with sun exposure (and thus latitude), and may thus pinpoint a narrow latitudinal zone where ancestral modern humans may have lived.

From a related story:

The most dramatic discovery concerned a gene known as MFSD12. Two mutations that decrease expression of this gene were found in high frequencies in people with the darkest skin. These variants arose about a half-million years ago, suggesting that human ancestors before that time may have had moderately dark skin, rather than the deep black hue created today by these mutations.

Science 12 Oct 2017: eaan8433 DOI: 10.1126/science.aan8433

Loci associated with skin pigmentation identified in African populations

Nicholas G. Crawford et al.

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

Link

Out of North Africa

I had previously called Irhoud 1 "The Father of Mankind" and proposed a "two deserts" theory of human evolution whereby our species originated in North Africa, and was pumped out of it to both the Middle East (and especially Arabia, the 2nd desert) and Sub-Saharan Africa during periods of Saharan aridity. This Out-of-North Africa theory (together with the secondary Out-of-Arabia expansion ~70kya) is responsible for the spread of Homo sapiens around the world.

The discovery and re-dating of modern human remains from Irhoud of course adds support to this theory and places North Africa as the most probable cradle of our species, with a comfortable 100kya buffer to the next place where modern humans are detected (the Omo remains of East Africa), and another comfortable 100kya buffer to the next place (Israel and the Skhul/Qafzeh hominins).

The interpretation of these findings in terms of Homo sapiens emerging out of a sort of multi-regional evolution involving all Africa is of course wrong. There is no reason to think of a single species evolving across the huge African continent. The early distribution of sapiens remains are in North Africa, East Africa, and the Near East, and such remains are absent in West/Central/South Africa.

The multi-regionalists lost the game in Eurasia, as it turned out that Eurasians only have ~2% archaic admixture, and they are inventing Multiregionalism-in-Africa.

Whatever finds we do have from Sub-Saharan Africa, some of them quite late (such as the Iwo Eleru remains from Nigeria), others of similar age as Irhoud (such as Florisbad and the recently described H. naledi from South Africa) did not belong to our species. The first modern humans appeared in South Africa with the Later Stone Age (probably associated with the migration of Y-chromosome haplogroup E into Africa), and the Hofmeyr skull (which resembled Eurasians and not the eternally romanticized Khoe-San). Even in East Africa the advent of modernity was not clear-cut (see Omo I vs. II and the more archaic later Herto specimen).

It seems that people were misled into thinking of Sub-Saharan Africa as the origin of our species by the genetic observation of greater genetic diversity of Sub-Saharan Africans. But, this diversity could have come about by admixture between people from North Africa and pre-existing people of Sub-Saharan Africa (both early waves of AMH and non-AMH).

It's not certain that North Africa will be the end of the story. Fashions shifted from the Near East to East Africa, to North Africa, with every new find. But, the fact that we do find the earliest modern humans in these areas, while we find non-AMH elsewhere (e.g. Europe or South Africa) is gradually constraining the solution to the problem of our origins. My bet remains North Africa; time will tell.

Population history with physically phased genomes

bioRxiv doi: http://dx.doi.org/10.1101/008367

Modeling human population separation history using physically phased genomes

Shiya Song, Elzbieta Sliwerska, Sarah Emery, Jeffrey M Kidd

Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Massai and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati and CEPH European populations and analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We find that statistically phased haplotypes yield an earlier split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation (ABC) approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard Isolation-with-Migration model. We inferred that the separation between hunter-gather populations and other populations happened around 120,000 to 140,000 years ago with gene flow continuing until 30,000 to 40,000 years ago; separation between west African and out of African populations happened around 70,000 to 80,000 years ago, while the separation between Massai and out of African populations happened around 50,000 years ago.

Link

Panorama of African admixture

I remember how in the early days of online discussions of anthropology a constant topic of contention was whether African variation was the result of admixture, some of it within Africa, some of it from Caucasoids, or whether it was the result of climatic adaptation manifested in gradual clines (as opposed to clusters corresponding to physical types).

Well, I won't dismiss the role of climate altogether, but it's hard to argue for it much anymore now that we know that the two big fish in the African ocean of human diversity were the spread of Niger-Congo languages (from the west), and of Caucasoids (from the east) over the last few thousands of years, with a healthy seasoning of minor admixtures before and after. Once again it seems that old-style anthropology was right and the more fashionable and trendy attempts to dismiss it as "typology", "imposition of European colonialism through science" and the like were wrong.



eLife 2016;5:e15266

Admixture into and within sub-Saharan Africa

George BJ Busby et al.

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Link

35,000 year old mtDNA haplogroup U6 from Romania

I wouldn't be very surprised if many of the markers supposedly signifying recent gene flow Africa and Eurasia were actually quite old in Eurasia. The trouble is that reports of such gene flow were often based on simply observing that marker "X" occurs at a higher frequency in Africa than in Eurasia, so a common sense explanation is that it reflects limited recent gene flow between the continents. But, it is now known that common sense is not always the best guide, as e.g., ancient Europeans had mtDNA haplogroup M (in the past considered evidence of Asian admixture), Y-chromosome haplogroup C (ditto), and now U6.

The same should also apply to the Middle East where there has been admixture with Africans since the Islamic period at least. The existence of such admixture does not mean that every single lineage that occurs at low frequency in the Middle East and high frequency in Africa is diagnostic of this later period of admixture. Some of them could well be relics of old Middle Eastern populations. Who knows what people inhabited the presently inhospitable landscape of the Saharan-Arabian desert zone? The living populations can certainly make no claim to being the first ones there, but the genetic heritage of those earlier occupants may still persist in them in traces.

Similarly for the New World; in that case, there is a better case that European-looking lineages are indeed due to the colonization of the Americas over the last five centuries. However, that does not mean that all of them are, and we should be mindful of the possibility of pre-Columbian contact between the Old and New worlds.

Scientific Reports 6, Article number: 25501 (2016)

The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa

M. Hervella et al.

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

Link

Archaic introgression in Pygmies

We must remember that detecting archaic admixture in Africa is a statistical power game where only a particular type of such introgression can be detected:

First, it needs to be from highly diverged Palaeoafrican sources so that it will look very different from plain H. sapiens DNA. Unlike Eurasia, there's no genome of an ancient Palaeoafrican one can compare against. All inference is based on African genomes having an improbable amount of heterozygosity in parts of their genome.

Second, it needs to have happened recently enough so that it will come in big chunks that can be distinguished from the plain H. sapiens background. Given enough time, recombination breaks down archaic segments into ever tinier bits. You can argue that an unusually long divergent haplotype with a deep TMRCA is archaic, but you can't argue that a single SNP is.

I have little doubt that most if not all of the supposedly "old divergences" between African populations are a mirage created by admixture between modern humans and archaic "Palaeoafricans" diverging and admixing at different time depths. The palaeoanthropological record is quite clear that modern humans were not the only game in town for most of the 200 thousand years since modern humans first appeared in the continent's northeastern corner.

A handful or two of archaic genomes from Eurasia needs an ever-more-complex web of admixtures to make sense of; Africa will need no less, and -if morphological variability persistence is any criterion- a lot more.

Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.196634.115

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

PingHsun Hsieh et al.

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

Link

Genome Research Published in Advance February 17, 2016, doi: 10.1101/gr.192971.115

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PingHsun Hsieh et al.

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Link

Admixture within and into Africa

bioRxiv, http://dx.doi.org/10.1101/038406

Admixture into and within sub-Saharan Africa

George Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Emil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk Rockett, Domnic Kwiatkowski, Chris Spencer, The Malaria Genomic Epidemiology Network

Understanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa. We show that coastal African populations have experienced an influx of Eurasian haplotypes as a series of admixture events over the last 7,000 years, and that Niger-Congo speaking groups from East and Southern Africa share ancestry with Central West Africans as a result of recent population expansions associated with the adoption of new agricultural technologies. We demonstrate that most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of large-scale population movements over the last 4,000 years. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.

Link

Helicobacter pylori in the Iceman

Science 8 January 2016:
Vol. 351 no. 6269 pp. 162-165

The 5300-year-old Helicobacter pylori genome of the Iceman
Frank Maixner1,*,†, Ben Krause-Kyora2,†, Dmitrij Turaev3,†, Alexander Herbig4,5, et al.

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.

Link

Refining Y-chromosome phylogeny with South African sequences

bioRxiv http://dx.doi.org/10.1101/034983

Refining the Y chromosome phylogeny with southern African sequences

Chiara Barbieri, Alexander Hübner, Enrico Macholdt, Shengyu Ni, Sebastian Lippold, Roland Schröder, Sununguko Wata Mpoloka, Josephine Purps, Lutz Roewer, Mark Stoneking, Brigitte Pakendorf

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.

Link

West Eurasian admixture throughout Africa (?)

In 2012, I wrote:

It is no longer tenable to view West Eurasian back-migrations as limited events that affected only North and East Africa: their effects are clearly evident throughout Africa, having affected different populations to a different extent.

A new paper in Science seems to confirm West Eurasian admixture related to Early Neolithic farmers throughout Africa, including the Yoruba, and Mbuti. I haven't read the paper yet, but it would be a striking discovery if confirmed.

UPDATE (1/26/2016). An erratum has now appeared that rejects the claim for Eurasian admixture in all Africans which was the result of the bioinformatic error. I continue to think that there was Eurasian back-migration into Africa, but it was a long shot that this had happened in the last 4,500 years (hence the ? in the title of this entry). A time series of African DNA may show whether the null model of Sub-Saharan Africans receiving virtually no admixture from Eurasia for the entirety of the existence of H. sapiens can remain valid.

Science DOI: 10.1126/science.aad2879

Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent

M. Gallego Llorente et al

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Link

Phylogeographic refinement of haplogroup E

Genome Biol Evol (2015) 7 (7): 1940-1950.

Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent

Beniamino Trombetta et al.

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12 ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers.

Link

Complex demographic history of Western Central African Pygmies

bioRxiv doi: http://dx.doi.org/10.1101/022194

Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PingHsun Hsieh et al.

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Link

Nilo-Saharan component

Scientific Reports 5, Article number: 9996 doi:10.1038/srep09996

The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

Begoña Dobon et al.

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

Link

Out of Egypt or Out of Ethiopia?

I am skeptical that once you remove non-African ancestry from Egyptians (even if you were able to do so perfectly), what you are left with is indigenous Northeastern Africans, the direct descendants of people who left Africa tens of thousands of years ago.

For one thing, Egypt has not only experienced gene flow from Europe and the Middle East, but also from elsewhere in Africa, more recently because of enslaved black Africans.

For another, even if you perfectly identified and removed both Eurasian and African non-native influences on the Egyptian population, you're left with some kind of indigenous northeastern African. But, did such a population with long-term continuity exist in Egypt since Out-of-Africa? The Eurasian experience (where ancient DNA falsifies continuity left and right even in a 1/10th of the OOA time scale) makes me doubt this. The Nile may have facilitated gene flow in a north-south direction, and the relatively recent emergence of the Sahara desert may very well have pumped populations into Egypt.


AJHG DOI: http://dx.doi.org/10.1016/j.ajhg.2015.04.019

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

Luca Pagani et al.

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

Link

DNA of 17th century African slaves frome the Caribbean

PNAS doi: 10.1073/pnas.1421784112

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Hannes Schroeder, María C. Ávila-Arcos et al.

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

Link

African Genome Variation project paper

A choice quote:

To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST = 0.027) may be a remnant of East African diversity pre-dating the Bantu expansion10.

I think this should be highlighted for a couple of reasons.

1. In too many papers to count, decreasing genetic diversity from East Africa was taken as evidence of an origin of H. sapiens in that locality and its expansion from there to Eurasia. This "East Africa=cradle of mankind" theory has, as far as I can tell, nothing really to stand on. Granted, the oldest anatomically modern human remains have been found in East Africa 200-150 thousand years ago. But, the fact that old sapiens have been found in East Africa and not elsewhere is easily explained by the excellent conditions for preservation (as opposed, e.g., deserts or rainforests of Africa or elsewhere), and by the extraordinary effort by palaeoanthropologists in that area. One also needs to overlook a century of physical anthropology that concluded that East Africa was a contact zone between Caucasoids and Sub-Saharan Africans. We now know that there is no deep lineage of humans in modern east Africans. Take out the Eurasian ancestry and only a paltry Fst=0.027 remains with other Sub-Saharan Africans, a fraction of the Fst between, say, Europeans and East Asians.

2. There has been enormous literature about phenotypic variation in Africans. The ultra-migrationism of old was replaced by ultra-selectionism that sought to explain every phenotypic marker of Eurasian admixture in Africa not as evidence of such admixture, but as a parallel process of evolution whereby some Africans tended to resemble some Eurasians not because of admixture but because of adaptation to similar environmental conditions.

But:

This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6).

This study also confirms the presence of Eurasian admixture in the Yoruba

Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.

Nature (2014) doi:10.1038/nature13997

The African Genome Variation Project shapes medical genetics in Africa

Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, et al.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

Link

Armed conflict in the Sahara, ~13 thousand years ago

An interesting story from the Independent:

Scientists are investigating what may be the oldest identified race war 13,000 years after it raged on the fringes of the Sahara. French scientists working in collaboration with the British Museum have been examining dozens of skeletons, a majority of whom appear to have been killed by archers using flint-tipped arrows.

...

Parallel research over recent years has also been shedding new light as to who, in ethnic and racial terms, these victims were.

Work carried out at Liverpool John Moores University, the University of Alaska and New Orleans’ Tulane University indicates that they were part of the general sub-Saharan originating population – the ancestors of modern Black Africans.

The identity of their killers is however less easy to determine. But it is conceivable that they were people from a totally different racial and ethnic group – part of a North African/ Levantine/European people who lived around much of the Mediterranean Basin.

The two groups – although both part of our species, Homo sapiens – would have looked quite different from each other and were also almost certainly different culturally and linguistically. The sub-Saharan originating group had long limbs, relatively short torsos and projecting upper and lower jaws along with rounded foreheads and broad noses, while the North African/Levantine/European originating group had shorter limbs, longer torsos and flatter faces. Both groups were very muscular and strongly built.

An older layer of Eurasian admixture in Eastern Africa

The authors propose that a genetic component found in Horn of Africa populations back-migrated to Africa from Eurasia ~23 thousand years ago. I did not read this carefully yet, but it seems reasonably plausible. The migration uncovered by Pagani et al. and Pickrell et al. (~3kya) is probably not the whole story of Eurasian back-migration into Africa; that episode probably involved only Semitic speakers (it's hard to imagine any other language being carried from the Middle East at that time frame). But the Eurasian affiliation of East Africans extends well beyond Semitic speakers. In North Africa this is even clearer as the native (pre-Arab) population is definitely broadly West Eurasian and this must have come about by back-migration.

The back-migration of M1 and U6 into Africa seems to be at a similar time depth as the one proposed by these authors (post-initial UP, but pre-Neolithic). I have proposed that haplogroup E may represent an even earlier layer of Eurasian back-migration, while the signals identified by Pagani et al. and Pickrell et al. in East Africa, Pickrell et al. for Southern Africa, and the limited (but present) Neandertal ancestry in Yoruba and Pygmies documented by Pruefer et al. represent later events. The arrival of Arabs and Europeans are later events still.

For a time, there was a taboo against imagining back-migration into Africa; in a sense this was reasonable on parsimony grounds: Africans have most autosomal genetic diversity and the basal clades of mtDNA and Y-chromosomes; a model with Out-of-Africa is simpler than one with both Out-of and Into-Africa. However, we now know that pretty much all Africans have Eurasian ancestry, ranging from at least traces in theYoruba and Pygmies (to account for the Neandertal admixture) to intermediate values in East Africans, to quite  a lot in North Africans.

Eurasian admixture in Africa seems to be general, variable, and to have occurred at different time scales. It's still the best hypothesis that modern humans originated in Africa initially and migrated into Eurasia. However, it is no longer clear that Africa was always the pump and never the destination of human migrations.

PLoS Genet 10(6): e1004393. doi:10.1371/journal.pgen.1004393

Early Back-to-Africa Migration into the Horn of Africa

Jason A. Hodgson

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka, and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-to-Africa migration is most likely pre-agricultural.

Link

The history of mtDNA haplogroup U6

BMC Evolutionary Biology 2014, 14:109 doi:10.1186/1471-2148-14-109

The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents

Bernard Secher et al.

Abstract (provisional)

Background

Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.

Results

Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.

Conclusions

The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.

Link