More statistical Palaeoafricans

More statistical evidence for a deep Palaeoafrican layer in modern Sub-Saharan Africans in the preprint by Ragsdale and Gravel (below). When I proposed that modern Africans are a mixture of Afrasians and diverse Palaeoafricans I only had two things to go on: greater African genetic diversity (produced by admixture between diverse Palaeoafricans and Afrasians), and cranioskeletal archaicity in known African specimens.

Current models of African origins have African groups tracing their ancestry to groups that split off 200-300 thousand years from the rest of mankind, as well as even more archaic Africans (such as the ones proposed in this preprint) that split off as early as 500 thousand years ago. I'm pretty sure there are multiple layers in-between yet to be discovered: counterintuitively archaic admixture is easiest to discover if it is more distant (as it's more distinctive). But, it's unimaginable that Afrasians admixed with people that split off 200 thousand years ago, 500 thousand years ago, and none in-between.

We now know that Eurasians are not pure Afrasian either: they have some admixture with archaic Eurasians. Interestingly, archaic Eurasians are the most deeply splitting branches of humans to have contributed to modern mankind. All African genetic lineages (both Palaeoafrican and Afrasian) are nested within Eurasian genetic variation, with the jury still out on whether this happened when (1) African Afrasian populations left Africa and met archaic Eurasians, or (2) Eurasian Afrasian populations left West Eurasia and met archaic Africans.


Related:

• Statistical Palaeoafricans

Models of archaic admixture and recent history from two-locus statistics 
Aaron P Ragsdale, Simon Gravel
doi: https://doi.org/10.1101/489401

We learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that individuals in two African populations have 6−8% ancestry through admixture from an unidentified archaic population that diverged from the ancestors of modern humans 500 thousand years ago.

Link

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

Out of Africa: a theory in crisis

The sensational discovery of modern humans in the Levant 177-194 thousand years ago should cause a rethink of the currently held Out-of-Africa orthodoxy.

By Out-of-Africa, I mean here the origin of anatomically modern humans, as opposed to the earlier origin of the genus Homo or the later origin of behaviorally fully modern humans.

Two main pieces of evidence supported the conventional OOA theory:

1. The observation that modern Eurasians possess a subset of the genetic variation of modern Africans.
2. The greater antiquity of AMH humans in the African rather than the Eurasian palaeoanthropological record.

Both these observations are in crisis.

1a. The oldest African fossil AMH is in North Africa (Morocco, Jebel Irhoud); modern genetic variation does not single out this region as a potential source of modern humans. In short, modern genetic variation has nothing to say about where AMH originated.
1b. Eurasians can no longer be seen as a subset of Africans, given that they possess genetic variation from Denisovans, a layer of ancestry earlier than all extant AMH. While it is still true that most Eurasian genetic material is a subset of that of modern Africans, it is also true that the deepest known lineage of humans is the Denisovan-Sima de los huesos, with no evidence for any deeper African lineage. Within humans as a whole, Africans possess a subset of Eurasian genetic variation.
2a. African priority received a boost by 0.1My by the redating of Jebel Irhoud last year. And, non-African AMH received a boost of 0.05My by the Hershkovitz et al. paper yesterday. A very short time ago, Ethiopia boasted the oldest AMH by 0.07My and now it's tied with the Levant and beaten by Morocco. It's a bit silly to argue for temporal priority based on the spotty and ever-shifting palaeoanthropological record.
2b. It is virtually untenable to consider the ~120,000 year old Shkul/Qafzeh hominins as a failed Out-of-Africa, since it now seems that they may have been descendants from the Mislya Cave population of >50,000 or even >100,000 years earlier.

I had previously supported a "two deserts" theory of human origins in which AMH originated in North Africa (Sahara) and then left Africa >100kya as evidenced by the Shkul/Qafzeh hominins and/or the Nubian technocomplex in Arabia. While I am still convinced that AMH originated somewhere in North Africa or the Near East, I am less certain as to where.

Science 26 Jan 2018: Vol. 359, Issue 6374, pp. 456-459 DOI: 10.1126/science.aap8369

The earliest modern humans outside Africa

Israel Hershkovitz et al.

To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.

Link

Deepest Neandertal mtDNA split

The authors interpret the new result from HST as placing a lower boundary on an introgression from Africans to Neandertals at more than 290kya, which explains why Africans are genomically closer to Neandertals than to Denisovans.

Of course, when one looks at the mitochondrial phylogeny, it has the form:

(Denisovans, (Neandertals, Modern Humans))

Within the Modern Humans, Eurasians are a branch of a tree which is mostly African. This has been interpreted for decades as evidence for the Out of Africa hypothesis for the origin of Modern Humans. But, within the phylogeny as a whole, Modern Humans are a branch of the Eurasian tree. This has not (why?) in general been interpreted as evidence for Out of Eurasia for the common ancestor of Modern Humans and Neandertals.

It seems to me that this hypothesis, that Modern Humans and Neandertals stem from a non-African ancestor (a non-African population of H. heidelbergensis, for example), has much to recommend it.

Eurasia has twice the size of Africa and has been home to hominins for ~1.8 million years. It was inhabited by diverse hominins, and thanks to blind luck we discovered that as late as a few tens of thousands years ago, it also sported two of the populations that split off before anyone else: first H. floresiensis, and second Denisovans.

While a North African source of modern humans is plausible, the data seems to favor a Eurasian origin of the (Modern Human, Neandertal) ancestor.

Nature Communications 8, Article number: 16046 (2017) doi:10.1038/ncomms16046

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.

Link

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

Bursts in human male demography

From the paper:

When the tree is calibrated with a mutation rate estimate of 0.76 × 10-9 mutations per base pair per year9, the time to the most recent common ancestor (TMRCA) of the tree is ~190,000 years, but we consider the implications of alternative mutation rate estimates below. Of the clades resulting from the four deepest branching events, all but one are exclusive to Africa, and the TMRCA of all non-African lineages (that is, the TMRCA of haplogroups DE and CF) is ~76,000 years (Fig. 1, Supplementary Figs. 18 and 19, Supplementary Table 10, and Supplementary Note). We saw a notable increase in the number of lineages outside Africa ~50–55 kya, perhaps reflecting the geographical expansion and differentiation of Eurasian populations as they settled the vast expanse of these continents. Consistent with previous proposals14, a parsimonious interpretation of the phylogeny is that the predominant African haplogroup, haplogroup E, arose outside the continent. This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). Furthermore, the timing of this putative return to Africa—between the emergence of haplogroup E and its differentiation within Africa by 58 kya—is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and nearby regions of Asia 50–80 kya15.

I've long argued for the Y-chromosome haplogroup E migration into Africa and it is nice to see this common-sense interpretation finally adopted. Too much focus has been placed on figuring out which routes modern humans took out of Africa, and not at all to figure out how Eurasian males came to overwhelm the African Y-chromosome gene pool so decisively. The Eurasian migration into Africa must have taken place in the ~70-60kya window, constrained by the D/E split and  the deepest intra-African E splits. I think that the Out-of-Arabia scenario I outlined in 2012 continues to make a lot of sense. It would be awesome to get data from the first Later Stone Age people from Africa which are probably the best bet to trace this migration from Eurasia into Sub-Saharan Africa.

Nature Genetics (2016) doi:10.1038/ng.3559

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

G David Poznik et al.

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.

Link

Nubian assemblages from the Negev

Nubian assemblages from the Levant are quite important because they provide an intermediate link (along land routes) between those from Africa and Arabia. It's also more difficult now to consider the Arabian finds as a limited event without broader implications about modern human dispersals. From the paper:

Mapping the earliest dated sites that contain a Nubian component does not permit an unequivocal identification of a region of origin for the Nubian Technology.

Quaternary International doi:10.1016/j.quaint.2016.02.008

“Diffusion with modifications”: Nubian assemblages in the central Negev highlands of Israel and their implications for Middle Paleolithic inter-regional interactions

Mae Goder-Goldberger, Natalia Gubenko, Erella Hovers

Nubian Levallois cores, now known from sites in eastern Africa, the Nile Valley and Arabia, have been used as a material culture marker for Upper Pleistocene dispersals of hominins out of Africa. The Levantine corridor, being the only land route connecting Africa to Eurasia, has been viewed as a possible dispersal route. We report here on lithic assemblages from the Negev highlands of Israel that contain both Levallois centripetal and Nubian-type cores. Wetter conditions over the Sahara and Negev deserts during MIS 6a–5e provided a generally continuous environmental corridor into the Levant that enabled the dispersal of hominin groups bearing the Nubian variant of prepared core technologies. The Negev assemblages draw renewed attention to the place of the Levant as one of the dispersal routes out of Africa during the Late Pleistocene and could suggest that processes of human dispersals and cultural diffusion resulted in the spread of Nubian technology across eastern Africa, the western Sahara and the Nile Valley, the southern Levant and Arabia.

Link

Adaptation in the light of ancient genomes

Nature Communications 7, Article number: 10775 doi:10.1038/ncomms10775

Human adaptation and population differentiation in the light of ancient genomes

Felix M. Key, Qiaomei Fu, Frédéric Romagné, Michael Lachmann and Aida M. Andrés

The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation.

Link

Are living Africans nested within Eurasian genetic variation (?)

The picture on the left (source) shows quite nicely that according to current understanding, Africans are nested within Eurasian genetic variation. The modern humans have the following structure:

(Early modern human lineage detected as admixture in the Altai Neandertal, ((Asians, Europeans), Africans)),

and then there are two deeper layers of Eurasian hominins (Neandertal/Denisovans) and the "Mystery hominin" that mixed into Denisovans.

Africans are thus just a leaf of the Eurasian family tree, casting serious doubt -if this model is to be believed- to the position that H. sapiens originated in Africa and are descended from people who never left the continent. It seems much simpler to derive them from an early migration (~200kya?) from Asia which would nicely explain why the continent's first sapiens populations appear tentatively in the northeastern corner, and why they do not replace archaic hominins for most of the 200 thousand years until today. In a reversal of perspective it is not Skhul/Qafzeh that are the "migration that failed", but rather the Omo 1 outlier is.

One might argue that this is just a consequence of the fact that lots of ancient genomes have been published from Eurasia, but none from Africa. So, there are all these branches of deep archaic Eurasians simply because there are no genomes of deep archaic Africans.

But, this explanation does not really work. If Africans had any significant ancestry deeper than the split of "Early modern human lineage", then this lineage would be closer to (Asians, Europeans) than to Africans. However, Kulhwilm et al. assert that it is "equally related to present-day Africans and non-Africans". If they had any ancestry deeper than ((Denisovans, Neandertals), H. sapiens), then (Denisovans, Neandertals) would be closer to non-Africans than to Africans. Well, they are, but this is now satisfactorily explained by admixture from (Denisovans, Neandertals) into non-Africans, thanks to genomes like Ust Ishim, K14, and Oase which have big chunks of Neandertal ancestry that can't be explained any other way. No need to invoke any such lineage when a simpler well-documented alternative exists.

The presented phylogeny negates the possibility of the existence of collateral archaic African kin of the extant Africans that admixed with them, and leads to the conclusion that Africans are nested within Eurasian variation because they really are. This is, of course, incompatible with the statistically inferred archaic introgression into Africans which indeed postulates the existence of such archaic Africans and their contribution to extant ones.

I don't see any obvious flaw with Kulhwilm et al. but if its model is right, then it does lead to some rather extreme conclusions. It contradicts the evidence for archaic introgression; if Hsieh et al. is wrong (and I don't seen any evidence for that either), then Kulhwilm et al. can be saved, but only if Africans are really nested within several layers of Eurasian variation and did not admix at all with the morphologically diverse archaic Africans of the paleoanthropological record. This also doesn't seem right now that we know that sapiens-archaic admixture was a common occurrence in Eurasia. The reversal of perspective alluded to above may help here by removing the opportunity for admixture, but that too is, of course, an extraordinary claim.

In sum, I am rather convinced that the latest discoveries have muddled the origin story of our species and some major rethink is needed to evaluate the totality of the evidence.

Ancestors of Eastern Neandertals admixed with modern humans 100 thousand years ago

If true, this is very hard to reconcile with late (60kya) out of Africa and may be a smoking gun for pre-100kya presence of anatomically modern humans in Eurasia. From the paper:

The inferred demographic model confirms and provides quantitative estimates of previously inferred gene flow events among modern and archaic humans2, 3 (Extended Data Fig. 1). These include Neanderthal gene flow into modern humans outside Africa (3.3–5.8%) and gene flow from an unknown archaic hominin into the ancestors of Denisovans (0.0–0.5%). Interestingly, we also detect a signal of gene flow from modern humans into the ancestors of the Altai Neanderthal (1.0–7.1%). The precise source of this gene flow is unclear, but it appears to come from a population that either split from the ancestors of all present-day Africans or from one of the early African lineages, as significant admixture rates are estimated from San as well as Yoruba individuals. This introgression thus occurred in the opposite direction from the previously reported gene flow from Neanderthals to modern humans outside Africa

And:

However, it is clear that the source of the gene flow is a population equally related to present-day Africans and non-Africans (Extended Data Fig. 3). We conclude that the introgressing population diverged from other modern human populations before or shortly after the split between the ancestors of San and other Africans (Fig. 3a), which occurred approximately 200,000 years ago11.

The implications of this inference (if correct) for modern human origins are potentially monumental as they suggest a Eurasian modern human lineage (only detected in the Altai Neandertal) that diverges from other modern humans as early (if not earlier) than any two African ones.

If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.

Things are bound to get more interesting.

Nature (2016) doi:10.1038/nature16544

Ancient gene flow from early modern humans into Eastern Neanderthals

Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.

Link

Modern humans in China ~80,000 years ago (?)

Another (?)-worthy paper has just appeared in Nature in the heels of the African ancient genome paper. Time will tell how these worldview-altering discoveries will change the story of Mankind, and a degree of skepticism is warranted. In the view I've held for a few years, modern humans expanded to Arabia before 100 thousand years ago, started leaving it 70 thousand years ago as the ecological situation worsened due to desertification and broke through the "Neandertal barrier" between 70-50 thousand years ago when they developed the skills and technology to overcome them.

The new paper claims that modern humans were in China 80 thousand years ago and came to Europe much later because Neandertal represented a barrier to successful entry to Europe. This begs the question of how they reached China without encountering Neandertals, as Neandertals were also in West Asia where -presumably- they passed through to get to China. A coastal route to south China would explain away this problem, but the coastal migration is usually envisioned much later, at around 60 thousand years ago. On top of that, how did Chinese end up having equal (or more) levels of Neandertals admixture if modern humans first went to China and later moved west and successfully outcompeted the Neandertals. How were they able to do so eventually? (There is no evidence that the kind of advantages associated with behavioral modernity first emerged in East Asia). It's possible that there were 80 thousand year-old modern humans in China (just as there were 100 thousand year-old modern humans in Israel), but that the later East Asians are not descended from them.

One would think that science would present an increasingly reasonable and consistent picture of the past, but it seems that we're a very long way from the point where the dust settles and the puzzle pieces start falling into place.

Nature (2015) doi:10.1038/nature15696

The earliest unequivocally modern humans in southern China

Wu Liu, María Martinón-Torres, Yan-jun Cai, Song Xing, Hao-wen Tong, Shu-wen Pei, Mark Jan Sier, Xiao-hong Wu, R. Lawrence Edwards, Hai Cheng, Yi-yuan Li, Xiong-xin Yang, José María Bermúdez de Castro & Xiu-jie Wu

The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking1, 2, 3, 4. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe5, 6, 7. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.

Link

Rethinking the dispersal of Homo sapiens out of Africa

An excellent review which -among its other graces- demolishes the view that mtDNA haplogroup L3 provides a terminus post quem of 70 thousand years for the Out-of-Africa expansion, a question I've discussed in this blog before.

I think the evidence is overwhelming at this point that there were modern humans outside Africa before 100,000 years ago. The argument that they were a  failed expansion is shoddy and is based, as far as I can tell on things like the age of L3, the assumption that Y-chromosome haplogroup E is native to Africa and not derived from back-to-Africa migrants, the assumption that Out-of-Africa coincided with the Upper Paleolithic cultural efflorescence (disproven by the earlier dating of Neandertal admixture), or the failed hypothesis of a coastal route Out of Africa 60 thousand years ago that seems to be repeated in inverse proportion to the evidence for it. The halving of the human autosomal mutation rate relative to what was inferred before has certainly not helped either.

Evolutionary Anthropology: Issues, News, and Reviews Volume 24, Issue 4, pages 149–164, July/August 2015

Rethinking the dispersal of Homo sapiens out of Africa

Huw S. Groucutt, Michael D. Petraglia, Geoff Bailey, Eleanor M. L. Scerri, Ash Parton, Laine Clark-Balzan, Richard P. Jennings, Laura Lewis, James Blinkhorn, Nick A. Drake, Paul S. Breeze, Robyn H. Inglis, Maud H. Devès, Matthew Meredith-Williams, Nicole Boivin, Mark G. Thomas andAylwyn Scally

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.

Link and here

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

Multiple opportunities for Out-of-Africa

Geology doi: 10.1130/G36401.1

Alluvial fan records from southeast Arabia reveal multiple windows for human dispersal

Ash Parton et al.

The dispersal of human populations out of Africa into Arabia was most likely linked to episodes of climatic amelioration, when increased monsoon rainfall led to the activation of drainage systems, improved freshwater availability, and the development of regional vegetation. Here we present the first dated terrestrial record from southeast Arabia that provides evidence for increased rainfall and the expansion of vegetation during both glacial and interglacial periods. Findings from extensive alluvial fan deposits indicate that drainage system activation occurred during Marine Isotope Stage (MIS) 6 (ca. 160–150 ka), MIS 5 (ca. 130–75 ka), and during early MIS 3 (ca. 55 ka). The development of active freshwater systems during these periods corresponds with monsoon intensity increases during insolation maxima, suggesting that humid periods in Arabia were not confined to eccentricity-paced deglaciations, and providing paleoenvironmental support for multiple windows of opportunity for dispersal out of Africa during the late Pleistocene.

Link

An archaeological scenario for Out of Arabia

Jeffrey Rose and Anthony Marks have a preprint in which he details an archaeological scenario for the emergence of the Emiran (arguably the best candidate for the ur-Upper Paleolithic at the moment) from Arabian progenitors who themselves had Northeast African Nubian Levallois progenitors. I proposed Out of Arabia a few years ago and followed research suggestive of such a trajectory of modern humans in various posts under the Out of Arabia label.

In a nutshell, it seems to me that the 50kya OoAfrica model is wrong, falsified by (i) the dating of Neandertal adixture (which precedes it and could only have happened outside of Africa), (ii) the dating of human mtDNA and NRY trees in numerous papers that show a split that precedes 50kya. This in itself proves that the Upper Paleolithic (which is attested in the post-50kya period and rapidly spreads across Eurasia in a genetic Big Bang of expansion leading to the full disappearance of Neandertals by ~40kya) must have local Eurasian origins rather than being an import from Africa.

If UP is not linked to the Out-of-Africa event, then two questions arise: (i) how did the UP arise in Eurasia, and (ii) when did the Out-of-Africa event take place? The increasing adoption of a "slow mutation rate", the discovery of a potential ~100kya layer of ancestry separating Europeans from East Asians, and, on the archaeology side, the proliferation of evidence against the "coastal migration route" all hint in OoAfrica taking place much earlier than the UP revolution in answer to question (ii).  Indeed, one of the few stumbling blocks of a much earlier Out-of-Africa (the date of L3~70kya) may actually be falling, if it turns out that African L3 is nested within Eurasian M+N and not vice versa. The new preprint by Rose snf Marks helps answer question (i) by proposing an archaeological scenario that derives the UP of the Levant from the MP of Arabia.

From the paper:

In sum, the tool assemblages of the early Emiran include a combination of both classic UP tool types and MP Levallois points; it cannot be accurately characterized as fully UP, rather, an amalgamation of MP and UP forms. Viewed solely within a Levantine context, the technological and typological patterning of the early Emiran might suggest it derived from local innovation without significant external demographic input. 

... 

So, with no clear cut antecedents in the Levant, do the three Emiran technological traits that have no deep Levantine ancestry (i.e., bidirectional core preparation, the use of cresting, and the presence of lateral modification on Levallois points), have  demonstrable origins elsewhere? Conversely, do those deeply rooted Levantine characteristics of the Emiran (i.e., elongated Levallois point production and UP tool  manufacture) have comparable analogues in adjacent areas? 

...  

Given these technological and typological considerations, we find no direct relationship between any northeast African MIS 5 industry and the early Emiran. The African data do suggest that the Emiran preferential bidirectional Levallois point production strategy ultimately arose in northeast Africa during late MIS 6. This reduction strategy became increasingly widespread during MIS 5, where it spread as far south as the Ethiopian Rift and east into the Arabian Peninsula. This wide distribution suggests extensive cultural contact, either direct or indirect, along the Nile Valley and across the Red Sea during the Last Interglacial, when climatic conditions were optimal. 

...  

By MIS 5.3 (~ 100 ka), perhaps, even as early as the Last Interglacial, the African Nubian Complex was widespread in Arabia, from the Yemeni Hadramawt to the eastern edge of the Nejd Plateau in southern Oman. Additional manifestations of this technocomplex have been found in the Rub' al Khali, central Saudi Arabia, and the Al Jawf basin of northern Saudi Arabia, less than 300 km southeast of ‘Ain Difla. Given the Nilotic origin of the Nubian Complex, its presence in Arabia may be firmly understood as a huntergatherer range expansion out of northeast Africa.  

...  

The techno-typological patterns we have observed point to an origin of the Emiran that was neither wholly rooted in the Levant nor the result of a complete demographic replacement from groups expanding out of Africa; rather, the Emiran combines elements of the Nubian Levallois system with typological elements from the southern Levantine Mousterian. This scenario envisions a zone stretching across the interface of northwestern Arabia and the southern Levant, where the territories of Levantine and Arabian huntergatherer populations overlapped during MIS 5. Bilateral exchange over time resulted in the incorporation of an Afro-Arabian core reduction strategy with a Levantine toolmaking tradition that extends back to the Early Mousterian. 

...  

African Nubian Complex toolmakers, at least, were modern humans. AMH specimens have been documented in North Africa from 150 ka onward (Smith et al., 2007; Hublin and McPherron, 2012), while no other species has yet been found there. An AMH child burial was excavated from an extraction pit associated with Activity Phase III at Taramsa Hill 1 (Vermeersch et al., 1998; Van Peer et al., 2010), with a terminus post quem of ca. 70 ka. Given the technological similarity of the Classic Dhofar Nubian and the Late Nubian Complex of the Middle Nile Valley in Egypt, as well as the fact that there is no evidence for prior MP human occupation in southern Oman, it is reasonable to associate the distribution of Nubian Complex sites with a population of AMHs spread across northeast Africa and the Arabian Peninsula. The presence of Nubian Levallois technology in southern Arabia and the Horn of Africa (Clark, 1954; Kurashina, 1978; Clark, 1988; Beyin, 2013), as well as northern Arabia and in the Red Sea hills of Egypt, suggests that early human groups traveled to and from Africa via both the Arabian and Levantine Corridors.

It is unfortunate that Arabia is so poor (to wholly deficient?) in ancient human remains from this critical period. Nonetheless, it makes sense that if modern humans were present in Northeast Africa in association with Nubian Complex tools, they would be the ones who carried them to Arabia. The presence of AMH in the Levant (associated with Mousterian tools) was often dismissed until recently as the Out-of-Africa that failed, partly because the Shkul/Qafzeh hominins were the only pre-UP modern humans in Eurasia (making their extinction plausible) and partly because of the widespread view that Out-of-Africa happened ~70-50kya (which by definition would imply that the Mount Carmel hominins weren't the Out-of-Africa.

However, if AMH were also present in Arabia during the MP it is much more difficult to argue for extinction of Eurasian modern humans and later replacement by a "late" Out-of-Africa event: this would imply that both the Levantine and Arabian humans would disappear. Moreover, the genetics no longer requires a late Out-of-Africa event and the UP is no longer plausibly concurrent with the OoAfrica event. In short, a quite simple explanation is that one group of AMH (from Arabia) mixed with another group of AMH (from the Levant) and the UP arose in this population. The latter group (from the Levant) lived in proximity to Neandertals and thus the evidence for Neandertal admixture in non-Africans is easily explained (no need to invoke unattested Neandertals admixing with "coastal route" migrating humans).

"Out of Arabia" and the Middle-Upper Palaeolithic transition in the southern Levant 

Jeffrey I. Rose, Anthony E. Marks

Beginning some 50 thousand years ago, a technological transition spread across the Near East and into Eurasia, in the most general terms characterized by a shift from preferential, prepared core reduction systems to the serial production of elongated points via opposed platform cores. The earliest known occurrence of such a technological shift is the Emiran Industry, whose earliest manifestations are found in the southern Levant. The cultural and demographic source(s) of this industry, however, remain unresolved. Looking to archaeogenetic research, the emerging picture indicates a major dispersal of our species out of Africa between 100 and 50 thousand years ago. Ancient DNA evidence points to low levels of admixture between Neanderthal and these pioneering modern human populations, which some suggest occurred in the Near East between 60 and 40 thousand years ago. These propositions underscore the significance of the Emiran and beg a reassessment of its origins. In this paper, we ask whether the Emiran was a local development, a cultural/demographic replacement, or the fusion of indigenous and exogenous lithic traditions. Our analysis considers the techno-typological features of the early Emiran in relation to late Middle Palaeolithic and contemporaneous assemblages from adjacent territories in Northeast Africa and the Arabian Peninsula, in order to identify overlapping cultural features and potential antecedents. Parsimonious with the archaeogenetic scenario of admixture, the Emiran seems to represent a fusion of local southern Levantine Mousterian typological elements with the Afro-Arabian Nubian Levallois reduction strategy. We conclude that the Emiran is primarily rooted in the Early Nubian Complex of the Nile Valley, which spread into the Arabian Peninsula during the Last Interglacial and developed at the interface of these two contextual areas between 100 and 50 thousand years ago.

Link

MSMC preprint (Schiffels and Durbin)

From the paper:

In particular, the early beginning of the drop would be consistent with an initial formation of distinct populations prior to 150kya, while the late end of the decline would be consistent with a final split around 50kya. This suggests a long period of partial divergence with ongoing genetic exchange between Yoruban and Non-African ancestors that began beyond 150kya, with population structure within Africa, and lasted for over 100,000 years, with a median point around 60-80kya at which time there was still substantial genetic exchange, with half the coalescences between populations and half within (see Discussion). We also observe that the rate of genetic divergence is not uniform but can be roughly divided into two phases. First, up until about 100kya, the two populations separated more slowly, while after 100kya genetic exchange dropped faster.

If divergence between Yoruba and non-Africans began 150kya, then I wonder when divergence between Bushmen or the non-farmer ancestors of Pygmies and the Yoruba started. These dates are well within the time period when anatomical modernity was already in existence, but well before the time period when behavioral modernity first appears. This is important, as some people imagine that humans lived together for most of the time period since their first appearance ~200kya and only split recently at ~50kya, but this is obviously wrong. ~50kya seems to be the time for cessation of gene flow, with 100ky more of impeded gene flow.

Also:

As expected, the oldest split amongst out-of-Africa populations is between European and East Asian (CHB and MXL) populations, most of which occurs between 20-40kya (Figure 4b). Intriguingly there may be a small component (10% or less) of this separation extending much further back towards 100kya, not compatible with a single out-of-Africa event around 50kya.

This is the most intriguing part of this preprint as it suggests that European/East Asian genetic differentiation may not only be due to the their post-UP divergence, but also to older strands of ancestry. Such deep differentiation may be related to the ~100kya settlement of the Near East (but not East Asia) by anatomically modern humans and the recent evidence for a deep "Basal Eurasian" lineage in Europeans but not East Asians.

bioRxiv, doi: http://dx.doi.org/10.1101/005348

Inferring human population size and separation history from multiple genome sequences

Stephan Schiffels, Richard Durbin

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.

Link

Chris Stringer on Recent Out-of-Africa

An interesting new opinion piece by Chris Stringer in which he affirms the recent Out-of-Africa theory. Some predictions of the multiregionalists were certainly wrong (e.g., they did not predict that East Asians would have any Neandertal ancestry, let alone more than Europeans; and the ancestry of mankind may be even more jumbled than they'd imagined as e.g., it is not Siberians that have regional continuity with Denisovans but rather the faraway Papuans and Australians). On the other hand, the evidence does seem to point for a mostly African origin of Homo sapiens with important details of when and how that remain to be filled.

The fundamental question for me is the balance of divergence and synthesis in human history. Certainly, the fact that Denisova cave and thereabouts in Siberia had at least four divergent human lineages in the last 100-40 thousand years (unknown archaic Eurasians, Denisovans, Neandertals, and finally modern humans) makes modern Eurasians look like twins by comparison. In more recent times, Europeans of a few thousand years ago living in Sweden were more divergent from each other than any two European populations living today. And, while many models would have modern humans and Neandertals splitting from each other and going their separate ways until very recent times, this is hard to reconcile with the fact that apparently Neandertals and Africans became more similar over time during the period where they were supposedly diverging from each other. Was the situation in Africa any different? Morphology does not suggest homogeneity for that continent either.

Certainly, both replacement and gene flow have played a role in human history. The "English" and "Spanish" packages were assembled in Europe by gene flows from hunter-gatherers, farmers, and more recently Anglo-Saxons, Celts, Vikings, Goths, Romans, and Celtiberians (to name a few), but was then exported from Europe. Human history probably abounds in examples of populations that emerge out of a multiregional matrix (even if that matrix does not encompass the entire globe) and then explode in population numbers due to a lucky break or some behavioral or technological advantage.

Trends in Ecology & Evolution Volume 29, Issue 5, p248–251, May 2014
DOI: http://dx.doi.org/10.1016/j.tree.2014.03.001

Why we are not all multiregionalists now

Chris Stringer

Highlights

•DNA data show that archaic introgression into modern human genomes occurred.
•Such introgression is claimed to support the multiregional model for modern human origins.
•This introgression is also claimed to support the lumping of distinct human species into Homo sapiens.
•Comparing models and data still validates a recent African origin model for modern humans and the use of a restricted diagnosis for H. sapiens.

Recent revelations that human genomes contain DNA introgressed through interbreeding with archaic populations outside of Africa have led to reassessments of models for the origins of our species. The fact that small portions of the DNA of recent Homo sapiens derive from ancient populations in more than one region of the world makes our origins ‘multiregional’, but does that mean that the multiregional model of modern human origins has been proved correct? The extent of archaic assimilation in living humans remains modest, and fossil evidence outside of Africa shows little sign of the long-term morphological continuity through to recent humans expected from the multiregional model. Thus, rather than multiregionalism, a recent African origin (RAO) model for modern humans is still supported by the data.

Link

Svante Paabo talk at NIH

A very interesting bit is from 18:30 and forward, in which he discusses the 45,000y BP modern human from Ust-Ishim. Here is a screenshot from this part of the talk (20:32):

According to Dr. Paabo, Ust-Ishim has longer Neandertal chunks than modern humans and this can be used to estimate that the admixture with Neandertals happened 331+/-99 generations before its time of 45,000y BP, or around 50-60,000y BP.

The coalescence of mtDNA haplogroups M and N has been estimated as ~50 and ~59ky BP respectively using modern human variation, so this seems quite compatible with that. This pretty much proves that there were modern humans in Eurasia before the Upper Paleolithic revolution and disproves Richard Klein's theory that modern humans together with UP technologies spread Out-of-Africa only after 50,000 years ago.

Green Arabia 2014 conference

The program of an upcoming conference that will take in about a month. I don't see abstracts but the list of talks seems interesting and hopefully there will be a twitter stream by attendees in April.

Resurrecting Neandertal Lineages (Vernot and Akey 2014)

Coinciding with the publication of Sankararaman et al. (2014) in Nature, another paper on Neandertal ancestry into modern humans appeared in Science. From the paper:

On average, we found 23 Mb of introgressed sequence per individual (Fig. 1F), with East Asian individuals inheriting 21% more Neandertal sequence than Europeans. Within subpopulations, we found small but statistically significant variation in the amount of introgressed sequence among Europeans (Kruskal-Wallis rank sum test; p-value = 4.2 × 10−12), but not among East Asians (p-value = 0.43).

and:

Consistent with recent inferences (5, 9), observed patterns of introgression were incom-patible with a one pulse model (Fig. 3B), suggesting that gene flow be-tween Neandertals and humans occurred multiple times. Although we varied many parameters of each model (10) (fig. S14), only the ratio of ancestral effective population size between East Asians and Europeans (NeASN/NeEUR) and the relative amount of introgression between the sec-ond and first pulse (m2/m1) had appreciable effects on model fit (Fig. 3B). We estimate that NeASN/NeEUR is 1.29 (95% CI of 1.15-1.57), and that East Asians received an additional 20.2% (95% CI of 13.4%-27.1%) more Neandertal sequence in the second pulse (10).

Science DOI: 10.1126/science.1245938

Resurrecting Surviving Neandertal Lineages from Modern Human Genomes

Benjamin Vernot, Joshua M. Akey

Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.

Link