December 12, 2018

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:

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

April 13, 2018

R1ans still at large (or, the story of India)

Ten ago, in the pre-ancient DNA "Dark Ages" a big debate raged on about the origin of R1a  men in India. The stage had been set even earlier, by the pioneering Eurasian heartland paper which was the first (to my memory) to link M17 with steppe migrations and Indo-Iranians. Yet, there was pushback as the distribution of M17 was better described, and people started using Y-STRs to try to date and place phylogeographically its migrations.

The two poles of the debate were the "Out-of-India", which relied primarily on Y-STR based time estimates that seemed very old (even Paleolithic, if one used the wrong mutation rate) in India, and the "Into-India" which thought that the R1a distribution pointed to its being brought into India by the Indo-Aryans in the conventional ~3,500BC time frame of the "Aryan Invasion Theory" (AIT).

AIT has been much maligned because it has been received as a Western colonialist imposition on Indian history: a way to claim that Indian civilization was not native but European in origin. Europeans were certainly guilty of misusing AIT: for British colonials it represented a precedent for their colonization of India; for German National Socialists it was evidence for the greatness of the Aryan race and its past expansions eastward. It also played into internal Indian politics, espoused by some as a means of furthering their superiority as either descendants of "Aryan conquerors" or as oppressed victims of the same.

Of course, a misuse of a theory does not mean it is wrong, and if a new preprint based on ancient and modern DNA is correct, it means that AIT was basically correct: Indo-Aryans did come to India in the Late Bronze Age, via the steppe, and ultimately from central Europe.

The opposing Out-of-India theory is all but dead, although failed theories often have a long half-life, especially if they are espoused for psycho-political reasons. I would argue that Out-of-India was dead for thousands of years before it was conceived, since even in Homer's time it was known that "India" was not "one thing" but was peopled by Indians in the north and "Eastern Ethiopians" in the south (which differed from their western "actual" Ethiopians of Africa by their possession of straight rather than curly hair). These were the "Ancestral North Indians" and "Ancestral South Indians" that modern science has revealed. Out-of-India is little more than a nationalistic myth functioning as an antidote to this basic dichotomy, a way to imbue India's diverse citizens with a myth of common origins.

Yet, proponents of AIT (who have a non-trivial overlap with R1an enthusiasts) are also scratching their heads because of the 27 ancient South Asian males from South Asia studied in the preprint there is exactly one R1a, who also happened to live after the time of the Buddha and not during the Bronze Age.

Both OIT enthusiasts (who expected copious and abundant R1a in India and its environs since the Paleolithic) and AIT/R1an enthusiasts (who expected to see it come in c. 3,500BC) are bound to be disappointed.

Perhaps the R1a Indo-Aryans did come to South Asia in a conventional AIT time frame and they haven't been sampled. Or, maybe they were, indeed, there, but were not R1ans. Or, maybe both sides missed the bigger story which is that the Indo-Aryans (so closely associated with India today) were simply not there as early as people have thought. 

bioRxiv: doi: https://doi.org/10.1101/292581

The Genomic Formation of South and Central Asia

Vagheesh M Narasimhan, Nick J Patterson et al.

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

Link


April 10, 2018

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

March 25, 2018

Statistical Palaeoafricans

According to a new preprint by Durvasula and Sankararaman (D+S):
Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population
This ~8% matches well the ~9% of "West Africa A" in Yoruba of the model of Skoglund et al. Figure 3D. If "West Africa A" corresponds to the Archaic Ghost of D+S, then the Mende have the most of it at ~13%.

I have long maintained that the higher genetic diversity of extant Sub-Saharan Africans is the result of admixture between "Afrasians" (a population that spawned Eurasians and much of the ancestry of Sub-Saharans and which had "low" (Eurasian-level) of genetic diversity) and multiple layers of "Palaeoafricans". It would seem that one such layer has now been discovered.

Where did the Afrasians live? Recent developments pushed back the presence of modern humans in both North Africa and the Middle East, making both regions highly competitive as the cradle of the Afrasians. The odds for Sub-Saharan Africa have greatly diminished also by the discovery of late non-sapiens H. naledi in South Africa (which was naively postulated as a cradle based on the presence there today of genetically diverse San Bushmen, but who are not descendants of even Late Pleistocene South Africans), as well as of the archaic component in the genomes of West Africans. These discoveries pile up on top of known archaic skulls of late provenance in both Central and West Africa.

Remember though, that the archaic admixture in West Africans is "less archaic" (more closely related to H. sapiens) than the Neandertal/Denisovan ancestry which contributed to extant Eurasians. All Africans (modern or archaic) are a branch within the phylogeny of Eurasians, with Australoids (and now apparently East Asians too) having the deepest known strain of human ancestry inherited from the elusive Denisovans.