Out of Africa Details Continue To Evade Resolution

Eurogenes calls attention to a new conference paper out humanity's out of Africa dispersals.

When and how modern humans left the African continent is still a debated question. 

Recently, three projects have analysed new genetic data from modern populations in Papua New Guinea and Australia, which has provided new insights on this topic. I will present analyses from one of these publications (Malaspinas et al. 2016), and compare results with findings from the two other projects (Mallick et al. 2016, Pagani et al. 2016). Here, we used MSMC2, a novel computational framework to analyse the distribution of times to the most recent common ancestor along multiple sequences. 

We find that all non-African populations that we analysed, including Australians, experienced a very similar population bottleneck in the past, consistent with only one out-of-Africa migration for all extant non-African populations. At the same time, we find evidence that some African populations are more distantly related to Australians than to Eurasian populations, and we show that this result is robust to haplotype phasing errors and archaic introgression. 

We interpret our result as evidence for gene flow between some Africans and Eurasians after the initial split, which is also consistent with results from other population genetic methods. Our analysis suggests that in order to understand human dispersal out of Africa, we need to better understand ancient population substructure within Africa, which is an important direction for future research.

Stephan Schiffels, "Analysing Australian genomes to learn about early modern human dispersal out of Africa, Human Dispersals in the Late Pleistocene - Interdisciplinary Approaches Towards Understanding the Worldwide Expansion of Homo sapiens" (Human Dispersals in the Late Pleistocene - Interdisciplinary Approaches Towards Understanding the Worldwide Expansion of Homo sapiens conference, November 2016).

Much of the "hot debate" revolves around archaeological evidence of a modern human presence as early as 125,000 years ago in Arabia, at least 100,000 years ago in the Levant, and some time prior to the Toba volcanic eruption of 75,000 years ago in India. And, there is evidence of modern human admixture in the ancient DNA of Altai Neanderthals that would have to date from at least 100,000 years ago, and the is also some evidence of modern humans or modern human hybrids in China well before the 50,000 to 65,000 years before present date expected for modern humans in Australia, Papua New Guinea and Southeast Asia based upon existing archaeological data.

But, both mutation rate DNA estimates, and linkage disequilibrium methods from ancient DNA have suggested a most common recent out of Africa ancestor for Eurasians of closer to 50,000 years ago than 75,000 years ago, and certainly not 100,000 to 125,000 years ago. Some argue that this reflects an "out of Africa that failed". 

Another possibility is that the single wave Out of Africa population was confined to Arabia or some other small geographic area that was a single population genetic unit until the most recent common ancestor date. 

Another possibility is massive dilution of earlier waves of modern humans that has eliminated almost all genetic trace of them (which is one possible interpretation of this paper).

Also, while most modern humans may derive from one wave, and the Y-DNA DE split seems to be close in time to the Y-DNA CF split that includes the vast majority of non-Africans, sampling issues may be hiding a northern route Y-DNA DE and D associated population that could have been another out of Africa wave. This is further complicated by increasingly credible suggestions of northern route expansions into Eurasia by modern humans, with a light archaeological footprint and genetic traces of which may have been largely erased by Ice Age of the Last Glacial Maximum around 20,000 years ago.

Given the seemingly contradictory and unresolved state of the evidence, understanding modern human out of Africa migrations during pre-history may take a lot longer to figure out.