Three major events have shaped the distribution and abundance of modern humans across planet earth over the past 50,000 years. First, the “Out of Africa” event. Second, the Last Glacial Maximum ~20,000 years ago. And third, the changes wrought by the Holocene, foremost amongst them agriculture, but also including other developments, such as the utilization of the horse to increase human mobility.
There are two major phylogenetic and population genetic consequences of these dynamics. First, human phylogeny is highly reticulated. That is, it can be better thought of as a graph rather than a branching tree over the past ~50,000 years, due to repeated pulses of massive gene flow between tips of the diversifying human lineages. Second, abiotic and biotic selection pressures in the context of population turnover mean that adaptation has been a continuous process. Additionally, the complex feedback loops engendered by cultural evolution mean that biological evolution through adaptation is driven by endogenous forces, emerging from changes within human societies, rather than simply external exogenous shocks.
Two new papers on Australian archaeology and genetics illustrate this. First, today, Cultural innovation and megafauna interaction in the early settlement of arid Australia:
Elucidating the material culture of early people in arid Australia and the nature of their environmental interactions is essential for understanding the adaptability of populations and the potential causes of megafaunal extinctions 50–40 thousand years ago (ka). Humans colonized the continent by 50 ka1, 2, but an apparent lack of cultural innovations compared to people in Europe and Africa3, 4 has been deemed a barrier to early settlement in the extensive arid zone2, 3. Here we present evidence from Warratyi rock shelter in the southern interior that shows that humans occupied arid Australia by around 49 ka, 10 thousand years (kyr) earlier than previously reported2. The site preserves the only reliably dated, stratified evidence of extinct Australian megafauna5, 6, including the giant marsupial Diprotodon optatum, alongside artefacts more than 46 kyr old. We also report on the earliest-known use of ochre in Australia and Southeast Asia (at or before 49–46 ka), gypsum pigment (40–33 ka), bone tools (40–38 ka), hafted tools (38–35 ka), and backed artefacts (30–24 ka), each up to 10 kyr older than any other known occurrence7, 8. Thus, our evidence shows that people not only settled in the arid interior within a few millennia of entering the continent9, but also developed key technologies much earlier than previously recorded for Australia and Southeast Asia8.
The paper is archaeology, with a lot of stuff on dating and stratigraphy, which I can’t add much to. But, it confirms hints that modern humans really spread rapidly once they had a chance. It does seem that the pulse of migration out of the fringe of Africa that resulted in all non-Africans (or most of their ancestry) moved very rapidly across the world once it got a head of steam going. The genetic and archaeological evidence seems to indicate that movement did not predate 50,000 years B.P. by that much (this doesn’t mean there weren’t earlier waves which were absorbed or died off from the same region of a similar ancestral population).
Then, from a few months ago, A genomic history of Aboriginal Australia:
The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
There are a few things going on in this paper. First, they had a lot of whole genomes, rather than just SNP data. They used this whole genome data to get a really good sense that once you correct for excess Denisovan ancestry the “two-wave” model out of Africa is just not that well supported in comparison to a single expansion.
Second, because the Australians and Papuans were isolated from other populations for most of history, it turns out you can see evidence of gene flow between Sub-Saharan Africans and Eurasians, in particular West Eurasians, after the divergence of the non-African groups. This is not entirely surprising. And, that gene flow is found in the Dinka and Yoruba samples, but not the San. Again, not surprising. Note, more recent Holocene gene flow form Eurasians into Sub-Saharan populations is clear in Nilotic populations, such as the Masai. This is something different. Perhaps it is older gene flow back into Africa, or, perhaps it is evidence of substantial African gene flow into Eurasia, possibly during the Pleistocene.
But big inferences were about the timing and divergence of Australian and Papuan groups. As noted in the paper Australia was not separate from New Guinea for much of the Pleistocene. They were one continent, Sahul. But the divergence between modern Australians and Papuans seems to predate the rising of the sea levels by tens of thousands of years. Part of this is probably some level of ecological isolation, as the highlands of New Guinea would always have been very distinct from the much drier Australian landmass. But I suspect that part of is that there was a lot of ancient structure in Sahul. The existence of two major lineages is probably simply a function of the fact that meta-population dynamics in humans are subject to a lot of local extinction events, and most of the deeply diverged lineages are gone.
Modern Australians seem to date from a common population which may have arisen around the Last Glacial Maximum. This comports with the model above. Basically, a lot of the other groups in the broader family of Australian populations probably went extinct for various reasons. This means ancient DNA from Australia which is substantially old enough will be from highly diverged lineages with no modern descendants. Think of the ancient samples from Siberia and Romania which seem to have had minimal impact on the modern Eurasian populations.