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What Sahul tells us about world genetic history


The paper Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul came out a few months ago. It’s fine. But one thing jumped out at me:

All estimated effective population size curves show a bottleneck around 60–70 ka, as found for European and Asian populations (supplementary fig. 16, Supplementary Material online). Around 50 ka, estimated effective population sizes for populations from Wallacea and Sahul are between 1,671 and 2,100 individuals, and between 2,540 and 2,999 individuals in Eurasia and 9,506 individuals in Africa. All divergence dates for Wallacea/Sahul groups from Africa, represented by Yoruba genomes, show similar results (74 ± 4.2 ka, supplementary fig. 17, Supplementary Material online). We note here that this date is older than that obtained between Eurasian and African genomes (66.5 ± 3.7 ka), a result previously reported and interpreted as a potential methodological bias or the signal of an even earlier human migration from Africa (Malaspinas et al. 2016; Mallick et al. 2016; Pagani et al. 2016; Bergstrom et al. 2017).

First, the bottleneck precedes the massive expansion after 60 ka. Second, perhaps there was Eurasian back-migration into Africa and that’s impacting the difference coalescence dates? Basically, the Yoruba can be thought as a population strongly influenced by “out-of-Africa” gene flow.

10 thoughts on “What Sahul tells us about world genetic history

  1. 74,000 years ago Toba caused an ecological vacuum. Genes flowed into the vacuum from Africa. Toba was the largest volcano in 25,000,000 years.

  2. Nice article, but I still have an important question to ask regarding the genetic relationship Australo-Melanesians have to the other “out-of-Africa” populations.
    Do they form a totally different lineage from the rest of Eurasians, or are they formed from an earlier split of ancestral Eastern Eurasians?

  3. Is it possible that the Denisovan admixture in Australo-Melanesians – much higher than in other Eurasians – (if that was not accounted for) contributes to their measured (the appearance of) “earlier divergence” from Africans (along with the factor of possible admixture in Australo-Melanesians from an earlier mostly extinct OOA AMH group, as the study/other studies have suggested)?

  4. @ Roberto Santos

    “Do they form a totally different lineage from the rest of Eurasians, or are they formed from an earlier split of ancestral Eastern Eurasians?”

    I think as it stands it seems that Oceanians do have a deep relationship with conventional East Eurasians but it’s not totally clear to what extent. I’ve seen models where Papuans are strict descendant of a sister lineage related to Tianyuan, but they can also be modeled as a 50-50 split of something Tianyuan-like and some sort of other “basal” Eurasian lineage that isn’t related to either conventional West or East Eurasians.

  5. @Jm8

    They did indeed account for the Denisovan/Neanderthal ancestry:

    “We added further detail to this scenario by reconstructing the effective population sizes of these groups, and estimating divergence dates between all studied groups using MSMC2 (Schiffels and Durbin 2014). Since archaic admixture can be a confounding factor in these analyses (Mallick et al. 2016), we masked both Neandertal and Denisovan genomic tracks using ChromoPainter (Lawson et al. 2012). The archaic genetic ancestry in the newly sequenced genomes ranges between 1.8% and 2.8% of Denisovan ancestry and ranges between 2.3% and 2.5% of Neandertal ancestry, corresponding to previous estimations (Vernot et al. 2016; Jacobs et al. 2019).”

  6. Oceanians cannot be from an earlier Out of Africa migration. At least such a stream of ancestry would not be a significant component of their auDNA. If it were, we would find some special Y or mt DNA haplogroup among Oceanians associated with such ancestry. So far all we see is just the usual OoA haplogroups like C1b, K2 on the paternal side and M & N for mt-DNA.

  7. @ J Khan

    The admixture component found/proposed from an earlier OOA in Oceanians would be (has been estimated to be) fairly small, but it would be pretty divergent from other non-African moderns, having left Africa significantly earlier than the later OOA (perhaps between 200-100,00 ya or 150-100,000 ya), so possibly could affect estimated divergence times.

  8. Cont.:
    From Pagani et al 2016.:
    “We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa….our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago…Fossil and archaeological evidence and craniometric studies of African and Asian populations, demonstrate that Homo sapiens was present outside of Africa ca. 120-70 kya11.
    “…modern human[s] reached Eurasia at around 100kya12.”
    https://escholarship.org/content/qt6568472d/qt6568472d_noSplash_3ac6cee920de10c4e8f1c37a66a8e82e.pdf

    The majority (usually all) of non-African modern ancestry derives from a later OOA (ca 50-70kya), but a small fraction in Australo-Melanesians seems to remain from an earlier OOA that occurred around 100kya (some evidence also supports an even earlier expansion of AMH from Africa).

  9. Edit to last comment:
    “(some evidence supports an even earlier – also extinct or mostly extinct -expansion of AMH from Africa)”

  10. @ Mick

    Is it possible that other/some fraction of the archaic admixture was undetected? If I remember, there was more than one admixture event involving the ancestors of Oceanians with more than one hominin in the “Denisovan family” native to Asia and the Pacific region (1.8%-2.8% is lower than the approximately 3%-4% usually estimated for Oceanians.).

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