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The Wallacean Hominin Wonderland

A new preprint, Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia, attempts to synthesize paleontology, biogeography, and human evolutionary genomics. It’s a pretty impressive effort, and short and compact:

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic super-archaic species, Homo luzonensis and H. floresiensis, were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA, a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.

Most paleonathropologists seem convinced now that Flores and the island of Luzon in the Phillipines were host to deeply diverged lineages of humans. By “deeply diverged” we’re talking well over one million years. Homo itself is only two million years ago. If they are deeply diverged there are ways to probe the genome for outlier segments of DNA which seem to have “come in” from outside lineages in relation to the main branch of ancestry. The more deeply diverged the ancestry, the easier it is to pick up the signal with even small amounts of admixture.

The authors could not find such ancestry in the various population across Southeast Asia and Australia, at least not to a greater extent than elsewhere. This implies that if luzonensis and floresiensis are deeply diverged they did not mix with anatomically modern humans. Or, the other option is that luzonensis and floresiensis are themselves Denisovans! In other words, luzonensis and floresiensis underwent strong adaptation to local conditions and changed so much that a standard morphological comparison will yield greater phylogenetic distance than what the whole genome might indicate. As we do not have ancient DNA from luzonensis and floresiensis this hypothesis cannot be tested.

But the model which the preprint seems to favor is that there are regions of island Southeast Asia with rich megafaunal survival, Sulawesi and Mindoro (an island off the coast of Luzon), that are also likely candidates for Denisovan remains. I would like the biogeographic element of the preprint fleshed out more before publication, though perhaps my relative confusion here is due to the fact that the evolutionary genomics is quite familiar to me.

I will note that the authors cite super-archaic admixture into the Andamanese, but from what I can tell most researchers in the area are skeptical of that particular paper. Basically, it looks like direct super-archaic admixture is unlikely. That being said, there are more complex models of indirect admixture through Neanderthals and Denisovans, and “first wave” modern humans, which I find possible.

8 thoughts on “The Wallacean Hominin Wonderland

  1. What do you think in general about the settlement of South/SE Asia? I heard it was depopulated after the LGM. What explains the lack of AASI ydna (besides MAYBE C1b?)

  2. Yes, makes sense to say H. floresiensis were Denosovians. They lived at the right place at the right time. Time to sequence their ancient DNA.

  3. The idea of SE Asia being depulated after(or during or before) LGM is… immensely funny.
    AASI’s yDNA may have been P or other K2’s.

  4. Is getting ancient DNA out of Flores or Luzon samples which we already have or ones which we may find in future possible ? It will be very fascinating if possible

  5. Tropical highlands can have climates comparable to parts of Europe that have a lot of ancient DNA finds. Presumably, there shouldn’t be much of a preservation problem if they look in the right parts of the islands.

  6. Kind of find it tough for the SE Asian small mystery hominins to be Denisovan… The morphology is supposedly pretty distant while Ds.

    Plus methylation maps/studies of D associated variants in living Australasian people don’t reconstruct a lot of size reduction… Given that this is a difference which is twice as significant as between living human groups, and trait are relatively well mapped in humans and animal models, we should be able to see something?

    Could be that variants related to size reduction were systematically purged out tho.

    Perhaps a study to see if there are “gene deserts” of Denisovan ancestry in Australasians at regions associated with body size tho.?

  7. Alas, the paper seems to have surprisingly little new insight.

    After reading all, or almost all of the papers on H. floresiensis, I am pretty won over to a super-archaic characterization of that species, which would be inconsistent with Denisovan being a sister clade to Neanderthals. The data for H. luzonensis, in contrast, seems too thin still to make a confident assessment.

    The assumption that megafauna should be more common, rather than less common, where Denisovan’s thrived, also seems rather arbitrary. I can imagine very plausible hypotheses for both possibilities.

    It also remains plausible that Denisovan were a mainland species that introgressed into the first wave of modern humans in the form of the pre-Australo-Papuan population, with subsequent waves of modern humans almost completely replacing them but lacking the seafaring technology to cross the Wallace line.

  8. John Hawks wrote a very detailed description of the wrist bone morphology of LB1, and gave the opinion that it was too primitive to have been derived from H. erectus – it was much more like australopithecines. So, I’m skeptical that H. floresiensis resulted from island dwarfing of Denisovans. H. luzonensis has also been noted to have some traits similar to australopithecines.

    They tried unsuccessfully three times to get DNA from the remains found at Liang Bua. I assume the same applies to luzonensis, otherwise we should have heard by now.

    I checked out Flores on Google Earth – it has some higher topography, but I don’t think high enough to provide a good preservational environment – no real highlands as such, unlike New Guinea, which is obviously very much bigger.

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