Multiple Deeply Divergent Denisovan ancestries in Papuans

See: Guy S. Jacobs et al
https://www.cell.com/cell/fulltext/S0092-8674(19)30218-1#.XK8tW74GOQ

[h=2]Highlights[/h]

• •A new dataset of 161 genomes covering the understudied Indonesia-New Guinea region
  
• •Introgressing Denisovans comprise at least three genetically divergent groups
  
• •Papuans carry haplotypes from two Denisovan groups, with one unique to Oceania
  
• •Some Denisovan introgression was recent and likely occurred in New Guinea or Wallacea

[h=2]Summary[/h]Genome sequences are known for two archaic hominins—Neanderthals and Denisovans—which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

[h=2]Graphical Abstract[/h]

The discovery and characterization of archaic hominins has typically begun with the analysis of fossil remains (Meyer et al., 2012, Prüfer et al., 2014, Prüfer et al., 2017, Slon et al., 2018). However, as Denisovan admixture has its center of gravity in ISEA and Papua where DNA rarely survives more than a few thousand years in the humid tropical environment (Lipson et al., 2018, McColl et al., 2018), studying the genetic record from modern humans remains the sole way to shed light on the substructure and phylogeography of archaic hominins in this important but understudied region.
Here, we use a statistical approach on new genomes from ISEA and Papua to identify two new Denisovan groups (D1 and D2) and describe the relationships between these archaic hominins long before they first interacted with anatomically modern humans. Both groups branched off early from the Altai Denisovan clade at 283 and 363 kya and were reproductively isolated from the individuals at Denisova cave in Siberia and from each other. Yet both groups bred with modern humans, contributing around 4% of the genomes of Papuans, including over 400 gene variants enriched for traits involving immunity and diet. Some of this introgression is restricted to modern New Guinea and its surrounding islands and may have occurred as late as the very end of the Pleistocene, making the admixing D1 Denisovan population among the last surviving archaic hominins in the world.
The genetic diversity within the Denisovan clade is consistent with their deep divergence and separation into at least three geographically disparate branches, with one contributing an introgression signal in Oceania and to a lesser extent across Asia (D2), another apparently restricted to New Guinea and nearby islands (D1), and a third in East Asia and Siberia (D0). This suggests that Denisovans were capable of crossing major geographical barriers, including the persistent sea lanes that separated Asia from Wallacea and New Guinea. They therefore spanned an incredible diversity of environments, from temperate continental steppes to tropical equatorial islands. The emerging picture suggests that far from moving into sparsely inhabited country, modern humans experienced repeated and persistent interactions as they expanded out of Africa into this highly structured archaic landscape across Eurasia. This genetic contact yielded a rich legacy, including hundreds of gene variants that continue to contribute to the adaptive success of anatomically modern humans today.

If they also had sampled DNA from Australian Aboriginees, the picture would have been mord detailed.

Interesting study. How about homo floresiensis as a candidate for D1? This is the only hominin apart from modern humans known to have crossed the Wallace Line. The archaeological horizon for them is estimated at 190,000 to 50,000bp on Flores. This could be compatible with the estimated split between D1 and D2 at 350,000bp in South East Asia, west of the Wallace Line. If the ancestors of homo floresiensis were capable of making an ocean crossing to Flores, it was probably not the only island they reached. Some may have survived to the late Pleistocene on other islands.

Some might argue on the basis of morphology that homo floresiensis was too distantly related to have admixed with homo sapiens because they probably split with the human lineage two or even three million years ago. However, there is also evidence that they used fire for cooking, hunted big game cooperatively and made sophisticated Upper Paleolithic tools similar to those made by modern humans in East Timor.

I think the relationship between homo floresiensis and homo sapiens will remain an open question until someone manages to extract aDNA from a homo floresiensis skeleton.

Tamakore said:

Interesting study. How about homo floresiensis as a candidate for D1? This is the only hominin apart from modern humans known to have crossed the Wallace Line. The archaeological horizon for them is estimated at 190,000 to 50,000bp on Flores. This could be compatible with the estimated split between D1 and D2 at 350,000bp in South East Asia, west of the Wallace Line. If the ancestors of homo floresiensis were capable of making an ocean crossing to Flores, it was probably not the only island they reached. Some may have survived to the late Pleistocene on other islands.

Some might argue on the basis of morphology that homo floresiensis was too distantly related to have admixed with homo sapiens because they probably split with the human lineage two or even three million years ago. However, there is also evidence that they used fire for cooking, hunted big game cooperatively and made sophisticated Upper Paleolithic tools similar to those made by modern humans in East Timor.

I think the relationship between homo floresiensis and homo sapiens will remain an open question until someone manages to extract aDNA from a homo floresiensis skeleton.

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some think the newly discovered homo Luzoniensis in Callao cave is related to Florensis

https://www.philstar.com/headlines/...new-human-species-discovered-philippines-cave

bicicleur said:

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46 ka is also +/- the TMRCA for the starlike expansion of haplogroup K, ancestral to both Papuans and Aboriginees

https://www.yfull.com/tree/K/

bicicleur said:

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looks like australoid is an ancestor of caucasoid and mongoloid.
So I think the papuan was split into east asian and west asian, not european.

Does the papuan have both admixture of west and east genes like malta?
How about ANE people? Were they created after the split or before?
I mean amalgamation or intermediate.
I think the ANE was after the split considering their mutations.