Illustration originally from mine and @mathiesoniain's review of the evidencehttps://www.dropbox.com/s/ddzg6q5e14dg6ad/Ancient%20Genomics.pdf …
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There is an undiscussed but potentially explosive implication of this paper: the 2nd Denisovan gene flow signal in East Asia seems to be absent from Native American ancestry--could Denisovans have survived after the isolation of these lineages <30 kya?? https://twitter.com/pontus_skoglund/status/974321894970351618 …pic.twitter.com/stWVJVObMQ
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Thanks. Twitter will use this to make your timeline better. UndoUndo
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Actually, it looks like *neither* Denisovan signal is in any of the Native American groups. That contradicts earlier work, I think.
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Yes neither indeed. Although I wrote this http://www.pnas.org/content/108/45/18301.short … a while ago, I had come to believe that the excess in Asia could have been entirely Neanderthal in origin. Until this paper, IMO the solid evidence was for only 2 admixture episodes+the instance in Oase's genealogy
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Not completely zero though, right? Don't almost all Eskimos and many Native Americans have the Denisovan "brown fat"-related gene?
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That genomic region matched Denisova closer than Neanderthal, but was noted by
@FerRacimo@emiliahsc@ras_nielsen to be "just as diverged to the Denisovan as a typical Neanderthal region is to a typical Denisovan region". So could be from Neandertals.https://academic.oup.com/mbe/article/34/3/509/2731791 … -
So to rephrase it could be thought of as matching the known Denisova genome closer than the hitherto sequenced Neandertal genomes available to
@FerRacimo et al at the time. But future genomes could reveal it to be from Neandertals. -
Wow! Thanks. Interesting it wasn't found in WHG or EEF, but in Yamnaya.
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It would be very interesting to know whether the Surui, Karitiana and Xavante peoples of Brazil’s Amazonia region carry either/both gene flow signatures. We already see strong data suggesting they have distinct ancestry.
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I agree! We found that these groups and others in the Amazon have intriguing connections to the Denisova-ancestry-carrying groups of Oceania and SE Asia. https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/nature14895_Skoglund_2015_1.pdf … It will be great to see the Browning analysis applied to their genomes, but more data is likely needed
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This could help us understand when the mysterious other ancestors of these tribes migrated, and also which direction was taken. The detection of Denisova DNA would tell us the migration is not likely earlier than the interbreeding with Southern Denisovans approx 40Kya.
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Cool! But could also have been lost with into America's bottleneck? Gosh us humans always hooking up through history
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If admixture happened many generations before the bottleneck I think the signal should be well-spread across the genome and unlikely to be lost. BUT it seems that methodologically there could be some interaction with the lower diversity of Native American populations. Interesting
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Is this relevant? "The match rate to the Altai Neanderthal and Altai Denisovan genomes is lower in the American [...]. This is likely because the American populations are admixed and thus have higher background levels of LD that could cause false-positive results.
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Possibly! Need to read up and understand the method here more closely.
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Could this explain why Andean Amerindians didn't get that EPAS version found in Tibetans?
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Certainly, cc
@emiliahsc -
Denisovans in Sundaland wouldn't have had selection for high altitude tolerance.
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I agree with
@pontus_skoglund. However, there are some Denisovan signals that we (with@FerRacimo) found in Mexicans, but need to check whether they are high/median affinity to Altai Denisovan. The density plot for Mexicans (Figure 4) does show a little of both in Mexicans -
It's possible that the Denisovan EPAS allele is disadvantageous in other environments, say low-altitude. Might not have made it all the way to South America.
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