Denisovan Ancestry in Papua New Guinea (PNG)

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Denisovan Ancestry in Papua New Guinea (PNG) Jan 21, 2018 18:58:21 GMT

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Post by Admin on Jan 21, 2018 18:58:21 GMT

Denisovan Introgression in East/South Asian, Siberian, and Native American Populations
To detect Denisovan introgression in EE/NA populations, we computed the ratio of two f4f4 statistics ( RD(X)RD(X) ): f4(Yoruba,Denisovan;French, X)f4(Yoruba,Denisovan;French, X) and f4(Yoruba,Neanderthal;French, X)f4(Yoruba,Neanderthal;French, X) , for each EE/NA population. Populations with RD(X)>1RD(X)>1 are likely to have Denisovan ancestry (see Materials and Methods). Before we applied the approach to empirical data, we evaluated the performance of this statistic through simulations (see Materials and Methods and supplementary fig. S7, Supplementary Material online). For simulated populations with or without Denisovan ancestry, we applied a strict threshold of RD(X)>1,RD(X)>1, which yields low false positive rates and underestimates true Denisovan ancestry (supplementary fig. S8A and Supplementary Data, Supplementary Material online), and hence is a conservative indicator of Denisovan ancestry. Moreover, gene flow between African and European populations will not inflate the false positive rate and has no obvious impact on the performance of this indicator (supplementary fig. S8C–F, Supplementary Material online). We then computed RD(X)RD(X) for all EE/NA populations exhibiting significant admixture signals with Denisovans and/or Neanderthals in formal admixture tests (fig. 1B and supplementary table S3, Supplementary Material online). As expected, we observed large ratios (RD(X) > 1) in all Oceanian populations (fig. 4). Variable results were obtained for the other EE/NA populations, with RD(X) > 1 observed in several populations, including most Native American populations. Overall, this analysis indicates that there are EE/NA populations outside Oceania with a clear signal of Denisovan ancestry. Similar results are obtained with the use of different reference populations (supplementary table S6, Supplementary Material online).

FIG. 4.
Widespread Denisovan ancestry in EE/NA populations. Values of the RD(X)RD(X) ratio are plotted for all EE/NA populations which give significant signals of admixture with Neanderthal or Denisovan in formal tests; values greater than 1 (dashed line) are indicative of Denisovan ancestry.

Is this presumptive Denisovan ancestry in EE/NA populations from the same admixture event that contributed Denisovan ancestry to Oceanian populations, or does it rather represent a separate admixture event (or events) between modern humans and Denisovans? We postulated that if it reflects the same event that contributed Denisovan ancestry to Oceanians, then the amount of Denisovan ancestry in EE/NA populations should be correlated with the amount of New Guinean ancestry. Because the estimated amount of Denisovan ancestry is quite small in EE/NA populations, and difficult to distinguish from Neanderthal ancestry, we instead compared the overall amount of archaic admixture in EE/NA populations (as a fraction of that in New Guinean), which is calculated by the ratio of f4(Yoruba,Denisovan;French,X)f4(Yoruba,Denisovan;French,X) and f4(Yoruba,Denisovan;French,NewGuinean)f4(Yoruba,Denisovan;French,NewGuinean) , to the statistic f4(Yoruba,NewGuinean;French,X)f4(Yoruba,NewGuinean;French,X) . These two values are significantly correlated (fig. 5A, Pearson R2=0.23R2=0.23 , P=2.5×10−3P=2.5×10−3 ). However, this analysis could be confounded by admixture between East Asians and New Guineans, which has occurred as a consequence of the Austronesian expansion (Wollstein et al. 2010; Duggan and Stoneking 2014) and perhaps other population movements. We therefore removed the East Asian populations and repeated the analysis just for Siberians and Native Americans, and obtained an even higher correlation (fig. 5B, Pearson R2=0.54R2=0.54 , P=3.8×10−6P=3.8×10−6 ). Thus, archaic ancestry in EE/NA populations is significantly correlated with their New Guinea ancestry, suggesting that the Denisovan ancestry in EE/NA and Oceanian populations reflects the same admixture event.

Last Edit: Apr 12, 2018 20:26:36 GMT by Admin

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Denisovan Ancestry in Papua New Guinea (PNG) Jan 23, 2018 19:03:22 GMT

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Post by Admin on Jan 23, 2018 19:03:22 GMT

FIG. 5.

Denisovan introgression in EE/NA populations is correlated with their genetic affinity with Oceanians. Genetic affinity is measured by f4(Yoruba,New Guinean;French,X)f4(Yoruba,New Guinean;French,X) . We observed a significant correlation between Denisovan ancestry and New Guinea ancestry with (A) R2=0.23R2=0.23 ( P=2.5×10−3P=2.5×10−3 ) for all EE/NA populations with RD(X)>1RD(X)>1 , and (B) R2=0.54R2=0.54 ( P=3.8×10−6P=3.8×10−6 ) when we remove East Asians. Significant correlations were also observed when New Guinean was replaced by Australian with (C) R2=0.19 R2=0.19 ( P=6.7×10−3P=6.7×10−3 ) and (D) R2=0.48R2=0.48 ( P=2.0×10−5P=2.0×10−5 ) when we remove East Asians.

However, there are (at least) two potential alternate scenarios that could explain these results. First, Denisovan admixture could have occurred in a population that was ancestral to both EE/NA and Oceanian populations; second, admixture could have occurred in a population that was ancestral specifically to Mamanwa, Australians, and New Guineans (as suggested previously; Reich et al. 2011), followed by a back-migration from New Guinea to mainland East Asia. This putative back-migration would then have spread both New Guinea and Denisovan ancestry throughout East Asia and Siberia, and ultimately to the Americas. To distinguish between these two scenarios, we repeated the previous analysis but substituted Australians for New Guineans, comparing the archaic admixture in EE/NA populations (as a fraction of that in Australians) to the statistic f4(Yoruba,Australian;French, X)f4(Yoruba,Australian;French, X) . The results are virtually identical to those obtained with New Guineans as the comparison (fig. 5C and D). Moreover, although Oceanian populations are more closely related to New Guineans than to Australians, EE/NA populations are equally related to Australians and New Guineans (supplementary table S5, Supplementary Material online). These results indicate that the archaic ancestry in EE/NA populations is shared with the common ancestor of Australians and New Guineans, and hence reflects the same admixture event. A more detailed model for archaic introgression in modern humans, combining results from this and previous studies (Prüfer et al. 2014; Vernot and Akey 2015), is presented in figure 6.

FIG. 6.

A model of admixture events between archaic hominins and modern humans. Solid lines represent descent without admixture, and dashed lines represent admixture events. Admixture proportions relating the archaic introgression as estimated from both this study and previous studies are shown.

Last Edit: Apr 12, 2018 20:26:55 GMT by Admin

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Denisovan Ancestry in Papua New Guinea (PNG) Jan 24, 2018 19:03:35 GMT

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Post by Admin on Jan 24, 2018 19:03:35 GMT

Discussion
Our analyses demonstrate that, in addition to being prevalent in Oceanian populations, Denisovan introgression is present in East Eurasian and Native American populations, even though the amount of Denisovan alleles in these latter populations is relatively small. These results thus confirm and extend previous studies suggesting Denisovan ancestry outside of Oceania (Skoglund and Jakobsson 2011; Huerta-Sánchez et al. 2014; Prüfer et al. 2014). In particular, as found previously (Reich et al. 2011), Denisovan ancestry in Oceania is highly correlated with New Guinea ancestry. This suggests that these populations have either shared ancestry or contact with New Guinea that is more recent than the Denisovan admixture event. However, previous studies did not exclude the possibility that more ancient shared ancestry with New Guinean (after the Denisovan admixture event but before the divergence between New Guinean and Australian) explains the correlated signals of Denisovan and New Guinean ancestry in Oceania. Another potential explanation would be migrations from Australian rather than New Guinean, which could still produce a significant correlation between Denisovan and New Guinean ancestry as a consequence of the genetic relationship of Australians and New Guineans. To test these other possibilities, we compared amounts of Denisovan and Australian ancestry in Oceanian populations, and found that New Guinean ancestry does indeed provide a better explanation for the Denisovan ancestry in these Oceanian populations than does Australian ancestry (supplementary table S5, Supplementary Material online).

Our results also show a consistent signal of a low-level of Denisovan ancestry outside of Oceania, in populations of East Eurasia and the Americas. Although this signal does not reach significance in all populations (fig. 4), given how widespread the signal is, it seems most reasonable to assume that all EE/NA populations probably do harbor some Denisovan ancestry. The actual amount of Denisovan ancestry is difficult to estimate directly as it is so low. As it was previously estimated that the Denisovan-related ancestry in EE/NA populations is 3.8–4.8% of that in Oceania (Prüfer et al. 2014), combining this information with our new estimate of approximately 3.5% Denisovan ancestry in New Guinea and Australian leads to estimates of Denisovan ancestry in EE/NA populations of 0.13–0.17%. We would expect full genome sequences to provide more accurate estimates.

As with Oceanian populations, the Denisovan ancestry in EE/NA populations is correlated with their New Guinean ancestry. However, unlike Oceanian populations, the Denisovan ancestry in EE/NA populations is equally correlated with their Australian ancestry, and moreover EE/NA populations are just as closely related to Australians as they are to New Guineans (fig. 5 and supplementary table S5, Supplementary Material online).

There are (at least) two potential scenarios that could account for these results. First, there was introgression from a population related to Denisovans into a modern human population that was ancestral to all EE/NA and Oceanian populations. After the separation of the ancestral EE/NA and Oceanian populations, subsequent migration(s) then brought other modern human ancestry into the ancestors of EE/NA (but not Australian or New Guinean) populations, thereby “diluting” Denisovan ancestry in EE/NA populations. This scenario has two important consequences. First, it means that the introgression between Denisovans and modern humans did not necessarily occur in island Southeast Asia as postulated previously (Reich et al. 2011), but instead could have occurred closer to the vicinity of Denisova Cave, in southern Siberia. Second, identifying the source(s) of the other modern human ancestry in EE/NA populations would be of great interest for further understanding the genetic history of human populations.

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Denisovan Ancestry in Papua New Guinea (PNG) Jan 25, 2018 19:09:37 GMT

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Post by Admin on Jan 25, 2018 19:09:37 GMT

The second scenario that could explain the different amounts of Denisovan ancestry in Oceanians versus EE/NA populations would be that Denisovan introgression occurred specifically in a population ancestral to Australians, New Guineans, and the Mamanwa, as hypothesized previously (Reich et al. 2011). After the Denisovan admixture, but before the divergence of Australians and New Guineans, there would then have been a back-migration from Oceania to mainland East Asia, which would have contributed both Denisovan and shared Australian/New Guinea ancestry to the ancestors of present day EE/NA populations. Although we are not aware of any previous suggestions of such a back-migration from archaeological, anthropological, or genetic evidence, we also are not aware of any evidence that would disprove such a back-migration.

It thus seems that at present these two scenarios are equally plausible explanations for our results. However, ancient DNA analyses could potentially distinguish between them. Current results indicate that modern humans colonizing Oceania split from ancestral Eurasian as early as 62,000–75,000 years before present (BP) (Rasmussen et al. 2011), whereas East Asians subsequently diverged from Europeans much later, around 23,000–38,000 years BP (Keinan et al. 2007; Gutenkunst et al. 2009; Gravel et al. 2011).

If ancient DNA from East Asian fossils that predate the divergence between East Asians and Europeans contains high levels of Denisovan ancestry (related to the Denisovan ancestry in Oceania), this would support the first scenario. But if high levels of Denisovan ancestry remain restricted to Oceania, with only low levels found outside Oceania even in ancient DNA, then this would support the second scenario.

In any event, the inescapable conclusion is that Denisovan ancestry is more widespread in modern human populations than thought previously to be the case, and moreover human genetic history must consequently also be more complicated than previously believed. Mapping the segments of Denisovan ancestry in modern human populations, as has been done for Neanderthal ancestry (Prüfer et al. 2014; Sankararaman et al. 2014; Vernot and Akey 2014), should provide more insights into the history and consequences of the interactions between Denisovans and modern humans.

Molecular Biology and Evolution, Volume 32, Issue 10, 1 October 2015, Pages 2665–2674, doi.org/10.1093/molbev/msv141

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Denisovan Ancestry in Papua New Guinea (PNG) Jan 17, 2019 4:20:19 GMT

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Post by Admin on Jan 17, 2019 4:20:19 GMT

The Xujiayao site in the Nihewan Basin of northern China was excavated in the late 1970s. In all, 20 ancient human fossils were found there, including skull fragments, jawbones and teeth from a number of individuals.

There have been two attempts to nail down when these prehistoric people lived. Dating of teeth from animal remains found alongside the hominin bones suggests they lived around 100,000 years ago.

But measurements of trapped electrons in the sediments that contain the fossils point to a more ancient time period.

“We believe it's the older age, at the end of the middle Pleistocene, around 160,000 [years ago],” says lead author Song Xing from the Institute of Vertebrate Palaeontology and Palaeoanthropology at the Chinese Academy of Sciences.

“They have some primitive features connected with Homo erectus and some derived features that fall into the variation of modern human, and also some minor Neanderthal features, too. It's definitely not Neanderthal. It's not Homo erectus, and not modern human,” says Xing.

“The story in Asia has been really interesting over the last few years,” says Smith. “This [study] gives us more insight into the characteristics of one of these anomalous relatives.”

One possibility is that the remains could be from Denisovans, the elusive group known from just a couple of teeth and bone shards and an incredibly complete genome sequence.