Denisovan Ancestry in East Eurasian and Native American Populations

Abstract

2 Although initial studies suggested that Denisovan ancestry was found only in modern 3 human populations from island Southeast Asia and Oceania, more recent studies have 4 suggested that Denisovan ancestry may be more widespread. However, the 5 geographic extent of Denisovan ancestry has not been determined, and moreover the 6 relationship between the Denisovan ancestry in Oceania and that elsewhere has not 7 been studied. Here we analyze genome-wide SNP data from 2493 individuals from 8 221 worldwide populations, and show that there is a widespread signal of a very low 9 level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) 10 populations. We also verify a higher level of Denisovan ancestry in Oceania than that 11 in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New 12 Guinea ancestry, but not the amount of Australian ancestry, indicating that recent 13 gene flow from New Guinea likely accounts for signals of Denisovan ancestry across 14 Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated 15 with their New Guinea or their Australian ancestry, suggesting a common source for 16 the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that 17 Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene 18 flow from, the common ancestor of New Guineans and Australians, indicating a more 19 complex history involving East Eurasians and Oceanians than previously suspected. 20 21 Keywords: Denisovans; Neanderthals; Archaic admixture; Modern humans. 2 bioRxiv preprint doi: https://doi.org/10.1101/017475; this version posted April 3, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 1 Significance Statement 2 Archaic hominins genetically interacted with the ancestors of present-day humans, but 3 the scope and magnitude of this interaction has not been fully documented. Our study 4 reveals that ancestry from Denisovans, (an archaic human group identified in the Altai 5 Mountains of southern Siberia), is prevalent in populations across eastern Eurasia and 6 the Americas, rather than only in island populations of Southeast Asia and Oceania as 7 previously reported. We show that the Denisovan ancestry in Eastern Eurasians and 8 Native Americans is probably derived from either common ancestry with, or ancient 9 gene flow from, the common ancestor of present-day New Guineans and Australians, 10 thereby demonstrating a more complex relationship of these human populations than 11 previously suspected. 12