The data presented here are consistent with a single ini-tial migration of all Native Americans and with later gene flow from sources related to East Asians and, more distant-ly, Australo-Melanesians. From that single migration, there was a diversification of ancestral Native Americans leading to the formation of ‘northern’ and ‘southern’ branches, which appears to have taken place ca. 13 KYA within the Americas. This split is consistent with the patterns of unip-arental genomic regions of mtDNA haplogroup X and some Y chromosome C haplotypes being present in northern, but not southern, populations in the Americas (18, 62). This di-versification event coincides roughly with the opening of habitable routes along the coastal and the interior corridors into unglaciated North America some 16 KYA and 14 KYA, respectively (63, 64), suggesting a possible role of one or both these routes in the isolation and subsequent dispersal of Native Americans across the continent.
We found that some American populations, including the Aleutian Islanders, Surui, and Athabascans are closer to Australo-Melanesians compared to other Native Americans, such as North American Ojibwa, Cree and Algonquin, and the South American Purepecha, Arhuaco and Wayuu (fig. S10). The Surui are, in fact, one of closest Native American populations to East Asians and Australo-Melanesians, the latter including Papuans, non-Papuan Melanesians, Solo-mon Islanders, and South East Asian hunter-gatherers such as Aeta (fig. S10). We acknowledge that this observation is based on the analysis of a small fraction of the whole ge-nome and SNP chip genotype datasets, especially for the Aleutian Islander data that is heavily masked due to recent admixture with Europeans (28), and that the trends in the data are weak.
Nonetheless, if it proves correct, these results suggest there may be a distant Old World signal related to Australo-Melanesians and East Asians in some Native Americans. The widely scattered and differential affinity of Native Americans to the Australo-Melanesians, ranging from a strong signal in the Surui to much weaker signal in north-ern Amerindians such as Ojibwa, points to this gene flow occurring after the initial peopling by Native American an-cestors.
However, how this signal may have ultimately reached South America remains unclear. One possible means is along a northern route via the Aleutian Islanders, previously found to be closely related to the Inuit (39), who have a rela-tively greater affinity to East Asians, Oceanians and Den-isovan than Native Americans in both whole genome and SNP chip genotype data-based D-tests (table S10 and figs. S10 and S11). On the basis of archaeological evidence and mtDNA data from ancient and modern samples, the Aleu-tian Islands are hypothesized to have been peopled as early as ca. 9 KYA by ‘Paleo-Aleuts’ who were succeeded by the ‘Neo-Aleuts’, with present-day Aleutian Islanders potentially resulting from admixture between these two populations (52, 53). Perhaps their complex genetic history included in-put from a population related to Australo-Melanesians through an East Asian continental route, and this genomic signal might have been subsequently transferred to parts of the Americas, including South America, through past gene flow events (Fig. 1). Evidence for this gene flow is supported by diCal2.0 and MSMC analyses showing a weak but recent gene flow into South Americans from populations related to present-day Northeast Asians (Koryak) (Fig. 2C and table S11C), who might be considered a proxy for the related Aleu-tian Islanders.
The detection of an Australo-Melanesian genetic signal in the Americas, however subtle, returns the discussion to the Paleoamerican model, which hypothesizes, on the basis of cranial morphology, that two temporally and source-distinct populations colonized the Americas. The earlier population reportedly originated in Asia in the Late Pleisto-cene and gave rise to both Paleoamericans and present-day Australo-Melanesians, whose shared cranial morphological attributes are presumed to indicate their common ancestry (23). The Paleoamericans were, in turn, thought to have been largely replaced by ancestors of present-day Amerindi-ans, whose crania resemble modern East Asians and who are argued to be descendants of later arriving Mongoloid populations (14, 23, 26, 54). The presence of Paleoamericans is inferred primarily from ancient archaeological specimens in North and South America, and a few relict populations of more recent age, which include the extinct Pericúes and Fuego-Patagonians (24, 25, 55).
The Paleoamerican hypothesis predicts that these groups should be genetically closer to Australo-Melanesians than other Amerindians. Previous studies of mtDNA and Y chro-mosome data obtained from Fuego-Patagonian and Paleo-american skeletons have identified haplogroups similar to those of modern Native Americans (55–57). Although these results indicate some shared maternal and paternal ancestry with contemporary Native Americans, uniparental markers can be misleading when drawing conclusions about the de-mographic history of populations. To conclusively identify the broader population of ancestors who may have contrib-uted to the Paleoamerican gene pool, autosomal genomic data are required.