Peopling of the Americas

Luzia: Brazil Buhl Woman: Idaho PoW: coastal Alaska Spirit cave: Nevada Kennewick: WA

QuesBons that archaeology hasn’t answered •  Pre-Clovis: shortly before? Or long before? •  Early (>8 KYA) Paleoindian skulls (e.g., Kennewick) look different from later skulls. Why? Did early seTlers go exBnct?

Kennewick man aDNA

Rasmussen et al. 2015

LinguisBc evidence Controversial “three-migraBon” hypothesis: Three NaBve American language families indicate three waves of migrants into the New World. Amerind (early migraBon): Contains all the hundreds of languages spoken by all other north and south NaBve Americans. Highly controversial. Na-Dene (intermediate migraBon): Spoken in parts of North America; might be related to Siberian Yeniseian language family (AKA “Athapascan”, “Apache”). Less controversial. Eskimo-Aluet (late migraBon): Spoken in far north America, Greenland and parts of Siberia. Not controversial.

GeneBc evidence

Pairwise Fst values from classical polymorphisms

mtDNA evidence

Y chromosome data

Autosomal data

HEG model

2015 geneBc analyses

Paleoamerican “relic” model Fig. S38. Simplified schematic of the scenario proposed by (23) where the Americas are peopled by two waves of migration. Under this hypothesis, the first migration (1, indicated in green) consists of the “Paleoamericans”, a population that shares a recent common ancestor with Papuans. The second wave of migration (2, indicated in blue) occurs later by the morphologically different Amerindians that share recent common ancestry with East Asians. The Amerindians largely replaced the Paleoamericans, however, some populations (e.g. the Pericúes/Fuego-Patagonians) have been described as relict Paleoamericans on morphological grounds. The expected tree topology is given (centre) and key locations (including our sample sites) are labeled. Potential gene flow between the arrows is omitted.

Raghavan et al. 2015 Four quesBons: 1. Timing of divergence from ancestral populaBon? 2. Number of migraBons into the Americas? 3. 15K years of isolaBon in Berengia? 4. Post-Pleistocene survival of relic Australo-Melanesian populaBon in Americas? (based on differences in cranial morphology)

Methods: 31 high coverage modern genomes from the Americas, Siberia, and Oceania 23 Ancient genomic sequences from from the Americas, 0.2 to 6 ka. SNP chip data from 79 individuals from 28 modern populaBons from the Americas and Siberia ExisBng geneBc data Reanalysis of skull morphology

Raghavan et al. 2015

Fig. 1. Origins and population history of Native Americans. (A) Our results show that the ancestors of all present-day Native Americans, including Amerindians and Athabascans, derived from a single migration wave into the Americas (purple), separate from the Inuit (green).This migration from East Asia occurred no earlier than 23 ka and is in agreement with archaeological evidence from sites such as Monte Verde (50). A split between the northern and southern branches of Native Americans occurred ~13 ka, with the former comprising Athabascans and northern Amerindians and the latter consisting of Amerindians in southern North America and Central and South America, including the Anzick-1 individual (5). There is an admixture signal between Inuit and Athabascans as well as some northern Amerindians (yellow line); however, the gene flow direction is unresolved because of the complexity of the admixture events (28). Additionally, we see a weak signal related to Australo-Melanesians in some Native Americans, which may have been mediated through East Asians and Aleutian Islanders (yellow arrows). Also shown is the Mal’ta gene flow into Native American ancestors some 23 ka (yellow arrow) (4). It is currently not possible for us to ascertain the exact geographical locations of the depicted events; hence, the positioning of the arrows should not be considered a reflection of these. (B) Admixture plot created on the basis of TreeMix results (fig. S5) shows that all Native Americans form a clade, separate from the Inuit, with gene flow between some Native Americans and the North American Arctic. The number of genome-sequenced individuals included in the analysis is shown in brackets.

Test of Paleoamerican model R ES E A RC H | R E S EA R C H A R T I C LE

Skoglund et al. 2015 One quesBon: •  Were there one or two founding populaBons of NaBve Americans?

Methods: •  63 individuals “without discernable evidence of European or African ancestry” from 21 NaBve American populaBons •  Genotyped at 600,000 SNPs

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Figure 1 | South Americans share ancestry with Australasian populations that is not seen in Mesoamericans or North Americans. a, Quantile–quantile plot of the Z-scores for the D-statistic symmetry test for whether Mixe and Suruı´ share an equal rate of derived alleles with a candidate non-American population, X, compared to the expected ranked quantiles for the same number of normally distributed values. b, Z-scores for the h4-statistic. c, Z-scores for

the ChromoPainter statistic. d, Heatmap of ChromoPainter statistics. For nonAmericans we display the symmetry statistic S(non-American; Mixe, Suruı´ and Karitiana) for donating as many haplotypes to Mixe as to Suruı´ and Karitiana. For the Americas we plot S(Onge; Mixe, American) for receiving as many haplotypes from the Onge as do the Mixe. 3 S E P T E M B E R 2 0 1 5 | VO L 5 2 5 | N AT U R E | 1 0 5

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Macmillan Publishers Limited. All rights reserved

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Figure 2 | A model of population history that can explain the excess affinity to Oceanians observed in Amazonian populations. a, We fit an admixture graph model where a population related to the Andamanese Onge contributed a fraction a of the ancestry of ‘Population Y’, which later contributed a fraction c to the ancestry of Amazonian groups today

(the remainder of which is related to Mesoamerican Mixe). b, Twodimensional grid of combinations of the admixture proportions a and c which are compatible with the data in terms of how many predicted f4-statistics deviate by Z $ 3.0 from empirical values.

Karitiana) that contributed Australasian-related ancestry to Amazonians was already mixed with a lineage related to First Americans at the time it reached Amazonia. When we model such a scenario, we obtain a fit for models that specify 2–85% of the ancestry of the Suruı´, Karitiana and Xavante as coming from Population Y (Fig. 2). These results show that quite a high fraction of Amazonian ancestry today might be derived from Population Y. At the same time, the results constrain the fraction of

possible through genome-wide analysis of ancient remains from across the Americas. Online Content Methods, along with any additional Extended Data display items and Source Data, are available in the online version of the paper; references unique to these sections appear only in the online paper. Received 5 February; accepted 14 July 2015.