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POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

July 2015
Science 349(6250)

DOI:10.1126/science.aab3884

Authors:

Maanasa Raghavan

University of Chicago

Matthias Steinrücken

University of Chicago

Kelley Harris

Stanford University

Stephan Schiffels

Max Planck Institute for Evolutionary Anthropology

Show all 101 authorsHide

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Divergence estimates between Native Americans and Siberian Koryak. (A) The demographic model used allows for continuous gene flow between populations 1 and 2, starting from the time TDIV of divergence and ending at TM. The backward probability of migration per individual per generation is denoted by m. The bottleneck at TB captures the out-of-Africa event. (B) The red and black solid curves depict empirical distributions of IBS tracts shared between Karitiana-Koryak and Athabascan-Koryak, respectively. The orange, pink, dashed blue and dashed green curves depict IBS tracts shared between the two population pairs, simulated under two demographic models based on results from diCal2.0. Overall, for Karitiana-Koryak and Athabascan-Koryak, the migration scenarios (orange and pink, respectively) match the empirical curves (red and black, respectively) better than the clean split scenarios (dashed blue and dashed green, respectively), with more long IBS tracts showing evidence of recent common ancestry between Koryaks and Native Americans. (C and D) Relative cross coalescence rates (CCR) for the Karitiana-Koryak and Athabascan-Koryak divergence (red), respectively, including data simulated under the two demographic models in panel B. In both cases, the model with gene flow (orange) fits the data (red) better than the clean split model (blue). The migration model explains a broader CCR tail in the case of Karitiana-Koryak and the relatively late onset of the CCR decay for Athabascan-Koryak.

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Research Articles

It is generally agreed that ancestral Native Americans are

descendants of Siberian peoples who traversed the Bering

Land Bridge (Beringia) from northeast Asia in Late Pleisto-

cene times, and though consensus has yet to be reached, it is

mostly conceded that the Clovis archaeological complex,

dating to ca. 13 KYA, does not represent the first migration

as long supposed (1–7). Archaeological evidence accumulat-

ed over the last two decades indicates that people were

Genomic evidence for the Pleistocene and recent

population history of Native Americans

Maanasa Raghavan,1* Matthias Steinrücken,2,3,4* Kelley Harris,5* Stephan Schiffels,6* Simon

Rasmussen,7* Michael DeGiorgio,8* Anders Albrechtsen,9* Cristina Valdiosera,1,10* María C.

Ávila-Arcos,1,11* Anna-Sapfo Malaspinas,1* Anders Eriksson,12,13 Ida Moltke,9 Mait

Metspalu,14,15 Julian R. Homburger,11 Jeff Wall,16 Omar E. Cornejo,17 J. Víctor Moreno-Mayar,1

Thorfinn S. Korneliussen,1 Tracey Pierre,1 Morten Rasmussen,1,11 Paula F. Campos,1,18 Peter de

Barros Damgaard,1 Morten E. Allentoft,1 John Lindo,19 Ene Metspalu,14,15 Ricardo Rodríguez-

Varela,20 Josefina Mansilla,21 Celeste Henrickson,22 Andaine Seguin-Orlando,1 Helena

Malmström,23 Thomas Stafford Jr.,1,24 Suyash S. Shringarpure,11 Andrés Moreno-Estrada,11,25

Monika Karmin,14,15 Kristiina Tambets,14 Anders Bergström,6 Yali Xue,6 Vera Warmuth,26,27

Andrew D. Friend,28 Joy Singarayer,29 Paul Valdes,30 Francois Balloux,26 Ilán Leboreiro,21 Jose

Luis Vera,31 Hector Rangel-Villalobos,32 Davide Pettener,33 Donata Luiselli,33 Loren G. Davis,34

Evelyne Heyer,35 Christoph P. E. Zollikofer,36 Marcia S. Ponce de León,36 Colin I. Smith,10

Vaughan Grimes,37,38 Kelly-Anne Pike,37 Michael Deal,37 Benjamin T. Fuller,39 Bernardo

Arriaza,40 Vivien Standen,41 Maria F. Luz,42 Francois Ricaut,43 Niede Guidon,42 Ludmila

Osipova,44,45 Mikhail I. Voevoda,44,46,47 Olga L. Posukh,44,45 Oleg Balanovsky,48,49 Maria

Lavryashina,50 Yuri Bogunov,48 Elza Khusnutdinova,51,52 Marina Gubina,42 Elena

Balanovska,49 Sardana Fedorova,53,54 Sergey Litvinov,14,51 Boris Malyarchuk,55 Miroslava

Derenko,55 M. J. Mosher,56 David Archer,57 Jerome Cybulski,58,59,60 Barbara Petzelt,61

Joycelynn Mitchell,61 Rosita Worl,62 Paul J. Norman,63 Peter Parham,63 Brian M. Kemp,17,64

Toomas Kivisild,14,65 Chris Tyler-Smith,6 Manjinder S. Sandhu,6, 66 Michael Crawford,67

Richard Villems,14,15 David Glenn Smith,68 Michael R. Waters,69,70,71 Ted Goebel,69 John R.

Johnson,72 Ripan S. Malhi,19,73 Mattias Jakobsson,23 David J. Meltzer,1,74 Andrea Manica,12

Richard Durbin,6 Carlos D. Bustamante,11 Yun S. Song,2,3,75† Rasmus Nielsen,75† Eske

Willerslev,1†

*These authors contributed equally to this work.

†Corresponding authors. E-mail: yss@berkeley.edu (Y.S.S.); rasmus_nielsen@berkeley.edu (R.N.); ewillierslev@snm.ku.dk

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide

data, we find that the ancestors of all present-day Native Americans, including Athabascans and

Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand

years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to

the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one

that is now dispersed across North and South America and the other is restricted to North America.

Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians

(including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict

populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not

directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

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south of the North American continental ice sheets more

than a millennium earlier and had reached as far south as

southern South America by at least ca. 14.6 KYA (1–3). In-

terpretations differ, however, regarding the precise spatio-

temporal dynamics of the peopling process, owing to ar-

chaeological claims for a significantly earlier human pres-

ence pre-dating the Last Glacial Maximum (LGM; ca. 20

KYA) (8–10), and conflicting interpretations of the number

and timing of migrations from Beringia based on anatomi-

cal and genetic evidence (11–16). Much of the genetic evi-

dence is from studies of mitochondrial DNA (mtDNA) and

Y-chromosome, which as single, uniparentally inherited loci

are particularly subject to genetic drift and sex-biased de-

mographic and cultural practices.

Among the principal issues still to be resolved regarding

the Pleistocene and recent population history of Native

Americans are: (i) the timing of their divergence from their

Eurasian ancestors; (ii) whether the peopling was in a single

wave or multiple waves, and, consequently, if the genetic

differences seen between major subgroups of Native Ameri-

cans (e.g., Amerindian and Athabascan) result from differ-

ent migrations or in situ diversification in the Americas (5,

6, 17, 18); (iii) if the migration involved ca. 15,000 years of

isolation in the Bering Strait region, as proposed by the Ber-

ingian Incubation Model to explain the high frequency of

unique and widespread American mitogenomes and private

genetic variants (19–22); and, finally, (iv) if there was post-

divergence gene flow from Eurasia and possibly even popu-

lation replacement in the Americas, the latter suggested by

the apparent differences in skull morphology between some

early (‘Paleoamerican’) remains and those of more recent

Native Americans (23–27). We address these issues using

genomic data derived from modern populations, supple-

mented by ancient specimens that provide chronologically

controlled snapshots of the genetics of the peopling process

as it unfolded.

We sequenced 31 genomes from present-day individuals

from the Americas, Siberia and Oceania to an average depth

of ca. 20X: Siberians – Altai (n = 2), Buryat (n = 2), Ket

(n=2), Koryak (n = 2), Sakha (n = 2), Siberian Yupik (n = 2);

North American Native Americans – Tsimshian (n =);

southern North American and Central and South American

Natives – Pima (n = 1), Huichol (n = 1), Aymara (n = 1),

Yukpa (n = 1); and, Oceanians – Papuan (n = 14) (28) (Table

S1). All the genome-sequenced present-day individuals were

previously genotyped using single nucleotide polymorphism

(SNP) chips (4, 29–35) except for the Aymara individual that

was SNP chip genotyped in this study (tables S3 and S4).

They were selected on the basis of their ancestry profiles

obtained with ADMIXTURE (36) to best represent their re-

spective populations, and to minimize recent genetic admix-

ture from populations of western Eurasian origin (28). For

populations represented by more than one individual, we

also verified from the genotype data that the sequenced in-

dividuals did not represent close relatives (28). We addi-

tionally sequenced 23 genomes from ancient individuals

dating between ca. 0.2-6 KYA from North and South Ameri-

ca, with an average depth ranging between 0.003X and 1.7X,

including specimens affiliated to putative relict Paleoameri-

can groups such as the Pericúes from Mexico and Fuego-

Patagonians from the southernmost tip of South America

(23, 26–28) (table S5). Finally, we generated SNP chip geno-

type data from 79 present-day individuals belonging to 28

populations from the Americas and Siberia (28) (table S4).

All the aforementioned datasets were analyzed together

with previously published genomes and SNP chip genotype

data (Tables S1, S3, and S4), masking the data for recent

European admixture in some present-day Native American

populations (28).

The structure of Native American populations and

the timing of their initial divergence

We explored the genetic structure of Native American

populations in the context of worldwide populations using

ADMIXTURE (36), employing a reference panel consisting

of 3,053 individuals from 169 populations (table S3) (28).

The panel included SNP chip genotype data from present-

day individuals generated in this study and previously pub-

lished studies, as well as the 4,000 year-old Saqqaq individ-

ual from Greenland (29) and the 12,600 year-old Anzick-1

(Clovis culture) individual from Montana (5) (table S3).

When assuming four ancestral populations (K=4), we found

a Native American-specific genetic component, indicating a

shared genetic ancestry for all Native Americans including

Amerindians and Athabascans (fig. S4). Assuming K=15,

there is structure within the Native Americans. Athabascans

and northern Amerindians (primarily from Canada) differ

from the rest of the Native Americans in sharing their own

genetic component (fig. S4). As reported previously, Anzick-

1 falls within the genetic variation of southern Native Amer-

icans (5), while the Saqqaq individual shares genetic com-

ponents with Siberian populations (fig. S4) (29).

To ascertain the population history of present-day Amer-

ican populations in relation to worldwide populations, we

generated admixture graphs with TreeMix (28, 37). All the

modern Siberian and Native American genomes sequenced

in this study, except for the North American Tsimshian ge-

nome that showed evidence of recent western Eurasian ad-

mixture (28), were used for this analysis, together with

previously published genomes from Africa (Yoruba) (38),

Europe (Sardinian, French) (38), East Asia (Dai, Han) (38),

Siberia (Nivkh) (39) and the Americas (Karitiana, Athabas-

can, Greenlandic Inuit) (5, 38, 39) (table S1). The ancient

individuals included in the analysis were Saqqaq, Anzick-1

and the 24,000 year-old Mal’ta child from south-central Si-

beria (4). TreeMix affirms that all Native Americans form a

monophyletic group across all ten migration parameter val-

ues, with further diversification into two branches, one rep-

resenting Amerindians (represented in this analysis by

Amerindians from southern North America and Central and

South America) and the other Athabascans (Fig. 1B and fig.

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S5). Paleo-Eskimos and Inuit were supported as a separate

clade relative to the Native Americans, as reported previous-

ly (Fig. 1B and fig. S5) (29, 39). Our results show that the

Siberian Yupik and Koryak are the closest Eurasian popula-

tions to the Americas, with the Yupik likely representing

back-migration of the Inuit into Siberia (Fig. 1B and fig. S5).

To assess the pattern of the earliest human dispersal into

the Americas, we estimated the timing of the divergence of

ancestral Native Americans from East Asians (hereafter,

including Siberians) using multiple methods. There is still

some debate regarding mutation rates in the human ge-

nome (40), and this uncertainty could affect our estimates

and results.

We applied diCal2.0 (28) (Method 1), a new version of

diCal (41) extended to handle complex demographic models

involving multiple populations with migration (42), and an

identity-by-state (IBS) tract method (43) (Method 2) to the

modern genome dataset (28). With these, we first estimated

divergence times between Native Americans and the Koryak

of Siberia, one of the genetically closest sampled East Asian

populations to Native Americans (fig. S5), using demograph-

ic models that reflect a clean split between the populations

(28). With both diCal2.0 and IBS tract method, the split of

Native Americans (including Amerindians and Athabascans)

from the Koryak dates to ca. 20 KYA (28) (tables S11A and

S12 and fig. S15).

We further applied diCal2.0 to models with gene flow

post-dating the split between Native Americans and Koryak

(Fig. 2A) and found that they provided a better fit to the

data than the models without gene flow (28). Overall, simu-

lated databased on the models inferred using diCal2.0 and

real data show very similar IBS tract length distributions

(Fig. 2B) and relative cross coalescence rates (CCR) between

pairs of individuals estimated using the Multiple Sequential-

ly Markovian Coalescent (MSMC) method (Method 3) (28,

44) (Figs. 2, C and D). This serves as a confirmation for the

model estimates from diCal2.0. We evaluated all the three

methods using simulations under complex demographic

models, and additionally investigated the effects of switch-

errors in haplotype phasing on the estimates (28).

We then applied the diCal2.0 model that allows for gene

flow between populations after their split to estimate diver-

gence times for Native Americans from more geographically

and genetically distant East Asian groups, including the Si-

berian Nivkh and Han Chinese. As before, the divergence

estimates for Amerindians and Athabascans were very simi-

lar to one another, ca. 23 KYA (table S11B and figs. S18 and

S21).

Hence, our results suggest that Amerindians and Atha-

bascans were, by three different methods, consistently equi-

distant in time to populations that were sampled from

different regions of East Asia, including some proximate to

Beringia, and with varied population histories. This suggests

that these two major Native American sub-groups are de-

scendants of the same source population that split off from

ancestral East Asians during the LGM. It is conceivable that

harsh climatic conditions during the LGM may have con-

tributed to the isolation of ancestral Native Americans, ul-

timately leading to their genetic divergence from their East

Asian ancestors.

We also modeled the peopling of the Americas using a

climate-informed spatial genetic model (CISGeM), in which

the genetic history and local demography is informed by

paleoclimatic and paleovegetation reconstructions (28, 45),

and found the results to be in accordance with the conclu-

sion of a single migration source for all Native Americans.

Using present-day and ancient high coverage genomes, we

found that Athabascans and Anzick-1, but not Greenlandic

Inuit and Saqqaq (29, 39), belong to the same initial migra-

tion wave that also gave rise to present-day Amerindians

from southern North America and Central and South Amer-

ica (Fig. 3), and that this migration likely followed a coastal

route, given our current understanding of the glacial geolog-

ical and paleoenvironmental parameters of the Late Pleisto-

cene (fig. S31).

In all cases, the best fit of the demographic models to the

IBS tract distribution and relative CCR by MSMC required

gene flow between Siberian and Native American popula-

tions after their initial split (Figs. 2, B to D). We also found

strong evidence for gene flow between Athabascans and the

Inuit (table S11B) supported by results from ADMIXTURE

(fig. S4), TreeMix (fig. S5), D-statistics employing both whole

genome and SNP chip genotype data (28, 46, 47) (figs. S6

and S8A), and outgroup f3 statistics using whole genome

data (28, 47) (Fig. S12). We attempted to estimate the diver-

gence times between Inuit and Siberians as well as Inuit

and Native Americans (table S11 and figs. S19 and S25 to

S27), but our analyses were complicated by gene flow be-

tween Inuit and Athabascans as well as complex admixture

patterns among Arctic groups (fig. S5).

We tested the duration and magnitude of post-split gene

flow between Native Americans and Siberians using di-

Cal2.0 by introducing stopping time of gene flow as a free

parameter (28). We still obtained the highest likelihood for

a divergence time of 22 KYA between Amerindians and Si-

berians as well as Athabascans and Siberians, although es-

timates for gene flow rate and end of the gene flow differ

(table S11C and fig. S22). Significant gene flow between Ath-

abascans and Siberians seems to have stopped ca. 12 KYA

(Table S11C), suggesting a link to the breaching of the Ber-

ingian Land Bridge by rising sea levels (48).

Overall, our results support a common Siberian origin

for all Native Americans, contradicting claims for an early

migration to the Americas from Europe (49), with their ini-

tial isolation and entrance into the Americas occurring no

earlier than 23 KYA, but with subsequent admixture with

East Asian populations. This additionally suggests that the

Mal’ta-related admixture into the early Americans (4), rep-

resenting ancestors of both Amerindians and Athabascans

(Fig. 1 and fig. S5), occurred sometime after 23 KYA, follow-

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ing the Native American split from East Asians.

Subsequent in situ diversification of Native Ameri-

can groups

That Amerindian and Athabascan groups were part of

the same migration implies that present-day genetic differ-

ences observed between them must have arisen later, after

ca. 23 KYA. Using the clean-split model in diCal2.0 on the

modern genomes dataset, we estimated that Athabascans

and Karitiana diverged ca. 13 KYA (95% confidence interval

of ca. 11.5-14.5 KYA, estimated from parametric bootstrap

results) (table S11A, fig. S16), which is consistent with results

from MSMC (fig. S27) (28).

Where the divergence between Karitiana and Athabas-

cans occurred is not known. However, several independent

lines of evidence suggest that it is more likely to have oc-

curred in lower latitude North America instead of eastern

Beringia (Alaska). These include the equidistant split times

of Amerindians and Athabascans to Asian populations, the

relatively brief interval between their estimated divergence

date range and the age of Anzick-1 (12.6 KYA) (5), and lastly,

the geographic location of Anzick-1 to the south of the North

American ice sheets and its clear affiliation with the ‘south-

ern branch’ of Native Americans (taken broadly to include

Amerindians from southern North America and Central and

South America) (5), as determined with outgroup f3 statistics

using SNP chip genotype data from present-day worldwide

populations (47) (Fig. 4 and figs. S13 and S14). Divergence in

North America would also be consistent with the known

pre-Clovis age sites in the Americas, such as Monte Verde

(14.6 KYA) (50). The most parsimonious model would be

that both Amerindians and Athabascans are descendants of

the same ancestral Native American population that entered

the Americas then subsequently diversified. However, we

cannot discount alternative and more complex scenarios,

which could be tested with additional ancient samples.

By the Clovis period (ca. 12.6 KYA), the ancestral Native

American population had already diversified into 'northern'

and 'southern' branches, with the former including ances-

tors of present-day Athabascans and northern Amerindian

groups such as Chipewyan, Cree and Ojibwa and the latter

including Amerindians from southern North America and

Central and South America (Fig. 4 and fig. S14). We tested

whether later gene flow from East Asian sources, such as the

Inuit, might explain the genetic differences between these

two branches. Using D-statistics on SNP chip genotype data

(47) masked for non-Native ancestry, we observed a signal of

gene flow between the Inuit and northwest Pacific Coast

Amerindians such as Coastal Tsimshian and Nisga’a, resid-

ing in the same region as the northern Athabascans (28)

(fig. S8B). However, this signal of admixture with the Inuit,

also detected in Athabascans (figs. S6 and S8A), was not

evident among northern Amerindian populations located

further east such as Cree, Ojibwa and Chipewyan (28) (fig.

S8C). This suggests that the observed difference between the

‘northern’ and ‘southern’ branches is not a consequence of

post-split East Asian gene flow into the ‘northern branch’,

and also provides a possible explanation as to why the

’southern branch’ Amerindians such as Karitiana are genet-

ically closer to the northern Amerindians located further

east than to northwest coast Amerindians and Athabascans

(fig. S9).

In contrast to Anzick-1, several of the Holocene individu-

als from the Americas, including those sequenced in this

study as well as the 8,500 year old Kennewick Man (51), are

closely related to present-day Native American populations

from the same geographical regions (Fig. 4 and figs. S13 and

S14). This implies genetic continuity of ancient and modern

populations in some parts of the Americas over at least the

last 8.5 KYA, which is in agreement with recent results from

Kennewick Man (51).

Evidence of more distant Old World gene flow into

some Native Americans

When testing for gene flow between Athabascans and

Inuit with masked SNP chip genotype data-based D-

statistics (47) (fig. S8), we observed a weak tendency for the

Inuit to be much closer to the Athabascans than to certain

Amerindians like the North American Algonquin and Cree,

and the Yaqui and Arhuaco of Central and South America

(respectively), as compared to other Amerindians such as

the Palikur and Surui of Brazil (fig. S8).

To further investigate this trend, we tested for additional

gene flow from Eurasian populations into the Americas with

D-statistics using the masked SNP chip genotype dataset

(47). 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

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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.

Testing the Paleoamerican model

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.

We, therefore, sequenced 17 ancient individuals affiliated

to the now-extinct Pericúes from Mexico and Fuego-

Patagonians from Chile and Argentina (28), who, on the

basis of their distinctive skull morphologies, are claimed to

be relicts of Paleoamericans (23, 27, 58, 59). Additionally, we

sequenced two pre-Columbian mummies from northern

Mexico (Sierra Tarahumara) to serve as morphological con-

trols, since they are expected to fall within the range of Na-

tive American morphological cranial variation (28). We

found that the ancient samples cluster with other Native

American groups and are outside the range of Oceanian ge-

netic variation (28) (Fig. 5 and figs. S32, S33, and S34). Simi-

larly, outgroup f3 statistics (47) reveal low shared genetic

ancestry between the ancient samples and Oceanians (28)

(Figs. S36, S37), and genome-based and masked SNP chip

genotype data-based D-statistics (46, 47) show no evidence

for gene flow from Oceanians into the Pericúes or Fuego-

Patagonians (28) (fig. S39).

As the Paleoamerican model is based on cranial mor-

phology (23, 27, 58, 59), we also measured craniometric data

for the ancient samples and assessed their phenotypic affin-

ities to supposed Paleoamericans, Amerindians and world-

wide populations (28). The results revealed that the

analyzed Fuego-Patagonians showed closest craniometric

affinity to Arctic populations and the Paleoamericans, while

the analyzed female Pericúes showed closest craniometric

affinities to populations from North America, the Arctic re-

gion and Northern Japan (table S15). More importantly, our

analyses demonstrated that the presumed ancestral ancient

Paleoamerican reference sample from Lagoa Santa, Brazil

(24) had closest affinities to Arctic and East Asian popula-

tions (table S15). Consequently, for the Fuego-Patagonians,

the female Pericúes and the Lagoa Santa Paleoamerican

sample, we were not able to replicate previous results (24)

that report close similarity of Paleoamerican and Australo-

Melanesian cranial morphologies. We note that male

Pericúes samples displayed more craniometric affinities

with populations from Africa and Australia relative to the

female individuals of their population (fig. S41). The results

of analyses based on craniometric data are, thus, highly sen-

sitive to sample structure and the statistical approach and

data filtering used (51). Our morphometric analyses suggest

that these ancient samples are not true relicts of a distinct

migration, as claimed, and hence do not support the Paleo-

american model. Similarly, our genomic data also provide

no support for an early migration of populations directly

related to Australo-Melanesians into the Americas.

Discussion

That Native Americans diverged from their East Asian

ancestors during the LGM and no earlier than 23 KYA pro-

vides an upper bound, and perhaps the climatic and envi-

ronmental context, for the initial isolation of their ancestral

population, and a maximum estimate for the entrance and

subsequent spread into the Americas. This result is con-

sistent with the model that people entered the Americas

prior to the development of the Clovis complex and had

reached as far as southern South America by 14.6 KYA. As

/ sciencemag.org/content/early/recent / 23 July 2015 / Page 5 / 10.1126/science.aab3884

archaeological evidence provides only a minimum age for

human presence in the Americas, we can anticipate the pos-

sible discovery of sites that approach the time of the diver-

gence of East Asians and Native Americans. However, our

estimate for the initial divergence and entry of Native Amer-

ican ancestors does not support archaeological claims for an

initial peopling significantly earlier than the LGM (8–10).

While our data cannot provide the precise geographical

context for the initial peopling process, it has allowed us to

more accurately estimate its temporal dynamics. This, in

turn, has enabled us to re-assess the Beringian Incubation

Model, which, based on mtDNA data and the timing and

geographical distribution of archaeological sites, hypothe-

sized a ca. 15,000 year-long period of isolation of ancestral

Native Americans in Beringia during the LGM (19–21). Our

results, along with recent findings of mtDNA haplogroup C1

in Iceland and ancient northwest Russia (60), do not fit with

the proposed 15,000-year span of the Beringian Incubation

Model (19–21). It is possible that a shorter period of isola-

tion occurred (ca. 8 KYA), but whether it occurred in Siberia

or Beringia will have to be determined by future ancient

DNA and archaeological findings. Given the genetic continu-

ity between Native Americans and some East Asian popula-

tions (figs. S4 and S5), other demographic factors, such as

surfing during population expansions into unoccupied re-

gions (61), may ultimately need to be taken into account to

better understand the presence of a large number of high

frequency private variants in the indigenous populations of

the Americas.

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.

Methods

DNA was extracted from 31 present-day individuals from

the Americas, Siberia and Oceania and 23 ancient samples

from the Americas, and converted to Illumina libraries and

shotgun-sequenced (28). Three of the ancient samples were

radiocarbon dated, of which two were corrected for marine

reservoir offset (28). SNP chip genotype data was generated

from 79 present-day Siberians and Native Americans affili-

ated to 28 populations (28). Raw data from SNP chip and

shotgun sequencing were processed using standard compu-

tational procedures (28). Error rate analysis, DNA damage

analysis, contamination estimation, sex determination,

mtDNA and Y chromosome haplogroup assignment,

ADMIXTURE analysis, ancestry painting and admixture

masking, Principal Component Analysis using SNP chip

genotype data, TreeMix analysis on genomic sequence data,

D-statistic and outgroup f3-statistic tests on SNP chip geno-

type and genomic sequence data, divergence time estima-

tion using diCal2.0, an IBS tract method and MSMC,

Climate-Informed Spatial Genetic Model analysis, and, cra-

niometric analysis were performed as described (28).

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ACKNOWLEDGMENTS

We thank J. Valdés for providing craniometric measurements of the Pericúes at the

National Museum of Anthropology in México; A. Monteverde from CINAH-Baja

California Sur and V. Laborde at the Musée de l´Homme in Paris for providing

documentation on Pericú and Fuego-Patagonian samples, respectively; T.

Gilbert, M. McCoy, C. Sarkissian, M. Sikora, L. Orlando for helpful discussions

and input; D. Yao and C. Barbieri for helping with the collection of the Aymara

population sample; B. Henn and J. Kidd for providing early access to the Mayan

sequencing data; Canadian Museum of History; Metlakatla and Lax Kw'alaams

First Nations; Listuguj Mi’gmaq Band Council; A. Pye of TERRA Facility, Core

Research Equipment & Instrument Training (CREAIT) Network at Memorial

University; the Danish National High-throughput DNA Sequencing Centre

(Copenhagen) for help with sequencing; and, Fondation Jean Dausset-Centre

de'Etude du Polymorphism Humain (CEPH) for providing DNA for the Human

Genome Diversity Project (HGDP) samples that were genome-sequenced in this

study. This study was supported by several funding bodies; Lundbeck

Foundation and the Danish National Research (Centre for GeoGenetics

members), Wellcome Trust grant 098051 (S.S., A.B., Y.X., C.T.-S., M.S.S., R.D.),

Marie Curie Intra-European Fellowship-FP7- People-PIEF-GA-2009-255503 and

the Transforming Human Societies Research Focus Areas Fellowship from La

Trobe University (C.V.), George Rosenkranz Prize for Health Care Research in

Developing Countries and National Science Foundation award DMS-1201234

(M.C.A.A), Swiss National Science Foundation (PBSKP3_143529) (A.-S.M.),

Ministerio de Ciencia e Innovación (MICINN) Project CGL2009-12703-C03-03

and MICINN (BES-2010-030127) (R.R.-V.), Consejo Nacional de Ciencia y

Tecnología (Mexico) (J.V.M.M.), Biotechnology and Biological Sciences Research

Council BB/H005854/1 (V.W., F.B., A.M.), European Research Council and Marie

Curie Actions Grant 300554 (M.E.A.), Wenner-Gren Foundations and the

Australian Research Council Future Fellowship FT0992258 (C.I.S.), European

Research Council ERC-2011-AdG 295733 grant (Langelin) (D.P. and D.L.),

Bernice Peltier Huber Charitable Trust (C.H., L.G.D.), Russian Foundation for

Basic Research grant 13-06-00670 (E.B.), Russian Foundation for Basic

Research grant 14-0400725 (E.K.), European Union European Regional

Development Fund through the Centre of Excellence in Genomics to Estonian

Biocentre and Estonian Institutional Research grant IUT24-1 (E.M., K.T., M.M.,

M.K., R.V.), Estonian Science Foundation grant 8973 (M.M.), Stanford Graduate

Fellowship (J.R.H.), Washington State University (B.M.K.), French National

Research Agency grant ANR-14-CE31-0013-01 (F-X.R), European Research

Council grant 261213 (T.K.), National Science Foundation BCS- 1025139

(R.S.M.), Social Science Research Council of Canada (K.-A.P., V.G.), National

Institutes of Health grants R01-GM094402 (M.S., Y.S.S.); R01 - AI17892 (P.J.N.,

P.P.); 2R01HG003229-09 (R.N., C.D.B.), Packard Fellowship for Science and

Engineering (Y.S.S.), Russian Science Fund grant 14-04-00827 and Presidium of

Russian Academy of Sciences Molecular and Cell Biology Programme (O.B.), and

Russian Foundation for Basic Research grant 14-06-00384 (Y.B.). Informed

consent was obtained for the sequencing of the modern individuals, with ethical

approval from The National Committee on Health Research Ethics, Denmark (H-

3-2012-FSP21). SNP chip genotype data and whole genome data for select

present-day individuals are available only for demographic research under data

access agreement with E.W. (see Tables S1 and S4 for a list of these samples).

Raw reads from the ancient and the remainder of the present-day genomes are

available for download through European Nucleotide Archive (ENA) accession

no. PRJEB9733, and the corresponding alignment files are available at

http://www.cbs.dtu.dk/suppl/NativeAmerican/. The remainder of the SNP chip

genotype data can be accessed through Gene Expression Omnibus (GEO) series

accession no. GSE70987 and at www.ebc.ee/free_data. The authors declare no

competing financial interests. C.D.B. is on the advisory board of Personalis, Inc.;

Identify Genomics; Etalon DX; and Ancestry.com.

SUPPLEMENTARY MATERIALS

www.sciencemag.org/cgi/content/full/science.aab3884/DC1

Materials and Methods

Supplementary Text

Figs. S1 to S41

Tables S1 to S15

References (65–205)

4 May 2015; accepted 15 July 2015

Published online 23 July 2015

10.1126/science.aab3884

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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 later than 23 KYA 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 ca. 13 KYA, with the former comprising Athabascans and northern

Amerindians and the latter consisting of Amerindians in northern North America and Central and South America

including the Anzick-1 individual (5). There is an admixture signal between Inuit and Athabascans and some northern

Amerindians (yellow line); however, the gene flow direction is unresolved due to 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 KYA (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.

/ sciencemag.org/content/early/recent / 23 July 2015 / Page 15 / 10.1126/science.aab3884

Fig. 2. Divergence estimates between Native Americans and Siberian Koryak. (A) The

demographic model used allows for continuous gene flow between populations 1 and 2, starting from

the time TDIV of divergence and ending at TM. The backward probability of migration per individual per

generation is denoted by m. The bottleneck at TB captures the out-of-Africa event. (

) The red and

black solid curves depict empirical distributions of IBS tracts shared between Karitiana-Koryak and

Athabascan-Koryak, respectively. The orange, pink, dashed blue and dashed green curves depict IBS

tracts shared between the two population pairs, simulated under two demographic models based on

results from diCal2.0. Overall, for Karitiana-Koryak and Athabascan-Koryak, the migration scenarios

(orange and pink, respectively) match the empirical curves (red and black, respectively) better than

the clean split scenarios (dashed blue and dashed green, respectively), with more long IBS tracts

showing evidence of recent common ancestry between Koryaks and Native Americans. (

and

)

Relative cross coalescence rates (CCR) for the Karitiana-Koryak and Athabascan-Koryak divergence

(red), respectively, including data simulated under the two demographic models in panel B. In both

cases, the model with gene flow (orange) fits the data (red) better than the clean split model (blue).

The migration model explains a broader CCR tail in the case of Karitiana-Koryak and the relatively late

onset of the CCR decay for Athabascan-Koryak.

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Fig. 3. Testing migrations into the Americas using a climate-informed model. Estimates of difference in

genetic divergence between Amerindians (from southern North America and Central and South America) or

Koryak versus Athabascan and Greenlandic Inuit and the ancient Saqqaq and Anzick-1 genomes (black vertical

lines), compared to posterior probability distribution predicted from a climate-informed spatial genetic model

reconstructing a single wave into the Americas (curves, the colored part represents the 95% credibility interval).

ΔT for population X is defined as T(X,Koryak)-T(X,Central and South Amerindians) (28). Both Anzick-1 and the

Athabascans were part of the same wave into the Americas to which other Amerindian populations from southern

North America and Central and South America belonged, while the Inuit and Saqqaq are the descendants of

different waves (observed values outside the 95% credibility interval).

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Fig. 4. Diversification within the Americas. SNP chip genotype data-based outgroup f

statistics (47) of the

form f3(X, Ancient; Yoruba) were used to estimate the shared ancestry between ancient samples from the

Americas and a large panel of worldwide present-day populations (X), including Athabascan and Amerindian

groups from North America (table S3), some of which were masked for non-Native ancestry prior to the

analysis (28). The outgroup f3 statistics are depicted as heat maps with the sampling location of the ancient

sample marked by the dotted lines, and corresponding ranked plots with error bars are shown in fig. S14. BP

refers to time before present. We find the Anzick-1 sample to share most ancestry with the ‘southern’ branch

of Native Americans when using multiple northern Native Americans sequenced in this study, consistent with

(5). The seven Holocene aged samples share most ancestry with Native Americans, with a general tendency to

be genetically closer to present-day Native American populations from the same geographical region.

/ sciencemag.org/content/early/recent / 23 July 2015 / Page 19 / 10.1126/science.aab3884

Fig. 5. The Paleoamerican model. (A) Principal Component Analysis plot of 19 ancient samples combined

with a worldwide reference panel, including 1,823 individuals from (6). Our samples plot exclusively with

American samples. For plots with other reference panels consisting of Native American populations, see fig.

S32. (

) Population structure in the ancient Pericú, Mexican mummy and Fuego-Patagonian individuals from

this study. Ancestry proportions are shown when assuming six ancestral populations (K = 6). The top bar

shows the ancestry proportions of the 19 ancient individuals, Anzick-1 (5), and two present-day Native

American genomes from this study (Huichol and Aymara). The plot at the bottom illustrates the ancestry

proportions for 1,823 individuals from (6). Our samples show primarily Native American (ivory, >92%) and

Siberian (red, ca. 5%) ancestry. For the plot with K=13, see fig. S33.

/ sciencemag.org/content/early/recent / 23 July 2015 / Page 20 / 10.1126/science.aab3884

Revised SOM 06.24.2015

Data

August 2015

Maanasa Raghavan · Matthias Steinrücken · Kelley Harris · Stephan Schiffels · Eske Willerslev

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From North Asia to South America: Tracing the longest human migration through genomic sequencing

Article

Full-text available

May 2025
SCIENCE

Genome sequencing of 1537 individuals from 139 ethnic groups reveals the genetic characteristics of understudied populations in North Asia and South America. Our analysis demonstrates that West Siberian ancestry, represented by the Kets and Nenets, contributed to the genetic ancestry of most Siberian populations. West Beringians, including the Koryaks, Inuit, and Luoravetlans, exhibit genetic adaptation to Arctic climate, including medically relevant variants. In South America, early migrants split into four groups—Amazonians, Andeans, Chaco Amerindians, and Patagonians—~13,900 years ago. Their longest migration led to population decline, whereas settlement in South America’s diverse environments caused instant spatial isolation, reducing genetic and immunogenic diversity. These findings highlight how population history and environmental pressures shaped the genetic architecture of human populations across North Asia and South America.

How did Evolutionary Processes Influence the Genetic Structure of Humans in the Neotropics?

Chapter

Apr 2025

The Neotropics, encompassing Central and South America, stand out for their extraordinary biodiversity and cultural richness. Indigenous Americans exhibit remarkable cultural and linguistic diversity, but their genetic diversity is among the lowest among human populations. Environmental factors, including altitude, temperature, and biodiversity, have influenced the genetic makeup of Indigenous Americans since the earliest peopling of the America. Additionally, human impact, such as hunting, harvesting, and wildlife management, has significantly affected neotropical biodiversity. Niche construction, driven by plant and animal domestication and landscape modification, has played a crucial role in agriculture and has heavily influenced the genetic diversity of the region. The interplay between humans and their environment has shaped human genetic adaptations concerning diet and susceptibility to infectious diseases, affecting contemporary indigenous and admixed populations. Furthermore, migrations have played a significant role in shaping the genetic structure of neotropical human populations. Over time, multiple migration waves have contributed to the genetic diversity observed in present-day populations. The peopling of the America involved successive migrations dating back at least 15,000 years, followed by later post-contact migrations from various world regions. The study of genetic variation in neotropical populations has provided insights into their evolutionary history, demographic changes, and the impact of historical events like colonization and the transatlantic slave trade. Understanding the complex interplay of genetic, environmental, and historical factors is vital for conserving the biodiversity of humans and ecosystems. This chapter discusses the importance of migrations, demographic changes and natural selection in shaping the genetic diversity of neotropical human populations.

Genetic Diversity and Forensic Parameters of 27 Y-STRs in Two Mestizo Populations from Western Mexico

Article

Full-text available

Mar 2025

Background: Analyzing Y-chromosome short tandem repeats (Y-STRs) is essential in forensic genetics and population studies. The Yfiler™ Plus kit, which includes 27 Y-STR markers, enhances the discrimination power for forensic and kinship applications. However, this genetic system has not been analyzed in Mexican populations, which limits its application and representativeness in international databases. Objectives: We wished to examine the genetic diversity and forensic parameters of the 27 Y-STRs included in the YFiler™ Plus kit in two populations from Western Mexico (Jalisco and Michoacán). Methods: Male DNA samples were amplified using the Yfiler™ Plus kit, followed by a fragment analysis via capillary electrophoresis (CE). The haplotype frequencies and forensic parameters were calculated. The haplogroups of all samples were predicted, and the distribution and percentages of ancestries were determined. The Rst genetic distances, including reference populations, were calculated and graphically represented in a multidimensional scaling (MDS) plot. Results: A total of 224 haplotypes were identified in all of the samples, of which 98.66% corresponded to unique haplotypes. Bi- and tri-allelic patterns were observed in both populations. The observed discriminatory capacity was 98.4% for Jalisco and 98.9% for Michoacán, while the haplotype diversity values were 0.9998 and 0.9997, respectively. The most frequent haplogroup was R1b, followed by Q, representing the European and Native American ancestries, in both populations. Conclusions: This study is the first to report the haplotype diversity and forensic parameters of the 27 Y-STRs included in the Yfiler™ Plus kit in Mexican populations. These findings confirm the forensic utility of these markers for human identification, biological relationship testing, and criminal investigations, reinforcing their applicability in forensic casework.

Descendants or Inheritors?

Chapter

Jun 2025

Christopher S. Davis

This chapter examines the origins of sun and moon worship among early Paleoindian South American cultures, in comparison with the rock art and archaeological findings at Monte Alegre. Disruptions in contact-period records reveal imprecise references to local populations, while missionary accounts suggest a continuity of artistic traditions. The rock art analysis in the previous chapters connects radiocarbon dating to climate changes, theorizing how these conditions may have motivated early human migration. Additionally, it explores motifs in rock art that likely signify solar observations and seasonal changes. This evidence positions rock art as a critical tool for understanding environmental interactions and cultural practices at the beginning of the Younger Dryas period, providing new insights about the comet-impact hypothesis.

A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia

Article

Full-text available

May 2025

Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.

Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden

Article

Full-text available

May 2025
GENOME BIOL

Background Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration, and disease pandemics during and after the Middle Ages had on these processes. Results We perform low-coverage sequencing of the genomes of 338 individuals spanning the eighth to the eighteenth centuries in the city of Sint-Truiden in Flanders, in the northern part of Belgium. The early/high medieval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less genetic relatedness than observed today between individuals in present-day Flanders. We find differences in gene variants associated with high vitamin D blood levels between individuals with Gaulish or Germanic ancestry. Although we find evidence of a Yersinia pestis infection in 5 of the 58 late medieval burials, we were unable to detect a major population-scale impact of the second plague pandemic on genetic diversity or on the elevated differentiation of immunity genes. Conclusions This study reveals that the genetic homogenization process in a medieval city population in the Low Countries was protracted for centuries. Over time, the Sint-Truiden population became more similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the high medieval period, and the continuous process of local admixture of Germanic and Gaulish ancestries which formed the genetic cline observable today in the Low Countries.

Exploring Halophiles for Reclamation of Saline Soils: Biotechnological Interventions for Sustainable Agriculture

Article

May 2025
J BASIC MICROB

Soil salinization is a major constraint on agricultural productivity, particularly in arid and semi‐arid regions where limited rainfall cannot wash salts from plant root zones. This leads to disruptions in water uptake, ion balance, photosynthesis, respiration, nutrient absorption, hormone regulation and rhizosphere microbiome disturbances in plants. Chemical and biological methods can help mitigate soil salinity, but biological approaches, like using halophytes and salt‐tolerant microorganisms, are preferred for environmental sustainability. Halophytes, however, represent only about 1% of flora and are habitat specific, so halophilic plant growth‐promoting (PGP) microbes have emerged as a key eco‐friendly solution. Halophilic PGP bacteria have shown promise in remediating saline soils, enhancing fertility and boosting crop resilience by inducing salinity tolerance (IST) and promoting plant growth traits. In the era of modern agriculture where chemical inputs are at their peak of application rendering the soil infertile, halophilic PGP bacteria represent a promising, sustainable approach to support food security, aligning with Sustainable Development Goals for zero hunger.

Picuris Pueblo oral history and genomics reveal continuity in US Southwest

Article

Full-text available

Apr 2025
NATURE

Indigenous groups often encounter significant challenges when asserting ancestral claims and cultural affiliations based on oral histories, particularly in the USA where such narratives have historically been undervalued. Although ancient DNA offers a tool to complement traditional knowledge and address gaps in oral history, longstanding disregard for Indigenous sovereignty and beliefs has understandably led many Indigenous communities to distrust DNA studies1, 2, 3–4. Earlier research often focused on repatriation claims5, 6–7, whereas more recent work has increasingly moved towards enhancing Tribal histories8,9. Here we present a collaborative study initiated by a federally recognized Native American tribe, the sovereign nation of Picuris Pueblo in the Northern Rio Grande region of New Mexico, USA, to address gaps in traditional knowledge and further their understanding of their population history and ancestry. We generated genomes from 16 ancient Picuris individuals and 13 present-day members of Picuris Pueblo, providing genomic data spanning the last millennium. We show genetic continuity between ancient and present-day Picuris, and more broadly with Ancestral Puebloans from Pueblo Bonito in Chaco Canyon¹⁰, 275 km to the west. This suggests a firm spatiotemporal link among these Puebloan populations of the North American Southwest. Furthermore, we see no evidence of population decline before European arrival11, 12–13, and no Athabascan ancestry in individuals predating 1500 ce, challenging earlier migration hypotheses14, 15–16. This work prioritizes Indigenous control of genetic data and brings together oral tradition, archaeology, ethnography and genetics.

"Rigorous and Systematic Qualitative Data Analysis in Biological Anthropology"

Article

Full-text available

Dec 2024

Biological anthropologists have long engaged in qualitative data analysis (QDA), though such work is not always foregrounded. In this article, we discuss the role of rigorous and systematic QDA in biological anthropology and consider how it can be understood and advanced. We first establish what kinds of qualitative data and analysis are used in biological anthropology. We then review the ways QDA has been used in six subfields of biological anthropology: primatology, human biology, paleoanthropology, dental and skeletal biology, bioarchaeology, and anthropological genetics. We follow that with an overview of how to use QDA methods: three simple QDA methods (i.e., word‐based analysis, theme analysis, and coding) and three QDA approaches for model‐building and model‐testing (i.e., content analysis, semantic network analysis, and grounded theory). With this foundation in place, we discuss how QDA can support transformative research in biological anthropology—emphasizing the valuable role of QDA in inductive and community‐based research. We discuss how QDA supports transformative research using mixed‐methods research designs, participatory action research, and abolition and Black feminist research. Finally, we consider how to close a QDA project, reflecting on the logistics, ethics, and limitations of qualitative data sharing, including how researchers can use the CARE Principles (Collective Benefit, Authority to Control, Responsibility, and Ethics) to support Indigenous data sovereignty.

Preparing for shotgun sequencing in forensic genetics – Evaluation of DNA extraction and library building methods

Article

Feb 2025
FORENSIC SCI INT-GEN

First Peoples in a New World: Colonizing Ice Age America

Book

May 2009

David J. Meltzer

The origin of the first Americans: An analysis based on the cranial morphology of early South American human remains

Article

Jan 1990
AM J PHYS ANTHROPOL

Inference of Population Structure Using Multilocus Genotype Data

Article

Jun 2000
GENETICS

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.

Population Structure and Eigenanalysis

Article

Jan 2006

A-la-recherche-de-la-Petite-Rochelle: Memory and identity in Restigouche

Article

Mar 1999
Acadiensis

PD Clarke

Mitochondrial DNA variation in two South Siberian aboriginal populations: Implications for the genetic history of North Asia

Article

Dec 2000

The mtDNAs of 76 individuals representing the aboriginal populations of South Siberia, the Tuvinians and Buryats, were subjected to restriction fragment length polymorphism (RFLP) analysis and control region hypervariable segment I (HVS-I) sequencing, and the resulting data were combined with those available for other Siberian and East Asian populations and subjected to statistical and phylogenetic analysis. This analysis showed that the majority of the Tuvinian and Buryat mtDNAs (94.4% and 92.5%, respectively) belong to haplogroups A, B, C, D, E, F, and M*, which are characteristic of Mongoloid populations. Furthermore, the Tuvinians and Buryats harbor four Asian- and Native American-specific haplogroups (A-D) with frequencies (72.2% and 55%, respectively) exceeding those reported previously for Mongolians, Chinese, and Tibetans. They represent, therefore, the populations that are most closely related to New World indigenous groups. Despite their geographical proximity, the Tuvinians and Buryats: shared no HVS-I sequences in common, although individually they shared such sequences with a variety of other Siberian and East Asian populations. Tn addition, phylogenetic and principal component analyses data of mtDNA sequences show that the Tuvinians clustered more closely with Turkie-speaking Yakuts, whereas the Mongolic-speaking Buryats clustered closer to Korean populations. Furthermore, HVS-I sequences, comprising one-fourth of the Buryat lineages and characterized by the only C-to-T transition at nucleotide position 16223, were identified as different RFLP haplotypes (B, C, D, E, M*, and H). This finding appears to indicate the putative ancestral state of the 16223T HVS-I sequences to Mongoloid macrohaplogroup M, at least. Finally, the results of nucleotide diversity analysis in East Asian and Siberian populations suggest that Central and East Asia were the source areas from which the genetically heterogeneous Tuvinians and Buryats first emerged.

Predicting the molecular complexity of sequencing libraries

Article

Apr 2013

Predicting the molecular complexity of a genomic sequencing library is a critical but difficult problem in modern sequencing applications. Methods to determine how deeply to sequence to achieve complete coverage or to predict the benefits of additional sequencing are lacking. We introduce an empirical Bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing.

Kennewick man the scientific investigation of an ancient American skeleton

Article

Jan 2014

Almost from the day of its accidental discovery along the banks of the Columbia River in Washington State in July 1996, the ancient skeleton of Kennewick Man has garnered significant attention from scientific and Native American communities as well as public media outlets. This volume represents a collaboration among physical and forensic anthropologists, archaeologists, geologists, and geochemists, among others, and presents the results of the scientific study of this remarkable find. Scholars address a range of topics, from basic aspects of osteological analysis to advanced? research focused on Kennewick Man’s origins and his relationships to other populations. Interdisciplinary studies, comprehensive data collection and preservation, and applications of technology are all critical to telling Kennewick Man’s story. Kennewick Man: The Scientific Investigation of an Ancient American Skeletonis written for a discerning professional audience, yet the absorbing story of the remains, their discovery, their curation history, and the extensive amount of detail that skilled scientists have been able to glean from them will appeal to interested and informed general readers. These bones lay silent for nearly nine thousand years, but now, with the aid of dedicated researchers, they can speak about the life of one of the earliest human occupants of North America.

The mammoth steppe hypothesis: The middle Wisconsin (oxygen isotope stage 3) peopling of North America

Article

Jan 2014

In this chapter we introduce the Mammoth Steppe Hypothesis suggesting an Oxygen Isotope Stage 3 (OIS3), human movement into the Americas sometime between 40,000 and 30,000 years ago. OIS3 was characterized by a relatively mild climate that created a vast contiguous grassland, which was capable of supporting abundant fauna. Humans had adapted to this Mammoth Steppe biome during the latter part of OIS3 as demonstrated by material cultural evidence from the Yana Rhino Horn site and other northern Siberian sites. Ecological data from the Mammoth Steppe support the assertion that humans could have followed the Mammoth Steppe into the Americas during OIS3. We suggest that human populations from northern Siberia were able to disperse across Beringia and down the eastern edge of the Rocky Mountains when an interior corridor was open prior to 22,000 14C yr BP. Support for the hypothesis is based on evidence from multiple North American mid-continent archaeological sites dating to OIS3 and the Last Glacial Maximum (LGM). Evidence from 14 sites, 5 of which contain stone artifacts, is summarized. The dispersal of small pre- LGM populations left a sparse archaeological record in North America that warrants ongoing investigation through systematic research in geological deposits greater than ca. 20,000 14C yr BP. © 2014 by Kelly E. Graf, Caroline V. Ketron, and Michael R. Waters. All rights reserved.

The First Americans: Race, Evolution and the Origin of Native Americans

Article

Oct 2005

Joseph F. Powell

The recent discoveries of 9000-12000 year old skeletal remains in the Americas have begun to change our understanding of who originally entered the Americas at the end of the last Ice Age. Discoveries such as Washington state's ‘Kennewick Man’, Brazil's ‘Luzia’, and Alaska's ‘Prince of Wales Island Man’ have challenged the archaeological and geological status quo. The First Americans explores these new discoveries by using racial classifications and micro-evolutionary techniques to better understand the complex relationships between the first Americans and living Native Indian groups.

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

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Supplementary resource (1)

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Genomic evidence for the Pleistocene and recent population history of Native Americans

Genomic evidence for the Pleistocene and recent population history of Native Americans

Genomic evidence for the Pleistocene and recent population history of Native Americans

Revised SOM 06.24.2015