The formation of human populations in South and Central Asia

Abstract

Ancient human movements through Asia
Ancient DNA has allowed us to begin tracing the history of human movements across the globe. Narasimhan et al. identify a complex pattern of human migrations and admixture events in South and Central Asia by performing genetic analysis of more than 500 people who lived over the past 8000 years (see the Perspective by Schaefer and Shapiro). They establish key phases in the population prehistory of Eurasia, including the spread of farming peoples from the Near East, with movements both westward and eastward. The people known as the Yamnaya in the Bronze Age also moved both westward and eastward from a focal area located north of the Black Sea. The overall patterns of genetic clines reflect similar and parallel patterns in South Asia and Europe.
Science , this issue p. eaat7487 ; see also p. 981

Full text

RESEARCH ARTICLE SUMMARY
◥
HUMAN EVOLUTION
The formation of human populations
in South and Central Asia
Vagheesh M. Narasimhan et al.
RATIONALE: To elucidate the extent to which
the major cultural transformations of farming,
pastoralism, and shifts in the distribution of
languages in Eurasia were accompanied by
movement of people, we report genome-wide
ancient DNA data from 523 individuals span-
ning the last 8000 years, mostly from Central
Asia and northernmost South Asia.
RESULTS: The movement of people follow-
ing the advent of farming resulted in genetic
gradients across Eurasia that can be modeled
as mixtures of seven deeply divergent popula-
tions. A key gradient formed in southwestern
Asia beginning in the Neolithic and continu-
ing into the Bronze Age, with more Anatolian
farmer–related ancestryin the west and more
Iranian farmer–related ancestry in the east.
This cline extended to the desert oases of
Central Asia and was the primary source of
ancestry in peoples of the Bronze Age Bactria
Margiana Archaeological Complex (BMAC).
This supports the idea that the archaeolog-
ically documented dispersal of domesticates
was accompanied by the spread of people from
multiple centers of domestication.
The main population of the BMAC carried no
ancestry from Steppe pastoralists and did not
contribute substantially to later South Asians.
However, Steppe pastoralist ancestry appeared
in outlier individuals at BMAC sites by the turn
of the second millennium BCE around the same
time as it appeared on the southern Steppe.
Using data from ancient individuals from the
Swat Valley of northernmost South Asia, we show
that Steppe ancestry then integrated further south
in the first half of the second millennium BCE,
contributing up to 30% of the ancestry of modern
groups in South Asia. The Steppe ancestry in
South Asia has the same profile as that in Bronze
Age Eastern Europe, tracking a movement of
people that affected both regions and that likely
spread the unique features shared between Indo-
Iranian and Balto-Slavic languages.
The primary ancestral population of modern
South Asians is a mixture of people related to
early Holocene populations of Iran and South
Asia that we detect in outlier individuals from
two sites in cultural contact with the Indus
Valley Civilization (IVC), making it plausible
that it was characteristic of the IVC. After the
IVC’s decline, this population mixed with north-
western groups with Steppe
ancestry to form the “An-
cestral North Indians”(ANI)
and also mixed with south-
eastern groups to form the
“Ancestral South Indians”
(ASI), whose direct descend-
ants today live in tribal groups in southern
India. Mixtures of these two post-IVC groups—
the ANI and ASI—drive the main gradient of
genetic variation in South Asia today.
CONCLUSION: Earlier work recorded mas-
sive population movement from the Eurasian
Steppe into Europe early in the third millen-
nium BCE, likely spreading Indo-European
languages. We reveal a parallel series of eve nts
leading to the spread of Steppe ancestry to
South Asia, thereby documenting movements
of people that were likely conduits for the
spread of Indo-European languages.▪
RESEARCH
Narasimhan et al., Science 365, 999 (2019) 6 September 2019 1of1
The list of authors and affiliations is available in the full
article online.
Corresponding authors: Vagheesh M. Narasimhan (vagheesh@
mail.harvard.edu); Nick Patterson (nickp@broadinstitute.org);
Michael Frachetti (frachetti@wustl.edu); Ron Pinhasi (ron.
pinhasi@univie.ac.at); David Reich (reich@genetics.med.
harvard.edu)
Cite this article as V. M. Narasimhan et al., Science 365,
eaat7487 (2019). DOI: 10.1126/science.aat7487
Arabian
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Ancestral
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2000–1000 BCE
Ancestral
North Indians
2000–1000 BCE
Ancestral
North Indians
2000–1000 BCE
~1000 BCE
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~2000 BCE
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~1700 BCE
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Yamnaya
~3300 BCE
Yamnaya
~3300 BCE
Yamnaya
~3300 BCE
~2700 BCE
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~2300 BCE Ancestral
South Indians
2000–1000 BCE
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The Impact of Yamnaya Steppe Pastoralists
Path by which
this ancestry arrived
in South Asia is
uncertain.
Location of the
initial formation of
Yamnaya ancestry
is uncertain.
Location of the
initial formation of
Yamnaya ancestry
is uncertain.
Location of the
initial formation of
Yamnaya ancestry
is uncertain.
KAZAKHSTAN
0 800 km
Other ancestry
Yamnaya
Flow of Yamnaya-derived ancestry
All arrows are approximate.
Eurasian Steppe
The Bronze Age spread of Yamnaya Steppe pastoralist ancestry into two subcontinents—Europe and South Asia. Pie charts reflect the
proportion of Yamnaya ancestry, and dates reflect the earliest available ancient DNA with Yamnaya ancestry in each region. Ancient DNA has not
yet been found for the ANI and ASI, so for these the range is inferred statistically.
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RESEARCH ARTICLE
◥
HUMAN EVOLUTION
The formation of human populations
in South and Central Asia
Vagheesh M. Narasimhan
1
*†, Nick Patterson
2,3
*†, Priya Moorjani
4,5
‡, Nadin Rohland
1,2
‡,
Rebecca Bernardos
1
, Swapan Mallick
1,2,6
‡, Iosif Lazaridis
1
, Nathan Nakatsuka
1,7
,
Iñigo Olalde
1
, Mark Lipson
1
, Alexander M. Kim
1,8
, Luca M. Olivieri
9
, Alfredo Coppa
10
,
Massimo Vidale
9,11
, James Mallory
12
, Vyacheslav Moiseyev
13
, Egor Kitov
14,15,16
,
Janet Monge
17
, Nicole Adamski
1,6
, Neel Alex
18
, Nasreen Broomandkhoshbacht
1,6
§,
Francesca Candilio
19,20
, Kimberly Callan
1,6
, Olivia Cheronet
19,21,22
,
Brendan J. Culleton
23
, Matthew Ferry
1,6
, Daniel Fernandes
19,21,22,24
, Suzanne Freilich
22
,
Beatriz Gamarra
19,21,25
||¶, Daniel Gaudio
19,21
, Mateja Hajdinjak
26
, Éadaoin Harney
1,6,27
,
Thomas K. Harper
28
, Denise Keating
19
, Ann Marie Lawson
1,6
, Matthew Mah
1,2,6
,
Kirsten Mandl
22
, Megan Michel
1,6
#**, Mario Novak
19,29
, Jonas Oppenheimer
1,6
††,
Niraj Rai
30,31
, Kendra Sirak
1,19,32
, Viviane Slon
26
, Kristin Stewardson
1,6
,
Fatma Zalzala
1,6
, Zhao Zhang
1
, Gaziz Akhatov
15
, Anatoly N. Bagashev
33
,
Alessandra Bagnera
9
, Bauryzhan Baitanayev
15
, Julio Bendezu-Sarmiento
34
,
Arman A. Bissembaev
15,35
, Gian Luca Bonora
36
, Temirlan T. Chargynov
37
,
Tatiana Chikisheva
38
, Petr K. Dashkovskiy
39
, Anatoly Derevianko
38
, Miroslav Dobeš
40
,
Katerina Douka
41,42
, Nadezhda Dubova
14
, Meiram N. Duisengali
35
, Dmitry Enshin
33
,
Andrey Epimakhov
43,44
, Alexey V. Fribus
45
, Dorian Fuller
46,47
, Alexander Goryachev
33
,
Andrey Gromov
13
, Sergey P. Grushin
48
, Bryan Hanks
49
, Margaret Judd
49
,
Erlan Kazizov
15
, Aleksander Khokhlov
50
, Aleksander P. Krygin
51
, Elena Kupriyanova
52
,
Pavel Kuznetsov
50
, Donata Luiselli
53
, Farhod Maksudov
54
, Aslan M. Mamedov
55
,
Talgat B. Mamirov
15
, Christopher Meiklejohn
56
, Deborah C. Merrett
57
,
Roberto Micheli
9,58
, Oleg Mochalov
50
, Samariddin Mustafokulov
54,59
, Ayushi Nayak
41
,
Davide Pettener
60
, Richard Potts
61
, Dmitry Razhev
33
, Marina Rykun
62
,
Stefania Sarno
60
, Tatyana M. Savenkova
63
, Kulyan Sikhymbaeva
64
,
Sergey M. Slepchenko
33
, Oroz A. Soltobaev
37
, Nadezhda Stepanova
38
,
Svetlana Svyatko
13,65
, Kubatbek Tabaldiev
66
, Maria Teschler-Nicola
22,67
,
Alexey A. Tishkin
68
, Vitaly V. Tkachev
69
, Sergey Vasilyev
14,70
, Petr Velemínský
71
,
Dmitriy Voyakin
15,72
, Antonina Yermolayeva
15
, Muhammad Zahir
41,73
,
Valery S. Zubkov
74
, Alisa Zubova
13
, Vasant S. Shinde
75
, Carles Lalueza-Fox
76
,
Matthias Meyer
26
, David Anthony
77
, Nicole Boivin
41
‡, Kumarasamy Thangaraj
30
‡,
Douglas J. Kennett
23,28,78
‡, Michael Frachetti
79,80
†,
Ron Pinhasi
19,22
†, David Reich
1,2,6,81
†
By sequencing 523 ancient humans, we show that the primary source of ancestry in
modern South Asians is a prehistoric genetic gradient between people related to early
hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s
decline, its people mixed with individuals in the southeast to form one of the two main
ancestral populations of South Asia, whose direct descendants live in southern India.
Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around
4000 years ago, spread via Central Asia to form the other main ancestral population.
The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern
Europe, tracking a movement of people that affected both regions and that likely spread
the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
The past 10,000 years have witnessed pro-
found economic changes driven by the
transition from foraging to food produc-
tion,aswellasmajorchangesincultural
practice that are evident from archaeology,
the distribution of languages, and the written
record. The extent to which these changes were
associated with movements of people has been
amysteryinCentralAsiaandSouthAsia,inpart
because of a paucity of ancient DNA. We report
genome-wide data from 523 individuals from
Central Asia and northernmost South Asia from
the Mesolithic period onward (1), which we co-
analyze with previously published ancient DNA
from across Eurasia and with data from diverse
present-day people.
In Central Asia, we studied the extent to which
the spread of farming and herding practices from
the Iranian plateau to the desert oases south of
the Eurasian Steppe was accompanied by move-
ments of people or adoption of ideas from neigh-
boring groups (2–4). For the urban communities
of the Bactria Margiana Archaeological Complex
(BMAC) in the Bronze Age, we assessed whether
the people buried in its cemeteries descended
directly from earlier smaller-scale food producers,
andwealsodocumentedtheirgenetichetero-
geneity (5). Farther to the north and east, we
showed that the Early Bronze Age spread of crops
and domesticated animals between Southwest
Asia and eastern Eurasia along the Inner Asian
Mountain Corridor (6) was accompanied by
movements of people. Finally, we examined
when descendants of the Yamnaya, who spread
across the Eurasian Steppe beginning around
3300 BCE (7–9), began to appear in Central Asia
south of the Steppe.
In northernmost South Asia, we report a time
transect of >100 individuals beginning ~1200 BCE,
which we coanalyze along with modern data from
hundreds of present-day South Asian groups, as
well as ancient DNA from neighboring regions
(10). Previous analyses place the majority of
present-day South Asians along a genetic cline (11)
that can be modeled as having arisen from mixture
of two highly divergent populations after around
4000 years ago: the Ancestral North Indians
(ANI), who harbor large proportions of ancestry
related to West Eurasians, and the Ancestral South
Indians (ASI), who are much less closely related to
West Eurasians (12). We leveraged ancient DNA to
place constraints on the genetic structure of the
ANI and ASI and, in conjunction with other lines
of evidence, to make inferences about when and
where they formed. By modeling modern South
Asians along with ancient individuals from sites
in cultural contact with the Indus Valley Civili-
zation (IVC), we inferred a likely genetic signa-
ture for people of the IVC that reached its
maturity in northwestern South Asia between
2600and1900BCE.WealsoexaminedwhenSteppe
pastoralist–derived ancestry (9) mixed into groups
in South Asia, and placed constraints on whether
Steppe-related ancestry or Iranian-related ances-
try is more plausibly associated with the spread
of Indo-European languages in South Asia.
Dataset and analysis strategy
We generated whole-genome ancient DNA data
from 523 previously unsampled ancient individ-
uals and increased the quality of data from 19
previously sequenced individuals. The individu-
als derive from three broad geographical regions:
182 from Iran and the southern part of Central
Asia that we call Turan (present-day Turkmenistan,
Uzbekistan, Tajikistan, Afghanistan, and Kyrgyzstan),
209 from the Steppe and northern forest zone mostly
in present-day Kazakhstan and Russia, and 132 from
northern Pakistan. The ancient individuals are from
(i) Mesolithic, Copper, Bronze,and Iron Age Iran
and Turan (12,000 to 1 BCE, from 19 sites) includ-
ing the BMAC; (ii) early ceramic-using hunter-
gatherers from the western Siberian forest zone,
who we show represent a point along an early
Holocene cline of North Eurasians and who
RESEARCH
Narasimhan et al., Science 365, eaat7487 (2019) 6 September 2019 1of15
on September 5, 2019 http://science.sciencemag.org/Downloaded from

emerge as a valuable source population for mod-
eling the ancestry of Central and South Asians
(6400 to 3900 BCE from 2 sites); (iii) Copper and
Bronze Age pastoralists from the Central Steppe,
including from Bronze Age Kazakhstan (3400 to
800 BCE from 56 sites); and (iv) northernmost
South Asia, specifically Late Bronze Age, Iron Age,
and historical settlements in the Swat and Chitral
districts of present-day Pakistan (~1200 BCE to
1700 CE from 12 sites) (Fig. 1 and table S1) (1,13).
We prepared samples in dedicated clean rooms,
extracted DNA (14,15), and constructed libraries
for Illumina sequencing (16,17). We enriched the
libraries for DNA overlapping around 1.2 million
single-nucleotide polymorphisms (SNPs), se-
quenced the products on Illumina instruments,
and performed quality control (table S2) (7,18,19).
Our final dataset after merging with previously
reported data (7–9,16,18,20,21–31) spans 83 7
ancient individuals who passed all our analysis
filters. These filters included restricting to the
92% of individuals who were represented by at
least 15,000 of the targeted SNPs (the number
at which we began to be able to reliably estimate
proportions of the deeply divergent ancestry
sources) (table S1). These filters also included
removing individuals determined genetically to
be first-degree relatives of other higher-coverage
individuals (table S3). The media n numb er of
SNPs analyzed per individual was ~617,000. We
also merged with previously reported whole-
genome sequencing data from 686 present-day
individuals (table S1) and coanalyzed with 1789
present-day people from 246 ethnographically
distinct groups in South Asia genotyped at
~600,000 SNPs (table S5) (10,13,27,32).
We grouped individuals on the basis of
archaeological and chronological information,
taking advantage of 269 direct radiocarbon
dates on skeletal material that we generated
specifically for this study (table S4). We further
clustered individuals who were genetically in-
distinguishable within these groupings and
labeled outliers with ancestry that was signif-
icantly different from that of others at the same
site and time period (13).For our primary analy-
ses, we did not include individuals who were the
sole representatives of their ancestry profiles,
thereby reducing the chance that our conclu-
sions were being driven by single individuals
with contaminated DNA or misattributed ar-
chaeological context. This also ensured that
each major analysis grouping was represented
by many more SNPs than our minimum cutoff of
15,000 per individual. Thus, all but one analysis
cluster included at least one individual covered
by >200,000 SNPs, which is sufficient to support
high-resolution analysis of population history
(18) (the exception is a pair of genetically similar
outliers from the site of Gonur that are not the
focus of any main analyses). We use italic font to
refer to genetic groupings and nonitalic font to
indicate archaeological cultures or sites.
To make inferences about population structure,
we began by carrying out principal components
analysis (PCA) projecting ancient individuals onto
the patterns of genetic variation in present-day
Eurasians, a procedure that allowed us to obtain
meaningful constraints even on ancestry of an-
cient individuals with limited coverage because
each SNP from each individual can be compared
to a large reference dataset (33–35). This revealed
three major clusters strongly correlating to the
geographic regions of the Forest Zone/Steppe,
Iran/Turan, and South Asia (Fig. 1), a pattern we
replicate in ADMIXTURE unsupervised cluster-
ing (36). To test if groups of ancient individuals
were heterogeneous in their ancestry, we used
f
4
-statistics to measure whether different parti-
tions of these groups into two subgroups differed
in their degree of allele sharing to a third group
(using a distantly related outgroup as a baseline).
We also used f
3
-statistics to test for admixture
(32). To model the ancestry of each group, we
Narasimhan et al., Science 365, eaat7487 (2019) 6 September 2019 2of15
1
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
2
Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
3
Radcliffe Institute for Advanced Study, Harvard
University, Cambridge, MA 02138, USA.
4
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
5
Center for Computational Biology, University of California,
Berkeley, CA 94720, USA.
6
Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
7
Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School,
Boston, MA 02115, USA.
8
Department of Anthropology, Harvard University, Cambridge, MA 02138, USA.
9
ISMEO - International Association of Mediterranean and Oriental Studies, Italian
Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.
10
Department of Environmental Biology, Sapienza University, Rome 00185, Italy.
11
Department of Cultural Heritage:
Archaeology and History of Art, Cinema and Music, University of Padua, Padua 35139, Italy.
12
School of Natural and Built Environment, Queen’s University Belfast, Belfast BT7 1NN, Northern
Ireland, UK.
13
Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia.
14
Center of Physical Anthropology,
Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.
15
A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.
16
Al-Farabi Kazakh
National University, Almaty 050040, Kazakhstan.
17
University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA.
18
Department of Electrical Engineering and
Computer Science, University of California, Berkeley, CA 94720, USA.
19
Earth Institute, University College Dublin, Dublin 4, Ireland.
20
Soprintendenza Archeologia, Belle Arti e Paesaggio per la
Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna, Cagliari 09124, Italy.
21
School of Archaeology, University College Dublin, Dublin 4, Ireland.
22
Department of Evolutionary
Anthropology, University of Vienna, 1090 Vienna, Austria.
23
Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.
24
CIAS, Department of Life
Sciences, University of Coimbra, Coimbra 3000-456, Portugal.
25
Catalan Institute of Human Paleoecology and Social Evolution (IPHES), Tarragona 43007, Spain.
26
Max Planck Institute for
Evolutionary Anthropology, Leipzig 04103, Germany.
27
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
28
Department of Anthropology,
Pennsylvania State University, University Park, PA 16802, USA.
29
Institute for Anthropological Research, Zagreb 10000, Croatia.
30
CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500
007, India.
31
Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India.
32
Department of Anthropology, Emory University, Atlanta, GA 30322, USA.
33
Tyumen Scientific Centre SB RAS,
Institute of the Problems of Northern Development, Tyumen 625003, Russia.
34
CNRS-EXT500, Directeur de la Delegation Archaologique Francaise en Afghanistan (DAFA), Embassy of France in
Kabul, Afghanistan.
35
Aktobe Regional Historical Museum, Aktobe 030006, Kazakhstan.
36
Archaeology of Asia Department, ISMEO - International Association of Mediterranean and Oriental
Studies, Rome RM00186, Italy.
37
Kyrgyz National University, 720033 Bishkek, Kyrgyzstan.
38
Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences,
Novosibirsk 630090, Russia.
39
Department of Political History, National and State-Confessional Relations, Altai State University, Barnaul 656049, Russia.
40
Institute of Archaeology, Czech
Academy of Sciences, Prague 118 01, Czech Republic.
41
Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
42
Oxford Radiocarbon
Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK.
43
Institute of History and Archaeology, Ural Branch RAS, Yekaterinburg
620990, Russia.
44
South Ural State University, Chelyabinsk 454080, Russia.
45
Department of Archaeology, Kemerovo State University, Kemerovo 650043, Russia.
46
Institute of Archaeology,
University College London, London WC1H 0PY, UK.
47
School of Cultural Heritage, Northwest University, Shanxi, 710069, China.
48
Department of Archaeology, Ethnography and Museology, Altai
State University, Barnaul 656049, Russia.
49
Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
50
Samara State University of Social Sciences and Education,
Samara 443099, Russia.
51
West Kazakhstan Regional Center for History and Archaeology, Uralsk 090000, Kazakhstan.
52
Scientific and Educational Center of Study on the Problem of Nature and
Man, Chelyabinsk State University, Chelyabinsk 454021, Russia.
53
Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy.
54
Institute for Archaeological Research, Uzbekistan
Academy of Sciences, Samarkand 140151, Uzbekistan.
55
Center for Research, Restoration and Protection of Historical and Cultural Heritage of Aktobe Region, Aktobe 030007, Kazakhstan.
56
Department of Anthropology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada.
57
Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
58
MiBAC –Ministero
per i Beni e le Attività Culturali - Soprintendenza Archeologia, belle arti e paesaggio del Friuli Venezia Giulia, 34135 Trieste, Italy.
59
Afrosiab Museum, Samarkand 140151, Uzbekistan.
60
Department of
Biological, Geological and Environmental Sciences, Alma Mater Studiorum –University of Bologna, Bologna 40126, Italy.
61
Human Origins Program, National Museum of Natural History, Smithsonian
Institution, Washington, DC 20013, USA.
62
National Research Tomsk State University, Tomsk 634050, Russia.
63
F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022,
Russia.
64
Central State Museum Republic of Kazakhstan, Samal-1 Microdistrict, Almaty 050010, Kazakhstan.
65
CHRONO Centre for Climate, the Environment, and Chronology, Queen's University
of Belfast, Belfast BT7 1NN, Northern Ireland, UK.
66
Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan.
67
Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria.
68
Department of Archaeology, Ethnography and Museology, The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul 656049,
Russia.
69
Institute of Steppe, Ural Branch RAS, Orenburg 460000, Russia.
70
Center for Egyptological Studies RAS, Moscow 119991, Russia.
71
Department of Anthropology, National Museum,
Prague 115 79, Czech Republic.
72
Archaeological Expertise LLP, Almaty 050060, Kazakhstan.
73
Department of Archaeology, Hazara University, Mansehra 21300, Pakistan.
74
N.F. Katanov
Khakassia State University, Abakan 655017, Russia.
75
Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
76
Institute of Evolutionary Biology,
CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain.
77
Anthropology Department, Hartwick College, Oneonta, NY 13820, USA.
78
Department of Anthropology, University of California, Santa
Barbara, CA 93106, USA.
79
Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USA.
80
Spatial Analysis, Interpretation, and Exploration Laboratory, Washington
University in St. Louis, St. Louis, MO 63112, USA.
81
Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA.
*These authors contributed equally to this work.
†Corresponding author. Email: vagheesh@mail.harvard.edu (V.M.N.); nickp@broadinstitute.org (N.P.); frachetti@wustl.edu (M.Fr.); ron.pinhasi@univie.ac.at (R.Pi.); reich@genetics.med.harvard.edu (D.Re.)
‡These authors contributed equally to this work. §Present address: Department of Anthropology, University of California, Santa Cruz, CA 95064, USA. ||Present address: Institut Català de Paleoecologia Humana i
Evolució Social (IPHES), 43007 Tarragona, Spain. ¶Present address: Universitat Rovira i Virgili (URV), Àrea de Prehistòria, 43002 Tarragona, Spain. #Present address: Max Planck-Harvard Research Center for the
Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA. **Present address: Department of Human Evolutionary Biology, Harvard University, Cambridge MA, 02138, USA. ††Present address:
Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
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used qpAdm, which evaluates whether a tested
group is consistent with deriving from a pre-
specified number of source populations (relative
to a set of outgroups) and, if so, estimates pro-
portions of ancestry (7). We first used qpAdm to
attempt to model groups from the Copper Age
and afterward as a mixture of seven “distal”
sources, using as surrogates for them six pre–
Copper Age populations and one modern Anda-
manese hunter-gatherer population (Box 1). (The
model assumes that each true ancestral popula-
tion is a clade with the population we use as a
surrogate for it in the sense of descending from
the same ancestral population, possibly deeply in
time.) In this paper, we use the term “farmers”to
refer to people who cultivated crops, herded
animals, or both; this definition covers not only
large settled communities but also smaller and
probably less sedentary communities like the early
herders of the Zagros Mountains of western Iran
fromthesiteofGanjDareh.Thelatterkeptdo-
mesticated animals but did not cultivate crops
and are a key reference population for this study,
as they had a distinctive ancestry profile that
spread widely after the Neolithic (9,28,37).
We also identified proximal models for each
group as mixtures of temporally preceding
groups. We implemented an algorithm called
DATES for estimating the age of the popula-
tion mixtures (13), which is related to previ-
ous methods that translate the average size of
ancestry blocks into time since mixture by
leveraging precise measurements of meiotic
recombination rate in humans (32,38,39).
DATES has the specific advantage that it is
optimized relative to previous methods in being
able to work with ancient DNA as well as with
single genomes (13). In Box 2, we summarize
the findings of these analyses (we use the same
headings in Box 2 and the main text to allow cross-
referencing), whereas our online data visualizer (1)
allows an interactive exploration of the data.
Iran and Turan
A west-to-east cline of decreasing
Anatolian farmer–related ancestry
We studied the genetic transformations accom-
panying the spread of agriculture eastward from
Iran beginning in the 7th millennium BCE (3,40,41).
We replicate previous findings that 9th to 8th
millenniumBCEherdersfromtheZagrosMoun-
tains of western Iran harbored a distinctive West
Eurasian–related ancestry profile (9,31), whereas
later groups across a broad region were admixed
between this ancestry and that related to early
Anatolian farmers. Our analysis reveals a west-
to-east cline of decreasing Anatolian farmer–
related admixture in the Copper and Bronze
Ages ranging from ~70% in Anatolia to ~31% in
eastern Iran to ~7% in far eastern Turan (Fig. 1,
Narasimhan et al., Science 365, eaat7487 (2019) 6 September 2019 3of15
Fig. 1. Overview of ancient DNA data. (A) Distribution of sites and
associated archeological or radiocarbon dates along with the number of
individuals meeting our analysis thresholds from each site. (B) Locations of
ancient individuals for whom we generated ancient DNA that passed our
analysis thresholds along with the locations of individuals from 140 groups
from present-day South Asia that we analyzed as forming the Modern Indian
Cline. Shapes distinguish the individuals from different sites. Data from
106 South Asian groups that do not fit along the Modern Indian Cline as well
as AHG are not shown. (C) PCA analysis of ancient and modern individuals
projected onto a basis formed by 1340 present-day Eurasians reflects
clustering of individuals that mirrors their geographical relationships. An
interactive version of this figure is presented in our online data visualizer (1).
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fig. S10, and tables S8 to S16) (13). This suggests
that the archaeologically documented spread
of a shared package of plants and animal domes-
ticates from diverse locations across this region
was accompanied by bidirectional spread of
people and mixture with the local groups they
encountered (3,40,42,43). We call this the
Southwest Asian Cline. In the far east of the
Southwest Asian Cline (eastern Iran and Turan)
in individuals from the third millennium BCE,
we detect not only the smallest proportions of
Anatolian farmer–related admixture but also
admixture related to West Siberian Hunter
Gatherers (WSHG), plausibly reflecting admix-
ture from unsampled hunter-gatherer groups
that inhabited this region before the spread of
Iranian farmer–related ancestry into it. This shows
that North Eurasian–related ancestry affected
Turan well before the spread of descendants of
Yamnaya Steppe pastoralists into the region. We
can exclude the possibility that the Yamnaya were
the source of this North Eurasian–related ances-
try, as they had more Eastern European Hunter
Gatherer (EEHG)–related than WSHG-related an-
cestry, and they also carried high frequencies of
mitochondrial DNA haplogroup type U5a as well
as Y chromosome haplogroup types R1b or R1a
that are absent in ancient DNA sampled from Iran
and Turan in this period (tables S93 and S94) (13).
People of the BMAC were not a major
source of ancestry for South Asians
From Bronze Age Iran and Turan, we obtained
genome-wide data for 84 ancient individuals
(3000 to 1400 BCE) who lived in four urban sites
oftheBMACanditsimmediatesuccessors.The
great majority of these individuals fall in a cluster
genetically similar to the preceding groups in
Turan, which is consistent with the hypothesis
that the BMAC coalesced from preceding pre-
urban populations (5). We infer three primary
genetic sources: early Iranian farmer–related
ancestry (~60 to 65%) and smaller proportions of
Anatolian farmer–related ancestry (~20 to 25%)
and WSHG-related ancestry (~10%). Unlike pre-
ceding Copper Age individuals from Turan, people
of the BMAC cluster also harbored an additional
~2 to 5% ancestry related (deeply in time) to
Andamanese hunter-gatherers (AHG). This evi-
dence of south-to-north gene flow from South
Asia is consistent with the archaeological evi-
dence of cultural contacts between the IVC and
the BMAC and the existence of an IVC trading
colony in northern Afghanistan (al though we
lack ancient DNA from that site) (44)andstands
in contrast to our qpAdm analyses showing
that a reciprocal north-to-south spread is un-
detectable. Specifically, our analyses reject the
BMAC and the people who lived before them in
Turan as plausible major sources of ancestry for
diverse ancient and modern South Asians by
showing that their ratio of Anatolian farmer–
related to Iranian farmer–related ancestry is
too high for them to be a plausible source for
South Asians [P< 0.0001, c
2
test; (13)] (figs. S50
and S51). A previous study (30)fitamodelin
which a population from Copper Age Turan was
used as a source of the Iranian farmer–related
ancestry in present-day South Asians, thus raising
the possibility that the people of the BMAC whom
the authors correctly hypothesized were primarily
derived from the groups that preceded them in
Turan were a major source population for South
Asians. However, that study only had access to
two samples from this period compared with the
36 we analyze inthis study, and it lacked ancient
DNA from individuals from the BMAC period
or from any ancient South Asians. With addi-
tional samples, we have the resolution to show
that none of the large number of Bronze and
Copper Age populations from Turan for which we
have ancient DNA fit as a source for the Iranian
farmer–related ancestry in South Asia.
Steppe pastoralist–derived ancestry
arrived in Turan by 2100 BCE
Our large sample sizes from Central Asia, includ-
ing individuals from BMAC sites, are a particular
strength of this study, allowi ng us to detect outlier
individuals whose ancestry differs from that of
those living at the same time and place and re-
vealing cultural contacts that would be otherwise
difficult to appreciate (Fig. 2). Around 2300 BCE,
we observe three outliers in BMAC-associated
sites carrying WSHG-related ancestry and we
report data from the third millennium BCE from
three sites in Kazakhstan and one in Kyrgyzstan
that fit as sources for them [related ancestry has
been found in ~3500-BCE Botai culture indi-
viduals (30)]. Yamnaya-derived ancestry arrived
by 2100 BCE, because from 2100 to 1700 BCE
we observe outliers from three BMAC-associated
sites carrying ancestry ultimately derived from
Western_Steppe_EMBA pastoralists, in the dis-
tinctive admixed form typically carried by many
Middle to Late Bronze Age Steppe groups (with
roughly two-thirds of the ancestry being of
Western_Steppe_EMBA origin, and the rest con-
sistent with deriving from European farmers).
Thus, our data document a southward movement
of ancestry ultimately descended from Yamnaya
Steppe pastoralists who spread into Central Asia
by the turn of the second millennium BCE.
An ancestry profile widespread during
the Indus Valley Civilization
We document 11 outliers—three with radiocar-
bon dates between 2500 and 2000 BCE from the
BMAC site of Gonur and eight with radiocarbon
dates or archaeological-context dates between
3300 and 2000 BCE from the eastern Iranian site
of Shahr-i-Sokhta—that harbored elevated propor-
tions of AHG-related ancestry (range: ~11 to 50%)
and the remainder from a distinctive mixture
of Iranian farmer–and WSHG-related ancestry
(~50 to 89%). These outliers had no detectable
Anatolian farmer–related ancestry, in contrast
with the main BMAC (~20 to 25% Anatolian-
related) and Shahr-i-Sokhta (~16 to 21%) clusters,
allowing us to reject both the main BMAC and
Shahr-i-Sokhta clusters as sources for the outliers
[P<10
−7
,c
2
test; (13)] (table S83). Without an-
cient DNA from individuals buried in IVC cultural
contexts, we cannot make a definitive statement
that the genetic gradie nt represented by these
11 outlier individuals, which we call the Indus
Periphery Cline, was also an ancestry profile com-
mon in the IVC. Nevertheless, our result provides
six circumstantial lines of evidence for this hy-
pothesis. (i) These individuals had no detectable
Anatolian farmer–related ancestry, suggesting
they descend from groups farther east along the
Anatolia-to-Iran cline of decreasing Anatolian
farmer–related ancestry than any individuals we
sampled from this period. (ii) All 11 outliers had
elevated proportions of AHG-related ancestry, and
two carried Y chromosome haplogroup H1a1d2,
which today is primarily found in southern India.
(iii) At both Gonur and Shahr-i-Sokhta there is
archaeological evidence of exchange with the
IVC (45,46), and all the outlier individuals we
dated directly fall within the time frame of the
mature IVC. (iv) Several outliers at Shahr-i-Sokhta
were buried with artifacts stylistically linked
to Baluchistan in South Asia, whereas burials
Narasimhan et al., Science 365, eaat7487 (2019) 6 September 2019 4of15
Box 1. Seven source populations used for distal ancestry modeling.
Anatolia_N, Anatolian farmer–related: Represented by seventh millennium BCEwestern Anatolian
farmers (18).
Ganj_Dareh_N, Iranian early farmer–related: Represented by eighth millennium BCE early goat
herders from the Zagros Mountains of Iran (9,24).
WEHG, Western European hunter-gatherer–related: Represented by ninth millennium BCE
Western Europeans (7,18,27,91). (WEHG and EEHG discussed below were denoted WHG and
EHG in previous studies, but as we coanalyze them with hunter-gatherers from Asia, we modify
the names to specify a European origin.)
EEHG, Eastern European hunter-gatherer–related: Represented by sixth millennium BCE
hunter-gatherers from Eastern Europe (18,27).
WSHG, West Siberian hunter-gatherer–related: A previously undescribed deep source of Eurasian
ancestry represented in this study by three individuals from the Forest Zone of Central Russia dated
to the sixth millennium BCE.
ESHG, East Siberian hunter-gatherer–related: Represented by sixth millennium BCE hunter-
gatherers from the Lake Baikal region with ancestry deeply related to East Asians (26).
AHG, Andamanese hunter-gatherer–related: Represented by present-day indigenous Andaman
Islanders (53) who we hypothesize are related to unsampled indigenous South Asians (AASI,
Ancient Ancestral South Indians).
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associated with the other ancestries did not
have these linkages (13). (v) In our modeling, the
11 outliers fit as a primary source of ancestry for
86 ancient individuals from post-IVC cultures
living near the headwaters of the Indus River
~1200 to 800 BCE as well as diverse present-day
South Asians, whereas no other ancient genetic
clusters from Turan fit as sources for all these
groups (13) (fig. S50). (vi) The estimated date of
admixture between Iranian farmer–related and
AHG-related ancestry in the outliers is several
millennia before the time they lived (71 ± 15
generations, corresponding to a 95% confidence
interval of ~5400 to 3700 BCE assuming 28 years
per generation) (13,47). Thus, AHG-andIranian
farmer–related groups were in contact well before
the time of the mature IVC at ~2600 to 1900 BCE,
as might be expected if the ancestry gradient was
a major feature of a group that was living in the
Indus Valley during the IVC.
The Steppe and Forest Zone
Ancestry clines in Eurasia established
after the advent of farming
The late hunter-gatherer individuals fromnorth-
ern Eurasia lie along a west-to-east hunter-gatherer
gradient of increasing relatedness to East Asians
Narasimhan et al., Science 365, eaat7487 (2019) 6 September 2019 5of15
Box 2. Summary of key findings.
Iran and Turan
1. A west-to-east cline of decreasing Anatolian farmer–related ancestry.There was a west-to-east gradient of ancestry across Eurasia in the Copper
and Bronze Ages—the Southwest Asian Cline—with more Anatolian farmer–related ancestry in the west and more WSHG-orAASI-related ancestry in the east,
superimposed on primary ancestry related to early Iranian farmers. The establishment of this gradient correlates in time to the spread of plant-based
agriculture across this region, raising the possibility that people of Anatolian ancestryspread this technology east just as they helped spread it west into Europe.
2. People of the BMAC were not a major source of ancestry for South Asians. The primary BMAC population largely derived from preceding
local Copper Age peoples who were, in turn, closely related to people from the Iranian plateau and had little of the Steppe ancestry that is
ubiquitous in South Asia today.
3. Steppe pastoralist–derived ancestry arrived in Turan by 2100 BCE. We find no evidence of Steppe pastoralist–derived ancestry in groups at
BMAC sites before 2100 BCE, but multiple outlier individuals buried at these sites show that by ~2100 to 1700 BCE, BMAC communities were
regularly interacting with peoples carrying such ancestry.
4. An ancestry profile widespread during the Indus Valley Civilization. We document a distinctive ancestry profile—~45 to 82% Iranian
farmer–related and ~11 to 50% AASI (with negligible Anatolian farmer–related admixture)—present at two sites in cultural contact with the Indus
Valley Culture (IVC). Combined with our detection of this same ancestry profile (in mixed form) about a millennium later in the post-IVC Swat Valley,
this documents an Indus Periphery Cline during the flourishing of the IVC. Ancestors of this group formed by admixture ~5400 to 3700 BCE.
The Steppe and Forest Zone
1. Ancestry clines in North Eurasia established after the advent of farming. Before the spread of farmers and herders, northern Eurasia was
characterized by a west-to-east gradient of very divergent hunter-gatherer populations with increasing proportions of relatedness to present-day
East Asians: from Western European hunter-gatherers (WEHG), to Eastern European hunter-gatherers (EEHG), to West Siberian hunter-gatherers
(WSHG), to East Siberian hunter-gatherers (ESHG). Mixture of people along this ancestry gradient and its counterpart to the south formed five later
clines after the advent of farming, of which the three northern ones are the European Cline, the Caucasus Cline, and the Central Asian Cline.
2. A distinctive ancestry profile stretching from Eastern Europe to Kazakhstan in the Bronze Age. We add >100 samples from the previously
described Western_Steppe_MLBA genetic cluster, including individuals associated with the Corded Ware, Srubnaya, Petrovka, and Sintashta
archaeological complexes, and characterized by a mixture of about two-thirds ancestry related to Yamnaya Steppe pastoralists (from the Caucasus
Cline) and European farmers (from the European Cline), suggesting that this population formed at the geographic interface of these two groups in
Eastern Europe. Our analysis suggests that in the Central Steppe and Minusinsk Basin in the Middle to Late Bronze Age, Western_Steppe_MLBA
ancestry mixed with ~9% ancestry from previously established people from the region carrying WSHG-related ancestry to form a distinctive
Central_Steppe_MLBA cluster that was the primary conduit for spreading Yamnaya Steppe pastoralist–derived ancestry to South Asia.
3. Bidirectional mobility along the Inner Asian Mountain Corridor. Beginning in the third millennium BCE and intensifying in the second
millennium BCE,we observe multiple individuals in the Central Steppe who lived along the Inner Asian Mountain Corridor and who harbored admixture
from Turan, documenting northward movement into the Steppe in this period. By the end of the second millennium BCE, these people were joined by
numerous outlier individuals with East Asian–related admixture that became ubiquitous in the region by the Iron Age (29,52). This East Asian–related
admixture is also seen in later groups with known cultural impacts on South Asia, including Huns, Kushans, and Sakas, and is hardly present in the two
primary ancestral populations of South Asia, suggesting that the Steppe ancestry widespread in South Asia derived from pre–Iron Age Central Asians.
South Asia
1. Three ancestry clines that succeeded each other in time in South Asia. We identify a distinctive trio of source populations that fits
geographically and temporally diverse South Asians since the Bronze Age: a mixture of AASI,anIndus Periphery Cline group with predominantly
Iranian farmer–related ancestry, and Central_Steppe_MLBA. Two-way clines that are well modeled as mixtures of pairs of populations that are
themselves formed of these three sources succeeded each other in time: before 2000 BCE, the Indus Periphery Cline had no detectable Steppe
ancestry, beginning after 2000 BCE the Steppe Cline, and finally the Modern Indian Cline.
2. The ASI and ANI arose as Indus Periphery Cline people mixed with groups to the north and east. An ancestry gradient of which the Indus
Periphery Cline individuals were a part played a pivotal role in the formation of both the two proximal sources of ancestry in South Asia: a minimum
of ~55% Indus Periphery Cline ancestry for the ASI and ~70% for the ANI. Today there are groups in South Asia with very similar ancestry to the
statistically reconstructed ASI, suggesting that they have essentially direct descendants today. Much of the formation of both the ASI and ANI
occurred in the second millennium BCE. Thus, the events that formed both the ASI and ANI overlapped the time of the decline of the IVC.
3. Steppe ancestry in modern South Asians is primarily from males and disproportionately high in Brahmin and Bhumihar groups. Most of
the Steppe ancestry in South Asia derives from males, pointing to asymmetric social interaction between descendants of Steppe pastoralists and
peoples of the Indus Periphery Cline. Groups that view themselves as being of traditionally priestly status, including Brahmins who are traditional
custodians of liturgical texts in the early Indo-European language Sanskrit, tend (with exceptions) to have more Steppe ancestry than expected on
the basis of ANI-ASI mixture, providing an independent line of evidence for a Steppe origin for South Asia’s Indo-European languages.
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Narasimhan et al., Science 365, eaat7487 (2019) 6 September 2019 6of15
Fig. 2. Outlier analysis reveals ancient contacts between sites. We plot
the average of principal component 1 (xaxis) and principal component
2(yaxis) for the West Eurasian and All Eurasian PCA plots, as we found that
this aids visual separation of the ancestry profiles. (A) In individuals of the
BMAC and successor sites, we observe a main cluster as well as numerous
outliers: outliers >2000 BCE with admixture related to WSHG, outliers
>2000 BCE on the Indus Periphery Cline (with an ancestry similar to the
outliers at Shahr-i-Sokhta), and outliers after 2000 BCE that reveal how
Central_Steppe_MLBA ancestry had arrived. (B) At Shahr-i-Sokhta in
eastern Iran, there are two primary groupings: one with ~20% Anatolian
farmer–related ancestry and no detectable AHG-related ancestry, and the
other with ~0% Anatolian farmer–related ancestry and substantial AHG-
related ancestry (Indus Periphery Cline). (C) In the Middle to Late Bronze
Age Steppe, we observe, in addition to the Western_Steppe_MLBA and
Central_Steppe_MLBA clusters (indistinguishable in this projection), out-
liers admixed with other ancestries. The BMAC-related admixture in
Kazakhstan documents northward gene flow onto the Steppe and
confirms the Inner Asian Mountain Corridor as a conduit for movement of
people. (D) In the Late Bronze Age and Iron Age of northernmost South
Asia, we observe a main cluster consistent with admixture between
peoples of the Indus Periphery Cline and Central_Steppe_MLBA and
variable Steppe pastoralist–related admixture.
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(Fig. 3). In the Neolithic and Copper Ages,
hunter-gatherers at different points along this
cline mixed with people with ancestry at differ-
ent points along a southern cline to form five
later clines, two of which were in the south (the
Southwest Asian Cline and the Indus Periphery
Cline described in the previous section) and three
of which were in northern Eurasia (Fig. 3). Fur -
thest to the west in the Steppe and Forest Zone
there was the European Cline, established by the
spread of farmers from Anatolia after ~7000 BCE
and mixture with Western European hunter-
gatherers (18). In far eastern Europe at latitudes
spanning the Black and Caspian Seas there was the
Caucasus Cline, consisting of a mixture of Eastern
European hunter-gatherers and Iranian farmer–
related ancestry with additional Anatolian farmer–
relatedancestryinsomegroups(48). East of the
Urals, we detect a Central Asian Cline, with WSHG
individuals at one extreme and Copper Age and Early
Bronze Age individuals from Turan at the other.
A distinctive ancestry profile stretching
from Eastern Europe to Kazakhstan in
the Bronze Age
Beginning around 3000 BCE, the ancestry profiles
of many groups in Eurasia were transformed by the
spread of Yamnaya Steppe pastoralist–related ances-
try (Western_Steppe_EMBA) from its source in the
Caucasus Cline (9,48) to a vast region stretching
from Hungary in the west to the Altai mountains
in the east (7,8) (Fig. 3). Over the next two millen-
nia, this ancestry spread further while admixing
with local groups, eventually reaching the Atlantic
shores of Europe in the west and South Asia in
the southeast. The source of the Western_Steppe_
EMBA ancestry that eventually reached Central
and South Asia was not the initial eastward ex-
pansion but instead a secondary expansion that
involved a group that had ~67% Western_Steppe_
EMBA ancestry and ~33% ancestry from a point
on the European Cline (8) (Fig. 3). We replicate
previousfindingsthatthisgroupincludedpeople
of the Corded Ware, Srubnaya, Petrovka, and
Sintashta archaeological complexes spreading
over a vast region from the border of Ea stern
Europe to northwestern Kazakhstan (8,18,30),
and our dataset adds more than one hundred
individuals from this Western_Steppe_MLBA
cluster. We also detect an additional cluster,
Central_Steppe_MLBA, which is differentiated
from Western_Steppe_MLBA (P=7×10
−6
by
qpAdm) because it carries ~9% additional an-
cestry derived from Bronze Age pastoralists of
the Central Steppe of primarily WSHG-related
ancestry (Central_Steppe_EMBA). Thus, indi-
viduals with Western_Steppe_MLBA ancestry
admixed with local populations as they inte-
grated eastward and southward.
Bidirectional mobility along the Inner
Asian Mountain Corridor
As in Iran/Turan, the outlier individuals provide
crucial information about human interaction.
Our analysis of 50 individuals from the Sintashta
culture cemetery of Kamennyi Ambar 5 reveals
multiple groups of outliers that we directly radio-
carbon dated to be contemporaries of the main
cluster but that were also genetically distinctive,
indicating that this was a cosmopolitan site (Fig. 2).
One set of outliers had elevated proportions of
Central_Steppe_EMBA (largely WSHG-related)
ancestry, another had elevated Western_Steppe_
EMBA (Yamnaya-related), and a third had ele-
vated EEHG-related ancestry.
In the Central Steppe (present-day Kazakhstan),
an individual from one site dated to between
2800 and 2500 BCE, and individuals from three
sites dated to between ~1600 and 1500 BCE, show
significant admixture from Iranian farmer–related
populations that is well-fitted by the main BMAC
cluster, demonstrating northward gene flow from
Turan into the Steppe at approximately the same
time as the southward movement of Central_
Steppe_MLBA-related ancestry through Turan to
South Asia. Thus, the archaeologically documented
spread of material culture and technology both
north andsouth along the Inner Asian Mountain
Corridor (3,49,50,51), which began as early as the
middle of the third millennium BCE, was associated
with substantial movements of people (Fig. 2).
We also observe individuals from Steppe
sites (Krasnoyarsk) dated to between ~1700 and
1500 BCE that derive up to ~25% ancestry from
a source related to East Asians (well-modeled
as ESHG), with the remainder best modeled as
Western_Steppe_MLBA. By the LateBronze Age,
ESHG-related admixture became ubiquitous, as
documented by our time transect from Kazakhstan
and ancient DNA data from the Iron Age and from
later periods in Turan and the Central Steppe, in-
cluding Scythians, Sarmatians, Kushans, and Huns
(29,52). Thus, these first millennium BCE to first
millennium CE archaeological cultures with docu-
mented cultural and political impacts on South
Asia cannot be important sources for the Steppe
pastoralist–related ancestry widespread in South
Asia today (because present-day South Asians
have too little East Asian–related ancestry to be
consistent with deriving from these groups), pro-
viding an example of how genetic data can rule out
scenarios that are plausible on the basis of the
archaeological and historical evidence alone (13)
(fig. S52). Instead, our analysis shows that the only
plausiblesourcefortheSteppeancestryisSteppe
MiddletoLateBronzeAgegroups,whonotonlyfit
as a source for South Asia but who we also docu-
ment as having spread into Turan and mixed with
BMAC-related individuals at sites in Kazakhstan in
this period. Taken together, these results identify a
narrow time window (first half of the second mil-
lennium BCE) when the Steppe ancestry that is
widespread today in South Asia must have arrived.
The genomic formation of human
populations in South Asia
Three ancestry clines that succeeded
each other in time in South Asia
Previous work has shown that South Asians har-
bor ancestry from peoples related to ancient
groups in northern Eurasia and Iran, East Asians,
and Australasians (9). Here we document the
process through which these deep sources of
ancestry mixed to form later groups.
We begin with the pre-2000-BCE Indus Periphery
Cline, describedinanearliersectionanddetected
in 11 outliers from two sites in cultural contact
with the IVC (Fig. 4).Wecanjointlymodelall
individuals in this cline as a mixture of two source
populations: One end of the cline is consistent
with being entirely AHG-related, and the other
is consistent with being ~90% Iranian farmer–
related and ~10% WSHG-related (Fig. 4) (13). Peo-
ple fitting on the Indus Periphery Cline constitute
the majority of the ancestors of present-day South
Asians. Through formal modeling, we demonstrate
that it is this contribution of Indus Periphery Cline
people to later South Asians, rather than westward
gene flow bringing an ancestry unique to South
Asia onto the Iranian plateau, that explains the
high degree of shared ancestry between present-
day South Asians and early Holocene Iranians
(9,13).
We next characterized the post-2000-BCE
Steppe Cline, represented in our analysis by 117
individuals dating to between 1400 BCE and
1700 CE from the Swat and Chitral districts of
northernmost South Asia (Figs. 2 and 4).We
found that we could jointly model all individuals
on the Steppe Cline as a mixture of two sources,
albeit different from the two sources in the earlier
cline. One end is consistent with a point along the
Indus Periphery Cline. The other end is consistent
with a mixture of ~41% Central_Steppe_MLBA an-
cestry and ~59% from a subgroup of the Indus
Periphery Cline with relatively high Iranian
farmer–related ancestry (13) (fig. S50).
To understand the formation of the Modern
Indian Cline, we searched for triples of popula-
tions that could fit as sources for diverse present-
daySouthAsiangroupsaswellaspeoplesofthe
Steppe Cline. All fitting models include as sources
Central_Steppe_MLBA (or a group with a similar
ancestry profile), a group of Indus Periphery Cline
individuals, and either AHG or a subgroup of
Indus Periphery Cline individuals with relatively
high AHG-related ancestry (13)(fig.S51).Co-
analyzing 140 diverse South Asian groups (10)
that fall on a gradient in PCA (13), we show that
while there are three deep sources, just as in the
case of the earlier two clines the great majority of
groups on the Modern Indian Cline can be jointly
modeled as a mixture of two populations that are
mixed from the earlier three. Although we do not
have ancient DNA data from either of the two
statistically reconstructed source populations for
the Modern Indian Cline, the ASI or the ANI,in
what follows, we coanalyze our ancient DNA data
in conjunction with modern data to characterize
the exact ancestry of the ASI and to provide
constraints on the ANI.
The ASI and ANI arose as Indus
Periphery Cline people mixed with
groups to the north and east
To gain insight into the formation of the ASI, we
extrapolated to the smallest possible proportion
of West Eurasian–related ancestry on the Modern
Indian Cline by setting the Central_Steppe_MLBA
ancestry proportion to zero in our model. We es-
timate a minimum of ~55% ancestry from people
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Fig. 3. Ancestry transformations in Holocene Eurasia. (A)Ancestry
clines before and after the advent of farming. We document a South Eurasian
Early Holocene Cline of increasing Iranian farmer–and West Siberian
hunter-gatherer–related ancestry moving west-to-east from Anatolia to Iran,
as well as a North Eurasian Early Holocene Cline of increasing relatedness
to East Asians moving west-to-east from Europe to Siberia. Mixtures of peoples
along these two clines following the spread of farming formed five later
gradients (shaded): moving west-to-east: the European Cline,theCaucasus
Cline from which the Yamnaya formed, the Central Asian Cline that
characterized much of Central Asia in the Copper and Bronze Ages, the
Southwest Asian Cline established by spreads of farmers in multiple directions
from several loci of domestication, and the Indus Periphery Cline.(B) Following
theappearanceoftheYamnayaSteppepastoralists,Western_Steppe_EMBA
(Yamnaya-like) ancestry then spread across this vast region.We use arrows
to show plausible directions of spread of increasingly