Genome sequence of a 45,000-year-old modern human from western Siberia

Abstract

We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 3 10 29 to 0.6 3 10 29 per site per year, a Y chromosomal mutation rate of 0.7 3 10 29 to 0.9 3 10 29 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 3 10 28 to 3.2 3 10 28 per site per year based on the age of the bone.

Full text

ARTICLE doi:10.1038/nature13810
Genome sequence of a 45,000-year-old
modern human from western Siberia
Qiaomei Fu
1,2
, Heng Li
3,4
, Priya Moorjani
3,5
, Flora Jay
6
, Sergey M. Slepchenko
7
, Aleksei A. Bondarev
8
, Philip L. F. Johnson
9
,
Ayinuer Aximu-Petri
2
, Kay Pru
¨fer
2
, Cesare de Filippo
2
, Matthias Meyer
2
, Nicolas Zwyns
10,11
, Domingo C. Salazar-Garcı
´a
10,12,13,14
,
Yaroslav V. Kuzmin
15
, Susan G. Keates
15
, Pavel A. Kosintsev
16
, Dmitry I. Razhev
7
, Michael P. Richards
10,17
, Nikolai V. Peristov
18
,
Michael Lachmann
2,19
, Katerina Douka
20
, Thomas F. G. Higham
20
, Montgomery Slatkin
6
, Jean-Jacques Hublin
10
,
David Reich
3,4,21
, Janet Kelso
2
, T. Bence Viola
2,10
& Svante Pa
¨a
¨bo
2
We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual
derives from a population that lived before—or simultaneously with—the separation of the populations in western and
eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic
segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating
that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We
estimate an autosomal mutation rate of 0.4 310
29
to 0.6 310
29
per site per year, a Y chromosomal mutation rate of
0.7 310
29
to 0.9 310
29
per site per year based on the additional substitutions that have occurred in present-day non-
Africans compared to this genome, and a mitochondrial mutation rate of 1.8 310
28
to 3.2 310
28
per site per year based
on the age of the bone.
In 2008, a relatively complete left human femoral diaphysis was discov-
ered on the banks of the river Irtysh (Fig. 1a, c, d), near the settlement
of Ust’-Ishim in western Siberia (Omsk Oblast, Russian Federation).
Although the exact locality is unclear, the femur was eroding out of al-
luvial deposits on the left bank of the river, north of Ust’-Ishim. Here,
Late Pleistocene and probably redeposited Middle Pleistocene fossils
are found in sand and gravel layers that are about 50,000–30,000 years
old (that is, from Marine Oxygen Isotope Stage 3).
Morphology, dating and diet
The proximal end of the bone shows a large gluteal buttress and gluteal
tuberosity, while the midshaft is dominated by a marked linea aspera,
resulting in a teardrop-shaped cross-section (Fig. 1e, f) (for details, see
Supplementary Information section 3). The morphology of the prox-
imal end of the shaft is similar to Upper Paleolithic modern humans and
distinct from Neanderthals (Supplementary Table 3.1, Supplementary
Fig. 3.2.),while the teardrop-shaped cross section of the midshaftis sim-
ilar to most Upper Paleolithic humans and early anatomically modern
humans
1
. Taken together, this suggests that the Ust’-Ishim femur derives
from a modern human.
Two samples of 890 mg and 450mg of the bone were removed on sep-
arate occasionsfor dating. Collagen preservationsatisfied all criteria for
dating
2
and after ultrafiltration we obtained ages of 41,400 61,300 years
before present (BP) (OxA-25516) and 41,400 61,400 BP (OxA-30190).
These two dates, when combined and corrected for fluctuations of atmo-
spheric
14
C through time, correspond to an age of about 45,000 calibrated
years BP (46,880–43,210 cal BP at 95.4% probability, Supplementary
Information section 1). The Ust’-Ishim individualis therefore the oldest
directly radiocarbon-datedmodern human outside Africa and the Mid-
dle East (Fig. 1b). Carbon and nitrogen isotope ratios indicate that the
diet of theUst’-Ishim individual (Supplementary Information section 4)
was based on terrestrial C
3
plants and animals that consumed them, but
also that an important part of his dietary protein may have come from
aquatic foods, probably freshwater fish, something that has been ob-
served in other early Upper Palaeolithic humans from Europe
3
.
DNA retrieval and sequencing
Nine samples of between41 and 130 mg of bone material wereremoved
from the distal part of the femur and used to construct DNA libraries
using a protocoldesigned to facilitatethe retrieval of short and damaged
DNA
4
. The percentage of DNA fragments in these libraries that could
be mapped to the human genome varied between 1.8% and 10.0% (Sup-
plementary Table 1.1).From the extract containing the highest propor-
tion of human DNA, eight further libraries were constructed. Each of
these libraries was treated with uracil-DNA glycosylase andendonucle-
ase VIII to remove deaminatedcytosine residues, and library molecules
with inserts shorter than approximately 35 base pairs(bp) were depleted
by preparative acrylamide gel electrophoresis before sequencing on the
Illumina HiSeq platform (Supplementary Information section 6). In total,
42-fold sequence coverage ofthe ,1.86 gigabases (Gb) of the autosomal
genome to which short fragments can be confidently mapped was gen-
erated. The coverage of the X and Y chromosomes was approximately
1
Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.
2
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary
Anthropology, D-04103 Leipzig, Germany.
3
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
4
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115,
USA.
5
Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
6
Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
7
Institute for Problems of the Development of the North, Siberian Branch of the Russian Academy of Sciences, Tyumen 625026, Russia.
8
Expert Criminalistics Center, Omsk Division of the Ministry of
Internal Affairs, Omsk 644007, Russia.
9
Department of Biology, Emory University, Atlanta, Georgia 30322, USA.
10
Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology,
D-04103 Leipzig, Germany.
11
Department of Anthropology, University of California, Davis, California 95616, USA.
12
Department of Archaeology, University of Cape Town, Cape Town 7701, South Africa.
13
Departament de Prehisto
`ria i Arqueologia, Universitat de Vale
`ncia, Valencia 46010, Spain.
14
Research Group on Plant Foods in Hominin Dietary Ecology, Max-Planck Institute for Evolutionary
Anthropology, D-04103 Leipzig, Germany.
15
Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
16
Institute of Plant and Animal Ecology,
Urals Branch of the Russian Academy of Sciences, Yekaterinburg 620144, Russia.
17
Laboratory of Archaeology, Department of Anthropology, University of British Columbia, Vancouver, British Columbia
V6T 1Z1, Canada.
18
Siberian Cultural Center, Omsk 644010, Russia.
19
Santa Fe Institute, Santa Fe, New Mexico 87501, USA.
20
Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology
and the History of Art, University of Oxford, Oxford OX1 3QY, UK.
21
Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
23 OCTOBER 2014 | VOL 514 | NATURE | 445
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©2014

half that of the autosomes (,22-fold), indicating that the bone comes
from a male. A likelihood method estimated present-day human mito-
chondrial DNA (mtDNA) contamination
5
to 0.50% (95% confidence
interval (CI) 0.26–0.94%), whereas a method that uses the frequency of
non-consensus bases in autosomal sequences estimated the contam-
ination to be less than 0.13% (Supplementary Information section 7).
Thus, less than 1% of the hominin DNA fragments sequenced are esti-
mated to be extraneous to the bone. After consensus genotype calling,
such low levels of contamination will tend to be eliminated.
Population relationships
About 7.7 positions per 10,000 are heterozygous in the Ust’-Ishim
genome, whereas between 9.6 and 10.5 positions are heterozygous in
present-day Africans and 5.5 and 7.7 in present-day non-Africans (Sup-
plementary Information section 12). Thus, with respect to genetic di-
versity, the population to which the Ust’-Ishim individual belonged was
more similar to present-day Eurasians than to present-day Africans,
which probably reflects the out-of-Africa bottleneck shared by non-
African populations. The Ust’-Ishim mtDNA sequence falls at the root
of a large group of related mtDNAs (the ‘R haplogroup’), which occurs
today across Eurasia (Supplementary Information section 8). The Y
chromosome sequence of the Ust’-Ishim individualis similarly inferred
to be ancestral to a group of related Y chromosomes (haplogroup K(xLT))
that occurs across Eurasia today
6
(Supplementary Information section 9).
As expected, the number of mutations inferred to have occurred on the
branch leading to the Ust’-Ishim mtDNA is lower than the numbers
inferred to have occurred on the branches leading to related present-
day mtDNAs (Supplementary Fig.8.1). Using this observation and nine
directly carbon-dated ancient modern human mtDNAs as calibration
points
5,7
in a relaxed molecular clock model, we estimate the age of the
Ust’-Ishim bone to be ,49,000 years BP (95% highest posterior den-
sity: 31,000–66,000 years BP), consistent with the radiocarbon date.
In a principal component analysis of the Ust’-Ishim autosomal ge-
nome along with genotyping data from 922 present-day individuals
from 53 populations
8
(Fig. 2a), the Ust’-Ishim individual clusters with
non-Africans rather than Africans. When only non-African popula-
tions are analysed (Fig. 2b), the Ust’-Ishim individual falls close to zero
on the two first principal component axes, suggesting that it does not share
much more ancestry with any particular group of present-day humans.
To determine how the Ust’-Ishim genome is related to the genomes of
present-day humans, we tested, using Dstatistics
8
, whether it shares more
derived alleles with one modern human than with another modern human
using pairs of human genomes from different parts of the world (Fig. 3).
Based on genotyping data for 87 African and 108 non-African indivi-
duals (Supplementary Information section 11), the Ust’-Ishim genome
shares more alleles with non-Africans than with sub-Saharan Africans
(jZj541–89), consistent with the principal component analysis, mtDNA
and Y chromosome results. Thus, the Ust’-Ishim individual represents
a population derived from, or related to, the population involved in the
dispersal of modern humans out of Africa. Among the non-Africans,
a
b
d
110° E
100° E
100° E
90° E
90° E
80° E
80° E
70° E
70° E60° E
60° N
60° N
50° N
50° N
1
234
5
30,00035,00040,00045,00050,000
Calibrated date (cal BP)
Siberia
Europe
China
Kostenki 14 (OxA-X-2395-15)
Kostenki 1 (OxA-15055)
Tianyuan Cave (BA-03222)
Pestera cu Oase 1 (GrA-22810)
Ust’-Ishim (OxA-25516 & 30190)
Cavallo B (Model age)
NGRIP 18O
–35
–40
–45
GI 12H5 H4
c
e
f
50 mm
Kent’s Cavern 4 (
Mo del ag e
)
Figure 1
|
Geographic location, morphology and dating. a, Map of Siberia
with major archaeological sites. Red triangles: Neanderthal fossils; white
circle within a red (Neanderthal) triangle: Denisovan fossils; blue square:
Initial Upper Palaeolithic sites; yellow asterisk: Ust’-Ishim. 1: Ust’-Ishim; 2:
Chagyrskaya Cave; 3: Okladnikov Cave; 4: Denisova Cave; 5: Kara-Bom.
b, Radiocarbon ages of early modernhuman fossils in northern Eurasia and the
NGRIP d
18
O palaeotemperature record. Specimens in light grey are indirectly
dated (OxCal v4.2.3(ref. 33); r:5 IntCal13 atmospheric curve
34
). H5: Heinrich 5
event, H4: Heinrich 4 event, GI 12: Greenland Interstadial 12. For a more
extensive comparison see Supplementary Information Fig. 2.1. c–f, The Ust’-
Ishim 1 femur. c, Lateral view. d, Posterior view. e, Cross-section at the 80
percent level. f, Cross-section at the midshaft. For other views see
Supplementary Fig. 3.1.
RESEARCH ARTICLE
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the Ust’-Ishim genome shares more derived alleles with present-day
people fromEast Asia than with present-dayEuropeans (jZj52.1–6.4).
However, when an ,8,000-year-old genome from western Europe (La
Bran
˜a)
9
or a 24,000-year-old genome from Siberia (Mal’ta 1)
10
were
analysed, there is no evidence that the Ust’-Ishim genome shares more
derived alleles with present-day East Asians than with theseprehistoric
individuals (jZj,2). This suggests that the population to which the Ust’-
Ishim individual belonged diverged from the ancestors of present-day
West Eurasian and East Eurasian populations before—or simultaneously
with—theirdivergence from eachother. The finding thatthe Ust’-Ishim
individual is equally closely related to present-day Asians and to 8,000-
to 24,000-year-old individualsfrom western Eurasia, but not to present-
day Europeans, is compatible with the hypothesis that present-day
Europeans derive some of their ancestry from a population that did
not participate in the initial dispersals of modern humans into Europe
and Asia
11
.
Mutation rate estimates
The high-quality Ust’-Ishim genome sequence, in combination withits
radiocarbon date, allows us to gauge the rate of mutations by estimating
the numbers of mutations that are ‘missing’ in theUst’-Ishim individual
relative to present-day humans. This results in a mutation rate estimate
of 0.44 310
29
to 0.63 310
29
per site per year using the high-coverage
genomes of 14 present-day humans. A challengefor inferring the muta-
tion rate in this way is that differences in error rates among genome
sequences can confound the inference (see discussion in ref. 12). We
therefore developed an alternative approach that leverages the Pairwise
Sequentially Markovian Coalescent (PSMC), a method which estimates
the distribution of coalescence times between the two chromosomes
across a diploid genome to estimate past changes in population size
13
,
and which is less influenced by differences in error rates. When the Ust’-
Ishim genomealong with 25 present-day human genomes are analysed
by PSMC, a recent reduction in population size similar to that seen for
11 present-day non-Africans is inferred for the Ust’-Ishim genome. How-
ever, the apparent age of this size reduction is more recent than in present-
day humans,consistent with theUst’-Ishim genomebeing older (Fig. 4).
We then compute the number of additional substitutions that are needed
to best fit the Ust’-Ishim PSMC curve to those of other non-African
genomes. Assuming that this corresponds to the number of mutations
that have accumulated over around 45,000 years, we estimate a muta-
tion rate o f 0.43 310
29
per site per year (95% CI 0.38 310
29
to 0.49 3
10
29
) that is consistent across all non-African genomes regardless of
their coverage (Supplementary Information section 14). This overall
rate, as well as the relative rates inferred for differentmutational classes
(transversions, non-CpG transitions, and CpG transitions), is similarto
the rate observed for de novo estimates from human pedigrees (,0.5 3
10
29
per site per year
14,15
) and to the direct estimate of branch shortening
(Supplementary Information section 10). As discussed elsewhere
14,16,17
,
these rates are slower than those estimated using calibrations based on
the fossil record and thus suggest older dates for the splits of modern
–0.050
–0.025
0.000
0.025
0.00 0.05 0.10
Ei
g
envector1 6.44 % of variance
Eigenvector2 3.94 % of variance
Europe
Central and South Asia
North Asia
East Asia
South East Asia
America
Oceania
Middle East
Ust_Ishim
North Africa
Sub-Saharan Africa
–0.10
–0.05
0.00
0.05
0.10
–0.025 0.000 0.025 0.050
Ei
g
envector1 5.26 % of variance
Eigenvector2 1.79 % of variance
a b
Figure 2
|
Principal Components(PC) analysis exploring the relationshipof
Ust’-Ishim to present-day humans. a, PC analysis using 922 present-day
individuals from 53 populations and the Ust’-Ishim individual. b, PC analysis
using Eurasian individuals and the Ust’-Ishim individual. The percentages of
the total variance explained by each eigenvector are given.
D(X Y; Ust’−Ishim Chimpanzee)
−0.10 0.00 0.10 0.20 0.30 0.40
Sardinian
Sardinian
Sardinian
Sardinian
Sardinian
French
French
French
French
French
La Braña
Han
Han
Karitiana
Karitiana
Karitiana
Onge
Onge
Onge
Onge
Dinka
Dinka
Dinka
Dinka
Dinka
Yoruba
Yoruba
Yoruba
Yoruba
Yoruba
Mbuti
Mbuti
Mbuti
Mbuti
Mbuti
Y
Mal’ta
La Braña
Han
Ka
r
itiana
Onge
Mal’ta
La Braña
Han
Ka
r
itiana
Onge
Mal’ta
Mal’ta
La Braña
Mal’ta
La Braña
Han
Mal’ta
La Braña
Han
Karitiana
Mal’ta
La Braña
Han
Onge
Mal’ta
La Braña
Han
Onge
Mal’ta
La Braña
Han
Karitiana
Karitiana
Karitiana
Onge
X
African Non-African
Other
non-African
Other
non-African
Other
non-African
Present-day
European
Figure 3
|
Statistics testing whether the Ust’-Ishim genome shares more
derived alleles with one or the other of two modern human genomes (X, Y).
We computed Dstatistics of the form D(X, Y, Ust’-Ishim, Chimpanzee) using
a subset of the genome-wide SNP array data from the Affymetrix Human
Origins array and restricting the analysis to transversions. Error bars
correspond to three standard errors. Red bars indicate that the Dstatistic is
significantly different from 0 (
|
Z
|
.2), such that the Ust’-Ishim genome
shares more derived alleles with the genome on the right (X) than the left (Y).
Ancient genomes are given in italics.
ARTICLE RESEARCH
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human and archaic populations. We caution, however, that rates may
have changed over time and may differ between human populations.
However, we expect this mutation rate estimate to apply at least to
non-African populations over the past 45,000 years.
We also estimated a phylogeny relating the non-recombining part of
the Ust’-Ishim Y chromosome to those of 23 present-day males. Using
this phylogeny, we measured the number of ‘missing’ mutations in the
Ust’-Ishim Y chromosomal lineage relative to the most closely related
present-day Y chromosome analysed. This results in an estimate of the
Y chromosome mutationrate of 0.76310
29
per site per year (95% CI
0.67 310
29
to 0.86 310
29
) (Supplementary Information section 9),
significantly higher than the autosomal mutation rate, consistent with
mutation rates in males being higher than in females
18–20
. Finally, using
the radiocarbon date of the Ust’-Ishim femur together with the mtDNAs
of 311 present-day humans,we estimated the mutation rate of the com-
plete mtDNA to be 2.53 310
28
substitutions per site per year (95%
highest posterior density: 1.76 310
28
to 3.23 310
28
) (Supplementary
Information section 8) for mtDNA, in agreement with a previous
study
5
.
Neanderthal admixture
The time of admixture between modernhumans and Neanderthals has
previously been estimated to 37,000–86,000 years BP based on the size
of the DNA segments contributed by Neanderthals to present-day non-
Africans
21
. Thus, the Ust’-Ishim individual could pre-datethe Neander-
thal admixture. From the extent of sharingof derived alleles betweenthe
Neanderthal and the Ust’-Ishim genomes we estimate the proportion
of Neanderthal admixture in the Ust’-Ishim individualto be 2.3 60.3%
(Supplementary Information section 16), similar to present-day east
Asians(1.7–2.1%) and present-day Europeans(1.6–1.8%).Thus, admix-
ture with Neanderthals had already occurred by 45,000 years ago. In
contrast, we fail to detect any contribution from Denisovans, although
such a contribution exists in present-day people not only in Oceania
22,23
,
but to a lesser extent also in mainland east Asia
12,24
(Supplementary
Information section 17).
The DNA segments contributed by Neanderthals to the Ust’-Ishim
individual are expected to be longer than such segments in present-
day people as the Ust’-Ishim individual lived closer in time to when the
admixture occurred, sothere was less time for the segments to be frag-
mented by recombination. To test if this is indeed the case, we identified
putative Neanderthal DNA segments in the Ust’-Ishim and present-
day genomes based on derived alleles shared with the Neanderthal ge-
nome at positions where Africans are fixed for ancestralalleles. Figure 5
shows that fragments of putative Neanderthal origin in the Ust’-Ishim
individual are substantially longer than those in present-day humans.
We use the covariance in such derived alleles of putative Neanderthal
origin across the Ust’-Ishim genome to infer that mean fragment sizes
in the Ust’-Ishimgenome are in the order of ,1.8–4.2 times longer than
in present-day genomes and that the Neanderthal gene flow occurred
232–430 generations before the Ust’-Ishim individual lived (Supplemen-
tary Information section 18; Fig. 6). Under the simplifying assumption
that the gene flow occurred as a singleevent, and assuming a generation
time of 29 years
16,25
, we estimate that the admixture between the ances-
tors of the Ust’-Ishim individual and Neanderthals occurred approxi-
mately 50,000 to 60,000 years BP, which is close to the time of the major
expansion of modern humans out of Africa and the Middle East. How-
ever, we also note that the presence of some longer fragments (Fig. 5) may
indicate that additional admixture occurred even later. Nevertheless,
these results suggest that the bulk of the Neanderthal contribution to
present-day people outside Africa does not go back to mixture between
Neanderthals and the anatomically modern humans who lived in the
Middle East at earlier times; for example, the modern humans whose
remains have been found at Skhul and Qafzeh
26,27
.
An Initial Upper Paleolithic individual?
A common model for the modern human colonization of Asia
23,28
assumes
that an early coastal migration gave rise to the present-day people of
Oceania, while a later more northern migration gave rise to Europeans
and mainland Asians. The fact that the 45,000-year-old individualfrom
Siberia is not more closely related to the Onge from the Andaman
A
ustralian_B2
A
ustralian_B1
Papuan_B
Papuan_A
Mixe_B
Karitiana_B
Karitiana_A
Dai_B
Dai_A
Han_B
Han_A
Sardinian_B
Sardinian_A
French_B
French_A
Ust’-Ishim
Figure 5
|
Regions of Neanderthal ancestry on chromosome 12 in the
Ust’-Ishim individual and fifteen present-day non-Africans. The analysis is
based on SNPs where African genomes carry the ancestral allele and the
Neanderthal genome carries the derived allele. Homozygous ancestral alleles
are black, heterozygous derived alleles yellow, and homozygous derived alleles
blue.
0
0.5
1
1.5
2
2.5
3
10–5 10–4 10–3 10–2
10 kya 100 kya 1 Mya 10 Mya
Population size (scaled in units of 4μNe × 103)
Time (scaled in units of 2μT)
San
Mbuti
Yoruba
Mandenda
Dinka
French
Sardinian
Han
Dai
Karitina
Papuan
Ust’-Ishim
Ust’-Ishim
corrected
Figure 4
|
Inferred population size changes over time. ‘Time’ on the xaxis
refers to the pairwise per-site sequence divergence. If we erroneously assume
that Ust’-Ishim lived today, its inferred population size history includes an
out-of-Africa-like population bottleneck that is more recent than that seen in
present-day non-Africans (red bold curve). By shifting the Ust’-Ishim curve
to align with those in present-day non-Africans (blue bold curve), and
assuming that the number of mutations necessary to do this corresponds to
45,000 years, we estimate the autosomal mutation rate to be 0.38 310
29
to
0.49 310
29
per site per year. The times indicated on the top of the figure
are based on this mutation rate.
RESEARCH ARTICLE
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©2014

Islands (putative descendants of an early coastal migration) than he is
to present-day East Asians or Native Americans (putative descendants
of a northern migration) (Fig. 3) shows that at least one other group to
which the ancestors of the Ust’-Ishim individual belonged colonized
Asia before 45,000 years ago. Interestingly, the Ust’-Ishim individual
probably lived during a warm period (Greenland Interstadial 12) that
has been proposed to be a time of expansion of modern humans into
Europe
29,30
. However, the latter hypothesis is based only on the appear-
ance of the so-called ‘Initial Upper Paleolithic’ industries (Supplemen-
tary Information section 5), and not on the identification of modern
human remains
31,32
. It is possible that the Ust’-Ishim individual was asso-
ciated with the Asian variant of Initial Upper Paleolithic industry, doc-
umented at sites such as Kara-Bom in the Altai Mountains at about
47,000 years BP. This individual would then represent an early modern
human radiation into Europe and Central Asia that may have failed to
leave descendants among present-day populations
29
.
Online Content Methods, along with any additional Extended Data display items
and SourceData, are available in theonline version of the paper;references unique
to these sections appear only in the online paper.
Received 15 May; accepted 29 August 2014.
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Supplementary Information is available in the online version of the paper.
Acknowledgements We are grateful to P. Gunz, M. Kircher, A. I. Krivoshapkin, P. Nigst,
M. Ongyerth, N. Patterson, G. Renaud, U. Stenzel, M. Stoneking and S. Talamo for
valuable input, comments and help; T. Pfisterer and H. Temming for technical
assistance.Q.F. is funded in part by the ChineseAcademy of Sciences (XDA05130202)
and the Ministryof Science and Technologyof China (2007FY110200); P.A.K. by Urals
Branch, Russian Academy of Sciences (12-C-4-1014) and Y.V.K. by the Russian
Foundation for Basic Sciences (12-06-00045); F.J. and M.S. by the National Institutes
of Health of the USA (R01-GM40282); P.J. by the NIH (K99-GM104158); and
T.F.G.H. by ERC advanced grant 324139. D.R. is a Howard Hughes Medical Institute
Investigator and supported by the National Science Foundation (1032255) and the
NIH (GM100233). Major funding for this work was provided by the Presidential
Innovation Fund of the Max Planck Society.
Author Contributions Q.F., S.M.S., A.A.B., Y.V.K., J.K., T.B.V. and S.P. designed the
research. A.A.P. and Q.F. performed the experiments; Q.F., H.L., P.M., F.J., P.L.F.J., K.P.,
C.d.F., M.M., M.L., M.S., D.R., J.K. and S.P. analysed genetic data; K.D. and T.F.G.H.
performed
14
C dating; D.C.S.-G. and M.P.R. analysed stable isotope data; N.V.P., P.A.K.
and D.I.R. contributed samples and data; S.M.S., A.A.B., N.Z., Y.V.K., S.G.K., J.-J.H. and
T.B.V. analysed archaeological andanthropological data;Q.F., J.K., T.B.V. and S.P. wrote
and edited the manuscript with input from all authors.
Author Information All sequence data have been submitted to the European
Nucleotide Archive (ENA) and are available under the following Ust’-Ishim
accession number: PRJEB6622. The data from the 25 present-day human
genomes are available from (http://www.simonsfoundation.org/life-sciences/
simons-genome-diversity-project/) and from (http://cdna.eva.mpg.de/neandertal/
altai/). Reprints and permissions information is available atwww.nature.com/reprints.
The authors declare no competing financial interests. Readers are welcome to
comment on the online version of the paper. Correspondence and requests for
materials should be addressed to Q.F. (qiaomei_fu@eva.mpg.de), D.R.
(reich@genetics.med.harvard.edu), J.K. (kelso@eva.mpg.de) or T.B.V.
(bence_viola@eva.mpg.de).
0.0 0.2 0.4 0.6 0.8 1.0
0.00
0.02
0.04
0.06
0.08
0.10
Genetic distance (cM)
Weighted covariance coefcient
Ust’−Ishim
French
Sardinian
Han
Dai
Figure 6
|
Dating the Neandertal admixture in Ust’-Ishim and present-day
non-Africans. Exponentially fitted curves showing the decay of pairwise
covariance for variable positions where Africans carry ancestral alleles and the
Neanderthal genome carries derived alleles.
ARTICLE RESEARCH
23 OCTOBER 2014 | VOL 514 | NATURE | 449
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METHODS
All sequencing was performed on the Illumina HiSeq 2000 and base-calling was
carried out using Ibis 1.1.6 9 (ref. 35). Reads were merged and remaining adaptor
sequences trimmed before being aligned to the Human reference genome (GRCh37/
1000 Genomes) using BWA (version0.5.10)
36
. GATK version1.3 (v1.3-14-g348f2b)
was used to produce genotype calls for each site. We excluded from analysis tan-
dem repeats and regions of the genome that are not unique. We considered only
genomic regions that fall withinthe 95% coverage distribution(Supplementary In-
formation section 7) and whereat least 99% of overlapping 35mers covering a pos-
ition map uniquely, allowing one mismatch.
35. Kircher, M., Stenzel,U. & Kelso, J. Improved base callingfor the Illumina Genome
Analyzer using machine learning strategies. Genome Biol. 10, R83 (2009).
36. Li, H. & Durbin, R. Fast and accurate short readalignment with Burrows–Wheeler
transform. Bioinformatics 25, 1754–1760 (2009).
RESEARCH ARTICLE
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©2014