Report

Ancient Wolf Genome Reveals an Early Divergence of

Domestic Dog Ancestors and Admixture into High-
Latitude Breeds
Graphical Abstract Authors
Pontus Skoglund, Erik Ersmark,
Eleftheria Palkopoulou, Love Dalén

Correspondence
skoglund@genetics.med.harvard.edu
(P.S.),
love.dalen@nrm.se (L.D.)

In Brief
Skoglund et al. recovered the genome
sequence of a 35,000-year-old Siberian
wolf. Calibration of the molecular clock
suggests that the ancestors of modern
dogs formed a distinct lineage prior to the
peak of the last ice age. Siberian huskies
and other northern dog breeds trace a
part of their ancestry to the ancient
Siberian wolf population.

Highlights Accession Numbers

d An ancient Siberian wolf yields a first draft genome sequence PRJEB7788
of a Pleistocene carnivore

d The 35,000-year-old wolf genome allowed recalibration of the

lupine mutation rate

d Dog ancestors diverged from modern wolf ancestors at least

27,000 years ago

d Ancient Siberian wolves contributed to the ancestry of high-

latitude dog breeds

Skoglund et al., 2015, Current Biology 25, 1515–1519

June 1, 2015 ª2015 Elsevier Ltd All rights reserved
http://dx.doi.org/10.1016/j.cub.2015.04.019
Current Biology

Report

Ancient Wolf Genome Reveals

an Early Divergence of Domestic Dog Ancestors
and Admixture into High-Latitude Breeds
Pontus Skoglund,1,2,3,* Erik Ersmark,4,5 Eleftheria Palkopoulou,4,5 and Love Dalén4,*
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
3Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
4Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
5Department of Zoology, Stockholm University, 10691 Stockholm, Sweden

*Correspondence: skoglund@genetics.med.harvard.edu (P.S.), love.dalen@nrm.se (L.D.)

http://dx.doi.org/10.1016/j.cub.2015.04.019

SUMMARY
The origin of domestic dogs is poorly understood
[1–15], with suggested evidence of dog-like features
in fossils that predate the Last Glacial Maximum [6, 9,
10, 14, 16] conflicting with genetic estimates of a
more recent divergence between dogs and world-
wide wolf populations [13, 15, 17–19]. Here, we
present a draft genome sequence from a 35,000-
year-old wolf from the Taimyr Peninsula in northern
Siberia. We find that this individual belonged to a
population that diverged from the common ancestor
of present-day wolves and dogs very close in time to
the appearance of the domestic dog lineage. We
use the directly dated ancient wolf genome to recali-
brate the molecular timescale of wolves and dogs
and find that the mutation rate is substantially slower
than assumed by most previous studies, suggesting
that the ancestors of dogs were separated from pre-
sent-day wolves before the Last Glacial Maximum.
We also find evidence of introgression from the
archaic Taimyr wolf lineage into present-day dog
breeds from northeast Siberia and Greenland,
contributing between 1.4% and 27.3% of their
ancestry. This demonstrates that the ancestry of pre-
sent-day dogs is derived from multiple regional wolf
populations.
RESULTS AND DISCUSSION
The closest living relative of domestic dogs is the gray wolf,
Canis lupus [1], but the number of domestication events, as
well as their antiquity and geographical origin, is highly conten-
tious [1–15]. While molecular estimates of the time of origin of
the dog lineage are contingent on principally unknown mutation
rates and generation times, the most recent genomic estimates
of the divergence between wolves and dogs date to 11,000 to
16, 000 years ago [13, 15, 17–19]. These estimates are in consid-
erable discord with reported archaeological evidence of dog-like
canids from before the Last Glacial Maximum, which date as far
back as 36,000 years before present (BP) [6, 9, 10, 14, 16].
Furthermore, a recent study showed that gray wolves from as
disparate locations as China, Israel, and Croatia were symmetri-
cally related to modern-day dogs [15]. This observation suggests
that dogs were domesticated prior to the diversification of
present-day gray wolf populations or that the wild ancestors of
dogs are now extinct. The latter scenario would be consistent
with an earlier finding of a morphologically distinct wolf popula-
tion adapted to megafaunal prey in Late Pleistocene Beringia
[20], as well as mitochondrial DNA evidence for a Holocene
replacement of European gray wolves [21]. One hypothesis
could thus be that the wild ancestors of dogs were a genetically
distinct wolf population that inhabited the Late Pleistocene
steppe-tundra biome and that this population was subsequently
replaced [18], possibly by a northward postglacial expansion of
smaller-bodied wolves that gave rise to modern-day wolf diver-
sity. To test this hypothesis, we sequenced a draft genome of a
Late Pleistocene wolf from northern Siberia.
Shotgun sequencing was performed on a canid rib originally
collected during an expedition to the Russian Taimyr Peninsula
in 2010, from here on referred to as Taimyr 1. This rib was iden-
tified as coming from a wolf through sequencing of a short region
of the mitochondrial 16S rRNA gene and was directly dated using
accelerator mass spectrometry (AMS) radiocarbon dating to
30,920 ± 380 14C years BP, equivalent to
34,900 calendar
years BP (35,000 years ago) (for details, see the Supplemental
Experimental Procedures). Genomic libraries were constructed
with and without treatment with the uracil-specific excision re-
agent (USER) enzyme mix [22]. This enzymatic treatment was
employed in order to remove postmortem-derived uracil resi-
dues that introduce errors into ancient genome datasets. We
sequenced these libraries on the Illumina HiSeq platform to a
total average 1-fold sequencing depth (Figure S1), the majority
of which is derived from the USER-treated libraries. Using the
retained postmortem damage patterns at methylated CpG sites,
we observed nucleotide misincorporation patterns in these se-
quences expected from DNA tens of thousands of years old (Fig-
ure S1) [23]. We assembled the mitochondrial genome to an
average 182-fold sequencing depth and reconstructed a phylog-
eny relating the Taimyr 1 individual’s mitochondrial DNA lineage
to those of modern-day dogs and wolves, as well as previously

Current Biology 25, 1515–1519, June 1, 2015 ª2015 Elsevier Ltd All rights reserved 1515

Figure 1. Mitochondrial DNA Phylogeny
The outgroups (one coyote and two Chinese wolf sequences) were excluded.
Nodes with posterior probability >0.9 are marked with asterisks, and stars
indicate ancient samples morphologically described as ‘‘dog like.’’ See also
Figure S1 and Table S1.
published mitochondrial DNA sequences from ancient canids
[14]. The mtDNA of Taimyr 1 forms a distinct lineage separated
from the dog lineages (Figure 1), in agreement with the generally
basal grouping of all ancient wolves that has been observed in
previous studies [14, 20]. The sequencing depth of chromosome
X is 50.4% of that expected of an autosome of similar size,
demonstrating that the Taimyr individual was male.
A previous study used seven present-day canid genomes to
show that all studied wolves share a common origin that ex-
cludes the ancestors of domestic dogs [15]. The divergence be-
tween the wolf and dog lineages was estimated to date back to
11,000–16,000 years ago, but this estimate relied on assump-
tions on the mutation rate, which has not been directly estimated
1516 Current Biology 25, 1515–1519, June 1, 2015 ª2015 Elsevier Ltd All rights reserved
for domestic dogs. A prediction of this model is that the
35,000-
year-old Taimyr individual would have lived long before the
divergence of dogs and gray wolves, and thus would be sym-
metrically related to both populations. In a principal component
analysis (Figure S2), the Taimyr individual is approximately inter-
mediate to gray wolves and dogs, but this could be expected just
from the extra genetic drift that has occurred in those lineages
since the death of the Taimyr individual. To formally test the hy-
pothesis that Taimyr 1 lived prior to the divergence between
dogs and gray wolves, we used D statistics [24, 25], expecting
symmetry (D = 0) under the null hypothesis corresponding to
the population history (Andean fox, (Taimyr 1, (dog, wolf))). This
test, as well as all other population genetic analyses reported
here, used the USER-treated portion of the sequence data in or-
der to minimize the effect of postmortem degradation. It should
be noted that we also found consistent results for an even more
conservative set of analyses restricted to transversion polymor-
phisms. Overall, we find that the data are consistent with the Tai-
myr wolf being symmetrically related to wolves and dogs for all
pairs of present-day canids (jZj < 3). Conversely, tests with the
Taimyr individual being assigned to a clade with one of the pre-
sent-day canids to the exclusion of another, corresponding to a
history (Andean fox, (canid1, (Taimyr 1, canid2))), were all rejected
(Z > 5).
To investigate the phylogenetic position of the Taimyr wolf
further, we fitted a population model to the genomes of the Tai-
myr wolf and modern canids. We find that gene flow between
present-day dogs and wolves after their initial divergence is
required to explain the data (Supplemental Experimental Proce-
dures). Once this gene flow is included in the model, the Taimyr
wolf can be successfully fitted as belonging to the wolf lineage,
the dog lineage, or the lineage ancestral to both wolves and
dogs (Figure 2; Supplemental Experimental Procedures). In
these three models, the Taimyr wolf is consistently placed very
close to the split between the dog and wolf lineages, as
measured in units of genetic drift (an FST of 0 to 0.007). Thus,
our data are consistent with a trifurcation of the dog, wolf, and
Taimyr lineages, indicating that they all diverged at about the
same time. This appears to be inconsistent with the hypothesis
that dogs and wolves diverged only 11,00016,000 years ago,
since under this model it might be expected that the Taimyr
wolf would be confidently placed on the lineage ancestral to
the dog-wolf split, due to the substantial amount of genetic drift
that most likely would have occurred since the death of the
Taimyr wolf (35,000 years ago) until the split between dogs and
wolves some 20,000 years later.
To estimate the divergence time between the Taimyr individual
and present-day canids directly, and accounting for changes
in effective population size, we estimated the probability
F(AderivedjBheterozygous) [25] of an individual A (such as the Taimyr
individual) sharing a derived allele discovered as a heterozygote
in a diploid present-day individual B. At sites where the Chinese
wolf is heterozygous, the Taimyr individual carries the derived
allele at 30.8% ± 0.1% of the sites, compared to
32% for the
Croatian wolf, dingo, and boxer (Figure 3; Table S2). We used
this as a summary statistic to estimate the divergence time of
the Taimyr lineage given a model of population history of the
Chinese wolf inferred using the pairwise sequential Markovian
coalescent method [26]. We find that calibration using the most
 A B

Figure 2. The 35,000 Year-Old Taimyr Individual Belonged to a Population that Was Genetically Close to the Ancestor of Present-Day Gray
Wolves and Domestic Dogs
(A) D statistics testing the phylogenetic relationship between the Taimyr wolf and present-day canids. The Andean fox is used as an outgroup in all tests. Error bars
correspond to one block jackknife SE on each side.
(B) A model of population history (admixture graph) fitted to the data. The Andean fox, which was used as an outgroup, is not shown. Although the graph shown
here indicates minor gene flow from domestic dogs into regional wolf populations, we note that an alternative graph with gene flow from the wolf lineages into the
domestic dog lineages provides equally good fit. In all fitted graphs, the branch length between the divergence of the Taimyr wolf lineage and the wolf-dog split is
very short. Branch lengths are measured as the allele frequency variance along each branch (genetic drift) rescaled to be proportional to FST.
See also Figures S2 and S3.

commonly assumed mutation rate of 1 3 108 per generation and
a 3-year gray wolf generation time [5, 15, 18, 19, 27] would imply
that the Taimyr wolf diverged from the Chinese wolf 10,000–
14,000 years ago (Figure 3), which is incompatible with its cali-
brated direct radiocarbon date of
35,000 years BP. Instead,
the mutation rate must be substantially slower in order to be
compatible with the age of the Taimyr individual, and we find
that the Taimyr divergence can be accommodated by a mutation
rate of 0.4 3 108 per generation (Figure 3). However, it should be
noted that this assumes that the Taimyr wolf is directly ancestral
to the Chinese gray wolf. If there was structure between the an-
cestors of the Chinese wolf and the Taimyr wolf, the mutation
rate would have to be even slower, and as such a rate of 0.4 3
108 per generation is conservative. We emphasize that this mu-
tation rate is for non-CpG sites, since SNPs in CpG dinucleotide
context were excluded from the variants called in the present-
day genome. Alternatively, our results could indicate that the gen-
eration time is longer than 3 years, or some combination of slower
mutation rate and a longer generation time. Regardless, this
direct evidence suggests a longer timescale of wolf-dog popula-
tion history and thus implies that the 11,00016,000 years ago
wolf-dog divergence inferred in a previous study [15] should be
recalibrated to
27,000–40,000 years ago.
To examine shared ancestry between the ancient Taimyr wolf
and a larger set of modern-day dog populations, we used data
from 48 dog breeds genotyped at
170,000 SNPs [28] and
computed D statistics to assess whether each breed shared
more alleles with the Taimyr wolf than a set of 15 modern-day
gray wolves (Figure 4; Table S3). We found clear evidence of a
closer relationship between the Taimyr wolf and the Siberian
Husky (Z = 4.3, p = 0.000009), Greenland Sledge Dogs (Z = 3.6,
p = 0.00016), and, to a lesser extent, Chinese Shar-Pei and Finnish
Spitz (p < 0.05) compared to other dog breeds (Supplemental
Experimental Procedures). To estimate the proportion of ancestry
derived from the Taimyr wolf lineage in the Greenland Sledge
Dogs, we fitted an admixture graph using the Andean fox, pre-
sent-day gray wolves, and German Shepherds. We find that the
best-fitting graph posits 3.5% Taimyr-derived ancestry in the
Greenland Sledge Dogs but that an ancestry proportion ranging
from 1.4% and 27.3% is consistent with the data (Supplemental
Experimental Procedures). These results can be explained either
by a very early presence of dogs in northern Eurasia or by the ge-
netic legacy of the Taimyr individual being preserved in northern
wolf populations until the arrival of dogs at high latitudes.
Extending our population history modeling to SNP array geno-
types from a large set of gray wolf populations [11, 29], we further
find that the majority of the ancestry of North American wolves
also diverged from other wolves later than the Taimyr wolf line-
age (Supplemental Experimental Procedures; Figure S4). This
suggests that all extant gray wolf populations share a relatively
recent origin, most likely sometime after the divergence of the
Taimyr wolf lineage but prior to the inundation of the Bering
Land Bridge and subsequent isolation of Eurasian and North
American wolves.
In conclusion, our results provide direct evidence for a longer
timescale for the divergence of the dog and wolf lineages than
previously assumed, and thus suggest that dogs may have orig-
inated much earlier than commonly accepted. Such an early
divergence is consistent with several paleontological reports of
dog-like canids up to 36,000 years old [6, 9, 10, 14, 16], as well
as the evidence that domesticated dogs most likely accompa-
nied early colonizers into the Americas [30]. However, the initial
divergence between the ancestors of dogs and gray wolves
would not necessarily have had to coincide with domestication
in the sense of selective breeding, since this human-mediated
process could have occurred later or over an extended period

Current Biology 25, 1515–1519, June 1, 2015 ª2015 Elsevier Ltd All rights reserved 1517
 introgression could have provided early dogs in high latitudes
38

0.1e−8
0.2e−8
0.3e−8
with phenotypic variation beneficial for adaptation to a new chal-
0.4e−8 lenging environment.
36

0.5e−8

Age of Taimyr 1
0.6e−8
0.7e−8
0.8e−8 ACCESSION NUMBERS
F(A|B) (%)

34

0.9e−8
1.0e−8
Sequence data for the Taimyr 1 genome has been submitted to the European
Nucleotide Archive (http://www.ebi.ac.uk/ena) under accession number
32

PRJEB7788.

F(Taimyr|Chinese wolf) ±2 SEs

30

SUPPLEMENTAL INFORMATION

Supplemental Information includes Supplemental Experimental Procedures,

28

four figures, and four tables and can be found with this article online at
http://dx.doi.org/10.1016/j.cub.2015.04.019.
0 10000 20000 30000 40000 50000

Population split time (years ago) AUTHOR CONTRIBUTIONS

P.S. and L.D. conceived and designed the study. L.D. conducted field work.
Figure 3. Recalibrating the Lupine Mutation Rate using the Directly
E.P. and E.E. performed laboratory analyses. E.E. and P.S. performed the
Dated Taimyr Genome
mtDNA analyses. P.S. analyzed the genomic data and interpreted the results
We estimated the probability F(AjB) for the Taimyr individual carrying the
with input from L.D. P.S. wrote the paper with input from all the other authors.
derived allele at positions where the Chinese wolf is heterozygous using
empirical data. This statistic is informative on the coalescent time passed in the
ACKNOWLEDGMENTS
ancestry of the Chinese wolf since its divergence from the Taimyr wolf’s
lineage. Since the Taimyr wolf must have separated at least 35,000 years ago,
We thank David Reich and Beth Shapiro for constructive comments on the
the age of the specimen obtained from a direct radiocarbon date, its diver-
population genetic analysis and a previous version of the manuscript. We
gence from the Chinese wolf can be used to calibrate the lupine mutation rate,
also wish to thank John Novembre, Rena Schweizer, Bridgett vonHoldt, Sofie
in the sense that we can infer the maximum mutation rate that is consistent
Wagenius, and Matthew Webster for data access and technical assistance
with the proximity of the Taimyr genome to the present-day Chinese wolf. To
and Tom Gilbert, Maria Avila-Arcos, Ludovic Orlando, Mark Lipson, Iosif Laz-
achieve this, we built calibration curves for F(AjB) given a model of Chinese
aridis, Iain Mathieson, Jan Storå, and Greger Larson for discussions. P.S. was
wolf effective population size history (inferred using pairwise sequentially
supported by a scholarship from the Swedish Research Council (VR grant
Markovian coalescent [PSMC] analysis) and different mutation rates. Mutation
2014-453). L.D. acknowledges funding from the Swedish Research Council
rates per generation are shown in the legend. A generation time of 3 years is
(VR grant 2012-3869), as well as logistical support from the Swedish Polar
assumed. See also Table S2.
Research Secretariat that organized the Taimyr 2010 expedition. The authors
would like to acknowledge support from the Science for Life Laboratory, Na-
of time. On the other hand, a scenario of a much more recent tional Genomics Infrastructure, NGI, and UPPMAX for providing assistance
timing of domestication would require that the majority of pre- in massive parallel sequencing and computational infrastructure (UPPNEX
sent-day dog ancestry originates from an extinct or presently un- project ID: b2014030). David Reich and Harvard Medical School provided
additional computational resources.
sampled wolf population. Regardless, we find that the ancestry
of present-day dog breeds descends from more than a single
Received: December 9, 2014
domestication event, since high-latitude dog breeds such as Revised: March 11, 2015
the Siberian Husky and Greenland Sledge Dogs can trace part Accepted: April 10, 2015
of their ancestry to the now-extinct Taimyr wolf lineage. This Published: May 21, 2015

Figure 4. Introgression from a Population Related to the Ancient Taimyr Wolf into Northeast Siberian and New World Arctic Dog Breeds
We computed the statistic D(ancient Taimyr wolf, present-day gray wolves; dog breed X, pool of European breeds) where the pool of European breeds was
comprised of 83 Boxer, Gordon Setter, Doberman Pinscher, and Newfoundland individuals. The color scale represents Z scores where the obtained D statistic
values were normalized by SEs estimated using a block jackknife. Positive statistics suggest an excess affinity to the Taimyr wolf over the modern-day gray
wolves for dog breed X. Negative statistics suggest an excess affinity to present-day gray wolves over the ancient Taimyr wolf for dog breed X. We tested 48
different dog breeds with information from
66,000 SNPs. The affinity of the Siberian Husky and Greenland Sledge Dogs to Taimyr is replicated also in statistics of
the form D(Andean fox, Taimyr; present-day gray wolves, dog breed X). See also Figure S4 and Tables S3 and S4.

1518 Current Biology 25, 1515–1519, June 1, 2015 ª2015 Elsevier Ltd All rights reserved
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Current Biology
Supplemental Information

Ancient Wolf Genome Reveals

an Early Divergence of Domestic Dog Ancestors
and Admixture into High-Latitude Breeds
Pontus Skoglund, Erik Ersmark, Eleftheria Palkopoulou, and Love Dalén
Supplemental Data

Figure S1. Features of the Taimyr 1 genome (related to Figure 1). Evidence for postmortem
damage for non-treated libraries and libraries treated with the USER enzyme mix, inside and
outside of CpG context.
 A

0.8
GoldenJackal
Gray wolves
Ancient Taimyr wolf
Dogs

0.6
0.4
PC2

0.2
0.0
−0.2
−0.4

−0.4 −0.2 0.0 0.2 0.4

PC1

B
0.1
0.0
PC2

−0.1

Gray wolves
−0.2

Ancient Taimyr wolf

Greenland sledge dog & Siberian Husky
Shar−Pei
Eurasian
Other domestic dogs

−0.05 0.00 0.05 0.10 0.15

PC1

Figure S2. Analysis of 7 present-day canid genomes and the ancient Taimyr wolf (related to
Figure 2). A) Principal component analysis. We used pseudo-haploid genotype calls of high-
coverage genomes overlapped with the ancient Taimyr individual (red). B) PCA using dogs and
wolves genotyped at ~170,000 SNPs.
Figure S3. Admixture graph
population history models of
the ancient Taimyr
individual and present-day
canids (related to Figure 2).
A) Rejected graph topology
without gene flow. Note that
even in this graph the internode
distance between the Taimyr
wolf and the dog-wolf ancestor
node is only FST=0.006 B)
Admixture graph with regional
dog-to-wolf gene flow and
Taimyr basal to the dog-wolf
ancestor. C) Admixture graph
with regional wolf-to-dog gene
flow and Taimyr basal to the
dog-wolf ancestor. D) Dog-to-
wolf gene flow and Taimyr on
the wolf lineage. E) Wolf-to-
dog gene flow and Taimyr on
the wolf lineage. F) Dog-to-
wolf gene flow and Taimyr on
the dog lineage. G) Wolf-to-
dog gene flow and Taimyr on
the dog lineage. All graphs
displayed in B-G provide a
good fit to the data in the sense
that the f4 statistics that they
predict are within 3 SEs of the
empirically observed SEs.
Nodes ANC, W0, D1 etc. are
hypothesized ancestral
populations in each graph.
Numbers given for branch
lengths are scaled as FST x
1000, but note that drift lengths
for admixture events (e.g. W2-
W6 in B) are not
mathematically determined.
Figure S4. Evidence of a recent origin of worldwide wolf populations (related to Figure 4).
A) Admixture graph fitted using TreeMix providing evidence that the Taimyr individual is
substantially closer to present-day gray wolves than to coyotes, but that worldwide present-day
gray wolves share substantial recent ancestry after the divergence of the Taimyr individual. Note
that the long branch of the Taimyr individual is an artifact of haploid genotype calling and that
this does not affect its relative covariance with other populations. B) D-statistics are consistent
with Taimyr 1 being basal to all worldwide wolf populations, and tests where Taimyr 1 is more
closely related to one gray wolf population than another are all rejected. Error bars are 3 standard
errors of the D-statistic.
Table S1 (related to Figure 1). Sequencing statistics of the Taimyr nuclear and mitochondrial
genome.
All data mitochondrial DNA
Seqs MAPQ≥ Total bp Mean Seqs MAPQ≥ Total bp Mean
30 depth 30 depth
Non- 7,582,638 6,509,172 615,051,149 0.26 8,454 7,755 685,449 40.98
treated
USER- 27,209,886 23,942,017 1,838,901,874 0.77 45,855 43,348 3,039,103 181.69
treated
Total 34,792,524 30,451,189 2,453,953,023 1.03 54,309 51,103 3,724,552 222.67
Note: An asterisk denotes that mean sequencing depth was obtained by dividing the number of
bp of sequences aligned to the genome (without mapping quality restrictions) with the number of
bp (2,392,715,236) in the canFam3.1 assembly
(http://useast.ensembl.org/Canis_familiaris/Info/Annotation, accessed 2 October 2014). Mean
sequencing depth for the mtDNA was obtained by dividing the number of bp of sequences
aligned to the mtDNA with 16,727, the number of bp in the canFam3.1 assembly of the dog
mtDNA genome.
Table S2. Statistics used to estimate the coalescent time separating the divergence of the
Taimyr individual from present-day gray wolves (related to Figure 3).
B A F(Aderived|Bheterozygote) Block jackknife SE Loci
Croatian wolf Taimyr 30.61% 0.11% 602,538
Croatian wolf Chinese wolf 31.35% 0.11% 1,353,073
Croatian wolf boxer 31.41% 0.11% 1,391,231
Croatian wolf dingo 31.35% 0.11% 1,308,264

Chinese wolf Taimyr 30.85% 0.12% 538,141

Chinese wolf Croatian wolf 31.90% 0.10% 1,133,764
Chinese wolf boxer 31.78% 0.11% 1,244,847
Chinese wolf dingo 32.14% 0.10% 1,154,013
Note: We estimate the probability F(Aderived|Bheterozygote) that a randomly chosen allele from
individual A is derived at positions where another individual B displays a heterozygotic
genotype. We estimate standard errors using a weighted block jackknife of 5 mb blocks, where
each block is weighted by the number of informative loci.
Table S3 (related to Figure 4). Excess allele sharing between the Taimyr wolf and Asian dog
breeds. D(T,W;X,DP) abbreviates D(Taimyr, Wolf; Breed X, Boxer, Gordon Setter, Dobermann
Pincher and Newfoundland). D(AF,T;W,X) abbreviates D(Andean fox, Taimyr; Wolf, Breed X).
Breed D(T,W;X,DP) D(AF,T; W, X) n Origin
D Z D Z
Australian Shepherd 0.0008 0.14 0.0028 0.33 1 USA
Belgian Tervuren -0.0048 -1.25 0.0058 0.72 10 Belgium
Beagle 0.0040 0.99 0.0017 0.23 12 Great Britain
Bernese Mountain Dog -0.0010 -0.22 0.0065 0.86 12 Swiss Alps
Border Collie 0.0043 1.21 0.0074 1.03 16 English-Scottish Border
Border Terrier 0.0031 0.74 0.0053 0.72 25 Northumberland, England
Boxer 0.0053 1.09 0.0168 2.09 8 Germany
Brittany Spaniel 0.0022 0.65 0.0096 1.40 12 Brittany, France
Chihuahua 0.0030 0.72 0.0028 0.33 5 Chihuahua, Mexico
Cavalier King Charles Spaniel -0.0032 -0.58 0.0076 1.04 2 Blenheim, England
Cocker Spaniel -0.0034 -1.00 0.0017 0.23 14 York, England
Czechoslovakian Wolf Dog -0.0139 -2.48 0.0019 0.22 12 Czechoslovakia
Dachshund 0.0012 0.40 0.0036 0.55 7 Germany
Dalmatian 0.0015 0.36 0.0023 0.31 25 Dalmatia, Croatia
Doberman Pinscher -0.0063 -1.71 -0.0027 -0.35 12 Apolda, Germany
English Bulldog -0.0008 -0.17 0.0056 0.70 13 England
English Bull Terrier -0.0071 -1.22 -0.0041 -0.44 8 Birmingham, England
English Cocker Spaniel -0.0061 -1.33 0.0032 0.38 2 England
Elkhound 0.0035 1.01 0.0074 1.05 12 Jämtland, Sweden
English Springer Spaniel -0.0126 -2.93 -0.0120 -1.60 3 England
English Setter -0.0016 -0.41 0.0099 1.41 12 England
Eurasian 0.0055 1.34 0.0079 1.12 12 Germany
Flatcoated Retriever 0.0035 0.71 0.0024 0.31 2 UK
Finnish Spitz 0.0101 2.29 0.0146 1.93 14 Finland
Gordon Setter 0.0015 0.58 0.0027 0.38 25 Scotland
Golden Retriever 0.0048 1.28 0.0114 1.62 12 Scotland
Greyhound 0.0025 0.59 0.0154 2.11 11 UK
German Shepherd -0.0053 -1.15 0.0012 0.15 12 Stuttgart, Germany
Greenland Sledge Dog 0.0173 3.64 0.0226 2.96 14 Greenland
Siberian Husky 0.0208 4.27 0.0175 2.20 1 Siberia, Russia
Irish Wolfhound -0.0023 -0.48 0.0005 0.07 2 Ireland
Jack Russell Terrier 0.0014 0.49 0.0086 1.34 25 Oxford, England
Large Munsterlander 0.0014 0.24 0.0111 1.33 23 Munster, Germany
Labrador Retriever 0.0013 0.38 0.0091 1.36 17 Labrador, Canada
Mops 0.0092 1.65 0.0096 1.13 12 China
Newfoundland 0.0026 0.89 0.0082 1.22 2 Newfoundland, Canada
Nova Scotia Duck Tolling Retr. 0.0018 0.44 0.0067 0.92 2 Nova Scotia, Canada
Rottweiler -0.0004 -0.08 0.0109 1.41 25 Rottweil, Germany
Samoyed 0.0067 1.36 0.0048 0.60 3 Nenentsia, Russia
Sarloos -0.0269 -5.15 -0.0142 -1.99 11 Netherlands
Schipperke 0.0024 0.63 0.0077 1.09 2 Belgium
Schnauzer -0.0039 -1.00 -0.0007 -0.09 12 Mecklenburg, Germany
Shar Pei 0.0127 2.98 0.0083 1.21 6 Guangdong, China
Standard Poodle 0.0006 0.17 0.0045 0.65 26 Germany
Yorkshire Terrier 0.0074 2.19 0.0075 1.06 12 Yorkshire, England
Weimaraner 0.0015 0.34 -0.0010 -0.13 0 Germany
Table S4 (related to Figure 4). Evidence for biased affinity to dogs for genome sequence data
overlapped with SNP array data.
Test genome full data boxer asc. boxer-poodle boxer-wolf asc.
asc.
D Z D Z D Z D Z
Taimyr -0.050 -4.006 -0.035 -1.937 -0.044 -2.480 -0.289 -3.097
CroatianWolf 0.028 3.609 0.052 4.479 0.021 2.029 -0.142 -2.170
ChineseWolf -0.038 -4.767 -0.023 -1.872 -0.046 -4.154 -0.014 -0.209
GoldenJackal -0.060 -6.276 -0.048 -3.638 -0.055 -4.204 -0.160 -1.875
Note: We show the statistic D(golden_jackal, Test genome; boxer, gray_wolf_Europe_Ukraine), computed on SNPs
obtained from different ascertainment schemes. Positive values are coloured in blue and negative values in red.
Supplemental Experimental Procedures
Sample description
During the Taimyr Peninsula 2010 expedition organised by the Swedish Polar Research
Secretariat, a partial rib (sample ID TX085) was collected at an ice complex site (N73o31’00’’,
E104o32’20’’) along the Bolshaya Balakhnaya River. The rib was found ex situ and was only
partial, making both its age and species identity uncertain. However, subsequent PCR
amplification and sequencing of a part of the mitochondrial 16S rRNA gene [S1] established the rib as
that from a gray wolf (Canis lupus) and AMS radiocarbon dating provided an age of 30,920±380
14
C years BP (OxA 28059). This age is equivalent to ~34,900 calendar years BP when calibrated
using the OxCal software v.4.2 [S2] and the IntCal 13 calibration curve [S3] (mean 34,888;
median 34,865; range (95.4%) 35,659 - 34,142).

DNA extraction and sequence library preparation

Extraction of the sample and library preparation was performed at a specifically designated
ancient DNA laboratory with high standards of sterility at the Swedish Museum of Natural
History in Stockholm, where no work had previously been performed on canids. DNA was
extracted using a silica-based method coupled with concentration on Vivaspin filters (Sartorius),
following a modified version of protocol C in Yang et al. [S4], as described in Brace et al. [S5]
Two sequencing libraries were prepared from 20µl of DNA extract using the multiplexed
double-stranded library preparation protocol for Illumina sequencing by Meyer and Kircher [S6].
One of the libraries was treated with the USER enzyme (New England Biolabs) during the blunt-
end repair step to remove uracils that derive from cytosine deamination [S7]. The non-USER-
treated library was indexed and amplified with AmpliTaq Gold® (Life technologies) and the
USER-treated library with the high-fidelity polymerase AccuPrimeTM Pfx (Life technologies).
Both libraries were purified with magnetic beads (Agencourt AMPure XP, Beckman Coulter)
and their concentration was measured on the Bioanalyzer 2100 (Agilent) using high-sensitivity
DNA chips. The non-USER-treated library was pooled together with a library from another
sample at equimolar concentrations and the pool was sequenced on a single lane of an Illumina
HiSeq 2500 flowcell with a paired-end 2x100bp setup in RapidRun mode. Sequencing of the
USER-treated library was performed on 2 lanes of the Illumina HiSeq 2500 flowcell with a
paired-end 2x100bp setup in HighOutput mode.

Ancient genomic data processing

For the sequencing data from libraries that were not treated with the USER enzyme mix, we
merged read pairs where the expected index was observed using MergeReadsFastQ_cc.py [S8],
requiring an overlap of at least 11 bp. We then mapped the sequence reads to the dog genome
assembly (builds canFam2 and canFam3.1) using BWA version 0.5.9 [S9] with parameters -l
16500 -n 0.01 -o 2, and collapsed PCR duplicate reads with identical start and end coordinates
into consensus sequences using FilterUniqueSAMCons.py [S8]. For the USER-treated
sequencing data, we merged all read pairs using the software package SeqPrep 1.1 (URL:
https://github.com/jstjohn/SeqPrep) using default parameters, and mapped to the dog genome
assemblies as above, collapsing PCR duplicates using samtools rmdup [S10] with default
parameters. For both data sets, we required mismatches to the reference genome to be less than
10% for each sequence, and discarded sequences of less than 35 bp.
Postmortem DNA damage
We computed postmortem DNA damage profiles from the libraries by modifying the PMDtools
program [S11], allowing for separation of the data into two categories: 1) positions aligned to a
nucleotide in CpG context and 2) positions aligned to a nucleotide in non-CpG context. This
stratification is available in PMDtools v0.56 at https://code.google.com/p/pmdtools/. We used
23,942,017 sequences from the USER-treated data and 168,327 from the non-USER-treated data
that mapped to chromosome 38 with a mapping quality of at least 30 to compute damage patterns
for these two categories. We also computed damage patterns on 44,150 sequences with mapping
quality of at least 30 from the USER-treated data that mapped to the mitochondrion, to test the
notion that cytosines in mtDNA are unmethylated and thus all cytosine deamination events result
in uracils. We required that each investigated base had a phred-scaled quality score of at least 30.

Biological sex
No Y-chromosome reference sequence is available from the canFam3.1 reference genome (the
sequenced individual was a female boxer [S12]), but we found that only 832,657 sequences with
mapping quality of at least 30 aligned to the 123,869,142 bp chromosome X sequence, compared
to 1,635,494 sequences which aligned to the 122,678,785 bp chromosome 1. Normalizing by the
length of the reference sequences, the number of X-chromosome alignments is (832,657
/123,869,142) / (1,635,494 /122,678,785) = 50.4% of what would be expected based on the
chromosome 1 observation. For the Chinese wolf genome, the same fraction is 98.6%, whereas
for the Dingo it is 53.2%. We thus conclude that the individual likely had only a single copy of
chromosome X and thus was male.

Modern reference data curation and merging with the ancient wolf genome
We obtained the genomes of 6 canids sequenced using Illumina and Solid technologies by
Freedman et al. [S13]. We obtained genotype calls directly from the authors and identified all
polymorphic alleles between the 6 canids and the Boxer reference genome that passed both
global and sample-specific quality filters implemented by the original study [S13]. Importantly,
the filters applied by the original study excluded all positions that could possibly have been in
CpG context. Since all discernible post-mortem derived damage in the USER-treated Taimyr
wolf is due to methylated CpG sites (Figure S1), the remaining errors in the Taimyr sequence
should all be on the magnitude expected from sequence errors, i.e. ~1/1000 given our phred-
scaled base quality threshold of 30. We added haploid genotypes from the USER-treated Taimyr
genome data by randomly sampling a single read at each locus to each identified reference locus
[S14], requiring a mapping quality for each sequence of at least 30, and a minimum base quality
of each base of 30. For the complete genomes, the number of SNPs where we called a base for
the Taimyr wolf was 3,639,567 (41.9% of the total number of 8,686,809 SNPs) after restricting
to the USER-treated data. To compare the Taimyr wolf to a broader diversity of modern-day dog
breeds, we obtained a data set of 532 dogs from 48 breeds and 15 gray wolves genotyped at
169,066 SNP loci on the Illumina CanineHD array [S15]. For this data set, approximately 66,000
SNPs were covered by the USER-treated Taimyr data after applying quality filters as above. To
compare the Taimyr wolf to a broader diversity of modern-day gray wolf populations, we used
the CanMap data set [S16, S17] typed on the Affymetrix Canine version 2 genome-wide SNP
mapping array, comprising a total of 1,235 canids genotyped at 47,934 SNPs, including 199 gray
wolves and genotypes extracted from the 6 genome sequences first published by Freedman et al.
[S13]. We obtained 21,687 autosomal SNPs for which we also had data from the Taimyr genome
(excluding non-USER-treated data). We processed the Andean fox data similarly to the Taimyr
genome, mapping the first read in each pair to canFam2, canFam3 and canFam3.1 using BWA
with default parameters.

Mitochondrial DNA analysis

We assembled a consensus sequence of the Taimyr mitochondrial genome restricting to data
obtained from the USER-treated library. We obtained 46,113 sequences mapping to the
mitochondrion of canFam2, 44,150 of which had a mapping quality of at least 30. The average
sequencing depth for the mitochondrial genome without filtering was 182X, and no site was
covered by less than three reads (two sites that were covered by three reads all agreed with the
consensus base). We used the vcfutils.pl tool in the samtools suite [S10] to call a consensus
sequence, with default parameters.

We performed a Bayesian phylogenetic analysis on the mitochondrial genome sequence of

Taimyr 1 together with previously published mitochondrial genome sequences of both modern
and ancient canids [S18]. A phylogeny was reconstructed using BEAST 1.8.0 [S19], applying the
HKY + G model of nucleotide substitution and assuming constant population size as a coalescent
tree prior. The posterior distribution of nodes, divergence times and substitution rates were
estimated by Markov chain Monte Carlo, where samples were drawn every 1000 MCMC steps
from a total of 10 million steps, following a discarded burn-in of 1 million steps. Convergence to
the stationary distribution and sufficient sampling were checked by inspection of posterior
samples and ESS values in Tracer 1.5.2 [S19]. Radiocarbon dates were used as internal
calibration points applying the ‘Estimate’ option with no prior on the substitution rate. Two
independent analyses were run and combined in LogCombiner 1.8.0, after which convergence
between the two runs was checked using Tracer 1.5.2 [S19].

Principal component analysis

We performed principal component analysis using EIGENSOFT v4.0 [S20], excluding one locus
from each pair in linkage disequilibrium, which was assessed with the r2 statistic (r2 > 0 was
excluded). Since we did not make diploid genotype calls for the ancient Taimyr wolf genome,
we pseudo-haploidized the modern-day data by randomly sampling a single allele at each site
[S21]. We find that the two first principal components (PC) computed using Taimyr and the 7
present-day canid genomes see Taimyr 1 clustering intermediately to wolves and dogs (Figure
S2A), as expected due to the 35,000 years of genetic drift that has occurred in dogs and wolves
since the death of the Taimyr wolf. We note that the Taimyr wolf was included in the PC
computations and not projected, as is often the practice for ancient humans [S22, S23]. This is
motivated by the lack of postmortem damage outside CpG context in the Taimyr genome as well
as the fact that only a single ancient individual is included, so there is no excess of missing data.
This also serves as quality control, since if the Taimyr wolf appeared highly differentiated from
all the present-day genomes in the PC analysis this would suggest that it is affected by
sequencing- or processing errors. However, we see that the most extreme outliers are the golden
jackal and the boxer, which might be expected from the evolutionary distance of the golden
jackal to the other canids, and the extensive bottlenecks that have occurred in recent European
dog breeds. Similar results are obtained for a PCA of Taimyr and present-day canids genotyped
on the Illumina CanineHD array (Figure S2B).
D-statistics
D-statistics quantify excess correlations in allele frequencies that deviate from the expectation of
a null model of a tree-like population history [S14, S24]. Given, for example, a history where
dogs and wolves became isolated at a specific point with no subsequent gene flow, we expect
that for a polymorphism discovered between two dogs, two wolf chromosomes that are
polymorphic should be equally probable to carry the derived or ancestral allele. Extended to
population-wide allele frequency data, we expect that the product (pwolf1-pwolf2)(pdog1-pdog2)
should be consistent with 0 when summed over many loci.

To compute D-statistics on empirical data, we used the estimation framework described in [S25]

Numerator = (pA-pB)-(pX-pY)
Denominator = (pA+ pB-2pApB)(pX+ pY-2pXpY)

where piA is the frequency of one arbitrarily chosen allele in population A at marker i. To obtain
genome-wide estimates, the Numerator and Denominator is summed for all n markers [S25,
S26] and D = Numerator / Denominator. We obtained standard errors by performing a weighted
block jackknife over 5 Mb blocks in the genome.

The use of an Andean fox (Lycalopex culpaeus) genome [S27] as the outgroup for most of these
analyses was motivated by the evidence for gene flow between the golden jackal and other
canids [S27], and we also excluded the Israeli wolf and Basenji genomes for this reason [S13],
but were still left with one dog and one wolf from both Western- (Boxer and Croatian wolf) and
Eastern Eurasia (Dingo and Chinese wolf).

Admixture graphs of population history using complete genomes

We used the program ADMIXTUREGRAPH [S24, S25] which uses f-statistics of allele frequency
correlations between samples to assess whether a fitted admixture graph of population history is
consistent with the data. ADMIXTUREGRAPH optimizes the fit of a proposed admixture graph
in which each node can be descended either from a mixture of two other nodes, or from a single
ancestral node from which it may be separated by genetic drift. ADMIXTUREGRAPH optimizes
the fit between predicted and empirical f2 statistics of the form f2(A, B) = (pA-pB), where pA and
pB are the allele frequencies of populations A and B, respectively, and the statistic is summed
over all n loci [S24, S25]. To assess the fit of a given model to the data, all possible f4 statistics
f4(A, B; X, Y) = (pA-pB)-(pX-pY) for the empirical data and the fitted model are compred.
Following previous studies, we consider statistics which deviate by normalized Z-scores > 3
between predicted and empirical statistics as evidence against the tested graph hypothesis.

We first tested a simple tree-like model where the Taimyr individual is basal to all present-day
wolves and dogs, with the two dogs and the two wolves forming separate clades (Figure S3A).
We found that this model was inconsistent with the data, with 8 f4 statistics predicted by the
model to be zero deviating by between 3 < |Z| < 7.3 standard errors from zero. We also note that
this model was in fact fitted as a trifurcation between the dog lineage, and the Chinese and
Croatian wolf lineages, respectively, since the drift inferred from the divergence of wolves and
dogs to the divergence of the two wolves was 0. Many statistics implied an excess affinity
between the dingo and the Chinese wolf, e.g. f4(Andean fox, dingo; Chinese wolf, Croatian wolf)
= -0.005328 (Z = -4.0), as well as an excess affinity between the Croatian wolf and the boxer,
e.g. f4(Andean fox, boxer; Chinese wolf, Croatian wolf) = 0.004249 (Z = -3.2). Thus we next
tested two modified models where either the dingo or the boxer had partial Chinese wolf-related
ancestry, and Croatian wolf-related ancestry, respectively, or, the Chinese wolf and the Croatian
wolf had partial dingo-related and boxer-related ancestry, respectively. Both these models were
good fits to the data with no f4 statistics deviating from predicted values by more than 3 standard
errors, respectively (Figure S3B and S3C). In addition, models of dog-to-wolf, or wolf-to-dog
gene flow, where Taimyr was on the lineage leading to either dogs or wolves also fit the data
with no significant deviations (Figure S3D, S3E, S3F, and S3G). However, all these posit drift
corresponding to FST < 0.01 between the Taimyr branch and the original divergence of wolves
and dogs. We therefore conclude that our graph modeling suggests that the wolf, dog, and
Taimyr lineages all diverged at about the same time. In the main text, we report the model that
posits dog-to-wolf gene flow and Taimyr as basal to the two other lineages (in effect a
trifurcation due to zero-length drift), since it requires admixture at a lower rate. However, some
bidirectional gene flow is probably more biologically realistic [S13], in which case some
combination of the two models, each with lower admixture proportions in any given direction, is
more likely.

Divergence time estimation and calibration of dog-wolf divergence

We used an approach for estimating the population divergence of the Taimyr individual’s lineage
from modern canids (scaled in coalescent time) that has previously been used to estimate the
divergence time between Neandertals and modern humans [S28]. This approach is based on
detection of heterozygous positions in the genome of a single present-day individual B, and then
estimating the probability F(A|B) of a second (ancient) genome A carrying the derived allele at a
randomly chosen chromosome. We estimate standard errors using a weighted block jackknife of
5 mb blocks, where each block is weighted by the number of informative loci. Since this
approach only samples a single chromosome from the ancient individual, population size
changes in the lineage specific to the population the ancient individual belonged to do not enter
into the probability of it carrying the derived allele. However, the proportion of derived alleles in
B that are not present in A is also affected by the genetic drift that has occurred in the ancestry of
B.

To account for genetic drift, we built a calibration curve for F(A|B) taking demographic history
into account by estimating historical changes in effective population size in the Chinese wolf
using the PSMC method [S29]. We chose the Chinese wolf for this analyses since a previous
study showed that the resolution of the inference for the other canid genomes was poorer due to
insufficient recombination events in the most recent time period [S13]. We used genotypes
inferred by the original authors, requiring a genotype quality of at least 20. We ran the PSMC
inference using the parameters ‘-N20 -t10 -r5 -p "64*1"’, limiting the last coalescence to 10
times the effective population size and inferring Ne over all 64 atomic time intervals. We then
simulated 900 mb under the inferred PSMC population size history using MaCS [S30], over a
grid of divergence times for a single haploid lineage A and computed F(A|B) for each simulation
replicate. Initial calibration of coalescent time units to chronological years assumed a generation
time of 3 years and a mutation rate of 1 x 10-8 per bp per generation, corresponding to 3.33 x 10-9
mutations per bp per year, which yields a starting Ne of the gray wolf of ~7000. We investigated
a range of calibrations of the per-generation mutation rate in order to identify a range that would
be compatible with the age of the Taimyr wolf. We note however that the slower mutation rate
that we infer could also be explained by a longer generation time interval than 3 years.
Regardless, this longer generation time would have the same effect of recalibrating models of
dog-wolf divergence to a longer time scale. We also note that SNPs in CpG context were
excluded from the present-day SNP panel, and so the upper bound on the mutation rate inferred
here excludes such sites.

Recent shared ancestry of worldwide gray wolves

To investigate the relationship between the Taimyr wolf and a larger set of gray wolf
populations, including New World gray wolves and coyotes typed on the Affymetrix Canine
version 2 genome-wide SNP mapping array [S16], we first fitted admixture graphs using the
heuristic approach employed by TreeMix. We excluded dogs from this analysis due to the
observation of biases towards dogs when overlapping genome sequence data to this data set (see
below). We fitted between 0 and 3 admixture edges using a selected set of wolf and coyote
populations from across the covered distribution that all had appreciable sample size, estimating
standard errors of the covariance matrix using blocks of 30 contiguous SNPs. We found that
assuming 0 or 1 migration edge resulted in fitted covariances that deviated from empirical values
of more than 3 SEs, suggesting poor fit, but that the maximum deviation for 2 migration edges
was 2.4, suggesting good fit. These two migration edges featured North American gray wolf
ancestry in the coyote, in agreement with previous results [S16], as well as gene flow from a
basal canid into the Israeli wolf, also in agreement with previous results [S13] and our
ADMIXTUREGRAPH modeling using the complete genome data (Figure S2).

This best-fitting model (Figure S4) places the ancient Taimyr wolf as being basal to all gray
wolves, but sharing a substantial amount of history with the present-day gray wolves after their
divergence from the coyote. To test this further, we computed D(golden jackal, Taimyr; wolf1,
wolf2) for the selected wolf populations (excluding the Israeli wolf due to its basal ancestry) and
found that these statistics were all consistent with 0 (Figure S4). In contrast, there is evidence for
all present-day wolf populations sharing genetic drift with each other, which is not shared with
the Taimyr wolf, since statistics of the form D(golden jackal; wolf1, wolf2, Taimyr) are
significantly negative. Since the Taimyr wolf genome is consistent with being basal to gray
wolves from the Middle East, China, Europe and North America, one possible historical scenario
is that the majority of gray wolf ancestry today stems from an ancestral population that lived less
than 35,000 years ago, but we note that we cannot exclude that this ancestral population diverged
from the population of the Taimyr wolf earlier than its lifetime.

Admixture into high-latitude dog breeds

To test for admixture between the Taimyr wolf and a large set of modern dog breeds, we first
tested the null hypothesis D(Andean fox, Taimyr; present-day gray wolves, dog breed X) using
15 present day gray wolves and 48 dog breeds genotyped on the Illumina CanineHD array (Table
S3). This null hypothesis assumes the topology inferred for the complete genome sequence data:
that the Taimyr individual is basal to present-day gray wolves and dogs. A significantly positive
statistic can be interpreted as excess derived allele sharing between the Taimyr individual and the
dog breed X. We found that the two most significant statistics were indeed positive, and involved
the Greenland sledge dog (Z = 2.96) and the Siberian Husky (Z = 2.2), two dog breeds that both
originate from arctic human populations.
To increase power to detect a genetic affinity to the Taimyr wolf, we computed D(present-day
gray wolves, Taimyr; dog pool, dog breed X) which tests if allele frequency differences between
a dog breed X and a pool of present day breeds (Newfoundland, Boxer, Gordon Setter and
Doberman Pincher) are correlated to the allele frequencies of either present-day gray wolves or
the Taimyr individual. Positive statistics can be interpreted as an excess affinity of dog breed X
to the Taimyr individual, whereas negative statistics can be interpreted as an excess affinity to
the present-day gray wolves. We again find strong evidence of Taimyr affinity in the Siberian
Husky (Z = 4.27) and Greenland sledge dog (Z = 3.64), but also in the Shar Pei (Z = 2.98) and
the Finnish Spitz (Z = 2.29), who are other ‘ancient’ breeds associated with high latitudes. In
contrast, the Dutch Saarloos wolfdog was closer to present-day gray wolves than Taimyr 1 (Z = -
5.2), in agreement with documented historical crossbreeding with wolves in this breed.

To estimate the proportion of Taimyr-derived ancestry in the Greenland sledge dog (the Siberian
Husky is represented by a single individual in our data so is limited in power for such an
inference), we used ADMIXTUREGRAPH to fit a graph consisting of the Andean fox outgroup,
the Taimyr individual, present-day gray wolves, the Greenland sledge dog and the German
Shepherd. We used exactly the same topology as inferred for our genome-wide data, that the
Taimyr wolf is basal to present-day gray wolves and dogs, but fitted the Greenland sledge dog as
being comprised both of dog and Taimyr-related ancestry. We then incrementally tested different
proportions of ancestry, and found that a proportion between 1.4% and 27.3% resulted in no
deviations of more than |Z| = 2 between empirical f4 statistics and those predicted by the model.

Comparison between complete genomes and the Affymetrix Canine SNP mapping array
We also wanted to corroborate the affinity between the Taimyr individual and gray wolves using
data from the Affymetrix Canine version 2 genome-wide SNP mapping array [S16, S17].
However, we found evidence for biases towards dogs in genome sequences merged into this data
set. This can be seen for example in the statistic D(golden jackal, Chinese wolf genome; boxer,
gray wolf Ukraine) = -0.038 (Z = 4.8), which suggests that even the high-quality Chinese wolf
genome shares more alleles with the boxers genotyped on the SNP array than with Ukrainian
gray wolves genotyped on the SNP array (the golden jackal data in these tests was also SNP
array genotypes).

Replacing the Chinese wolf genome with Taimyr, Croatian wolf, and golden jackal genomes, we
find that both the Taimyr individual and the golden jackal show a similar attraction to the boxer
(Table S4). In contrast, the Croatian wolf genome is correctly identified as being more closely
related to the Ukrainian wolf SNP array data. This suggests that the extra drift shared between
the two European wolves is enough to overcome the bias that is causing the attraction of e.g. the
Chinese wolf to dogs in the SNP array data. To study this further, we stratified the data by SNPs
that were ascertained by Lindblad-Toh et al. [S12] as either i) being polymorphic in the boxer
reference genome (13,302 SNPs) ii) polymorphic between the boxer reference genome and a
standard poodle individual (24,930 SNPs), and iii) polymorphic between the boxer reference
genome and shotgun sequences from wolves (634 SNPs). While the uncertainty is large, the bias
seems exacerbated for the SNPs ascertained as boxer-wolf differences, for which even the
Croatian wolf genome appears closer to the boxer than to Ukrainian wolves (D = -0.14, Z = 2.2)
(Table S1).
We conclude that using the SNP array data for this purpose is unreliable. One explanation could
be that this is due to reference alignment bias in the Chinese wolf genome, since the reference
genome is a boxer individual. Importantly however, this could not explain our results based on
genome sequences that the Taimyr individual is closer to wolves, since reference alignment bias
would be expected to cause it to be closer to dogs. Given the careful filtering of the genome
sequence data and lack of ascertainment bias, we suggest that the genome sequence data is more
trustworthy for these purposes, and the observation that e.g. D(goldenJackal, Chinese wolf;
basenji, boxer) using genome sequence data is consistent with 0 suggests that reference
alignment bias is not a major issue. Other explanations could include ascertainment bias, or
allelic biases in the array genotyping.

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