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Article
Genomic Analyses Reveal the Influence of
Geographic Origin, Migration, and Hybridization on
Modern Dog Breed Development
Graphical Abstract
Highlights
dNeighbor joining cladogram of 161 breeds establishes 23
supported clades
dCrossing between diverse clades was done recently to add
new traits
dMigration of a breed to a new region alters both immigrant
and indigenous breeds
dTracking recent crosses can identify the source of mutations
in multiple breeds
Authors
Heidi G. Parker, Dayna L. Dreger, Maud
Rimbault, Brian W. Davis, Alexandra B.
Mullen, Gretchen Carpintero-Ramirez,
Elaine A. Ostrander
Correspondence
eostrand@mail.nih.gov
In Brief
The domestic dog is divided into
hundreds of island-like populations
called breeds. Parker et al. examine 161
breeds and show that they were
developed through division and
admixture. The analyses define clades,
estimate admixture dates, distinguish
geographically diverse populations, and
help determine the source of shared
mutations among diverse populations.
Accession Numbers
GSE90441
GSE83160
GSE70454
GSE96736
Parker et al., 2017, Cell Reports 19, 697–708
April 25, 2017 ª2017 The Author(s).
http://dx.doi.org/10.1016/j.celrep.2017.03.079
Cell Reports
Article
Genomic Analyses Reveal the Influence
of Geographic Origin, Migration, and
Hybridization on Modern Dog Breed Development
Heidi G. Parker,
1
Dayna L. Dreger,
1
Maud Rimbault,
1
Brian W. Davis,
1
Alexandra B. Mullen,
1
Gretchen Carpintero-Ramirez,
1
and Elaine A. Ostrander
1,2,
*
1
Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health,
Bethesda, MD 20892, USA
2
Lead Contact
*Correspondence: eostrand@mail.nih.gov
http://dx.doi.org/10.1016/j.celrep.2017.03.079
SUMMARY
There are nearly 400 modern domestic dog breeds
with a unique histories and genetic profiles. To track
the genetic signatures of breed development, we
have assembled the most diverse dataset of dog
breeds, reflecting their extensive phenotypic varia-
tion and heritage. Combining genetic distance,
migration, and genome-wide haplotype sharing ana-
lyses, we uncover geographic patterns of develop-
ment and independent origins of common traits.
Our analyses reveal the hybrid history of breeds
and elucidate the effects of immigration, revealing
for the first time a suggestion of New World dog
within some modern breeds. Finally, we used cladis-
tics and haplotype sharing to show that some com-
mon traits have arisen more than once in the history
of the dog. These analyses characterize the com-
plexities of breed development, resolving longstand-
ing questions regarding individual breed origination,
the effect of migration on geographically distinct
breeds, and, by inference, transfer of trait and dis-
ease alleles among dog breeds.
INTRODUCTION
The dog, Canis familiaris, is the first domesticate earning a place
within nearly every society across the globe for thousands of
years (Druzhkova et al., 2013; Thalmann et al., 2013; Vila
`et al.,
1997, 1999). Over the millennia, dogs have assisted humans
with hunting and livestock management, guarding house and
field, and played crucial roles in major wars (Moody et al.,
2006). Providing a range of services from companionship to pro-
duction of fur and meat (Wilcox and Walkowicz, 1995), the diver-
sity of talents and phenotypes combined with an unequalled
emotional connection between dogs and humans has led to
the creation of more than 350 distinct breeds, each of which is
a closed breeding population that reflects a collage of defining
traits (http://www.akc.org).
Previous studies have addressed the genomic makeup of a
limited number of breeds, demonstrating that dogs from the
same breed share common alleles and can be grouped using
measures of population structure (Irion et al., 2003; Koskinen,
2003; Parker et al., 2004), and breeds that possess similar
form and function often share similar allelic patterns (Parker
et al., 2004, 2007; Vonholdt et al., 2010). However, none of these
studies have effectively accounted for the variety of mechanisms
through which modern breeds may have developed, such as
geographic separation and immigration; the role of hybridization
in the history of the breeds; and the timeline of the formation of
breeds. In this study, we overcome these barriers by presenting
an expansive dataset, including pure breeds sampled from mul-
tiple sections of the globe and genotyped on a dense scale. By
applying both phylogenetic methods and a genome-wide anal-
ysis of recent haplotype sharing, we have unraveled common
population confounders for many breeds, leading us to propose
a two-step process of breed creation beginning with ancient
separation by functional employment followed by recent selec-
tion for physical attributes. These data and analyses provide a
basis for understanding which and why numerous, sometimes
deleterious mutations are shared across seemingly unrelated
breeds.
RESULTS
We examined genomic data from the largest and most diverse
group of breeds studied to date, amassing a dataset of 1,346
dogs representing 161 breeds. Included are populations with
vastly different breed histories, originating from all continents
except Antarctica, and sampled from North America, Europe,
Africa, and Asia. We have specifically included breeds that
represent the full range of phenotypic variation present among
modern dogs, as well as three breeds sampled from both the
United States and their country of origin. Samples from 938
dogs representing 127 breeds and nine wild canids were geno-
typed using the Illumina CanineHD bead array following standard
protocols. Data were combined with publically available informa-
tion from 405 dogs genotyped using the same chip (Hayward
et al., 2016; Vaysse et al., 2011). For three dogs from one breed,
genotypes were retrieved from publically available sequence
Cell Reports 19, 697–708, April 25, 2017 ª2017 The Author(s). 697
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
files, and all were merged into a single dataset (Table S1). After
pruning for low quality or genotyping rate, 150,067 informative
SNPs were retained.
Ascertainment bias has been shown to skew population ge-
netic calculations that require estimation of allele frequencies
and diversity measures (Lachance and Tishkoff, 2013). It has
also been shown that ascertainment based on a single individual
provides less bias than a mixed group (Patterson et al., 2012).
The SNPs used in this study were identified primarily within the
boxer or from boxer compared to another genome (Vaysse
et al., 2011), which has exaggerated the boxer minor allele fre-
quency (MAF; 0.351 in boxer compared to 0.260 overall) but
has little affect the other breeds (MAF range, 0.247–0.284). To
minimize the effect this might have, we have chosen to use dis-
tance measures based on allele sharing rather than frequency
and to enhance these analyses with unbiased haplotype sharing
for a robust assessment of canine population structure.
A bootstrapped cladogram was obtained using an identity-by-
state distance matrix and a neighbor-joining tree algorithm (Sup-
plemental Experimental Procedures). After 100 bootstraps, 91%
of breeds (146/161) formed single, breed-specific nodes with
100% bootstrap support (Figure 1). Of the 15 breeds that did
not meet these criteria, seven (Belgian tervuren, Belgian
sheepdog, cane corso, bull terrier, miniature bull terrier, rat ter-
rier, and American hairless terrier) were part of two- or three-
breed clades that were supported at 98% or greater, and two
breeds (Lhasa apso and saluki) formed single-breed clades
that were supported at 50% and 78%, respectively. Four breeds
(redbone coonhound, sloughi, cane paratore, and Jack Russell
terrier) were split within single multi-breed clades, and the last
Basenji
Xigou
TibetanMastiff(Ch)
TibetanMastiff(Am)
SiberianHusky
AlaskanMalamute
GreenlandSledgeDog
ShibaInu
Papillon
BrusselsGriffon
PugDog
Pumi
Puli
Toy and Miniature
Poodle
StandardPoodle
CotoduTulear
Havanese
BichonFrise
PortugueseWaterDog
Maltese
RatTerrier
ToyFoxTerrier
AmericanHairlessTerrier
ChineseCrested
Chihuahua
*
*
+
^
+
GreatPyrenees
CirnecodelEtna
IbizanHound
PharaohHound
Komondor
MastinoAbruzzese
Azawakh
Kuvasz
LevrieroMeridionale
AnatolianShepherd
Sloughi
AfghanHound
Saluki
@
@
#
Dachshund
PetitBassetGriffonVendeen
BassetHound
OtterHound
RedboneCoonhound
Beagle
FoxHound
EnglishSetter
GordonS
etter
Briard
BouvierdesFlandres
BelgianMalinois
BelgianTervurenand
Sheepdog
ItalianGreyhound
Borzoi
IrishWolfhound
ScottishDeerhound
Whippet
Greyhound
OldEnglishSheepdog
AustralianCattleD
og
BeardedCollie
BullTerrier
MiniatureBullTerrier
Boxer
Bulldog
DoguedeBordeaux
BostonTerrier
FrenchBulldog
= 90-100
= 70-89
= 50-69
Figure 1. Cladogram of 161 Domestic Dog Breeds
Breeds that form unique clades supported by 100% of bootstraps are combined into triangles. For all other branches, a gold star indicates 90% or better, black
star 70%89%, and silver star 50%69% bootstrap support. Breeds are listed on the perimeter of the circle. A small number of dogs do not cluster with the rest
of their breed, indicated as follows: *cane paratore, +Peruv ian hairless dog, #sloughi, @country-of-origin salukis, and ^miniature xoloitzcuintle.
698 Cell Reports 19, 697–708, April 25, 2017
two breeds (xoloitzcuintli and Peruvian hairless dog) were split
between divergent clades. Nine of the breeds that were not
monophyletic were either newly recognized by the American
Kennel Club (AKC) or not recognized at the time of sample
collection and likely represent a breed under development.
Two other non-monophyletic breeds are composed of dogs
collected in two countries; the cane corsos collected in Italy
form a fully supported, single clade, as do the salukis collected
in the United States. However, the cane corsos collected in the
United States form a paraphyletic clade near the Neapolitan
mastiffs, and the salukis collected in the Middle East form
multiple paraphyletic groups within a clade that includes the
US salukis and Afghan hounds.
Not including those that are breed specific, this study defined
105 phylogenetic nodes supported by R90% of bootstrap
replicates, 133 by R70%, and 150 supported by R50% of
replicates. We identify 29 multi-breed clades that are supported
at R90%. Each of these clades includes 2–16 breeds and
together account for 78% of breeds in the dataset. 150 breeds,
or 93% of the dataset, can be divided into 23 clades of 2–18
breeds each, supported at >50%. These multi-breed clades
reflect common behaviors, physical appearance, and/or related
geographic origin (Figure 2).
Eleven breeds did not group with significance to any other
breeds. Five breeds form independent clades and six others
are paraphyletic to established clades with <50% bootstrap sup-
port (Table S2). The lack of grouping may indicate that we have
not sampled the closest relatives of these breeds or that these
breeds comprise outcrossings that are not shared by similar
breeds.
To assess hybridization across the clades, identical-by-
descent (IBD) haplotype sharing was calculated between all
pairs of dogs from the 161 breeds. Haplotypes were phased
using the program Beagle (Browning and Browning, 2013)in
100-SNP windows, resulting in a minimum haplotype size of
232 kb, well above the shared background level established in
previous studies (Lindblad-Toh et al., 2005; Sutter et al., 2004).
The large haplotypes specifically target admixture resulting
from breed formation rather than domestication, which previous
studies have not addressed. The total length of the shared hap-
lotypes was summed for each pair of dogs. Individuals from
within the same breed clade share nearly four times more of their
genome within large IBD haplotype blocks than dogs in different
breed clades (median shared haplotype lengths of 9,742,000 bp
and 2,184,000 bp, respectively; p [Kolmogorov-Smirnov (K-S)
and Wilcox] < 2.2e
16
;Figure 3A). Only 5% of the across-breed
pairings have a median greater than 9,744,974 bp. These excep-
tions argue for recent admixture events between breeds, as evi-
denced by the example of the Eurasier breed, created in the
1970s by mixing chow chow with other spitz-type breeds (Fogle,
2000)(Figure 3B). The data reveal not only the components of the
breed but also the explanation for its placement on the clado-
gram. The Eurasier (unclustered) shows significant haplotype
sharing with the samoyed (unclustered), keeshond (Nordic spitz),
and chow chow (Asian spitz) (Figure 3B). Because all three
breeds are located in different clades, unrelated to each other,
the Eurasier falls between the component breeds and forms its
own single-breed clade. Haplotype-sharing bar graphs for
each of 161 breeds, including 152 AKC breeds, are available in
Data S1. This provides a long-term resource for identifying
BDE
GI
MNOP Q
RS UV
F
H K L
W
C
A
J
T
Figure 2. Representatives from Each of the
23 Clades of Breeds
Breeds and clades are listed for each picture from
left to right, top to bottom.
(A) Akita/Asian spitz.
(B) Shih tzu/Asian toy (by Mary Bloom).
(C) Icelandic sheepdog/Nordic spitz (by Veronica
Druk).
(D) Miniature schnauzer/schnauzer.
(E) Pomeranian/small spitz.
(F) Brussels griffon/toy spitz (by Mary Bloom).
(G) Puli/Hungarian.
(H) Standard poodle/poodle.
(I) Chihuahua/American toy.
(J) Rat terrier/American terrier (by Stacy Zimmer-
man).
(K) Miniature pinscher/pinscher.
(L) Irish terrier/terrier.
(M) German shepherd dog/New World (by Mary
Bloom).
(N) Saluki/Mediterranean (by Mary Bloom).
(O) Basset hound/scent hound (by Mary Bloom).
(P) American cocker spaniel/spaniel (by Mary
Bloom).
(Q) Golden retriever/retriever (by Mary Bloom).
(R) German shorthaired pointer/pointer setter (by Mary Bloom).
(S) Briard/continental herder (by Mary Bloom).
(T) Shetland sheepdog/UK rural.
(U) Rottweiler/drover
(V) Saint Bernard/alpine.
(W) English mastiff/European mastiff (by Mary Bloom).
Cell Reports 19, 697–708, April 25, 2017 699
populations that likely share rare and common traits that will be
invaluable for mapping the origins of deleterious and beneficial
mutations.
Strong evidence of admixture across the clades was found in
117 breeds (Figure 4). A small number of these were identified in
previous studies using migration analysis (Pickrell and Pritchard,
2012; Shannon et al., 2015) 30% of these breeds share with only
one breed outside their clade. Therefore, more than half (54%) of
the breeds that make up the 23 established clades share large
haplotypes with one or zero breeds outside their clade, indi-
cating breed creation by selection based on the initial founder
population rather than recent admixture. Only 6 of the 161
breeds share extensive haplotypes with many (>8) different
groups, suggesting recent creation of these breeds from multiple
others or that they provide a popular modern breed component.
The overall low level of sharing across diverse breeds suggests
that interclade crosses are done thoughtfully and for specific
reasons, such as the introduction of a new trait or the immigra-
tion of a breed to a new geographic region.
As importation and establishment in a new country has been
shown to have a measurable effect on breed structure (Quignon
et al., 2007), we chose three breeds, the Tibetan mastiff, saluki,
and cane corso, for inclusion in the study, with each collected in
the country of origin as well as from established populations in
the United States. In each case, there is division of the breed
based on collection location. The split between the US and
AB
Figure 3. Gross Haplotype Sharing across Breeds
(A) Boxplot of total haplotype sharing between all pairs of dogs from breeds within the same clade, across different clades, and within the same breed. The
difference between the distributions is highly significant (p < 2e-16).
(B) Example of haplotype sharing between three breeds (samoyed, chow chow, and keeshond) and a fourth (Eurasier) that was created as a composite of the
other three. Combined haplotype length is displayed on the y axis, and 169 breeds and populations are listed on the x axis in the order they appear on the
cladogram, starting with the jackal and continuing counterclockwise. Haplotype sharing of zero is set at 250,000 for graphing, a value just below what is detected
in this analysis. Breeds are colored by clade. 95% significance level is indicated by the horizontal line. Breed abbreviations are listed under the graph in the order
they appear and colored by clade. Definitions of the breed abbreviations can be found in Table S1.
700 Cell Reports 19, 697–708, April 25, 2017
Chinese Tibetan mastiffs is likely due to independent lineage for-
mation stemming from an importation bottleneck, as is evident
from estimations of inbreeding coefficients (Chinese Tibetan
mastiffs average F = 0.07, and US Tibetan mastiffs average
F = 0.15). Similarly, the average inbreeding coefficient of salukis
collected in the United States is twice as high as those sampled
from the countries of origin (F = 0.21 and 0.10, respectively).
Since the US salukis form a more strongly bootstrapped clade
than the country-of-origin dogs, we suggest that there is a less
diverse gene pool in the United States. In comparison, the
cane corsos from Italy form a single clade, while the cane corsos
from the United States cluster with the Neapolitan mastiffs, also
collected in the United States. Significant shared haplotypes are
observed between the US cane corsos and the rottweiler that are
not evident in the Italian cane corsos, as well as increased shared
haplotypes with the other mastiffs. Cane corsos have been in the
United States for less than 30 years (American Kennel Club,
1998).
Our analyses were designed to detect recent admixture;
therefore, we were able to identify hybridization events that are
described in written breed histories and stud-book records.
Using the most reliably dated crosses that produced modern
breeds, we established a linear relationship between the total
length of haplotype sharing and the age of an admixture event,
occurring between 35 and 160 years before present (ybp) (Fig-
ure 5A). Applying this equation to the total shared haplotypes
calculated from the genotyping data, we have validated this rela-
tionship on a second set of recently created breeds arriving at
Figure 4. Haplotype Sharing between Breeds from Different Phylogenetic Clades
The circos plot is ordered and colored to match the tree in Figure 1. Ribbons connecting breeds indicate a median haplotype sharing between all dogs of each
breed in excess of 95% of all haplotype sharing across clades. Definitions of the breed abbreviations can be found in Table S1.
Cell Reports 19, 697–708, April 25, 2017 701
historically accurate time estimations (Figure 5B). Using the rela-
tionship equation y = 1,613,084.67x + 262,137,843.89, where y
is the total shared haplotype length and x is the number of years,
we can estimate the time at which undocumented crosses or di-
visions from older breeds took place. For example, based on a
median haplotype sharing value of 66,993,738, the golden
retriever was separated from the flat-coated retriever in 1895,
and the written history of the golden retriever dates to crosses
between multiple breeds taking place between 1868 and 1890
(Figure 5B), a near-perfect match.
To determine if the multi-breed clades are formed through
recent admixture rather than through common ancestral sour-
ces, we examined migration in 18 groups of four or more breeds.
These include 16 of the clades established on the tree, including
nearby unclustered breeds, and two groups of small clades
(American terrier/American toy and small spitz/toy spitz/schnau-
zer) that are monophyletic, but not well supported. Using the pro-
gram Treemix (Pickrell and Pritchard, 2012), and allowing 0–12
predicted migration events, we determined the effect of admix-
ture on clade formation by calculating the increase in maximum
A
B
Breed 1 Breed 2 Total sharing Esmated Yrs Ago Predicted Year Historical year
Figure 5. Total Haplotype SharingIs Inversely
Correlated with the Time of Hybridization
between Breeds that Have Developed within
the Last 200 Years
(A) The time of hybridization in years before present
is graphed on the x axis and the median total
haplotype sharing on the y axis for six breeds of dog
with reliable recent histories of admixture in breed
formation or recovery. The trendline shows a linear
correlation with r
2
=1.
(B) The slope and intercept of the trendline from A
was applied to the median haplotype sharing values
from the data for four additional breeds with reliable
breed creation dates to establish accuracy of esti-
mated hybridization dates.
likelihood score over a zero migration tree
(Figure 6A). Only 2 of the 18 clades, New
World and Asian toy (Figures 6B and 6C),
showed evidence of extensive hybridiza-
tion between the breeds. Thus, the mod-
ern breeds were likely created through se-
lection for unique traits within an ancient
breed type with possible admixture from
unrelated breeds to enhance the trait.
Our hybridization analysis reveals evi-
dence for disease sharing across the
clades. For instance, collie eye anomaly
(CEA) is a disease that affects the develop-
ment of the choroid in several herding
breeds, including the collie, Border collie,
Shetland sheepdog, and Australian shep-
herd, all members of the UK Rural clade
(Lowe et al., 2003). The mutation and
haplotype pattern displayed IBD across
all affected breeds, and we speculated
that all share a common obviously
affected ancestor (Parker et al., 2007).
We were unable to explain, however, the presence of the disease
in the Nova Scotia duck tolling retriever, a sporting dog devel-
oped in Canada from an unknown mixture of local breeds, which
also shares the same haplotype. This perplexing observation can
now be explained, as this analysis shows that collie and/or Shet-
land sheepdog were strong, undocumented, contributors to the
formation of the Nova Scotia duck tolling retriever and, therefore,
the likely source of the CEA mutation within that breed
(Figure 7A).
Similarly,a mutationin the MDR1 gene (multi-drug resistance 1),
which causes life-threatening reactions to multiple drugs in many
of the UK Rural breeds, has been reported in 10% of German
shepherd dogs (Mealey and Meurs, 2008). These data display a
link between the German shepherd dog and UK Rural breeds
through the Australian shepherd, highlighting the unexpected
role the Australian shepherd orits predecessor played inthe devel-
opment of the modern German shepherd dog (Figure 6B). Earlier
this year, the MDR1mutation was identified in the chinook at a fre-
quency of 15% (Donner et al., 2016). Our analysis reveals recent
admixture between this breed and the German shepherd dog as
702 Cell Reports 19, 697–708, April 25, 2017
Figure 6. Assessment of Migration between Breeds within Clades
Admixture was measured in Treemix for 18 groups of breeds representing clades or combinations of small clades.
(A) Improvement to the maximum likelihood tree of each group as the result of admixture. The y axis shows fold improvement over the zero admixture tree.
(B) Cladogram of the New World breeds with European herders allowing four migration events. Arrows show estimated migration between breeds colored by
weight (yellow to red = 0–0.5).
(C) Cladogram showing migration within the Asian toy clade, including a neighboring breed, the Tibetan terrier. Pictures by Terri Gueck (TIBT), Yuri Hooker (INCA),
Mary Bloom (GSD and SHIH), Maurizio Marziali (CPAT), Mary Malkiel (COOK), and John and Debbie Caponetto (large and small XOLO/MXOL).
Cell Reports 19, 697–708, April 25, 2017 703
Figure 7. Haplotypes Shared with Breeds that Carry
Known Deleterious Mutations
Breeds are connected if the median shared haplotype size
exceeds the 95% threshold for interclade sharing. Sharing
between breeds that are known to carry the mutation is
colored black, and sharing with other breeds is colored
according to the breed that carries the mutation.
(A) Collie eye anomaly is found in a number of herding
breeds developed in the United Kingdom and some
sporting breeds developed in the United States.
(B) Multi-drug resistance 1 mutation is carried by many UK
herding breeds as well as the German shepherd.
704 Cell Reports 19, 697–708, April 25, 2017
well as previously unknown addition of Collie, both carriers of
the MDR1 mutation. Haplotype sharing with the same affected
breeds is found in the xoloitzcuintli, which allows us to predict
that this rare breed may also carry the deleterious allele but has
yet to be tested.
DISCUSSION
Phylogenetic analyses have often been applied to determine the
relationships between dog breeds with the understanding that a
tree structure cannot fully explain the development of breeds.
Prior studies have shown that single mutations produce recog-
nizable traits that are shared across breeds from diverse clades,
suggesting that admixture across clades is a notable source of
morphologic diversity (Cadieu et al., 2009; Parker et al., 2009;
Sutter et al., 2007). Studies of linkage disequilibrium and haplo-
type sharing suggest further that within regions of 10–15 kb,
there exist a small number of haplotypes that are shared by
the majority of breeds, while breed specificity is revealed only
in large haplotypes (Lindblad-Toh et al., 2005; Sutter et al., 2004).
In this study, we observe that the majority of dog breeds either
do not share large haplotypes outside their clade or share with
only one remote breed. The small number of breeds that share
excessively outside their assigned clade could be recently
created from multiple diverse breeds or may have been popular
contributors to other breeds. For example, the pug dog groups
closely with the European toy breed, Brussels griffon (Figure 2F),
in the toy spitz clade but also shares extensive haplotypes with
the Asian toy breeds (Figure 2B) as well as many small dog
breeds from multiple other clades. This likely indicates the
pug’s early exportation from Asia and subsequent contribution
to many small breeds (Watson, 1906). Consider also the exten-
sive cross-clade haplotype sharing in the chinook, a recently
created breed with multiple ancestors from different breeds.
Our data both recapitulates and enhances the written history
of this breed (http://www.chinook.org/history.html)(Data S1).
Extreme examples such as these underscore the complications
implicit in relying on phylogeny alone to describe breed relation-
ships. Overall, our data show that admixture has played an
important role in the development of many breeds and, as new
hybrids are added to phylogenetic analyses, the topology of
the cladogram will likely rearrange to accommodate.
The ability to determine a time of hybridization for recent
admixture events can refine sparse historical accounts of breed
formation. For example, when dog fighting was a popular form of
entertainment, many combinations of terriers and mastiff or
bully-type breeds were crossed to create dogs that would excel
in that sport. In this analysis, all of the bull and terrier crosses
map to the terriers of Ireland and date to 1860–1870. This coin-
cides perfectly with the historical descriptions that, though they
do not clearly identify all breeds involved, report the popularity of
dog contests in Ireland and the lack of stud book veracity, hence
undocumented crosses, during this era of breed creation (Lee,
1894).
The dates estimated from these data are approximations, as
selection for or against traits that accompanied each cross, as
well as the size of the population at the time of the cross, would
have affected retention of the haplotypes within the genome.
Based on these estimates, the excess haplotype sharing that
we have identified represents the creation of breeds since the
Victorian era breed explosion. Most breeds within each clade
share haplotypes at this level (<200 ybp); however, the lack of
sharing across the clades, outside of very specific crosses, sug-
gests the clades were developed much earlier than the breed
registries. Dividing the data by clade, the median haplotype
sharing is lowest in the Asian spitz (median = 0) and the Mediter-
ranean clades (median = 516,900) (median range across all
clades = 0–3,459,000), indicating that these clades are most
divergent and possibly older than the rest. This fits well with pre-
vious studies that suggest the earliest dogs came from Central
and East Asia (Pang et al., 2009; Shannon et al., 2015). Interest-
ingly, the mean haplotype sharing is slightly higher in the Asian
spitz clade than it is in the Mediterranean clade (mean =
1,596,000 and 1,317,000, respectively) (Figure S1), implying
that the Asian spitz breeds have been used in recent crosses
while the Mediterranean breeds are currently more segregated.
These data describe a staggered pattern of dog breed creation
starting with separation by type based on required function
and the form necessary to carry out that function. This would
have taken place as the need arose during early human progres-
sion from hunter-gather to pastoral, agricultural, and finally ur-
ban lifestyles. During the last 200 years, these breed types
were refined into very specific breeds by dividing the original
functional dog into morphotypes based on small changes in
appearance and with occasional outcrosses to enhance appear-
ance or alter behavior (e.g., reduce aggression, increase
biddability).
Though most breeds within a clade appear to be the result of
descent from a common ancestor, the New World dogs and the
Asian toys showed nearly 200% improvement in the maximum
likelihood score by allowing for admixture between the breeds
within the clade. Based on this analysis, the Asian toy dogs
were likely not considered separate breeds when first exported
from their country of origin resulting in multiple admixture events
(Figure 6C). Unexpectedly, the New World clade admixture
events center exclusively on the German shepherd dog, which
informs both the development of this breed as well as immigra-
tion of dog breeds to the New World (Figure 6B). The inclusion of
German shepherd dog with cane paratore, an Italian working
farm dog, likely indicates a recent common ancestor among
these breeds, as the German shepherd dog was derived from
a herding dog of unknown ancestry in the late 1800s (http://
gsdca.org). However, the hybridization of the German shepherd
dog with the Peruvian hairless dog and the xoloitzcuintli, also a
hairless breed, is unexpected and could be the result of recent
admixture to enhance the larger varieties of these breeds or
could indicate admixture of generic herding dogs from Southern
Europe into South America during the Columbian Exchange.
Dogs have been in the Americas for more than 10,000 years,
likely traveling from East Asia with the first humans (Wang
et al., 2016). However, studies of mitochondrial DNA suggest
that the original New World dogs were almost entirely replaced
through European contact (Castroviejo-Fisher et al., 2011;
Wayne and Ostrander, 1999; Witt et al., 2014) and additional
Asian migrations (Brown et al., 2015). As colonists came to the
Americas from the 16
th
to the 19
th
centuries, they brought Old
Cell Reports 19, 697–708, April 25, 2017 705
World livestock, and therefore the dogs required to manage and
tend the livestock, to the New World (Crosby, 1972). Many of the
newly introduced animals outcompeted the native animals,
which may explain the surprising and very strong herding dog
signature in the native hairless breeds of South and Central
America that were not developed to herd. In this analysis, we
observe that the ancient hairless breeds show extensive hybrid-
ization with herding dogs from Europe and, to a lesser extent,
with each other. We also identify two additional clades of New
World breeds, the American terriers and the American toys (Fig-
ures 2I and 2J), two monophyletic clades of small-sized breeds
from North/Central America, which include a set of related ter-
riers, and the Chihuahua and Chinese crested. Written records
state that the terriers trace their ancestry to the feists, a
North American landrace dog bred for hunting (http://www.
americantreeingfeist.com,akc.org). The Chihuahua and Chinese
crested are both believed to have originated in Central America
(American Kennel Club, 1998; Parker et al., 2017), despite the
nomenclature of the latter, which implies Asian ancestry. In
contrast, most new breeds developed in the Americas were
created from crosses of European breeds and cluster accord-
ingly (i.e., Boston terrier [European mastiff], Nova Scotia duck
tolling retriever [retriever], and Australian shepherd [UK Rural]).
The separation of the older American breeds on the cladogram,
despite recent European admixture, suggests that both clades
may retain the aboriginal New World dog genomic signatures in-
termixed with the European breed haplotypes, similar to the
admixture among European, African, and Native American ge-
nomes that can be found in modern South American human pop-
ulations (Mathias et al., 2016; Ruiz-Linares et al., 2014). This is
the first indication that the New World dog signature may not
be entirely extinct in modern dog breeds, as has been previously
suggested (Leonard et al., 2002).
In addition to the effects on the native population, our analysis
of geographically distinct subsets of the same breeds shows that
some degree of admixture also occurs in the imported breeds
when first introduced into a new country. These data suggest
two outcomes of breed immigration that mirror human immigra-
tion into a new region: the immigrant population is less diverse
than the founding population, and there is often admixture with
the native population in early generations (Baharian et al.,
2016; Zhai et al., 2016).
We observe further evidence of the role geography plays in the
distribution of breeds within the clades. For instance, both the
UK Rural and the Mediterranean clades include both sighthound
and working dog breeds, two highly divergent groups in terms of
physical and behavioral phenotype. Sighthounds are lithe and
leggy hunters, built to run fast, and have a strong prey drive.
Working dogs include both the tall and heavy flock guards that
are bred to live among herds without human interaction, prevent-
ing predator attacks, and mid-sized herders (Figure 2T), which
are agile and bred to work closely with humans to control the
movement of the flock without harming them. Despite the
opposing phenotypes under selection, both breed types form
single clades stemming from distinct geographical regions.
Haplotype analysis shows no recent admixture between the
geographically distinct clades, suggesting that these groups
arose independently (Figures S2A and S2B). Archeological
depictions show sighthound-type hunting dogs that date back
4,000 ybp (Alderton, 2002; Fogle, 2000), and one of the earliest
known writings regarding segregation of dogs based by type
clearly delineates hunting dogs from working dogs (Columella,
1954). The new cladogram presented herein suggests that the
switch from hunting to agricultural pursuits may have initiated
early breed formation and that this occurred in multiple regions.
These data show that geographical region can define a founda-
tional canid population within which selection for universally rele-
vant behaviors occurred independently, separating the regional
groups also by function long ago.
The lack of admixture across clades that appear to share a
common trait suggests that these traits may have arisen inde-
pendently, multiple times. For example, these data show no
recent haplotype sharing between the giant flock guards of the
Mediterranean and the European mastiffs (Figure S2D). These
breed types required large size for guarding; however, each
used that size in a different way, a fact that was recognized at
least 2,000 years ago (Columella, 1954). The flock guards use
their size to defeat animal predators, while the mastiffs use their
size to keep human predators at bay, often through fierce coun-
tenance rather than action. The phylogenetic placement of these
breeds and lack of recent admixture suggests that giant size
developed independently in the different clades and that it may
have been one of the earliest traits by which breeds were segre-
gated thousands of years ago.
The cladogram of 161 breeds presented here represents the
most diverse dataset of domestic dog breeds analyzed to
date, displaying 23 well-supported clades of breeds represent-
ing breed types that existed before the advent of breed clubs
and registries. While the addition of more rare or niche breeds
will produce a denser tree, the results here address many unan-
swered questions regarding the origins of breeds. We show that
many traits such as herding, coursing, and intimidating size,
which are associated with specific canine occupations, have
likely been developed more than once in different geographical
locales during the history of modern dog. These data also
show that extensive haplotype sharing across clades is a likely
indicator of recent admixture that took place in the time since
the advent of breed registries, thus leading to the creation of
most of the modern breeds. However, the primary breed types
were developed well before this time, indicating selection and
segregation of dog populations in the absence of formal breed
recognition. Breed prototypes have been forming through selec-
tive pressures since ancient times depending on the job they
were most required to perform. A second round of hybridization
and selection has been applied within the last 200 years to create
the many unique combinations of traits that modern breeds
display. By combining genetic distance relationships with pat-
terns of haplotype sharing, we can now elucidate the complex
makeup of modern dogs breeds and guide the search for genetic
variants important to canine breed development, morphology,
behavior, and disease.
EXPERIMENTAL PROCEDURES
Further details and an outline of resources used in this work can be found in the
Supplemental Experimental Procedures.
706 Cell Reports 19, 697–708, April 25, 2017
ACCESSION NUMBERS
The accession numbers for the raw data files for the SNP genotype arrays
reported in this paper are GEO: GSE90441, GSE83160, GSE70454, and
GSE96736.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Supplemental Experimental Procedures,
two figures, two tables, and two data files and can be found with this article
online at http://dx.doi.org/10.1016/j.celrep.2017.03.079.
AUTHOR CONTRIBUTIONS
H.G.P. conceived of project, performed analyses, created figures, and pre-
pared the manuscript. D.L.D. created figures and assisted in manuscript prep-
aration. M.R. ran SNP chips and worked on early analysis. B.W.D. and A.B.
performed experiments. G.C.-R. performed sample collection and DNA isola-
tion. E.A.O. organized and directed the study and contributed to manuscript
preparation
ACKNOWLEDGMENTS
We gratefully acknowledge support from the Intramural Program of the Na-
tional Human Genome Research Institute. We thank Sir Terence Clark for col-
lecting DNA samples from multiple breeds of sighthounds from their countries
of origin in Africa and Asia; Mauricio Lima, Flavio Bruno, and Robert Gennari for
collecting samples from native Italian breeds; and Lei Song for collecting sam-
ples from native Tibetan mastiffs.
Received: January 3, 2017
Revised: February 10, 2017
Accepted: March 28, 2017
Published: April 25, 2017
REFERENCES
Alderton, D. (2002). Dogs (Dorling Kindersley, Ltd.).
American Kennel Club (1998). The Complete Dog Book, 19th Edition Revised
(Howell Book House).
Baharian, S., Barakatt, M., Gignoux, C.R., Shringarpure, S., Errington, J., Blot,
W.J., Bustamante, C.D., Kenny, E.E., Williams, S.M., Aldrich, M.C., and
Gravel, S. (2016). The great migration and African-American genomic diversit y.
PLoS Genet. 12, e1006059.
Brown, S.K., Darwent, C.M., Wictum, E.J., and Sacks, B.N. (2015). Using mul-
tiple markers to elucidate the ancient, historical and modern relationships
among North American Arctic dog breeds. Heredity (Edinb.) 115, 488–495.
Browning, B.L., and Browning, S.R. (2013). Improving the accuracy and effi-
ciency of identity-by-descent detection in population data. Genetics 194,
459–471.
Cadieu, E., Neff, M.W., Quignon, P., Walsh, K., Chase, K., Parker, H.G., Von-
holdt, B.M., Rhue, A., Boyko, A., Byers, A., et al. (2009). Coat variation in the
domestic dog is governed by variants in three genes. Science 326, 150–153.
Castroviejo-Fisher, S., Skoglund, P., Valadez, R., Vila
`, C., and Leonard, J.A.
(2011). Vanishing native American dog lineages. BMC Evol. Biol. 11,73.
Columella, L.J.M. (1954). On Agriculture (De Re Rustica), Vol. Books 5–9 (E.S.
Forster and E.H. Heffner, Trans.) (Harvard University Press).
Crosby, A.W., Jr. (1972). The Columbian Exchange (Greenwood Publishing
Company).
Donner, J., Kaukonen, M., Anderson, H., Mo
¨ller, F., Kyo
¨stila
¨, K., Sankari, S.,
Hyto
¨nen, M., Giger, U., and Lohi, H. (2016). Genetic panel screening of nearly
100 mutations reveals new insights into the breed distribution of risk variants
for canine hereditary disorders. PLoS ONE 11, e0161005.
Druzhkova, A.S., Thalmann, O., Trifonov, V.A., Leonard, J.A., Vorobieva, N.V.,
Ovodov, N.D., Graphodatsky, A.S., and Wayne, R.K. (2013). Ancient DNA anal-
ysis affirms the canid from Altai as a primitive dog. PLoS ONE 8, e57754.
Fogle, B. (2000). The New Encyclopedia of the Dog, Second Edition (Dorling
Kindersley Publishing, Inc.).
Hayward, J.J., Castelhano, M.G., Oliveira, K.C., Corey, E., Balkman, C.,
Baxter, T.L., Casal, M.L., Center, S.A., Fang, M., Garrison, S.J., et al. (2016).
Complex disease and phenotype mapping in the domestic dog. Nat. Commun.
7, 10460.
Irion, D.N., Schaffer, A.L., Famula, T.R., Eggleston, M.L., Hughes, S.S., and
Pedersen, N.C. (2003). Analysis of genetic variation in 28 dog breed popula-
tions with 100 microsatellite markers. J. Hered. 94, 81–87.
Koskinen, M.T. (2003). Individual assignment using microsatellite DNA reveals
unambiguous breed identification in the domestic dog. Anim. Genet. 34,
297–301.
Lachance, J., and Tishkoff, S.A. (2013). SNP ascertainment bias in population
genetic analyses: why it is important, and how to correct it. BioEssays 35,
780–786.
Lee, R.B. (1894). A History and Description of the Modern Dogs of Great Britain
and Ireland (Horace Cox).
Leonard, J.A., Wayne, R.K., Wheeler, J., Valadez, R., Guille
´n, S., and Vila
`,C.
(2002). Ancient DNA evidence for Old World origin of New World dogs. Science
298, 1613–1616.
Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B.,
Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J., 3rd, Zody, M.C., et al.
(2005). Genome sequence, comparative analysis and haplotype structure of
the domestic dog. Nature 438, 803–819.
Lowe, J.K., Kukekova, A.V., Kirkness, E.F., Langlois, M.C., Aguirre, G.D.,
Acland, G.M., and Ostrander, E.A. (2003). Linkage mapping of the primary dis-
ease locus for collie eye anomaly. Genomics 82, 86–95.
Mathias, R.A., Taub, M.A., Gignoux, C.R., Fu, W., Musharoff, S., O’Connor,
T.D., Vergara, C., Torgerson, D.G., Pino-Yanes, M., Shringarpure, S.S.,
et al.; CAAPA (2016). A continuum of admixture in the Western Hemisphere re-
vealed by the African Diaspora genome. Nat. Commun. 7, 12522.
Mealey, K.L., and Meurs, K.M. (2008). Breed distribution of the ABCB1-1Delta
(multidrug sensitivity) polymorphism among dogs undergoing ABCB1 geno-
typing. J. Am. Vet. Med. Assoc. 233, 921–924.
Moody, J.A., Clark, L.A., and Murphy, K.E. (2006). Canine history and breed
clubs. In The Dog and Its Genome, E.A. Ostrander, U. Giger, and K. Lind-
blad-Toh, eds. (Cold Spring Harbor Laboratory Press), pp. 1–18.
Pang, J.F., Kluetsch, C., Zou, X.J., Zhang, A.B., Luo, L.Y., Angleby, H., Arda-
lan, A., Ekstro
¨m, C., Sko
¨llermo, A., Lundeberg, J., et al. (2009). mtDNA data
indicate a single origin for dogs south of Yangtze River, less than 16,300 years
ago, from numerous wolves. Mol. Biol. Evol. 26, 2849–2864.
Parker, H.G., Kim, L.V., Sutter, N.B., Carlson, S., Lorentzen, T.D., Malek, T.B.,
Johnson, G.S., DeFrance, H.B., Ostrander, E.A., and Kruglyak, L. (2004).
Genetic structure of the purebred domestic dog. Science 304, 1160–1164.
Parker, H.G., Kukekova, A.V., Akey, D.T., Goldstein, O., Kirkness, E.F.,
Baysac, K.C., Mosher, D.S., Aguirre, G.D., Acland, G.M., and Ostrander,
E.A. (2007). Breed relationships facilitate fine-mapping studies: a 7.8-kb dele-
tion cosegregates with Collie eye anomaly across multiple dog breeds.
Genome Res. 17, 1562–1571.
Parker, H.G., VonHoldt, B.M., Quignon, P., Margulies, E.H., Shao, S., Mosher,
D.S., Spady, T.C., Elkahloun, A., Cargill, M., Jones, P.G., et al. (2009). An ex-
pressed fgf4 retrogene is associated with breed-defining chondrodysplasia in
domestic dogs. Science 325, 995–998.
Parker, H.G., Harris, A., Dreger, D.L., Davis, B.W., and Ostrander, E.A. (2017).
The bald and the beautiful: hairlessness in domestic dog breeds. Philos. Trans.
R. Soc. Lond. B Biol. Sci. 372, 372.
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Gen-
schoreck, T., Webster, T., and Reich, D. (2012). Ancient admixture in human
history. Genetics 192, 1065–1093.
Cell Reports 19, 697–708, April 25, 2017 707
Pickrell, J.K., and Pritchard, J.K. (2012). Inference of population splits and mix-
tures from genome-wide allele frequency data. PLoS Genet. 8, e1002967.
Quignon, P., Herbin, L., Cadieu, E., Kirkness, E.F., He
´dan, B., Mosher, D.S.,
Galibert, F., Andre
´, C., Ostrander, E.A., and Hitte, C. (2007). Canine population
structure: assessment and impact of intra-breed stratification on SNP-based
association studies. PLoS ONE 2, e1324.
Ruiz-Linares, A., Adhikari, K., Acun
˜a-Alonzo, V., Quinto-Sanchez, M., Jara-
millo, C., Arias, W., Fuentes, M., Pizarro, M., Everardo, P., de Avila, F., et al.
(2014). Admixture in Latin America: geographic structure, phenotypic diversity
and self-perception of ancestry based on 7,342 individuals. PLoS Genet. 10,
e1004572.
Shannon, L.M., Boyko, R.H., Castelhano, M., Corey, E., Hayward , J.J.,
McLean, C., White, M.E., Abi Said, M., Anita, B.A., Bondjengo, N.I., et al.
(2015). Genetic structure in village dogs reveals a Central Asian domestication
origin. Proc. Natl. Acad. Sci. USA 112, 13639–13644.
Sutter, N.B., Eberle, M.A., Parker, H.G., Pullar, B.J., Kirkness, E.F., Kruglyak,
L., and Ostrander, E.A. (2004). Extensive and breed-specific linkage disequi-
librium in Canis familiaris. Genome Res. 14, 2388–2396.
Sutter, N.B., Bustamante, C.D., Chase, K., Gray, M.M., Zhao, K., Zhu, L., Pad-
hukasahasram, B., Karlins, E., Davis, S., Jones, P.G., et al. (2007). A single
IGF1 allele is a major determinant of small size in dogs. Science 316, 112–115.
Thalmann, O., Shapiro, B., Cui, P., Schuenemann, V.J., Sawyer, S.K., Green-
field, D.L., Germonpre
´, M.B., Sablin, M.V., Lo
´pez-Gira
´ldez, F., Domingo-
Roura, X., et al. (2013). Complete mitochondrial genomes of ancient canids
suggest a European origin of domestic dogs. Science 342, 871–874.
Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Rosengren Pielberg, G.,
Sigurdsson, S., Fall, T., Seppa
¨la
¨, E.H., Hansen, M.S., Lawley, C.T., et al.;
LUPA Consortium (2011). Identification of genomic regions associated with
phenotypic variation between dog breeds using selection mapping. PLoS
Genet. 7, e1002316.
Vila
`, C., Savolainen, P., Maldonado, J.E., Amorim, I.R., Rice, J.E., Honeycutt,
R.L., Crandall, K.A., Lundeberg, J., and Wayne, R.K. (1997). Multiple and
ancient origins of the domestic dog. Science 276, 1687–1689.
Vila
`, C., Maldonado, J.E., and Wayne, R.K. (1999). Phylogenetic relationships,
evolution, and genetic diversity of the domestic dog. J. Hered. 90, 71–77.
Vonholdt, B.M., Pollinger, J.P., Lohmueller, K.E., Han, E., Parker, H.G.,
Quignon, P., Degenhardt, J.D., Boyko, A.R., Earl, D.A., Auton, A., et al.
(2010). Genome-wide SNP and haplotype analyses reveal a rich history under-
lying dog domestication. Nature 464, 898–902.
Wang, G.D., Zhai, W., Yang, H.C., Wang, L., Zhong, L., Liu, Y.H., Fan, R.X., Yin,
T.T., Zhu, C.L., Poyarkov, A.D., et al. (2016). Out of southern East Asia: the nat-
ural history of domestic dogs across the world. Cell Res. 26, 21–33.
Watson, J. (1906). The Dog Book, Volume II (Doubleday, Page & Company).
Wayne, R.K., and Ostrander, E.A. (1999). Origin, genetic diversity, and genome
structure of the domestic dog. BioEssays 21, 247–257.
Wilcox, B., and Walkowicz, C. (1995). Atlas of Dog Breeds of the World, Fifth
Edition (T.F.H. Publications).
Witt, K.E., Judd, K., Kitchen, A., Grier, C., Kohler, T.A., Ortman, S.G., Kemp,
B.M., and Malhi, R.S. (2014). DNA analysis of ancient dogs of the Americas:
identifying possible founding haplotypes and reconstructing population his-
tories. J. Hum. Evol. 79, 105–118.
Zhai, G., Zhou, J., Woods, M.O., Green, J.S., Parfrey, P., Rahman, P., and
Green, R.C. (2016). Genetic structure of the Newfoundland and Labrador
population: founder effects modulate variability. Eur. J. Hum. Genet. 24,
1063–1070.
708 Cell Reports 19, 697–708, April 25, 2017
