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Origins of the dog: Genetic insights into dog domestication



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Origins of the dog: Genetic insights into dog
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23 Bridgett M. vonHoldt and Carlos A. Driscoll
3.1 Introduction
Dogs are the oldest domesticated animal and today are second only to cats as the most popular pet
in western societies (Boyko, 2011 ; Leonard et al ., 2006 ; Wayne and vonHoldt, 2012 ). The dog has
taken on many signifi cant roles in human society, ranging from companion, sentry, and hunting
partner to its more recent function as a model for understanding human disease. By exploring the
genetic and evolutionary history of our canine companions, we can better understand not only the
natural history of dogs but also our own evolutionary history.
Inquiries into the dog’s natural history are now enlightened by molecular and genetic data to
an overwhelmingly greater degree then they were 20 years ago when the rst edition of this book
was published. This trend towards increasing molecular inference will certainly continue, though
morphology and archaeology will remain vitally important in completing our understanding of the
cultural context of the changes wrought by domestication.
3.2 The wolf, ancestor of the dog
The dog and its ancestor, the wolf ( Canis lupus ), belong to the family Canidae . The 34 living species
of canids are grouped into four clades: a red fox-like clade, a South American clade, a wolf-like
clade, and a clade comprising only the gray and island fox ( Urocyon cinereoargenteus and U. lit-
toralis , respectively) (Lindblad-Toh et al ., 2005 ; Perini et al ., 2009 ) ( Figure 3.1 ). Canids are found
in all terrestrial habitats and, with the human-assisted introduction of dogs and foxes to Australia
and New Zealand, Antarctica is now the only continent without a resident population. Currently,
seven species belong to the dog-like genus Canis ( Figure 3.2 ), which arose nearly six million years
ago (mya) in North America and, along with a number of other carnivore species, expanded into
Eurasia (4 mya) via the Beringian land bridge , and subsequently into Africa (3 mya) (Wang &
Tedford, 2008 ). The archaeological record indicates that the modern-day gray wolf ( Canis lupus
lupus ) evolved in Eurasia around 3–4 mya, re-invading North America about 500 000 years ago
(Wang & Tedford, 2008 ). Supremely adaptable, the wolf inhabits nearly every habitat and environ-
mental condition (Mech & Boitani, 2003 ). Wolves vary greatly in size depending on their environ-
mental distribution, from the gracile 13 kg wolves of the Middle Eastern deserts to the large robust
individuals (over 78 kg) of the Arctic tundra.
Members of the genus Canis vary in appearance, behavior and degree of sociality (Mech &
Boitani, 2003 ; Packard, 2003 ). Based on recent molecular genetic studies and corroborating mor-
phological evidence, it is now agreed that the sole ancestor of the dog is the gray wolf, Canis lupus .
Though this verdict settles hundreds of years of speculation on dog origins (e.g. Clutton-Brock,
1981 ; Darwin, 1868 ), resolving which particular group of wolves was directly ancestral to the dog
still proves challenging (Ding et al ., 2012 ; Franz et al ., 2016 ; Freedman et al ., 2014 ; Pang et al .,
2009 ; Savolainen et al ., 2002 ; Shannon et al ., 2015 ; vonHoldt et al ., 2010 ; Wang et al ., 2016 ).
Establishing an evolutionary timeframe for the initial domestication process is similarly problem-
atic, though estimates based on archaeological records and mitochondrial DNA indicate 16 000 and
12 000 years ago, respectively (Clutton-Brock, Chapter 2 ; Larson et al ., 2012 ). The taxonomic status
of the dog remains contentious in some quarters, with a minority calling for the dog to be listed as a
separate species, Canis familiaris , while others consider it a subspecies of the gray wolf (i.e. Canis
lupus familiaris ).
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24 Origins of the dog: Genetic insights into dog domestication
Island fox
Gray fox
Maned wolf
Bush dog
Darwin’s fox
Hoary fox
South American gray fox
Pampas fox
Sechuran fox
Crab-eating fox
Short-eared dog
Culpeo (Andean fox)
African wild dog
Gray wolf
Golden jackal
Side-striped jackal
Black-backed jackal
Bat-eared fox
Raccoon dog
Corsac fox
Red fox
Arctic fox
Kit fox
Fennec fox
South American species Wolf-like canids Red fox-like species
Figure 3.1 Canidae phylogeny
with estimated dates of
divergence in millions of years
indicated on the branches.
(Adapted by permission from
John Wiley & Sons: Journal
of Evolutionary Biology
(Perini, F. A. et al ., The evolution
of South American endemic
canids, etc.), copyright 2009.)
(A black and white version of
this fi gure will appear in some
formats. For the colour version,
please refer to the plate section.)
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25 Bridgett M. vonHoldt and Carlos A. Driscoll
3.3 The human handprint: Canine domestication
Just what is meant by domestication? Domestic is a colloquial term applied to many animals habit-
ually used by humans or habituated to human places. Domestication, in contrast, is a biological
process that leads to the development of unique human–animal relationships that vary greatly both
in quality and intensity. To borrow a concept from ecology, we could describe the relationship that
many people today believe they have with their dogs as a mutualistic one – i.e. one in which both
parties benefi t from the association. But we can also recognize dog–human relationships that might
be better described as commensal i.e. cases in which one member (the dog) benefi ts from the
association while the other is more or less unaffected. Both represent examples of domestication but
clearly to different degrees.
Domestication is fundamentally different from taming , which is the habituation of an individual
animal to human presence. Domestication alters the genetic (and morphological) characteristics
of a breeding population and, unlike taming, these changes are heritable (Coppinger et al ., 2009 ).
The domestication of wolves was an evolutionary process that favored any heritable predisposition
to tameness in a restricted population of ancestral wolves when in close proximity to human pop-
ulations (see Box 3.1 ). Subsequently, the process of domestication mandates a degree of genetic
isolation from the parent species in order to segregate alleles controlling the suite of behaviors and
morphology encompassing the “domestication syndrome” (see below).
For our purposes here, domestic dogs are wolves that have undergone a process of selection, cru-
cially relating to behavior and cognition, but also including morphology and metabolism, which has
Red wolf
(Canis rufus)
Canis latrans)
Gray wolf (Canis lupus)
Gray wolf (Canis lupus)
Golden jackal
(Canis aureus)
Side-striped jackal
(Canis adustus)
Black-backed jackal
(Canis mesomelas)
Ethiopian wolf
(Canis simensis)
Figure 3.2 Species of Canis from the wolf-like clade and their current geographic distribution (IUCN, 2012 ).
Distributions may overlap. Wolves were historically widespread across the Old and New Worlds, with current
fragmentation a result of humans. Abbreviations: Af, Africa; As, Asia; Aus, Australia; Eu, Europe; ME, Middle East;
NAm, North America; SAm, South America. (A black and white version of this fi gure will appear in some formats. For
the colour version, please refer to the plate section.)
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26 Origins of the dog: Genetic insights into dog domestication
resulted in heritable genetic changes in allele frequencies. There continues to be much debate and
speculation as to how this selection process occurred but, either way, it is likely to have happened in
a series of stages (Diamond, 2005 ; Driscoll et al ., 2009 ; Lord et al ., Chapter 4 ; Vigne et al ., 2011 ;
Zeder, 2012 ):
1. Selective affi liation of wolves with humans predisposed to tolerance and lower levels of aggres-
sion and fear in proximity to humans; a process shaped by a combination of natural selection and
human acceptance.
2. Fitness advantages accrue to those wolves that reproduce successfully in, or in close proximity
to, the human environment, probably reinforced by a degree of human provisioning (transition
from natural to unconscious artifi cial selection).
3. Early selection for “utility” leading to the initial emergence of primitive dogs by an unconscious
process of artifi cial selection.
4. Prehistoric type formation based on landraces or specifi c utilities (e.g. coursing, baying, short
legs, etc.) (a transition from unconscious to deliberate artifi cial selection).
5. Modern era of genetic isolation and rapid radiation of highly specialized breeds, often based on
physical conformation, rather than strict utility (methodical artifi cial selection).
Not all domestic dogs have been subjected to all ve of these stages. Some are best described as
semi-domestic in the sense that they have not been subjected to conscious selective breeding but
have, due to long association with humans and their environment, and long reproductive isolation
from their wolf ancestors, plainly become domestic animals (that is, they are clearly part of a human
landscape and are derived from it). Examples of such semi-domestic dogs include the dingo and
New Guinea singing dog, neither of which has been subjected to the kind of conscious selective
breeding associated with the modern radiation (stages 4–5) but which have experienced the early
stages of domestication (stages 1–3).
Box 3.1 Natural versus artifi cial selection
Charles Darwin discussed artifi cial selection as an analogue of evolution by natural selection
(Darwin, 1868 ), but both selection processes require that the desired traits are heritable with
some more advantageous than others. Natural selection is the environmentally driven mecha-
nistic process that works to preserve only the adaptive variants; artifi cial selection works in a
similar way, but with the key difference that humans determine which traits are to be passed
on to the next generation of pups (Diamond, 2005 ; Driscoll et al ., 2009 ). Human-imposed
selective breeding of only a subset of dogs shapes the canine population, shifting the frequen-
cies of morphological and behavioral traits. Therefore, the domestication of a species is an
evolutionary process accomplished through artifi cial selection
The dingo has been isolated in Australia for approximately 5000 years (Larson et al ., 2012 ;
Savolainen et al ., 2004 ). During this time, dingoes have evolved primarily through natural selection
post-domestication, since they have never been subjected to the highly managed breeding found
among modern purebred dogs. As a result, the dingo is still readily socialized or habituated to human
proximity and has, historically, participated in mutually benefi cial hunting parties with Australian
Aborigines , but it is also capable of living altogether independent of humans in self-sustaining
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27 Bridgett M. vonHoldt and Carlos A. Driscoll
populations. Dingoes have also experienced some admixture with modern domestic dogs following
the arrival of European colonists, leaving a genetic fi ngerprint that has infl uenced the interpretation
of their evolutionary history ( Figure 3.3 ) (Larson et al ., 2012 ; Savolainen et al ., 2004 ).
Likewise, the African village dogs recently described by Boyko et al . ( 2010 ) are a cryptic pop-
ulation of dogs living in association with humans that have not experienced the artifi cial selection
associated with modern breed formation. The term “cryptic” here refers to populations that are
morphologically indistinguishable from the surrounding population but which are still genetically
distinct, indicating that some degree of genetic isolation is being enforced either ecologically or
geographically. As a result of the absence of conscious artifi cial selection on these semi-domestic
populations, some hypothesize that such dogs harbor a closer representation of the early, domestic
dog genome, though this remains controversial.
Regardless of where wolf domestication occurred, the inter-specifi c bond between early dogs
and humans was probably loose enough to permit dogs to form transitory associations with local
gray wolves (Anderson et al ., 2009 ; Randi, 2008 ; Vilà and Wayne, 1999 ; Vilà et al ., 2005 ). This
fraternization allowed these dogs to hybridize with wolves, enriching the dog genome during early
phases of domestication, and thereby providing new genetic and phenotypic variants. A genome-
wide genetic study has confi rmed these secondary contacts with local wolf populations, providing
new sources of genetic diversity to the genomes of early dogs (vonHoldt et al ., 2010 ). Over suc-
ceeding generations, dogs acquired important status in human society, and often received benefi ts
from being part of the human “pack,” likely in the form of protection, access to resources, and
100,000 ya: Ancestral wolf population
13,000−45,000 ya: Earliest
dog fossils identified
12,000−9,500 ya: Stone Age
5,000 ya: Dingoes to Australia
circa 1800s: “Victorian Era”,
Modern dog breed radiation
odayFeral and semi-
domesticated dog
breeds (e.g. Dingo)
Modern dog breeds
(>350 recognized)
Dog Wolf
Figure 3.3 Model for dog domestication.
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28 Origins of the dog: Genetic insights into dog domestication
companionship. Dogs were quickly integrated into human culture, while breeding practices gradu-
ally shaped the dog’s function and form with each successive generation.
3.4 The human cultural context of domestication
Domesticated dogs come from one or more lineages of gray wolves that have been modifi ed by
chronic exposure to humans and human environments. A highly social species, the wolf relies upon
cooperative living and it is therefore easy to imagine that the rst proto-dogs were born to wolves
that had a propensity to associate with or tolerate some degree of proximity to human groups. As
these tolerant wolves reproduced, their pups inherited the genes for their parents’ temperament and
these proto-dogs established the rst population of early dogs (see Box 3.2 ). The stories of these fi rst
dogs can be deciphered from the fossil record and from the cultural context of human burial sites.
It seems that, rather than being domesticated in direct association with Near Eastern agriculture
roughly 10 000 years ago, as were other species (e.g. cattle, goats, pigs, and sheep), the archeolog-
ical record suggests that dogs may have appeared in an earlier hunter-gatherer past, and in a region
including Europe and eastern Siberia (Driscoll et al ., 2009 ; Crockford et al ., 2012 ; Germonpré et
al ., 2009 ; Ovodov et al ., 2011 ; Sablin & Khlopachev, 2002 ; Zeder, 2008 ) ( Figure 3.3 ). However,
in the Epipaleolithic (late Stone Age, ~ 15 kya), humans shifted towards a sedentary and eventually
agrarian-based society (Dayan, 1999 ; Morey, 1994 ). In these early civilizations humans were accom-
panied by their dogs, presumably fulfi lling various practical roles in local villages and elds, perhaps
serving as companions, and probably traded or bartered along trade routes (Sundqvist et al ., 2006 ).
Dating these early dog populations can be challenging. Although dates may be derived from
genetic data by invoking a “molecular clock,” these analyses often result in large margins of error.
For this reason, archaeologists tend to rely on carbon dating of fossil remains. The challenge then is
in the differentiation of dog fossils from those of other closely related canine species (see Clutton-
Brock, Chapter 2 ).
Box 3.2 The Russian farm-fox experiment
In one of the most interesting experiments of the last century, silver foxes ( Vulpes vulpes )
have undergone experimental domestication at a Russian breeding center in Siberia (Belyaev,
1969 ; Trut, 1999 ; Trut et al ., 2009 ). This “farm-fox experiment” provides some important
clues as to how domestication might have proceeded, and serves as a remarkable resource for
understanding how selective breeding can shape phenotypes.
The experiment was initiated in the 1950s by the scientist Dmitry Belyaev at the Russian
Academy of Sciences’s Institute of Cytology and Genetics (Belyaev, 1969 ; Spady and Os-
trander, 2008 ; Statham et al ., 2011 ; Trut, 1999 ; Trut et al ., 2009 ). The goal was to selectively
breed the foxes to become tamer. However, as the tame lineage of foxes were producing
tamer kits, the researchers noticed physical changes in the foxes’ appearance: size variation
increased; their coats became more diverse in coloration and fur structure (e.g. appearance of
wirehair and curly); ears opped over; tails became shortened and curly, and females became
polyestrous, allowing for multiple litters per year (Trut, 1999 ). Many if not all of these traits
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29 Bridgett M. vonHoldt and Carlos A. Driscoll
Figure 3.4 Tame-bred foxes have many physical
and behavioral traits that are dog-like. This tame
adult fox is playing with a ball. Photograph
courtesy of Anna Kukekova (see Spady and
Ostrander, 2007).
have been noted in other domesticated species (including cattle, goats, pigs and sheep) and
are now referred to as the “domestication syndrome” (Driscoll et al ., 2009 ; Trut, 1999 ; Trut et
al ., 2009 ) ( Table 3.1 ). Surprisingly, within 10 generations of selectively breeding the foxes for
tame behavior, they began to closely resemble domesticated dogs in both physical and behav-
ioral phenotypes ( Figure 3.4 ) (Hare et al ., 2005 ; Kukekova et al ., 2010 ; Spady and Ostrander,
2008 ; Statham et al ., 2011 ).
Table 3.1 The domestication syndrome – a suite of physical traits common to domesticated
species (adapted from Driscoll et al ., 2009 ; Dobney and Larson, 2006 ; Hare et al ., 2005 ;
Kukekova et al ., 2010 ; Spady and Ostrander, 2008 ; Trut, 1999 ; Trut et al ., 2009 ).
size variety
Wavy or
Curly hair
Curly or
Rolled tails
Change in
Dog • • • •
Donkey • •
Goat • •
Guinea pig • •
Horse • •
Mouse • •
Pig • •
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30 Origins of the dog: Genetic insights into dog domestication
3.5 The canine genetic toolkit
In 2003, the entire nuclear DNA sequence from a Standard Poodle was made publicly available. In
2005 the genome of a different dog, a Boxer, was published (Kirkness et al ., 2003 ; Lindblad-Toh et
al ., 2005 ). From these DNA sequences researchers identifi ed specifi c sites where nucleotides varied
within and between individuals. So far, over 2.5 million of these variants, referred to as single nucle-
otide polymorphisms or “SNPs,” have been catalogued in the dog genome (Kirkness et al ., 2003 ;
Lindblad-Toh et al ., 2005 ).
As researchers began exploring the genetics of domesticated animals, a few basic statistical meth-
ods were standardized in order to unravel the genetic history of species. Many researchers relied
upon DNA sequence data and theories from evolutionary genetics to infer relationships or phylog-
enies . For example, if the goal is to infer which population is the wild ancestor of a domesticate,
then the phylogenetic tree would provide a type of “family tree” in which the wild and domesticated
groups are expected to be more closely related then either is to more distantly related species. This
method has been applied towards understanding evolutionary relationships among wild and domes-
ticated species, including the dog (Dobney & Larson, 2006 ; Driscoll et al ., 2007 ; Frantz et al ., 2016 ;
Parker et al ., 2004 ; Savolainen et al ., 2002 ; Shannon et al ., 2015 ; Vilà et al ., 1997 , 2005 ; vonHoldt
et al ., 2010 ; Wang et al ., 2016 ; Zeder et al ., 2006 ).
3.6 Molecular evidence of the ancestral wolf populations
Moving a step beyond the analysis of archaeological remains from burial sites and dating of fossils
through radioactive decay methods, advancing technologies allow for detailed genetic analyses of
individuals from distinct geographic origins and evolutionary time periods. In addition to geography
and timing, we can also begin to assess the number of wolves involved in the early stages of domes-
tication (i.e. the number of founders), how many separate domestication events likely occurred, and
the genetic changes that can be linked to the physical changes wolves experienced in the process of
A number of recent molecular studies have sought to determine which geographic population(s)
of wolves is genetically closest to modern-day domestic dogs; doing so supplies strong inferential
evidence for the geographic and cultural origin of dogs. Several theoretical approaches have been
employed. One early study was based on analyzing matrilineal mitochondrial DNA from a handful
of Eurasian wolves and hundreds of dogs representing various geographic regions (Africa, America,
Europe, Asia, Siberia, and India) as well as ancestries (e.g. purebred, semi-domestic dogs, mixed
breed, stray, mongrels) (Savolainen et al ., 2002 ). By inferring phylogenetic relationships and assess-
ing genetic diversity, this and subsequent studies have concluded that all dogs share a common
ancestry with wolves from East Asia, specifi cally in the region south of the Yangtze River (Pang et
al ., 2009 ; Savolainen et al ., 2002 ; Wang et al ., 2016 ). The study relied upon measures of genetic
diversity as an indication of the geographic center of domestication. Based on the assumption that as
individuals disperse from a large population they take with them only a subset of the original genetic
diversity, the source population is presumed to be more diverse than that found in the colonizing
offshoots (Barrett & Schluter, 2008 ; Biswas & Akey, 2006 ; Innan & Kim, 2004 ).
An alternative approach has been to survey the genetic variation and genomic structure of prim-
itive and semi-domestic dogs, such as the dingo, New Guinea Singing dog, and the African village
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31 Bridgett M. vonHoldt and Carlos A. Driscoll
dog. The genomes of these dogs are often considered to represent surviving versions of “ancestral”
dog genomes, some of which exist in isolation from wild canids (e.g. dingoes and New Guinea
singing dogs) while others may survive as endogamous, cryptically differentiated populations that
do not currently interbreed with recently derived dog breeds, though they may have experienced
inter-breeding in the past (Boyko et al ., 2009 ). Additionally, village dogs thrive as free-roaming com-
mensals within local human communities and have not been subjected to strong selective breeding.
Therefore, a genetic survey of these unique dogs may provide insight into a putatively “ancestral”
dog genome. However, care needs to be taken to properly distinguish true village dogs (which may
have existed for millennia) from introduced free-roaming dogs of recent European derivation, since
results will likely be misinterpreted if these dogs are mistakenly included.
The collection and analysis of genome-wide single nucleotide polymorphism (SNP) data across
village and semi-domestic dogs has revealed a surprising result. When the genetic diversity was
assessed in African village and domesticated dogs from around the globe, researchers found com-
parable levels of diversity to that of East Asian dogs from previous studies, calling into question the
view that dogs originated in East Asia (Boyko et al ., 2009 ; Shannon et al ., 2015 ). A subsequent study
that genetically surveyed 85 dog breeds determined that wolves from the Middle East contributed
the most variation to the genome of the domestic dog, with other dog-specifi c genetic variants only
found in this wolf population (Gray et al ., 2010 ; Parker et al ., 2009 ; vonHoldt et al ., 2010 ). The
apparent association with this geographic region is not surprising since it tends to corroborate ear-
lier theories that most domesticated animals have at least one point of origin in the Fertile Crescent
(Dayan, 1999 ; Driscoll et al ., 2009 ; Zeder, 2008 ; Zeder et al ., 2006 ) (see Box 3.3 ).
Recently, Freedman et al . ( 2014 ) utilized whole genome sequencing to survey representative
individuals from the three putative centers of wolf domestication – China, the Near East, and
Europe – in addition to genome sequences from the supposedly ancient, semi-domestic dog breeds,
the Basenji and dingo . They inferred that numerous bottlenecks through dog domestication his-
tory have occurred, as well as instances of post-divergence gene ow, with the initial process of
domestication estimated to have started around 11 000–16 000 years ago, predating the agricultural
revolution. Moreover, the study found that modern wolves form a monophyletic sister clade to
domestic dogs, implying that the direct ancestor of dogs is extinct, impossibly confounding any
attempt at resolving the geographic origin of dogs when examining only extant lineages. This
result was recently corroborated by an independent study of a fossil dog specimen from a cave in
the Altai Mountains of Siberia (Druzhkova et al ., 2013 ). This study analyzed the mtDNA from a
33 000-year-old Pleistocene fossil dog and identifi ed that it showed an affi nity with modern dogs
and prehistoric wolves from North America. Due to the lack of phylogenetic proximity with any
contemporary wolf population, it is proposed that the population of wolves directly ancestral to
modern day dogs is indeed extinct. Further support for a European origin of domestic dogs comes
from Thalmann et al .’s ( 2013 ) recent sequencing of mitochondrial genomes from ancient and mod-
ern canids. Bayesian phylogenetic and dating analyses identifi ed that all modern dogs are more
closely related to ancient European canids, with the onset of dog domestication occurring between
18 800 and 32 100 years ago. This domestication event, they propose, coincides with the evolution-
ary time when humans preyed upon megafauna as hunter-gatherers . In fact, their ndings suggest
that the conditions for domestication are not unique. Many early lineages of proto-dogs were likely
initiated but with many failing to survive to modern day, thereby populating the fossil record with
aborted episodes of domestication.
Most recently, genomic analyses have confi rmed deep evolutionary divergence between two geo-
graphically disparate wolf populations (Fan et al ., 2016 ; Frantz et al ., 2016 ). Frantz and colleagues
( 2016 ) suggest this may represent two independent dog domestication events. They suggest that
9781107024144c03_p22-41.indd 31 24/08/16 4:03 PM
32 Origins of the dog: Genetic insights into dog domestication
eastern dogs dispersed westward alongside their human counterparts between 6400 and 14 000 years
ago. The arrival of these eastern dogs replaced the indigenous Paleolithic dog population in western
Europe. This potential genetic replacement through admixture presents challenges for inferring the
history of dog domestication.
Box 3.3 New World origins?
In the Americas, fossils reliably identifi ed as dog are signifi cantly younger (ca. 9000–10 000
ya) than those in the Old World (15 000–33 000 ya) although dogs were common in the New
World at the time of European colonization (Clutton-Brock, Chapter 2 ; Larson et al ., 2012 ;
Leonard et al ., 2002 ). An obvious question is whether these New World dogs represented
a separate lineage of domesticated dogs (i.e. domesticated in the Americas from American
wolves) or if they accompanied early humans in crossing the Bering land bridge , presumably
between 20 000 and 11 000 ya. To answer this question, DNA sequence of pre-Columbian
dog fossils from both the Old and New Worlds were analyzed and compared to modern day
dogs and gray wolves. Phylogenetic analyses revealed that fossil New World dogs were
more closely related to the European-derived modern dog breeds and thus did not repre-
sent a unique and separate domestication (Goebel et al ., 2008 ; Leonard et al ., 2002 ; Waters
et al ., 2007 ).
3.7 Breeds
The origin and relationships among domesticated dog breeds, whose histories are often anecdotal or
only partially documented, has been a persistent interest of genetic research long before the release
of the dog genome sequence. Early natural historians considered each dog breed to be derived from
a local canid population, be it wolf, coyote, jackal, or fox (Darwin, 1868 ). In Europe, dog breeds
have existed since at least the 1300s (certainly even earlier accounts of distinct varieties have been
described in classical Greek literature), mostly for hunting; a different dog breed was employed
for each different quarry: badger hounds, wolfhounds, otter hounds, and deer hounds, for example.
Note, however, that this is not the rst formation of dog varieties; sighthound-type coursing dogs
and mastiff-type hunting dogs represent two breed types of antiquity (Clutton-Brock, 1981 and
Chapter 2 ). There was, at that time, no evidence of strong line breeding: dogs being bred to task in
the fashion of a true working dog such that any dog with desirable qualities, regardless of parentage,
was introduced into the line. By the mid 1800s, however, dog breeding was driven primarily by a
focus on form rather than function.
The Victorian view of what a breed should be changed to emphasize conformation and pedigree,
and the weight given to actual functionality was often greatly lessened. This is where modern dog
breeding has its roots. Breed organizations, such as the American Kennel Club (AKC), established
strict regulations to control breeding practices in order to achieve and preserve specifi c desired aes-
thetics or function ( Figure 3.3 ), and virtually mandated the practice of line-breeding (Ritvo, 1989 ).
As universal breeding standards were applied, the number of dogs allowed to reproduce quickly
decreased and only show champions of a breed that possessed an outstanding award-winning record
9781107024144c03_p22-41.indd 32 24/08/16 4:03 PM
33 Bridgett M. vonHoldt and Carlos A. Driscoll
became popular sires . With the same champion being used many times in a pedigree, inbreeding was
frequently commonplace. A major consequence of this strong line-breeding practice is an increased
occurrence of medical conditions and breed-specifi c diseases (see Hubrecht et al ., Chapter 14 ).
Because breeders could select mutations with obvious phenotypes (e.g. dwarfi sm, see below) to
include in their lineage, and because fanciers tend to select for the extremes of a phenotype, such
breeding practices did allow for the rapid development of new sizes, shapes, colors, and behavioral
features. As a result, there are currently about 175 distinct breeds recognized by the AKC, while over
350 breeds have worldwide recognition (Lindblad-Toh et al ., 2005 ; Parker et al ., 2004 ; Spady &
Ostrander, 2008 ; Young & Bannasch, 2006 ).
In an early genetic study designed to identify individual breed histories, researchers surveyed
the dog genome and identifi ed repetitive DNA elements called microsatellites . Based on a survey
of 96 microsatellites in over 400 dogs representing 85 breeds, genetic relatedness-based measure-
ments were used to cluster individual breeds into larger breed “groups” related in heritage, such as
mastiff-related breeds , breeds convergent on the herding behavioral trait, and Nordic breeds, for
example (Parker et al ., 2004 ). These breed groups often represented major “functional categories”
and have been confi rmed by a more recent study (Parker, 2012 ; vonHoldt et al ., 2010 ) ( Figure 3.5 ).
However, inferences based on relatedness present a statistical challenge as the domesticated and
wild groups can interbreed and produce viable offspring. Such hybridization events between distinct
lineages increase the levels of gene-sharing and genetic diversity, which will ultimately bias evolu-
tionary interpretations.
Any analysis of dog breeds is complicated by the fact that breed histories are characterized by
periods of admixture between lines, followed by strict line breeding. Any occurrence of mixing
across breeds will infl ate genetic diversity and skew the resulting inferences of ancestral relation-
ships (AKC, 2006 ; Parker et al ., 2004 , 2010 ; Parker & Ostrander, 2005 ; Sutter & Ostrander, 2004 ).
Therefore, scientists must rely upon additional analytical methods if they are to avoid making incor-
rect inferences based solely on the measurement of genetic similarity and diversity.
Studies of morphological changes as documented from archaeological and burial sites have
described variations in skeletal sizes, proportions, and dentition, but assessing the genetic changes
in similar specimens will provide information about the molecular changes associated with artifi cial
selection under domestication (see Box 3.2 ).
3.8 Genetic studies: the evolution of dog morphology
Domesticated dogs display a breadth of phenotypic variability not observed in gray wolves, or
indeed in any other domesticated animal (Stockard, 1941 ). Conversely, signifi cant traits exist in
wolves that are lacking in their domestic derivatives. Female wolves, for example, experience one
estrous cycle per year, with the pups reared in a pack consisting of relatives (e.g. siblings, cousins)
in addition to unrelated adults that forego reproduction and provide regurgitated food for the pups
(vonHoldt et al ., 2008 ). Upon maturation, pups disperse out of their natal pack in an attempt to fi nd
a mate and potentially establish their own pack. Dogs, on the other hand, have had many of their
natural history traits altered through the domestication process in a way that distinguishes them from
their wild relatives (Spady & Ostrander, 2008 ; Statham et al ., 2011 ; Trut, 1999 ; Trut et al ., 2009 )
(see Box 3.2 ). Dogs reach sexual maturity more quickly than wolves (<1 versus 2 years, respec-
tively), and will continue to bark throughout their lives, a behavioral trait that is rare in adult wolves
(Clutton-Brock, 1981 ; Morey, 1994 ). Also, critical to dogs’ survival among humans is the reduction
9781107024144c03_p22-41.indd 33 24/08/16 4:03 PM
34 Origins of the dog: Genetic insights into dog domestication
of hunting impulses (at least in most breeds) that make it possible for dogs and domestic livestock
to live together peacefully.
With the development of genome resources in the past decade, many researchers have conducted
genome-wide analyses concomitantly and uncovered a large number of shared genomic regions
across various dog breeds that are associated with typical “dog-specifi c” phenotypes; that is, the col-
lection of traits that make a dog (Akey et al ., 2010 ; Boyko et al ., 2010 ; Chase et al ., 2009 ; Freedman
et al ., 2016 ; Jones et al ., 2008 ). Surprisingly, it turns out that seemingly complex traits in dogs (e.g.
body dimensions, dentition, skeletal proportions) are due to a small handful of genes that explain
Afghan Hound
oy P
Std. S
len ofImaal
ull mastiff
Mast iff
airn terr.
BerneseMtn. Dog
Shetland S
ardigan Corgi
cottish Deerhound
Irish W
est Highland t err.
ng.Springer S
Alask. Malamute
astern &
Figure 3.5 Breed phylogeny, where the colors of branches indicate a “functional” breed group: yellow,
ancient breeds; brown, spitz breeds; black, toy breeds, blue, mastiff-like breeds, red, modern breeds, gray,
wild canids; green, herding-sighthounds; purple, mountain breeds. Black bar indicates Toy breeds. Ancient
breeds were as defi ned in vonHoldt et al . ( 2010 ) and Parker ( 2012 ). Dots on internal branches indicate >95%
confi dence. (Adapted from vonHoldt et al ., 2010 ; Parker, 2012 .) (A black and white version of this fi gure will
appear in some formats. For the colour version, please refer to the plate section.)
9781107024144c03_p22-41.indd 34 24/08/16 4:03 PM
35 Bridgett M. vonHoldt and Carlos A. Driscoll
each trait, unlike the hundreds of genes required for the expression of similar traits in humans and
non-domesticated animals (Flint et al ., 2009 ; Visscher, 2008 ; Voight et al ., 2006 ; Wellcome Trust
Case Consortium, 2007 ). Additional studies have focused on very specifi c traits that are shared
among a handful of dog breeds. Here, we focus on three examples of trait-specifi c mapping efforts
and their evolutionary implications (see Box 3.4 ).
Box 3.4 Gene mapping
Gene mapping is a method in which scientists search for particular gene variants that are
statistically associated with a phenotype. In the case of diseases, such variants may serve as
therapeutic targets for treatment. Mapping a gene variant in humans is a complex statistical
challenge, often requiring genetic samples from thousands of individuals. The method relies
upon a set of genetic markers located across the genome, and then testing these markers
statistically for a non-random association with a phenotype of interest, such as a disease
or physical trait, across individuals with the trait (case) and those lacking it (controls) (see
also van den Berg, Chapter 5 ). Despite the high degree of line breeding (and lack of genetic
diversity) in the dog genome, genetic variants will exist as a result of random mutations, a
subset of which are associated with specifi c phenotypes (e.g. disease, curly tail, pigmenta-
tion patterns). For example, consider a dog breed that segregates two phenotypes (e.g. a bull
terrier of both the piebald and solid pigmented variety; see Barsh, 2007 ) ( Figure 3.6 ). After
locating and sampling a number of solid and piebald bull terriers, we would scan each of the
38 canine chromosomes in search for a region that is shared among all piebald Bullterriers
but lacking in the solid pigmented dogs. We could further improve our chances of locating
this genomic region if we expand our search to other breeds that segregate the piebald phe-
notype ( Figure 3.6 ).
3.8.1 Domestic trait 1: How to make a toy
The initial stages of dog domestication resulted in a dog that was proportionally reduced in size, a
distinct phenotype along the spectrum of dwarfi sm , or proportional reduction in size. Dwarfed dog
breeds are easily recognizable, and are collectively referred to as “Toy” breeds by the AKC based on
the sharing of one distinguishing feature: miniature body size. The genetics behind body size varia-
tion was originally investigated in the Portuguese water dog, as this breed was recently established
with detailed pedigree records and is sexually dimorphic (the female is smaller in size than the male)
(Chase et al ., 2002 , 2005 , 2009 ). An initial genetic survey identifi ed a large region (15 million bases
or nucleotides long) on chromosome 15 containing the insulin-like growth factor 1 gene ( IGF1 ) that
was signifi cantly associated with canine body size (Chase et al ., 2005 ). The function of this gene is
well described in humans as a growth factor that regulates postnatal skeletal growth (Baker et al .,
1993 ; Laron, 2001 ; Yakar et al ., 2002 ).
To further understand how this gene region is associated with small body size, a follow-up
ne-mapping analysis focused on the region in detail in search of a genetic change that produces
the trait of interest (body size) (Sutter et al ., 2007 ). The mapping study categorized dogs as giant
(>30 kg) and toy (<9 kg) breeds based on breed standards and searched for a fragment of DNA
9781107024144c03_p22-41.indd 35 24/08/16 4:03 PM
36 Origins of the dog: Genetic insights into dog domestication
sequence (referred to as a haplotype ) that was shared among all the toy individuals that was lacking
in the giant dogs, in addition to the molecular signals of selection (e.g. lack of genetic diversity
across the haplotype; Sutter et al ., 2007 ). A haplotype found only in toy dogs and lacking in giant
dogs was nearly perfectly associated with small body size. Upon a closer investigation the IGF1
gene in toy dogs was found to contain a mutation, specifi cally an insertion of DNA that was absent
in the giant dogs’ IGF1 gene (Sutter et al ., 2007 ). The “small-dog insertion” was further surveyed
across global wolf populations, in order to better understand its evolutionary history. The inser-
tion was found only among toy dogs, and was absent from the wolf genome, confi rming that this
mutation occured post-domestication and is a toy dog-specifi c genetic variant (Gray et al ., 2010 ).
Interestingly, when looking at the larger genomic region containing the IGF1 gene, all domesticated
dogs have closer kinship with Middle Eastern wolves than other wolf populations, corroborating the
earlier fi ndings of genomic contribution (Gray et al ., 2010 ; vonHoldt et al ., 2010 ).
Piebald Boxer Non-piebald Boxer
Piebald (Cases)
No gene region is shared
across breeds
Shared gene region
No gene region shared
Shared gene region
No gene region shared
A gene region is
shared across breeds
Solid (Controls)
Piebald Bullterrier Non-piebald Bullterrier
Boxer 1
Chromosome 20
Boxer 2
Boxer 7
Figure 3.6 Conceptual
framework of gene mapping
through association. Here, the
trait being mapped is piebald
coloration across two breeds, the
boxer and the bull terrier. Each
colored segment is considered
a different allele or variant on
the chromosome. (Adapted by
permission from Macmillan
Publishers Ltd: Nature Genetics
(Barsh, G.S., How the dog got
its spots), copyright 2007 .)
(A black and white version of
this fi gure will appear in some
formats. For the colour version,
please refer to the plate section.)
9781107024144c03_p22-41.indd 36 24/08/16 4:03 PM
37 Bridgett M. vonHoldt and Carlos A. Driscoll
Only a handful of genes, when altered, result in the miniaturized version of a dog. A breeder can
take advantage of this genetic variant with large phenotypic effect by crossing the miniature dog
with other non-miniature dogs in order to shop around this subset of size-altering genes. This strict
nature of controlled dog breeding allows for goal-directed changes in phenotypes, as is the case for
the miniature breeds found today (Sutter et al ., 2007 ).
3.8.2 Domestic trait 2: How to make shortened limbs
Just as in the case of miniature-sized dogs, many short-legged breeds were created for various func-
tional purposes, such as burrow hunting, traversing through thick brush, and nding scents low to
the ground. Many genes (specifi cally growth factors ) have been described that help regulate overall
body size and skeletal proportions in humans (Giustina et al ., 2008 ; Lefebvre & Bhattaram, 2010 ;
Su et al ., 2008 ). However, only recently was the genetic basis of canine leg length uncovered from
a genetic screen of short-legged and regularly sized dogs. All dogs with the short-legged phenotype
carried a single extra copy of the fi broblast growth factor 4 ( FGF4 ) gene, whose effects halted the
elongation of the long bones in limbs during embryonic development (Parker et al ., 2009 ). This sec-
ond full-length identical copy of FGF4 has a unique origin as a retrogene copy established through
a gene duplication event called retrotransposition .
Specifi c types of DNA elements (a subset called retrotransposons ) can undergo self-replication,
with the new copy inserting into a new location in the genome (Cordaux & Batzer, 2009 ; Kazazian,
2004 ; McClintock, 1956 ). The replication process of retrotransposons can be at times error-prone,
sometimes incorporating with their new copy bits of other DNA sequences. In the case of short-legged
dogs, the retrotransposon copy contained the entire protein-coding sequence of the FGF4 gene and,
upon inserting this copy over 30 million nucleotides away, was a new identical copy of the gene but
under new regulatory controls. Short-legged breeds then not only carry the original parental gene of
the parental FGF4 gene, but also an additional copy. Researchers also found that this new gene copy
functioned independently, with the over-expression of this new copy linked to the termination of long-
bone growth prematurely in development, producing short legs (Parker et al ., 2009 ).
The part of the chromosome that contains the FGF4 retrogene copy was additionally surveyed
in wolves from across the globe in order to help infer when this retrogene was likely to have rst
inserted and the rst short-legged dog appeared. Using the haplotype around the retrogene, the
major fi nding is that all short-legged breeds, no matter where they originated geographically, share
this same retrogene. Therefore, all short-legged dogs share a common ancestor with one origination
event of this retrogene duplication and insertion, which has been passed around to various dog line-
ages by deliberate cross-breeding.
3.8.3 Domestic trait 3: How to change hair type and structure
From smooth, long fur to coarse furnished (eyebrow and mustache growth) wirehair, dogs exhibit
a breadth of fur structure and type not found in their wild counterparts (Cadieu et al ., 2009 ). When
a genetic screen was conducted across 108 AKC-recognized breeds, seven hair phenotypes were
found to segregate with variants of three genes: fi broblast growth factor 5 ( FGF5 ; nucleotide muta-
tion), R-spondin-2 ( RSPO2; 167 nucleotide insertion), and a keratin ( KRT71 ; nucleotide mutation)
(Cadieu et al ., 2009 ). Each permutation of the genetic variants accounted for the vast majority of
canine coat texture/patterning. Regarding the evolutionary timing of these fur phenotypes, only
9781107024144c03_p22-41.indd 37 24/08/16 4:03 PM
38 Origins of the dog: Genetic insights into dog domestication
one is considered ancestral (short hair lacking curl, wirehair and furnishings), whereas the other
six phenotypes are derived , and have a more recent evolutionary history. The derived variants were
surveyed in the wolf genome and found to be lacking, further reinforcing the view that the canine
ancestral fur phenotype is short, straight, smooth and without furnishings (Cadieu et al ., 2009 ).
As with each of the domestic traits discussed, these phenotypes are exclusive to dogs compared
to their wild relatives and they likely arose only once (due to the genetic relationships among breeds
and the concordance of phenotype with genotype), with humans dispersing those mutations within
and across breed lineages through their selective breeding practices. These efforts were the primary
driving forces by which the appearance of dog diversity was created despite a paucity of genetic
diversity found in their genomes.
3.9 Conclusions
The origin of the domestic dog is a complex story, including many unresolved details on location
and timing. The aspects most clearly resolved are the genetic changes linked to the evolving canine
phenotype: the traits that are unique to domestic dogs. Many features of the dog phenotype can now
be viewed as an array of genetic variants, each infl uencing the size, shape and function of the ani-
mal. As our genetic sequencing technologies decrease in costs, we are better able to search multiple
dimensions of the genome for links to what makes a dog a dog. This is an exciting time for canine
geneticists who embark on the journey to understand the differences between the dog and wolf
genomes, and identify variants linked to behavior and disease, many of which have human analogs.
American Kennel Club ( 2006 ). The Complete Dog Book ,
20th edition. New York, NY : Ballantine Books .
Anderson , T. M. , vonHoldt , B. M. , Candille , S. I. et al .
( 2009 ). Molecular and evolutionary history of melanism
in North American gray wolves . Science , 323 : 1339–43 .
Akey , J. M. , Ruhe , A. L. , Akey , D. T. et al . ( 2010 ). Tracking
footprints of artifi cial selection in the dog genome .
Proceedings of the National Academy of Sciences USA ,
107 : 1160–5 .
Baker , J. , Liu , J. P. , Robertson , E. J. & Efstratiadis , A.
( 1993 ). Role of insulin-like growth factors in embryonic
and postnatal growth . Cell , 75 : 73 82 .
Barrett , R. D. H. & Schluter , D. ( 2008 ). Adaptation from
standing genetic variation . Trends in Ecology &
Evolution , 23 : 38 44 .
Barsh , G.S. ( 2007 ). How the dog got its spots . Nature
Genetics , 39 : 1304–6 .
Belyaev , D. K. ( 1969 ). Domestication of animals . Science ,
5 : 47 52 .
Biswas , S. & Akey , J. M. ( 2006 ). Genomic insights into
positive selection . Trends in Genetics , 22 : 437–46 .
Boyko , A. R. , Boyko , R.H. , Boyko , C.M. et al . ( 2009 ).
Complex population structure in African village dogs and
its implications for inferring dog domestication history .
Proceedings of the National Academy of Sciences USA ,
106 : 13903–8 .
Boyko , A. R. , Quignon , P. , Li , L. et al . ( 2010 ). A simple
genetic architecture underlies morphological variation in
dogs . PLoS Biology , 8 : e1000451 .
Boyko , A. R. ( 2011 ). The domestic dog: man’s best friend in
the genomic era . Genome Biology , 12 : 216 .
Cadieu , E. , Neff , M. , Quignon , P. et al . ( 2009 ). Coat
variation in the domestic dog is governed by variants in
three genes . Science , 326 : 150–3 .
Chase , K. , Carrier , D. R. , Adler , F. R. et al . ( 2002 ). Genetic
basis for systems of skeletal quantitative traits: principal
component analysis of the canid skeleton . Proceedings
of the National Academy of Sciences USA , 99 : 9930–5 .
Chase , K. , Carrier , D. R. , Adler , F. R. , Ostrander , E. A. & Lark ,
K. G. ( 2005 ). Interaction between the X chromosome
and an autosome regulates size sexual dimorphism in
Portuguese Water Dogs . Genome Research , 15 : 1820–4 .
Chase , K. , Jones , P. , Martin , A. , Ostrander , E. A. & Lark ,
K. G. ( 2009 ). Genetic mapping of fi xed phenotypes:
disease frequency as a breed characteristic . Journal of
Heredity , 100 : S37 41 .
Clutton-Brock , J. ( 1981 ). Domesticated Animals from Early
Times . Cambridge : Cambridge University Press .
9781107024144c03_p22-41.indd 38 24/08/16 4:03 PM
39 Bridgett M. vonHoldt and Carlos A. Driscoll
Coppinger , R. , Spector , L. & Miller , L. ( 2009 ). What,
if anything, is a wolf? In The World of Wolves: New
Perspectives on Ecology, Behaviour and Management ,
eds. M. Musiani , L. Boitani and P. Paquet . Calgary,
Alberta : The University of Calgary Press , pp. 51 65 .
Cordaux , R. & Batzer , M. A. ( 2009 ). The impact of
retrotransposons on human genome evolution . Nature
Reviews Genetics , 10 : 691 703 .
Crockford , S. J. & Kuzmin , Y. V. ( 2012 ) Comments on
Germonpré et al., Journal of Archaeological Science 26,
2009 “Fossil dogs and wolves from Palaeolithic sites in
Belgium, the Ukraine and Russia: osteometry, ancient
DNA and stable isotopes”, and Germonpré, Lázkicková-
Galetová, and Sablin, Journal of Archaeological Science
26, 2012 “Paleolithic dog skulls at the Gravettian
Predmostí site, the Czech Republic” . Journal of
Archaeological Science , 39 : 2797–801 .
Darwin , C. ( 1868 ). The Variation of Animals and Plants
under Domestication . London : John Murray .
Dayan , T. ( 1999 ). Early domesticated dogs of the Near East .
Journal of Archaeological Science , 21 : 633–40 .
Diamond , J. ( 2005 ). Guns, Germs, and Steel . New York :
Norton and Company, Inc .
Ding , Z. , Oskarsson , M. , Ardalan , A. et al . ( 2012 ). Origins
of domestic dog in Southern East Asia is supported by
analysis of Y-chromosome DNA . Heredity , 108 : 507–14 .
Dobney , K. & Larson , G. ( 2006 ). Genetics and animal
domestication: new windows on an elusive process .
Journal of Zoology , 269 : 261–71 .
Driscoll , C. A. , Menotti-Reymond , M. , Roca , A. L. et al .
( 2007 ). The Near Eastern origin of cat domestication .
Science , 317 : 519–23 .
Driscoll , C. A. , Macdonald , D. W. & O’Brien , S. J. ( 2009 ).
From wild animals to domestic pets, an evolutionary
view of domestication . Proceedings of the National
Academy of Sciences , 106 : S9971–8 .
Druzhkova , A. S. , Thalmann , O. , Trifonov , V. A. , Leonard ,
J. A. , Vorobieva , N.V. , Ovodov , N. D. , Graphodatsky ,
A. S. & Wayne , R. K. ( 2013 ). Ancient DNA analysis
affi rms the canid from Altai as a primitive dog . PLoS
One , 8 : e57754 .
Fan , Z. , Silva , P. , Gronau , I. , Wang , S. , Serres Armero , A. ,
Schweizer , R. M. , Ramirez , O. , et al . ( 2016 ). Worldwide
patterns of genomic variation and admixture in gray
wolves . Genome Research , 26 : 163–73 .
Flint , J. & Mackay , T. F. C. ( 2009 ). Genetic architecture of
quantitative traits in mice, fl ies and humans . Genome
Research , 19 : 723–33 .
Frantz , L. A. , Mullin , V. E. , Pionnier-Capitan , M. ,
Lebrasseur , O. , Olliver , M. , Perri , A. , et al . ( 2016 ).
Genomic and archaeological evidence suggest a dual
origin of domestic dogs . Science , 352 : 1228–31 .
Freedman , A. H. , Gronau , I , Schweizer , R. M. et al . ( 2014 ).
Genome Sequencing Highlights the Dynamic Early
History of Dogs . PLoS Genetics , 10 : e1004016
Freedman , A. H. , Schweizer , R. M . Ortega-Del Vecchyo ,
D. , Han , E. , Davis , B. W. , Gronau , I. , et al . ( 2016 ).
Demographically-based evaluation of genomic regions
under selection in domestic dogs . PLoS Genetics , 12 :
Germonpré , M. , Sablin , M. , Stevens , R. et al . ( 2009 ). Fossil
dogs and wolves from Palaeolithic sites in Belgium, the
Ukraine and Russia: osteometry, ancient DNA and stable
isotopes . Journal of Archaeological Science , 36 : 473–60 .
Giustina , A. , Mazziotti , G. & Canalis , E. ( 2008 ). Growth
hormone, insulin-like growth factors, and the skeleton .
Endocrine Reviews , 29 : 535–59 .
Goebel , T. , Waters , M. R. & O’Rourke , D. H. ( 2008 ). The
late Pleistocene dispersal of modern humans in the
Americas . Science , 319 : 1497–502 .
Gray , M. M. , Sutter , N. B. , Ostrander , E. A. & Wayne , R. K.
( 2010 ). The IGF1 small dog haplotype is derived from
Middle Eastern gray wolves . BMC Biology , 8 : 16 .
Hare , B. , Plyusnina , I. , Ignacio , N. et al . ( 2005 ). Social
cognitive evolution in captive foxes is a correlated by-
product of experimental domestication . Current Biology ,
15 : 226–30 .
Innan , H. & Kim , Y. ( 2004 ). Pattern of polymorphism after
strong artifi cial selection in a domestication event .
Proceedings of the National Academy of Sciences USA ,
101 : 10667–72 .
IUCN ( 2012 ). The IUCN Red List of threatened species.
Version 2012.1 [Online]. Available:
Jones , P. , Chase , K. , Martin , A. , Ostrander , E. A. & Lark ,
K. G. ( 2008 ). Single-nucleotide polymorphism-based
association mapping of dog stereotypes . Genetics , 179 :
1033–44 .
Kazazian , H. ( 2004 ). Mobile elements: drivers of genome
evolution . Science , 303 : 1626–32 .
Kirkness , E. F. , Bafna , V. , Halpern , A. L. et al . ( 2003 ).
The dog genome: survey sequencing and comparative
analysis . Science , 301 : 1898–903 .
Kukekova , A. V. , Trut , L. N. , Chase , K. et al . ( 2010 ).
Mapping loci for fox domestication: Deconstruction/
reconstruction of a behavioral phenotype . Behavorial
Genetics , 41 : 593 606 .
Laron , Z. ( 2001 ). Insulin-like growth factor 1 (IGF-1): a
growth hormone . Molecular Pathology , 54 : 311–16 .
Larson , G. , Karlsson , E. K. , Perri , A. et al . ( 2012 ). Rethinking
dog domestication by integrating genetics, archeology,
and biogeography . Proceedings of the National Academy
of Sciences USA , 109 : 8878–83 .
Lefebvre , V. & Bhattaram , P. ( 2010 ). Vertebrate
skeletogenesis . Current Topics in Developmental
Biology , 90 : 291 317 .
Leonard , J. A. , Wayne , R. K. , Wheeler , J. et al . ( 2002 ).
Ancient DNA evidence for Old World origin of New
World dogs . Science , 298 : 1613–16 .
Leonard , J. A. , Vilà , C. & Wayne , R. K. ( 2006 ). From wild
wolf to domestic dog . In The Dog and Its Genome , eds.
E. A. Ostrander , U. Giger & K. Lindblad-Toh . Cold
Spring Harbor, NY : Cold Spring Harbor Laboratory
Press , pp. 95 118 .
Lindblad-Toh , K. , Wade , C. M. , Mikkelsen , T. S. et al . ( 2005 ).
Genome sequence, comparative analysis and haplotype
structure of the domestic dog . Nature , 438 : 803–19 .
9781107024144c03_p22-41.indd 39 24/08/16 4:03 PM
40 Origins of the dog: Genetic insights into dog domestication
Mech , L. D. & Boitani , L. ( 2003 ). Wolf social ecology . In
Wolves: Behavior, Ecology, and Conservation , eds. L. D.
Mech & L. Boitani . Chicago, IL : The University of
Chicago Press , pp. 1 34 .
McClintock , B. ( 1956 ). Controlling element and the gene .
Cold Spring Harbor Symposia on Quantitative Biology ,
31 : 197 216 .
Morey , D. F. ( 1994 ). The early evolution of the domestic
dog . American Scientist , 82 : 336–47 .
Ovodov , M. D. , Crockford , S. J. , Kuzmin , Y. V. et al . ( 2011 ).
A 33 000 year-old incipient dog from the Altai Mountains
of Siberia: Evidence of the earliest domestication
disruption by the last glacial maximum . PLoS One , 6 :
e22821 .
Packard , J. M. ( 2003 ). Wolf behavior: Reproductive, social,
and intelligent . In Wolves: behavior, ecology, and
conservation . eds. L. D. Mech & L. Boitani . Chicago, IL :
The University of Chicago Press , pp. 35 65 .
Pang , J. F. , Kluetsch , C. , Zou , X. 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 . Molecular Biology & Evolution , 26 : 2849–64 .
Parker , H. G. ( 2012 ). Genomic analyses of modern dog
breeds . Mammalian Genome , 23 : 19 27 .
Parker , H. G. , Kim , L. V. , Sutter , N. B. et al . ( 2004 ). Genetic
structure of the purebred domestic dog . Science , 304 :
1160–4 .
Parker , H. G. & Ostrander , E. A. ( 2005 ). Canine genomics and
genetics: running with the pack . PLoS Genetics , 1 : e58 .
Parker , H. G. , vonHoldt , B. M. , Quignon , P. et al . ( 2009 ).
An expressed fgf4 retrogene is associated with breed-
defi ning chondrodysplasia in domestic dogs . Science ,
325 : 995–8 .
Parker , H. P. , Shearin , A. L. & Ostrander , E. A. ( 2010 ).
Man’s best friend becomes biology’s best in show:
genome analyses in the domestic dog . Annual Review of
Genetics , 44 : 309–36 .
Perini , F. A. , Russo , C. A. & Schrago , C. G. ( 2009 ). The
evolution of South American endemic canids: a history
of rapid diversifi cation and morphological parallelism .
Journal of Evolutionary Biology , 23 : 311–22 .
Randi , E. ( 2008 ). Detecting hybridization between wild
species and their domesticated relatives . Molecular
Ecology , 17 : 285–93 .
Ritvo , H. ( 1989 ). The Animal Estate: The English and Other
Creatures in the Victorian Age . Cambridge, MA : Harvard
University Press .
Sablin , M. & Khlopachev , G. ( 2002 ). The earliest Ice Age
dogs: evidence from Eliseevichi I . Current Anthropology ,
45 : 795 819 .
Savolainen , P. , Zhang , Y. P. , Luo , J. , Lundeberg , J. & Leitner ,
T. ( 2002 ) Genetic evidence for an East Asian origin of
domestic dogs . Science , 298 : 1610–13 .
Savolainen , P. , Leitner , T. , Wilton , A. N. , Matisoo-Smith ,
E. & Lundeberg , J. ( 2004 ). A detailed picture of the
origin of the Australian dingo, obtained from the study
of mitochondrial DNA . Proceedings of the National
Academy of Sciences USA , 101 : 12387–90 .
Shannon , L. M. , Boyko , R. H. , Castelhano , M. , Corey ,
E. , Hayward , J. J. , McLean , C. , et al . ( 2015 ) Genetic
structure in village dogs reveals a Central Asian
domestication origin . PNAS , 112 : 13639–44 .
Spady , T. C. & Ostrander , E. A. ( 2008 ). Canine behavioral
genetics: pointing out the phenotypes and herding up the
genes . American Journal of Human Genetics , 82 : 10 18 .
Statham , M. J. , Trut , L. N. , Sacks , B. N. et al . ( 2011 ). On the
origin of a domesticated species: indentifying the parent
population of Russian silver foxes ( Vulpes vulpes ) .
Biological Journal of the Linnean Society , 103 : 168–75 .
Stockard , C. R. ( 1941 ). The Genetic and Endocrinic Basis
for Differences in Form and Behavior: As Elucidated
by Studies of Contrasted Pure-line Dog Breeds and
their Hybrids . Philadelphia, PA : The Wistar Institute of
Anatomy and Biology .
Su , N. , Du , X. & Chen , L. ( 2008 ). FGF signaling: its role
in bone development and human skeleton diseases .
Frontiers in Bioscience , 13 : 2842–65 .
Sundqvist , A. K. , Bjornfeldt , S. , Leonard , J. A. et al . ( 2006 ).
Unequal contribution of sexes in the origin of dog breeds .
Genetics , 172 : 1121–8 .
Sutter , N. B. & Ostrander , E. A. ( 2004 ). Dog star rising:
the canine genetic system . Nature Reviews Genetics , 5 :
900–10 .
Sutter , N. B. , Bustamante , C. D. , Chase , K. et al . ( 2007 ). A
single IGF1 allele is a major determinant of small size in
dogs . Science , 316 : 112–15 .
Thalmann , O. , Shapiro , B. , Cui , P. et al . ( 2013 ) Complete
mitochondrial genomes of ancient canids suggest a
European origin of domestic dogs . Nature , 342 : 871–4 .
Trut , L. ( 1999 ). Early canid domestication: the farm-fox
experiment . American Scientist , 87 : 160–9 .
Trut , L. , Oskina , I. & Kharlamova , A. ( 2009 ). Animal
evolution during domestication: the domesticated fox as
a model . Bioessays , 31 : 349–60 .
Vigne , J. D. ( 2011 ). The origins of animal domestication and
husbandry: a major change in the history of humanity and
the biosphere . Comptes Rendus Biologie , 334 : 171–81 .
Vilà , C. , Savolainen , P. , Maldonado , J. E. et al . ( 1997 ).
Multiple and ancient origins of the domestic dog .
Science , 276 : 1687–9 .
Vilà , C. & Wayne , R. K. ( 1999 ). Hybridization between
wolves and dogs . Conservation Biology , 13 : 195–8 .
Vilà , C. , Seddon , J. & Ellegren , H. ( 2005 ). Genes of
domestic mammals augmented by backcrossing with
wild ancestors . Trends in Genetics , 21 : 214–18 .
Visscher , P. M. ( 2008 ). Sizing up human height variation .
Nature Genetics , 40 : 489–90 .
Voight , B. F. , Kudaravalli , S. , Wen , X. & Pritchard , J. K.
( 2006 ). A map of recent positive selection in the human
genome . PLoS Biology , 4 : e72 .
vonHoldt , B. M. , Stahler , D. R. , Smith , D. W. et al . ( 2008 ).
The genealogy and genetic viability of reintroduced
Yellowstone gray wolves . Molecular Ecology , 17 : 252–
74 .
vonHoldt , B. M. , Pollinger , J. P. , Lohmueller , K. E. et al .
( 2010 ). Genome-wide SNP and haplotype analyses
9781107024144c03_p22-41.indd 40 24/08/16 4:03 PM
41 Bridgett M. vonHoldt and Carlos A. Driscoll
reveal a rich history underlying dog domestication .
Nature , 464 : 898 902 .
Wang , G.-D. , Zhai , W. , Yang , H.-C. , Wang , L. , Zhong , L. ,
Liu , Y.-H. , et al . ( 2016 ) Out of southern East Asia: the
natural history of domestic dogs across the world . Cell
Research , 26 : 21 33 .
Wang , X. & Tedford , R. H. ( 2008 ). Dogs: Their Fossil
Relatives and Evolutionary History . New York, NY :
Columbia University Press .
Waters , M. R. & Stafford , T. W. Jr. ( 2007 ). Redefi ning
the age of Clovis: implications for the peopling of the
Americas . Science , 315 : 1122–6 .
Wayne , R. K. & vonHoldt , B. M. ( 2012 ). Evolutionary
genomics of dog domestication . Mammalian Genome ,
23 : 3 18 .
Wellcome Trust Case Consortium ( 2007 ). Genome-wide
association study of 14,000 cases of seven common
diseases and 3,000 shared controls . Nature , 447 : 661–78 .
Yakar , S. , Rosen , C. J. , Beamer , W. G. et al . ( 2002 ). Circulating
levels of IGF-1 directly regulate bone growth and density .
Journal of Clinical Investigation , 110 : 771–81 .
Young , A. & Bannasch , D. ( 2006 ). Morphological variation
in the dog . In The Dog and Its Genome , eds. E. A.
Ostrander , U. Giger & K. Lindblad-Toh . Cold Spring
Harbor, NY : Cold Spring Harbor Laboratory Press , pp.
47 65 .
Zeder , M. A. , Emshwiller , E. , Smith , B. D. & Bradley , D. G.
( 2006 ). Documenting domestication: the intersection of
genetics and archaeology . Trends in Genetics , 22 : 139–
55 .
Zeder , M. A. ( 2008 ). Domestication and early agriculture in
the Mediterranean Basin: origins, diffusion, and impact .
Proceedings of the National Academy of Sciences USA ,
105 : 11597–604 .
Zeder , M. A. ( 2012 ). The domestication of animals . Journal
of Anthropological Research 68 ( 2 ): 161 .
9781107024144c03_p22-41.indd 41 24/08/16 4:03 PM
... We rely on skeletal morphology but also on context. A suite of morphological and physiological traits are termed the "domestication syndrome," because they occur together and may be recognized in many domestic mammals (Trut, Oskima, & Kharlamova, 2009; and see von Holdt & Driscoll, 2017; but see Lord, Larson, Coppinger, & Karlson, 2019). Such traits include changes to body size (including both dwarf and giant forms), many specific somatic traits (e.g., floppy ears, tail curling or rolling; coat color patterns), and reproductive physiology. ...
... Clutton-Brock (1999) suggested that humans may have tamed and bred wolf pups from these neighboring canids. But more recently, a number of transitional stages have been suggested, as summarized by von Holdt and Driscoll (2017). First, selection may have favored wild canids that were tolerant of humans; they would have reaped the benefits of commensalism (symbiosis in which only one organism benefits). ...
... Domestication as a prolonged process may include a period in which ancestors of domestic dogs evolved on their own, in a period of "self-domestication." Or to put it another way, not all traits of domestic dogs are necessarily derived from intentional artificial selection (von Holdt & Driscoll, 2017). In this issue, Chirchir (2021) investigates trabecular bone fraction in dogs and wolves, in order to test the hypothesis that a gracilization of the skeleton, as evidenced by low trabecular bone fraction, is a byproduct of domestication. ...
This special issue of The Anatomical Record is the end result of a rare convergence of researchers scattered around the globe who came together to explore the mystery of the dog-human connection. Many of the discussions at the 12th International Congress of Vertebrate Morphology in Prague (July 23, 2019) are echoed within this issue. The enigmatic origins of dog domestication (as well as feralized descendants such as the dingo) are discussed, including phases of domestication that we might infer, and our historical knowledge of dog breeding. Emphasized by the morphological and genetic data are the forces of selection, both unintentional and intentional. In our modern life with dogs, we enjoy their companionship and benefit from the utility of many breeds, but we encounter unintended health care issues that are often breed-specific. Dogs are so different in their sensory specializations (especially olfaction), but have uniquely (among other domestic mammals) developed highly sophisticated means of interspecific communication with humans. In sum, the manuscripts within this issue discuss anatomical, paleontological, genetic, and behavioral evidence bearing on the antiquity of the domestic dog, the process of domestication, and the many ways in which dogs continue to affect human life.
... The tibia and fibula showed no major differences as seen in other domestic species [2,[13][14][15][16][17][18][19][20] Igado OO, [7]. The weight of various bones taken increased with age, the mean width, length and circumference of various segments also increases with age for all the groups and the values obtained were statistically significant except for the fibula, in which the values obtained were almost similar and statistically the same [20][21][22][23][24][25]. ...
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This study was aimed at investigating the age related changes in the morphometry and biometry of some selected bones of the hind limb of Nigerian local dog (canis lupus familiaris). In this study a total of fifteen dogs were used as sample and were grouped into five age categories (group A-E). The dogs were aged by estimation using dentition eruption and wearing. The segment of the hind limb was identified and separated from the rest from other parts. The gross study of the hind limb revealed that the hind limb was composed of: ossa coxarum, femur, patella, tibia, fibula, tarsal and metatarsal bones. The biometric study revealed that the weight, length, width and circumference were found to be increasing with advancement in age. The result revealed that mean weight, length and circumference of various segments of the ossa coxarum, femur and the tibia tends to increase with age across the group that is from group A to group E. However, there is variation in the length of the fibula, width of the obturator foramen and length of the obturator foramen. Base on the above results, it was concluded that base line data was established with the aim of enhancing learning.
... Crucially, as the field moves through this period of development, it is more important than ever that researchers employ rigorous experimental designs along with objective and transparent approaches to scoring and analysis, such that the products of this research can be adequately evaluated by both scientists and practitioners in the field (65). Along these lines, researchers should aim to [1] present methodological details such that all components of a study are fully reproducible, [2] conduct and report interrater reliability for measures used, [3] conduct and report retest reliability, [4] differentiate between approaches that describe statistical association vs. predictive validity, [5] employ wellpowered designs that control for confounding factors, and [6] ensure adequate blinding between research staff and dog training professionals. ...
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Dogs perform a variety of integral roles in our society, engaging in work ranging from assistance (e.g., service dogs, guide dogs) and therapy to detection (e.g., search-and-rescue dogs, explosive detection dogs) and protection (e.g., military and law enforcement dogs). However, success in these roles, which requires dogs to meet challenging behavioral criteria and to undergo extensive training, is far from guaranteed. Therefore, enhancing the selection process is critical for the effectiveness and efficiency of working dog programs and has the potential to optimize how resources are invested in these programs, increase the number of available working dogs, and improve working dog welfare. In this paper, we review two main approaches for achieving this goal: (1) developing selection tests and criteria that can efficiently and effectively identify ideal candidates from the overall pool of candidate dogs, and (2) developing approaches to enhance performance, both at the individual and population level, via improvements in rearing, training, and breeding. We summarize key findings from the empirical literature regarding best practices for assessing, selecting, and improving working dogs, and conclude with future steps and recommendations for working dog organizations, breeders, trainers, and researchers.
... Dog domestication may have occurred as a series of spatially disparate domestication (including failed) events (vonHoldt et al., 2012;Thalmann et al., 2013;Germonpr� e et al., 2015a;Skoglund et al., 2015;Frantz et al., 2016); a complicated admixture of newly forming dog and sympatric wolf populations (vonHoldt et al., 2012;Morey, 2014, but see Botigu� e et al., 2017. Dogs could even derive from a now-extinct lineage of wolves (Freedman et al., 2014;Larson and Bradley, 2014;Perri, 2016;vonHoldt and Driscoll, 2016). ...
Morphological and genetic evidence put dog domestication during the Paleolithic, sometime between 40,000 and 15,000 years ago, with identification of the earliest dogs debated. We predict that these earliest dogs (referred to herein as protodogs), while potentially difficult to distinguish morphologically from wolves, experienced behavioral shifts, including changes in diet. Specifically, protodogs may have consumed more bone and other less desirable scraps within human settlement areas. Here we apply Dental Microwear Texture Analysis (DMTA) to canids from the Gravettian site of P�redmostí (approx. 28,500 BP), which were previously assigned to the Paleolithic dog or Pleistocene wolf morphotypes. We test whether these groups separate out significantly by diet- related variation in microwear patterning. Results are consistent with differences in dietary breadth, with the Paleolithic dog morphotype showing evidence of greater durophagy than those assigned to the wolf morphotype. This supports the presence of two morphologically and behaviorally distinct canid types at this middle Upper Paleolithic site. Our primary goal here was to test whether these two morphotypes expressed notable differences in dietary behavior. However, in the context of a major Gravettian settlement, this may also support evidence of early stage dog domestication. Dental microwear is a behavioral signal that may appear generations before morphological changes are established in a population. It shows promise for distinguishing protodogs from wolves in the Pleistocene and domesticated dogs from wolves elsewhere in the archaeological record.
... Over the past decades, dogs have assumed many significant roles within human society, ranging from hunting partner to companion animal [1]. Nowadays, dogs are increasingly important within the family system [2] and they often gain a special role as social partners. ...
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Recent studies show evidence that human-dog companionship has healthy effects on humans. For example, findings demonstrate that owning a dog leads to a reduction in stress levels. Aspects that have not been taken into consideration so far are underlying theoretical principles of stress like the sense of coherence (SOC) by Aaron Antonovsky. The SOC consists of psycho-social, biochemical and physical conditions which indicate whether or not inner and outer stimuli are comprehensive, manageable and meaningful to an individual. In addition, it is still unclear if owning a dog affects the subjective assessment of critical life events (CLE), which is associated with the strength of the SOC (the stronger the SOC, the better the handling and assessment of stressful situations). Based on these aspects, the goal of the study was to examine if dog ownership, as well as values of the SOC, have an impact on the subjective evaluation of CLE (including daily hassles as well as unexpected critical life events). For this purpose, dog owners and non-dog owners were surveyed online and were compared based on their personal estimations regarding these constructs. Statistical analysis including t-tests, correlations and interaction-analyses were performed and a significant difference between dog owners and non-dog owners regarding the assessment of daily hassles was found. Contrary to expectations, results show that dog owners assessed daily stressors to be more stressful than non-dog owners did. Moreover, data show that the higher the number of stated relationships (inner-and cross-species), the more stressful life events were assessed to be. Calculations showed no evidence for the influence of dogs regarding the SOC. Based on the actual findings, it might be assumed, that an overestimation of the dog's protective role regarding stress has taken place in public media and in research as well.
... Experimental findings on young domesticated dogs and human-raised wolf pups indicate dogs have a greater sensitivity to the pointing gesture and human eye gaze than their undomesticated counterparts, a developmentalcognitive bias for human communicative signals (Miklósi et al 2003, Gácsi et al 2009, also see Range and Virány 2015). Given that dogs underwent domestication over the last 13,000 to 45,000 years (Vonholdt and Driscoll 2017), this would suggest that developmental bias in cognitive-conceptual capacities to communicative signals may arise relatively quickly in evolutionary terms once a communicative signal becomes culturally or environmentally available in a population. ...
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Gene-culture coevolutionary theory suggests language-like communication evolved to teach kin and provided the high-fidelity transmission necessary for the emergence of cumulative culture. If this view is correct, then a more fundamental evolutionary account of language origins will also require explaining both the adaptive emergence of teaching in an ancestral hominid and the absence of teaching in most species. I argue the barrier or impediment to language-like communication and teaching derives from the fundamental nature of animal communication: it does not drive positive selection for a cognitive bias for communication to be honest and cooperative in potential pupils nor does it provide potential teachers with unique signature signals encoding the identity of potential pupils. The absence of these characters increases the energetic cost of teaching for teachers, thereby blocking language-like communication and teaching in most species. The pathway to language-like communication and teaching required the exceptionally rare adaptation for a signature call and copy system as it provides both these capacities. I maintain this precursor reduced the energetic cost of teaching for teachers and enabled the adaptive emergence of the pointing gesture for teaching kin at the Ardipithecus-Australopithecus transition. This allowed the threshold of elementary complex traditions to be crossed, a population of teachers to emerge and provided the precursors necessary for the adaptive emergence of more complex traditions requiring high-fidelity transmission yielding cumulative culture in subsequent Australopithecines. Important implications for gene-culture coevolutionary theory, human self-domestication hypotheses and prevailing gesture-first theories of language origins are also discussed.
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During two retreats in 2017 and 2020, a group of international scientists convened to explore the Human-Animal Bond. The meetings, hosted by the Wallis Annenberg PetSpace Leadership Institute, took a broad view of the human-dog relationship and how interactions between the two may benefit us medically, psychologically or through their service as working dogs (e.g. guide dogs, explosive detection, search and rescue, cancer detection). This Frontiers’ Special Topic has collated the presentations into a broad collection of 14 theoretical and review papers summarizing the latest research and practice in the historical development of our deepening bond with dogs, the physiological and psychological changes that occur during human-dog interactions (to both humans and dogs) as well as the selection, training and welfare of companion animals and working dogs. The overarching goals of this collection are to contribute to the current standard of understanding of human-animal interaction, suggest future directions in applied research, and to consider the interdisciplinary societal implications of the findings.
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This research was conducted over period of 3 months with the aim of studying Age related changes of selected bones of forelimb (Scapula, Humerus, Radius and Ulna) in Local Mongrelian Dog (Canis lupus familiaris). The study entails biometrical and gross observations on the bones. The sample bones were acquired from the experimental animals of comparative anatomy in the department. The bones were categorized into various age groups for the research. The length, width, diameter and circumference of the samples (scapula, humerus, radius and ulna bones) were determined for all the groups. The shape, size, color, location, position and relation of each segment of the samples at various stages of development were determined. The differences across the age groups of different samples were observed and recorded. Based on the research result, it was concluded that, the biometric and morphometry data was found to be increasing with advancement of age. A baseline data was established with the view to enhance learning.
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The Jianchang duck is mainly distributed in Southwest China, and has the characteristics of fast growth rate and strong abilities in lipid deposition in the liver. In order to investigate the effects of domestication process on formation of the unique characteristics of Jianchang duck, the whole genome of sixteen individuals and three pooling of Jianchang duck were re-sequenced, and genome data of 70 mallards and 83 domestic ducks from thirteen different places in China were obtained from NCBI. The population stratification and evolution analysis showed gene exchanges existed between the Jianchang and other domestic duck populations, as well as Jianchang ducks and mallards. Genomic comparison between mallards and Jianchang ducks showed genes, including CNTN1 , CHRNA9 , and SHANK2 , which is involved in brain and nerve development, experienced strong positive selection in the process of Jianchang duck domestication. The genomic comparison between Jianchang and domestic duck populations showed that HSD17B12 and ESM1 , which affect lipid metabolism, experienced strong positive selection during the domestication process. FST analysis among populations of Jianchang duck with different plumage colors indicated that MITF was related to the phenotype of a white feather, while MC1R was related to the phenotype of hemp feather. Our results provided a base for the domestication process of Jianchang duck and the genomic genes for unique traits.
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Americas Redefining the Age of Clovis: Implications for the Peopling of the This copy is for your personal, non-commercial use only. clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others here. following the guidelines can be obtained by Permission to republish or repurpose articles or portions of articles): July 7, 2014 (this information is current as of The following resources related to this article are available online at
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The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
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Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers.
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The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. The specific evolutionary relationships of dogs and extant wolves are controversial and have been explored with a variety of genomic approaches. However, these studies suffer from a paucity of samples from throughout the Holarctic range of the wolf. To address questions about wolf relationships to each other and dogs, we assemble and analyze a dataset of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event, and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprising recent common ancestry, and experienced a dramatic population decline beginning at least ~30 kya. We suggest this crisis was related to the colonization of Eurasia by modern human hunter-gatherers who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.
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The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.Cell Research advance online publication 15 December 2015; doi:10.1038/cr.2015.147.
The dog ( Canis familiaris ) was the first species to be domesticated. This event was a crucial step in the history of humankind and it occurred more than 15,000 years ago when humans were generally nomadic hunter–gatherers (Price and Gebauer 1995). Dogs were domesticated at least several thousand years before any other plant or animal species, and the few ancient remains found so far come from Europe, North America, and the Near East, suggesting they rapidly spread throughout the world after initial domestication events. As a result of the scarce and highly fragmented archaeological evidence, little is known about the specific location, conditions, or causes of domestication. Knowledge of the pattern and process of domestication is essential to understanding human civilization at the end of the Stone Age and the transition from hunter–gatherer to agrarian societies. Domestic dogs are morphologically diverse, and differences in cranial and skeletal proportions among dog breeds exceed that among wild canids (Wayne 1986a,b). Domestic dogs are also behaviorally diverse and have behavioral patterns that are distinct from those of their wild ancestors (Coppinger and Coppinger 2001; Hare et al. 2002; Miklosi et al. 2003). Despite this dramatic diversity in phenotype, dogs have diverged very recently from their wild progenitor, the gray wolf ( Canis lupus ), and consequently, the two species have very similar genomes. Understanding the small subset of genes that have changed during domestication will provide insights into how rapid diversification occurs in domestic and wild species, as well as a more precise understanding...