Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA

Multiple Origins and Genomic Basis of Complex Traits in Sighthounds

Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.

Being a Dog: A Review of the Domestication Process

The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.

Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups

Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.

Conservation concerns associated with low genetic diversity for K'gari-Fraser Island dingoes

The dingo population on world heritage-listed K'gari-Fraser Island (K'gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K'gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (A_R, H_E, P_AR; p < 0.05) with a fourfold reduction in effective population size (N_e = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K'gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

Paternal Origins and Migratory Episodes of Domestic Sheep

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.

Deciphering the puzzles of dog domestication

The domestic dog, as a highly successful domestication model, is well known as a favored human companion. Exploring its domestication history should provide great insight into our understanding of the prehistoric development of human culture and productivity. Furthermore, investigation on the mechanisms underpinning the morphological and behavioral traits associated with canid domestication syndrome is of significance not only for scientific study but also for human medical research. Current development of a multidisciplinary canine genome database, which includes enormous omics data, has substantially improved our understanding of the genetic makeup of dogs. Here, we reviewed recent advances associated with the original history and genetic basis underlying environmental adaptations and phenotypic diversities in domestic dogs, which should provide perspectives on improving the communicative relationship between dogs and humans.

Complete Range of the Universal mtDNA Gene Pool and High Genetic Diversity in the Thai Dog Population

The dog population of Southern East Asia is unique in harboring virtually the full range of the universal mtDNA gene pool, and consequently, it has the highest genetic diversity worldwide. Despite this, limited research has been performed on dog genetics within this region. Here we present the first comprehensive study of a sub-region within Southern East Asia, analyzing 528bp of mtDNA for 265 dogs from Thailand, in the context of dogs from across the Old World. We found that Thailand was the only region in the world that has the full range of the universal mtDNA gene pool, that is, all 10 sub-haplogroups. Consequently, the statistics for diversity are among the highest, especially in North Thailand, which had high values for haplotype diversity and the number of haplotypes, and the lowest proportion of individuals with a universal type-derived haplotype (UTd) among all regions. As previously observed, genetic diversity is distinctly lower outside Southern East Asia and it decreases following a cline to the lowest values in western Eurasia. Thus, the limited geographical region of Thailand harbors a distinctly higher genetic diversity than much larger regions in western Eurasia, for example, Southwest Asia and Europe which have only five and four of the 10 sub-haplogroups, respectively. Within Thailand, diversity statistics for all four sub-regions follow the general pattern of Southern East Asia, but North Thailand stands out with its high diversity compared to the other regions. These results show that a small part of Southern East Asia harbors the full range of the mtDNA gene pool, and they emphasize the exceptional genetic status of Southern East Asia. This indicates that today's dogs can trace a major part of their ancestry to Southern East Asia or closely situated regions, highlighting Thailand as a region of special interest. Considering the large genetic diversity found in Thailand and that many neighboring regions, e.g., Myanmar and Laos, have not been studied for dog genetics, it is possible that large parts of the dog gene pool remain undiscovered. It will be an important task for future studies to fill in these blanks on the phylogeographic map.

Population structure and genetic history of Tibetan Terriers

Background

Tibetan Terrier is a popular medium-sized companion dog breed. According to the history of the breed, the western population of Tibetan Terriers includes two lineages, Lamleh and Luneville. These two lineages derive from a small number of founder animals from the native Tibetan Terrier population, which were brought to Europe in the 1920s. For almost a century, the western population of Tibetan Terriers and the native population in Tibet were reproductively isolated. In this study, we analysed the structure of the western population of Tibetan Terriers, the original native population from Tibet and of different crosses between these two populations. We also examined the genetic relationships of Tibetan Terriers with other dog breeds, especially terriers and some Asian breeds, and the within-breed structure of both Tibetan Terrier populations.

Results

Our analyses were based on high-density single nucleotide polymorphism (SNP) array (Illumina HD Canine 170 K) and microsatellite (18 loci) genotypes of 64 Tibetan Terriers belonging to different populations and lineages. For the comparative analysis, we used 348 publicly available SNP array genotypes of dogs from other breeds. We found that the western population of Tibetan Terriers and the native Tibetan Terriers clustered together with other Asian dog breeds, whereas all other terrier breeds were grouped into a separate group. We were also able to differentiate the western Tibetan Terrier lineages (Lamleh and Luneville) from the native Tibetan Terrier population.

Conclusions

Our results reveal the relationships between the western and native populations of Tibetan Terriers and support the hypothesis that Tibetan Terrier belongs to the group of ancient dog breeds of Asian origin, which are close to the ancestors of the modern dog that were involved in the early domestication process. Thus, we were able to reject the initial hypothesis that Tibetan Terriers belong to the group of terrier breeds. The existence of this native population of Tibetan Terriers at its original location represents an exceptional and valuable genetic resource.

Genetic diversity and population structure of the Sapsaree, a native Korean dog breed

BACKGROUND

The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed was rescued from extinction and population sizes have been gradually increasing over the past few decades. The aim of this study was to ascertain novel information about the genetic diversity, population structure, and demographic history of the Sapsaree breed using genome-wide single nucleotide polymorphism data. We characterized the genetic profile of the Sapsaree breed by comparison with seven foreign dog breeds with similar morphologies to estimate genetic differentiation within and among these breeds.

RESULTS

The results suggest that Sapsarees have higher genetic variance compared with the other breeds analyzed. The majority of the Sapsarees in this study share a discrete genetic pattern, although some individuals were slightly different, possibly as a consequence of the recent restoration process. Concordant results from analyses of linkage disequilibrium, effective population size, genetic diversity, and population structural analyses illustrate a relationship among the Sapsaree and the Tibetan breeds Tibetan terrier and Lhasa Apso, and a small genetic introgression from European breeds. The effective population size of the Sapsaree has contracted dramatically over the past generations, and is currently insufficient to maintain long-term viability of the breed's genetic diversity.

CONCLUSIONS

This study provides novel insights regarding the genetic diversity and population structure of the native Korean dog breed Sapsaree. Our results suggest the importance of a strategic and systematic approach to ensure the genetic diversity and the authenticity of the Sapsaree breed.

The horse Y chromosome as an informative marker for tracing sire lines

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

The evolutionary history of grey wolf Y chromosomes

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.

Haplotype diversity in mitochondrial DNA reveals the multiple origins of Tibetan horse

The Tibetan horse is a species endemic to the Tibetan plateau, with considerable economic value in the region. However, we currently have little genetic evidence to verify whether the breed originated in Tibet or if it entered the area via an ancient migratory route. In the present study, we analyzed the hypervariable segment I sequences of mitochondrial DNA (mtDNA) in 2,050 horses, including 290 individuals from five Tibetan populations and 1,760 from other areas across Asia. Network analysis revealed multiple maternal lineages in the Tibetan horse. Component analysis of sub-lineage F3 indicated that it decreased in frequency from east to west, a trend reflected both southward and northward from Inner Mongolia. Analysis of population genetics showed that the Deqen horse of eastern Tibet was more closely related to the Ningqiang horse of northern China than to other Tibetan horses or the Yunnan horse. These results indicated that the Tibetan horse migrated first from Central Asia to Mongolia, moved south to eastern Tibet (near Deqen), then finally westward to other regions of Tibet. We also identified a novel lineage K that mainly comprises Tibetan and Yunnan horses, suggesting autochthonous domesticated origin for some Tibetan horse breeds from local wild horses. In conclusion, our study demonstrated that modern Tibetan horse breeds originated from the introgression of local wild horses with exotic domesticated populations outside China.

Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences

Objectives

There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses.

Methods

To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed.

Results

Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35-10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe.

Conclusions

Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

Background

Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs.

Results

We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700–7000 years old) belong to distinct clades.

Conclusions

We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68–151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4749-z) contains supplementary material, which is available to authorized users.

Genome-wide analysis of the diversity and ancestry of Korean dogs

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.

New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula

This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.

Mitochondrial DNA sequence variation in Iranian native dogs

The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n = 443) and Southwest Asian (n = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise F_ST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.

The origin of chow chows in the light of the East Asian breeds

Background

East Asian dog breeds are one of the most ancient groups of dogs that radiated after the domestication of the dog and represent the most basal lineages of dog evolution. Among these, the Chow Chow is an ancient breed that embodies very distinct morphological and physiological features, such as sturdy build, dense coat, and blue/purple tongue.

Results

Using a Restricted site Associated DNA (RAD) sequencing approach, we sequenced the genomes of nine Chow Chows from China. Combined with a dataset of 37 canid whole genome sequencing (WGS) from several published works, we found that the Chow Chow is one of the most basal lineages, which originated together with other East Asian breeds, such as the Shar-Pei and Akita. Demographic analysis found that Chow Chows originated from the Chinese indigenous dog about 8300 years ago. The bottleneck leading to Chow Chows was not strong and genetic migration between Chow Chows and other populations is low. Two classes of genes show strong evidence of positive selection along the Chow Chow lineage, namely genes related to metabolism and digestion as well as muscle/heart development and differentiation.

Conclusions

Dog breeds from East Asia, including the Chow Chow, originated from Chinese indigenous dogs very early in time. The genetic bottleneck leading to Chow Chows and migrations with other populations are found to be quite mild. Our current study represents an early endeavor to characterize the origin of East Asian dog breeds and establishes an important reference point for understanding the origin of ancient breeds in Asia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3525-9) contains supplementary material, which is available to authorized users.

On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.

Lessons from the canine Oxtr gene: populations, variants and functional aspects

Oxytocin receptor (OXTR) acts as a key behavioral modulator of the central nervous system, affecting social behavior, stress, affiliation and cognitive functions. Variants of the Oxtr gene are known to influence behavior both in animals and humans; however, canine Oxtr polymorphisms are less characterized in terms of possible relevance to function, selection criteria in breeding and domestication. In this report, we provide a detailed characterization of common variants of the canine Oxtr gene. In particular (1) novel polymorphisms were identified by direct sequencing of wolf and dog samples, (2) allelic distributions and pairwise linkage disequilibrium patterns of several canine populations were compared, (3) neighbor joining (NJ) tree based on common single nucleotide polymorphisms (SNPs) was constructed, (4) mRNA expression features were assessed, (5) a novel splice variant was detected and (6) in vitro functional assays were performed. Results indicate marked differences regarding Oxtr variations between purebred dogs of different breeds, free-ranging dog populations, wolf subspecies and golden jackals. This, together with existence of explicitly dog-specific alleles and data obtained from the NJ tree implies that Oxtr could indeed have been a target gene during domestication and selection for human preferred aspects of temperament and social behavior. This assumption is further supported by the present observations on gene expression patterns within the brain and luciferase reporter experiments, providing a molecular level link between certain canine Oxtr polymorphisms and differences in nervous system function and behavior.

Deciphering the Origin of Dogs: From Fossils to Genomes

Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.

The Genetics of How Dogs Became Our Social Allies

Dogs were domesticated from wolves about 15,000 years ago, and an important selection pressure (intentional or unintentional) has been their ability to communicate and cooperate with people. They show extensive human-directed sociability, which varies within as well as between breeds and is not shared by ancestral wolves. Hence, dogs are potentially ideal models for studying the genetics of social behavior. Here, we review some recent research carried out by us and others on this subject. We present results showing that recent selection of different breed types can be used as a model system for investigating the genetic architecture of personalities. Furthermore, we review data showing that human-directed social behavior is significantly related to a small number of genes that have known connections to human social disorders such as autism and schizophrenia. We suggest that dogs are excellent study subjects for analyzing the evolution and genetics of social behavior and can serve as probes for human health and welfare.

The origin of Chinese domestic horses revealed with novel mtDNA variants

The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe.

Dietary Variation and Evolution of Gene Copy Number among Dog Breeds

Prolonged human interactions and artificial selection have influenced the genotypic and phenotypic diversity among dog breeds. Because humans and dogs occupy diverse habitats, ecological contexts have likely contributed to breed-specific positive selection. Prior to the advent of modern dog-feeding practices, there was likely substantial variation in dietary landscapes among disparate dog breeds. As such, we investigated one type of genetic variant, copy number variation, in three metabolic genes: glucokinase regulatory protein (GCKR), phytanol-CoA 2-hydroxylase (PHYH), and pancreatic α-amylase 2B (AMY2B). These genes code for proteins that are responsible for metabolizing dietary products that originate from distinctly different food types: sugar, meat, and starch, respectively. After surveying copy number variation among dogs with diverse dietary histories, we found no correlation between diet and positive selection in either GCKR or PHYH. Although it has been previously demonstrated that dogs experienced a copy number increase in AMY2B relative to wolves during or after the dog domestication process, we demonstrate that positive selection continued to act on amylase copy number in dog breeds that consumed starch-rich diets in time periods after domestication. Furthermore, we found that introgression with wolves is not responsible for deterioration of positive selection on AMY2B among diverse dog breeds. Together, this supports the hypothesis that the amylase copy number expansion is found universally in dogs.

Out of southern East Asia: the natural history of domestic dogs across the world

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.

Worldwide patterns of genomic variation and admixture in gray wolves

The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set 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 surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (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.

Genetic structure in village dogs reveals a Central Asian domestication origin

Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups--a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations--including those of Vietnam, India, and Egypt-show minimal evidence of European admixture. These populations exhibit a clear gradient of short--range linkage disequilibrium consistent with a Central Asian domestication origin.

Complete mitochondrial genome database and standardized classification system for Canis lupus familiaris

To contribute to the complete mitogenome database of the species Canis lupus familiaris and shed more light on its origin, we have sequenced mitochondrial genomes of 120 modern dogs from worldwide populations. Together with all the previously published mitogenome sequences of acceptable quality, we have reconstructed a global phylogenetic tree of 555 C. l. familiaris mitogenomes and standardized haplogroup nomenclature. The phylogenetic tree presented here and available online at http://clf.mtdna.tree.cm.umk.pl/ could be further used by forensic and evolutionary geneticists as well cynologists, for data quality control and unambiguous haplogroup classification. Our in-depth phylogeographic analysis of all C. l. familiaris mitogenomes confirmed that domestic dogs may have originated in East Asia during the Mesolithic and Upper Paleolithic time periods and started to expand to other parts of the world during Neolithic times.

Behavior genetics and the domestication of animals

Across species, a similar suite of traits tends to develop in response to domestication, including modifications in behavior. Reduced fear and increased stress tolerance were central in early domestication, and many domestication-related behaviors may have developed as traits correlated to reduced fear. Genetic mechanisms involved in domestication of behavior can be investigated by using top-down or bottom-up approaches, either starting from the behavior variation and searching for underlying genes or finding selected loci and then attempting to identify the associated phenotypes. Combinations of these approaches have proven powerful, and examples of results from such studies are presented and discussed. This includes loci associated with tameness in foxes and dogs, as well as loci correlated with reduced aggression and increased sociality in chickens. Finally, some examples are provided on epigenetic mechanisms in behavior, and it is suggested that selection of favorable epigenetic variants may have been an important mechanism in domestication.

Using multiple markers to elucidate the ancient, historical and modern relationships among North American Arctic dog breeds

Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown. During the Alaskan Gold Rush, additional sled dogs, possibly of post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky, were used in the Arctic. The genealogical relationships among and origins of these breeds are unknown. Here we use autosomal, paternal and maternal DNA markers to (1) test the hypothesis that Inuit dogs have retained their indigenous ancestry, (2) characterize their relationship to one another and to other Arctic breeds, and (3) estimate the age of North American indigenous matrilines and patrilines. On the basis of the agreement of all three markers we determined that Inuit dogs have maintained their indigenous nature, and that they likely derive from Thule dogs. In addition, we provide support for previous research that the Inuit dogs from Canada and Greenland dog should not be distinguished as two breeds. The Alaskan Husky displayed evidence of European introgression, in contrast to the Malamute and Siberian Husky, which appear to have maintained most of their ancient Siberian ancestry.

Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog

Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.

African origin for Madagascan dogs revealed by mtDNA analysis

Madagascar was one of the last major land masses to be inhabited by humans. It was initially colonized by Austronesian speaking Indonesians 1500-2000 years ago, but subsequent migration from Africa has resulted in approximately equal genetic contributions from Indonesia and Africa, and the material culture has mainly African influences. The dog, along with the pig and the chicken, was part of the Austronesian Neolithic culture, and was furthermore the only domestic animal to accompany humans to every continent in ancient times. To illuminate Madagascan cultural origins and track the initial worldwide dispersal of dogs, we here investigated the ancestry of Madagascan dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared it with that from potential ancestral populations in Island Southeast Asia (n=219) and sub-Saharan Africa (n=493). We found that 90% of the Madagascan dogs carried a haplotype that was also present in sub-Saharan Africa and that the remaining lineages could all be attributed to a likely origin in Africa. By contrast, only 26% of Madagascan dogs shared haplotypes with Indonesian dogs, and one haplotype typical for Austronesian dogs, carried by more than 40% of Indonesian and Polynesian dogs, was absent among the Madagascan dogs. Thus, in contrast to the human population, Madagascan dogs seem to trace their origin entirely from Africa. These results suggest that dogs were not brought to Madagascar by the initial Austronesian speaking colonizers on their transoceanic voyage, but were introduced at a later stage, together with human migration and cultural influence from Africa.

Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature

Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.

DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories

As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present.

The complete mitochondrial genome of the Simao Chinese indigenous dog

In this study, the whole mtDNA genome of Simao Chinese indigenous dog was amplified and sequenced. Our data showed that the whole mtDNA genome of Simao Chinese indigenous dog includes 16,730 base pairs (bps). The Simao Chinese indigenous dog mitochondrial genome included structural organization and base composition of the rRNAs, tRNAs and protein-coding genes, as well as characteristics of tRNAs.

Gene flow between wolf and shepherd dog populations in Georgia (Caucasus)

We studied the distribution of the mitochondrial DNA haplotypes and microsatellite genotypes at 8 loci in 102 gray wolves, 57 livestock guarding dogs, and 9 mongrel dogs from Georgia (Caucasus). Most of the studied dogs had mitochondrial haplotypes clustered with presumably East Asian dog lineages, and most of the studied wolves had the haplotypes clustered with European wolves, but 20% of wolves and 37% of dogs shared the same mitochondrial haplotypes. Bayesian inference with STRUCTURE software suggested that more than 13% of the studied wolves had detectable dog ancestry and more than 10% of the dogs had detectable wolf ancestry. About 2-3% of the sampled wolves and dogs were identified, with a high probability, as first-generation hybrids. These results were supported by the relatedness analysis, which showed that 10% of wolves and 20% of dogs had closest relatives from an opposite group. The results of the study suggest that wolf-dog hybridization is a common event in the areas where large livestock guarding dogs are held in a traditional way, and that gene flow between dogs and gray wolves was an important force influencing gene pool of dogs for millennia since early domestication events. This process may have been terminated 1) in areas outside the natural range of gray wolves and 2) since very recent time, when humans started to more tightly control contacts of purebred dogs.

The complete mitochondrial genome of the Chinese indigenous dog

In this study, the complete nucleotide sequence of Chinese indigenous dog mitochondrial genome was determined for the first time. Sequence analysis showed that the genome structure was in accordance with other dogs. It contained 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The base composition was A (31.6%), G (14.2%), C (25.5%) and T (28.7%), so the percentage of A and T (60.3%) was higher than that of G and C. The complete mitochondrial genome sequence of the Chinese indigenous dog would shed a new light on further studies in dog domestication.

The genomics of selection in dogs and the parallel evolution between dogs and humans

The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.

Genetic and morphometric evidence on a Galápagos Island exposes founder effects and diversification in the first-known (truly) feral western dog population

Domesticated animals that revert to a wild state can become invasive and significantly impact native biodiversity. Although dogs can be problematic locally, only the Australasian dingo is known to occur in isolation from humans. Western dogs have experienced more intense artificial selection, which potentially limits their invasiveness. However, feral dogs eradicated from Isabela Island, Galápagos in the 1980s could be the first-known exception. We used DNA and morphometric data from 92 of these dogs to test the hypotheses that (i) these dogs persisted independently of humans for up to a century and a half since descending from a handful of dogs introduced in the early 1800s, vs. (ii) similarly to other western feral dog populations, they reflected continuous recruitment of strays from human settlements on a portion of the Island. We detected one dominant maternal lineage and one dominant paternal lineage shared by the three subpopulations, along with low autosomal genetic diversity, consistent with the hypothesized common origins from a small founder population. Genetic diversity patterns among the three island subpopulations were consistent with stepping-stone founder effects, while morphometric differentiation suggested rapid phenotypic divergence, possibly due to drift and reinforced by selection corresponding to distinct microclimates and habitats on Isabela. Despite the continued presence of free-ranging dogs in the vicinity of settlements on Isabela and other Galápagos Islands, feral populations have not reestablished in remote areas since the 1980s, emphasizing the rarity of conditions necessary for feralization of modern western dogs.