Y chromosomestudies support that domestication of the dog started in Southern China

For this first comprehensive study of the Y-Chromosome, 151 male dogs of many breeds worldwide,12 male wolves and 2 male coyotes were sampled and 14437bp of Y-chromosome DNA analysed. None of the dog samples were from strays.

The geographical distribution and breeds of the dog samples are as follows (in bold the Sighthounds)
Africa: Niger/Mali (Azawakh) , Morocco/Algeria (Sloughi) , Benin/Congo/Sudan (Basenji), Cameroon (1 dog), Kenya (2 dogs), Lesotho (2 dogs)
Americas: Xoloitzcuintle, Chihuahua, Peruvian Inca Orchid, Alaskan malamute, Inuit sled dog, Greenland dog,
East Asia: China: dogs from Guangdong, Guangxi, Guizhou, Hainan, Hebei (Pug, Chinese crested dog, ChowChow, Shi Tzu), Heilonggjiang, Hunan, Jiangxi, Liaoning, Qinghai, Shaanxi, Shanxi, Sichuan, Tibet (Tibetan Terrier, Tibetan Spaniel, Tibetan Mastiff, Lhasa Apso), Yunnan
Japan (Akita, Iwate matagi, Kisyu, Shiba, Hokkaido); Siberia (Aboriginal sled Dog, East Siberian Laika, West Siberian laika, Siberian Husky, Samoyed, Chukotka Sled Dog)
Southeast Asia: Cambodia, Thailand (Thai Ridgeback, + other dogs) Vietnam (Phuquoc dog, + others), other (Sredneasiatskaja Ovtjarka)
Europe:
Britain (Yorkshireterrier, Golden retriever, English Springer Spaniel, Border Collie, Shetland Sheep Dog, Cavalier King Charles Spaniel.
Central Europe: German Shepherd Dog, Bouvier des Flandres, Chart Polski, Dachshund, Puli, Leonberger, Polski Owczarek Nizinny, Pumi, Groenendael, Slovensky Kopov
South Europe: Poodle, Lagotto Romagnolo, Maremmano abruzzese, Italian Greyhound, Volpino Italiano, Galgo espanol, Pyrenean Mastiff, Portuguese Water Spaniel, Cane Corso, Bracco Italiano
Scandinavia: Swedish Elkhound, Finnish Lapphund, Norwegian Lundehund, Norwegian Elkhound, Karelo-Finnish Laika; other Russo-European Laika
Southwest Asia: Afghanistan (Afghan Hound), Iran (10 from 10 different locations), Israel (Canaan dog) Turkey (7 from 6 locations across Turkey), other.

The geographical distribution of the wolf samples is
Europe (Scandinavia), America (North America), East Asia/China (Heilongjiang, Qinghai, Sichuan, Shanxi, Yunnan)

The geographical distribution of the coyote samples is Sonoma county and Butte county in California, USA

Results
      In total 49 nucleotide positions with binary substitutions and 11 indels were discovered. The 49 substitutions result in 32 Y-Chromosome haplotypes, 28 for dogs, 2 specific for Wolf and 2 specific for Coyote.
      The wolf haplotypes differed by 0-4 substitutions from the dog haplotypes, the coyote haplotypes differed by at least 15 substitutions from the closest dog haplotype, showing that the Wolf is closer to the Dog than the Coyote is to the Dog and supporting the notion that the Dog descends from the Wolf.
      The 12 wolf samples represent 3 haplotypes, haplotype H23 was shared between Dog and one Chinese Wolf, haplotype H26 (in one American Wolf) was 1 substitution away from 2 dog samples, and H27 (in 9 Chinese and 1 Scandinavian Wolf) differed by 4 substitutions from the closest dog haplotype.

The dog haplotypes clusted in 5 haplogroups named HG1, HG3, HG6, HG9, HG23 after their central haplotypes. Calculations of the rate of substitutions suggest that the Y-Chromosome genepool in these 151 dog samples descend from 13-24 male wolf founders. This finding agrees with the results of a similar study on the mtDNA which point out that the female lines descend from at least 51 female wolf lineages and a study on MHC data by Vila et al showing at least 21 founder wolves. Thus multiple data sets indicate that dogs descend from numerous domesticated wolves.
Two of the 5 Dog haplogroups, HG1 and HG23, were found in 62% of the dogs in the study. Their 3 central haplotypes H1, H1* (of HG1) and H23* (of HG23) were found in 46% of the dogs (75% in Europe, 44% in Southwest Asia, and 32% in China). HG 3 was found in East Asia and America, and at low frequency in Southwest Asia, Scandinavia and Britain, but not in Continental Europe or Africa. HG6 absent elsewhere was located in East Asia and at low frequency in Southwest Asia. HG9 in present in only 4 individuals far apart geographically (1 in East Siberia, 3 in Central Africa). All 4 main haplogroups were represented together only in East, Southwest and Southeast Asia.

Conclusion
The distribution and frequency of the various haplotypes, except for H1, H1* and H23* which were almost universal, was very different between regions. In Europe, with 7 haplotypes for 32 samples, a few haplotypes were very frequent: H1 (47% of the samples) , H1* (22% of the samples) and H23* (lower percentage) and others completely absent. Southwest Asia had a high frequency of the haplogroup HG23 (68%) and the largest number of its haplotypes (5). In Southeast Asia, there was a larger number of different haplogroups and haplotypes distributed in more even frequencies. As was the case for the mtDNA, the highest genetic diversity for the Y-Chromosome was found in Southeast Asia and showed the trend of diminishing as one moves towards the West, with Europe having the lowest genetic diversity. This trend suggest that the domestication of male wolves, like that of female wolves (mtDNA study) also occurred in Southeast Asia.

This genetic diversity in Southeast Asia both in mtDNA and Y-Chromosome makes it important in genetic studies about the origins of the domestic Dog to always include samples from Southeast Asia to avoid results biased towards other dog populations.

     According to the authors, this study cannot pinpoint exactly where the male wolf domestication occurred as some areas in Southeast Asia have not been sampled yet. The dominance of the HG23 haplogroup in Southwest Asia would tend to suggest that another domestication event took place there, but it cannot be ascertained as the neighboring regions do not show a high frequency of that haplogroup. In the mtDNA studies of female wolf lineages, more recent crossbreeding to wolves tend to be very localised and found at low frequencies, not at large frequencies like HG23. The geographical origin of that particular haplogroup is unclear but because it is also present in Southeast Asia, its origin there cannot be excluded.
     No Y-chromosome haplogroups were found to be restricted to any particular region. There was therefore no clear sign that a localized crossbreeding of female Dog with male Wolf actually took place and was important in the evolution of dog breeds, or if it happened it was not captured in the samples of this study.
     So far there are only very few clear genetic cases that Dog x Wolf crossbreeding happened after the Wolf became Dog. In the mtDNA studies of female lines, mtDNA haplogroups d1 (restricted to Scandinavia), d2 (restricted to Middle East and Mediterranean countries), and F ( a few extant Japanese dogs and extinct Japanese Wolf) are such examples.
    Regarding Europe with its many different breeds of dogs, both the Y-Chromosome and mtDNA lack of diversity probably occurred before the extensive selective breeding that took place to create so many breeds.

        Both the Y-Chromosome and the mtDNA studies indicate that the origins of the domestic dog involved the taming of many female and male wolves, probably a major cultural event in Southeast Asia. There is the possibility that the taming of wolves coincided with the shift from hunter-gathering to the farming and culture of rice, as mtDNA studies suggest that dogs have originated at about that time.
       Although the major region for the domestication of today's Dog lineages has probably been found, more studies are needed on denser sampling in some areas, and with the use of new generation DNA sequence analysis methods, to get a more detailed picture of the origins of the Dog.

Results of the Sighthounds

     The Azawakh, Chart Polski, Italian Greyhound and Sloughi are together in Haplogroup HG1, with the widespread haplotypes H1 or H1*. The Saluki and Afghan are together in Haplogroup, HG23, with haplotype H10 (Saluki) and H7 (Afghan)

The African Sighthounds, Sloughis and Azawakhs' male lineages are thus grouped with the Continental European dogs with the widespread haplotypes H1 and H1* of Haplogroup HG1. Instead, Salukis and Afghan Hound are grouped with the Middle Eastern dogs with haplotypes H10 (Saluki) and H7 (Afghan Hound) in another Haplogroup altogether: H23. These results add to the differences already known about the foundation female dog lineages and their mtDNA between these breeds.

I thank Peter Savolainen for fine-tuning this text, Carla Cruz, Claudia Gaede, Corine Lundqvist, Cora Nurnberger, Nina Turunen and all the photographers, who allow the use of their photographs through Wikimedia Commons, for their photographs.

Sighthound breeds in this study
AFRICA & EUROPE

Sloughi © de Caprona ~ Italian Greyhound © Nürnberger ~ Azawakh © Lundqvist

Galgo espanol © Gaede ~ Chart polski © Turunen

MIDDLE- EAST

Saluki © Nina Neswadba ~ Afghan © Schwab

SOME OF THE OTHER BREEDS IN THE STUDY

SOUTH AMERICA

Xoloitzcuintle haired & hairless (Mexico) © Christopher A./Amanda L. Dellario ~ Chihuahua © ExDumpling ~ Perro Sin Pelo del Peru (Peru) © Manuel González Olaechea y Franco

SCANDINAVIA - SIBERIA