33,000-year old dog from the Altai

From the paper:

In conclusion, our analyses support the hypothesis that the Altai specimen is more closely related to domestic dogs than to extant wolves, but we stress the point that these analyses were limited to a single, maternally inherited locus and more sequence data would be needed to obtain a statistically well supported phylogeny and unambiguously resolve the genetic relationship of the Altai specimen. However, this preliminary analysis affirms the conclusion that the Altai specimen is likely an ancient dog with a shallow divergence from ancient wolves. These results suggest a more ancient history of the dog outside the Middle East or East Asia, previously suggested as centres of dog origin. Additional discoveries of ancient dog-like remains are essential for further narrowing the time and region of origin for the domestic dog [5].

An ancient dog with shallow divergence from ancient wolves is probably what we might expect if dogs had been domesticated by some of the first Upper Paleolithic Eurasians a few thousand years prior to the date of this particular specimen.
PLoS ONE 8(3): e57754. doi:10.1371/journal.pone.0057754
Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog
Anna S. Druzhkova et al.
The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.
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Southeast Asian Neolithic dogs

Southeast Asian Neolithic dogs

From the paper:

Nevertheless, the close phylogenetic clustering of haplotypes from Thailand, Brunei, Bali, and the Philippines suggests these populations originated from the same source, consistent with a single migration event, whereas the dingoes, NGSDs, and dogs from Taiwan appear sufficiently distinct from these to reflect a distinct migration event (Fig. 2b-c). The clustering of the three Island Southeast Asian populations with Thailand also was more consistent with origination from Mainland Southeast Asia than Taiwan (in agreement with mtDNA findings of Oskarsson et al. 2011).

and:

In light of findings from the present study, it seems clear that both post-Victorian and Neolithic exchanges link eastern and western Eurasian dogs. However, the cause of post-Victorian haplotype sharing between Western breed dogs and Southeast Asian village dogs apparently reflects very recent introduction of Western dogs to the East rather than extraction of Eastern dogs to create Western breeds during the Victorian Era.

and:

Specifically, our aging of this European haplogroup to 5,800 (±SE = 1750) or 8,400 (±SE = 2500) years (depending on the dingo calibration to 3,500 or 5,000 years, respectively) suggests that the connection between pre-Victorian European and Southeast Asian dogs traces only to the Neolithic period and is not of sufficient antiquity to support the hypothesis of a single origin of dogs from Southeast Asia. Thus, although future studies are needed to combine the Y SNPs and STR markers in a geographically broader sampling of dogs than was considered here, our findings support the hypothesis for a massive Neolithic expansion of dogs from Southeast Asia rather than a Paleolithic origin of dogs from this region.

This massive Neolithic expansion of Southeast Asian dogs is testable by looking at early European dogs; these ought not to belong to haplogroup H1. It would also be interesting to speculate about the trade routes and/or population movements that facilitated the spread of dogs from SE Asia to Europe during the Neolithic.

Mol Biol Evol (2013) doi: 10.1093/molbev/mst027

Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals

Benjamin N. Sacks et al.

Dogs originated >14,000 BP, but the location(s) where they first arose is uncertain. The earliest archaeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5–7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archaeological evidence. We propose and investigate with Y chromosomes an alternative hypothesis for the proximate origins of dogs from Southeast Asia--a massive Neolithic expansion of dogs from this region that largely replaced more primitive dogs to the west and north. Previous attempts to test matrilineal findings with independent patrilineal markers have lacked the necessary genealogical resolution and mutation rate estimates. Here, we used Y chromosome genotypes, composed of 29 SNPs and 5 STRs, from 338 Australian dingoes, New Guinea singing dogs, and village dogs from Island Southeast Asia, along with modern European breed dogs, to estimate the evolutionary mutation rates of Y chromosome STRs based on calibration to the independently known age of the dingo population. Dingoes exhibited a unique haplogroup characterized by a single distinguishing SNP mutation and 14 STR haplotypes. The age of the European haplogroup was estimated to be only 1.7 times older than that of the dingo population, suggesting an origin during the Neolithic rather than the Paleolithic (as predicted by the Southeast Asian origins hypothesis). We hypothesize that isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation, enhancing their value in trade and as cargo, and enabling them to rapidly expand and replace more primitive dogs to the West. Our findings also suggest that dingoes could have arrived in Australia directly from Taiwan, independently of later dispersals of dogs through Thailand to Island Southeast Asia.

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Dog food

Dog food

Diet Shaped Dog Domestication

The analysis turned up 36 regions, with 122 genes in all, that may have contributed to dog evolution, the team reports online today in Nature. Nineteen of these regions contain genes important for the brain, eight of which are involved with nervous system development, which makes sense given the importance of behavioral changes in the transition to becoming man's best friend, Axelsson notes.

More surprising were genes for digesting starch. Dogs had four to 30 copies of the gene for amylase, a protein that starts the breakdown of starch in the intestine. Wolves have only two copies, one on each chromosome. As a result, that gene was 28-fold more active in dogs, the researchers found. More copies means more protein, and test-tube studies indicate that dogs should be fivefold better than wolves at digesting starch, the chief nutrient in agricultural grains such as wheat and rice. The number of copies of this gene also varies in people: Those eating high carbohydrate diets -- such as the Japanese and European Americans -- have more copies than people with starch-poor diets, such as the Mbuti in Africa. "We have adapted in a very similar way to the dramatic changes that happened when agriculture was developed," Axelsson says.

Nature (2013) doi:10.1038/nature11837

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

Erik Axelsson et al.

The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated1, 2, 3, 4, 5 and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication6. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.

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