Genome sequencing highlights the dynamic early history of dogs

Abstract

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.

Figure 1. Geographic distribution of sampled lineages.

Figure 2. Comparison of next generation sequencing with array typed samples, and historical changes in effective population size.

PCA plot of next-generation sequencing (NGS) samples generated in this study (open circles) along with corresponding samples genotyped on the Affymetrix canid array (colors and two letter codes: red M = Mid-East Wolf, green E = European Wolf, black Ch = Chinese Wolf, purple Ba = Basenji, brown Bo = Boxer, orange D = Dingo, cyan J = Golden Jackal).

Figure 3. Heterozygosity and historical changes in effective population size.

(A) Box plots of heterozygosity measured in 5000 100 kb windows for each sample. (B) Reconstruction of historical patterns of effective population size (N_e) for individual genome sequences. Based upon the genomic distribution of heterozygous sites using the pairwise sequential Markovian coalescent (PSMC) method of Li and Durbin 2011 . Time scale on the x-axis is calculated assuming a mutation rate of 1×10⁻⁸ per generation (see Text S8); estimates from the full data and 50 bootstraps are depicted by darker and lighter lines, respectively.

Figure 4. Neighbor-joining tree and admixture signatures from ABBA/BABA tests.

(A) NJ tree constructed from genome-wide pairwise divergence, calculated using equation E8.1 in . All nodes have 100% bootstrap support. Dashed lines indicate admixture edges that were statistically significant in ABBA/BABA tests. (B) ABBA/BABA tests with significant Z-scores (values ≥3 are significant). All comparisons made are shown in Table S11. For each row, boldfaced labels indicate admixing lineages.

Figure 5. Demographic model of domestication.

Divergence times, effective population sizes (N_e), and post-divergence gene flow inferred by G-PhoCS in joint analysis of the Boxer reference genome, and the sequenced genomes of two basal dog breeds, three wolves, and a golden jackal. The width of each population branch is proportional to inferred population size, and stated ranges of parameter estimates indicate 95% Bayesian credible intervals. Horizontal gray dashed lines indicate timing of lineage divergences, with associated means in bold, and 95% credible intervals in parentheses. Migration bands are shown in green with associated values indicating estimates of total migration rates, which equal the probability that a lineage will migrate through the band during the time period when the two populations co-occur. Panels show parameter estimates for (A) the population tree best supported by genome-wide sequence divergence (Fig. 4A) (B) a regional domestication model, and (C) a single wolf lineage origin model in which dogs diverged most recently from the Israeli wolf lineage (similar star-like divergences are found assuming alternative choices for the single wolf ancestor. Estimated divergence times and effective population sizes are calibrated assuming an average mutation rate of 1×10⁻⁸ substitutions per generation and an average generation time of three years. See Text S9 and Table S12 for details.

Figure 6. Copy number variation at amylase (AMY2B) locus.

(A) Copy number variation (CNV) at AMY2B estimated from whole genome sequence data, showing presence of elevated copy number in Basenji but not in other lineages. Results are based on SOLiD data, except for the Chinese wolf (see Text S6 for supporting results and Text S10 for CNV analyses in an additional 12 dog breeds). (B) qPCR results on CNV state in an expanded set of wolf and dog lineages. Abbreviations for lineages are: AFG, Afgan Hound; AFR, Africanis; AKI, Akita; BSJ, Basenji; BE, Beagle; BU, Bulldog, CAN, Canaan Dog; CU, Chihuahua; CC, Chinese Crested; FC, Flat-coated Retriever; GD, Great Dane; IH, Ibizan Hound; KUV, Kuvasz; MAS, Mastiff; NGS, New Guinea Singing Dog; PEK, Pekinese; PHU, Phu Quoc; SAL, Saluki; SAM, Samoyed; SCT, Scottish Terrier; SHA, Shar Pei; SIH, Siberian Husky; THD, Thai Dog; TOP, Toy Poodle; DNG, Dingo; CHW, Chinese wolf; INW, Indian wolf; ISW, Israeli wolf; ITW, Italian wolf; RUW, Russian wolf; SPW, Spanish wolf; YSW, Yellowstone wolf; GLW, Great Lakes wolf.