Genome Sequencing Highlights the Dynamic Early History of Dogs
Divergence times, effective population sizes (Ne), 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.