Consensus Neighbour Joining tree (1,000 bootstrap steps) built assuming the Tamura-Nei substitution model, the best fit model for the dataset comprising complete mitochondrial genomes from coyotes (Coyotes), wolves (OWW, NWW – Old and New World wolves, respectively) and dogs combined with partial control region sequences from the Altai specimen (Altai dog) and additional prehistoric canids (pre-Columbian dogs, eastern Beringian wolves).

<p>We highlighted all clades containing modern dogs in light blue and enlarged Clade A for better visibility. The position of the Altai specimen is marked with a light blue arrow in the enlargement. Bootstrap values are shown with an asterisk whenever larger than 50.</p

Map depicting the geographic origin of the Altai dog specimen.

<p>Map depicting the geographic origin of the Altai dog specimen.</p

Likelihood mapping analysis off all 142 canid sequences clustered into four groups.

<p>Upper panel shows the distribution pattern of all quartets and the lower panel depicts the fraction of each occupied region. Quartets situated in the centre part of the triangle support a star-shaped sequence evolution whereas quartets in the three corners support resolved topologies, respectively. A) Likelihood mapping pattern when clustering the sequences into Altai dog, dogs, wolves and coyotes. B) Likelihood mapping pattern when sequences were clustered as follows: Altai dog, dogs, wolves and prehistoric New World canids taken from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057754#pone.0057754-Leonard1" target="_blank">[23]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057754#pone.0057754-Leonard2" target="_blank">[24]</a>.</p

Node ages as estimated from BEAST analyses given in years and with 95% HPD.

<p>Shown is the averaged results from the three analyses excluding outgroups (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone-0055950-t002" target="_blank">Table 2</a>).</p

Phylogenetic RAxML trees (GTR+G+I) with 500 bootstraps and MrBayes (GTR+G+I) 50M generations on the full data set.

<p>Posterior probabilities are given in proportions and bootstrap support as a percentage on each branch of interest. * Branch is supported by maximum posterior probability and bootstrap (1/100). <b>A:</b> Including outgroups and based on 5 partitions. <b>B:</b> Excluding outgroups and based on 4 partitions.</p

Sample information.

<p>Number of amplicons refers to the number of amplicons sequenced on the GS FLX, and does not include amplicons sequenced by Sanger sequencing. For total number of amplicons see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone.0055950.s008" target="_blank">Table S5</a>. Sh. stands for shotgun sequencing and refers to cases where no amplicons have been generated. Sh.+C refers to cases where shotgun and target capture data have been merged. C. refers to in solution MYSelect capture. The number of reads used is the number of reads that mapped successfully to the reference used. Coverage is provided as the total number of bases sequenced and aligned against the horse reference mitogenome divided by the length of the horse reference mitogenome (Cov.) or the horse reference mitogenome after excluding a region of tandem repeats (Cov$). Column mitogenome length provides the total sequence length of the mitogenome that is covered by a minimal read depth of 2 and excluding tandem repeats (see Methods).</p

Average node ages from BEAST.

<p>Analyses run with and without outgroups (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone.0055950.s012" target="_blank">Table S9a</a>–b). All dates are in years with 95% confidence interval given in parentheses. N/a = not applicable. Sum = Sumatran rhino; Wool = woolly rhino; Zeb = zebras; Don = Donkey; Donkey = <i>E. africanus</i> and <i>E. asinus</i>; Asses = <i>E. hemionus</i> and <i>E. kiang</i>; Ass = Asses. Node letters in parentheses as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055950#pone-0055950-g001" target="_blank">Figure 1</a>.</p