Figure 4.

Dissection of the rebuilt founder canid's genome. (A) Maximum likelihood phylogeny of canine variation catalog using putative founder-inherited variant positions with clades colored by monophyly. The position of the CTVT germline genomes indicate that the founder was a post-wolf canine with closest similarity to a contemporary Arctic spitz breed. Observed acceleration on the CTVT branch is due to the use of all positions determined to vary from reference in the CTVT germline, therefore ensuring the proportion of these variant characters exceeds all other genomes. For the unrooted maximum likelihood tree with bootstrap support, see Supplemental Figure S3. (B) We used 135,833 SNPs from the Illumina HD chip and genotypes extracted from the tumor WGS to perform principal components analysis on the CTVT tumors and dogs from three Arctic spitz breeds. The CTVT founder was likely most genetically similar to the modern Alaskan malamute.