Fig. 5

Distribution of CfERV-Fc1(a) insertions in the genomes of modern canids. In silico genotyping was performed for 145 LTRs using Illumina read pairs across 347 sequenced canids representing extant members of all major Canidae lineages (Fig. 1). Sample names are indicated above by species or sub-population. Samples correspond to the Island and gray foxes (; n = 8), red fox (n = 1), Andean fox (n = 1), dhole (n = 1), golden jackal (n = 1), golden wolf (n = 1), coyote (n = 3), red wolf (n = 2), and representatives of gray wolf sub-populations (n = 33), village dogs (n = 111), ancient breed dogs (n = 38), and modern breed dogs (n = 154). ‘Insertion’ and ‘unoccupied’ alleles were recreated utilizing the CanFam3.1 reference and genotypes were inferred by re-mapping Illumina reads that spanned either recreated allele for each sample. Samples lacking remapped reads across a given site were excluded from genotyping at that site alone (indicated with a ‘.’). Allele frequencies were calculated for each species or sub-population (see “Methods”) and plotted as a heat map. The locus identifier for each insertion (left) corresponds to the chromosome and the leftmost insertion breakpoint, irrespective of insertion orientation. Non-reference and reference insertions are indicated by an ‘N’ and ‘R’, respectively. A green diamond is used to indicate loci with full-length alleles