Additional file 1: Figure S1. of The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

Phylogenies. The left panel shows the phylogenetic tree of all the samples, estimated from reads that are mapped to the boxer dog reference genome, while the right panel shows the phylogenetic tree estimated from the data after mapping reads to the denovo assembled wolf reference genome. Figure S2. Distribution of repeat elements. Total amount of bases in different repeat classes across the two reference genomes. Figure S3. Comparison of the divergence of the different repeat elements from their consensus sequence. The top panel shows the total number of bases against the divergence from the consensus sequence in each repeat family when using the de novo wolf reference genome for alignment. The bottom panel shows the same figures when using the boxer reference genome. Figure S4. Principal Components Analysis (PCA). Panels A and B show the first four principal components of the genotypes when using the de novo wolf reference assembly. For making these PCA plots, we used a missingness cutoff of 0.9 and a minor allele frequency cutoff of 0.2. Panels C and D show the first four principal components of the genotypes when using the boxer reference genome while using the same filtering thresholds. Figure S5. Picture of the skull of the Swedish wolf sample used for reference genome assembly. Table S1. Coverage and heterozygosity estimates. The coverage and heterozygosity are shown for each sample included in the study. For each animal, the higher estimate of coverage are bolded. (PDF 1652 kb)