Fig. 1

Mustela erminea clade geographic distributions and phylogenetic relationships. a–c Stoat clade distributions (clade names reflect refugial origins) based on amplicon mitochondrial haplotype distributions¹² and IUCN (International Union for Conservation of Nature, www.iucn.org) range information. Genomic samples are labeled with locality abbreviations: ANN (Annette Island, Alaska, USA), BC (southern British Columbia, Canada), KUP (Kupreanof Island, Alaska, USA), MON (Mongolia), NM (New Mexico, USA), POW (Prince of Wales Island, Alaska, USA), REV (Revillagigedo Island, Alaska, USA), SYT (Southern Yukon Territory, Canada), YTAK (northern Yukon-Alaska border), VT (Vermont, USA). Contact zones are denoted with yellow hatching, based on the presence of mixed mitochondrial haplotypes¹². Scale bars are in kilometers. a Global sampling scheme. b North American sampling localities. c Sampling within the northern North Pacific Coast (NPC) archipelagos. d Mid-point rooted maximum-likelihood phylogenies, scaled by genetic distance. d (left) Complete mitochondrial genomes and d (right) autosomal SNPs for ten M. erminea individuals. Phylogenies demonstrate strong support for four major refugial clades and mitonuclear discordance for hybrid samples (SYT, YTAK). Deep divergence between the NPC Island (POW) and Beringia (MON) clades is evident in the long branches in both phylogenies