Mitogenomics clarifies the position of the Nearctic magpies ( and ) within the Holarctic magpie radiation.

Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: ) serve as a good example of these problems. The Black-billed magpie is widely distributed in North America, whereas the Yellow-billed Magpie is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie () and the Oriental Magpie (), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of , and as a sister clade to the two Nearctic species. and form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with , with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between and , our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.