Response to Kishida et al. (2022): Asian black bears show stronger introgression signal with brown than American black bears

Abstract The expansion of whole genome sequencing from single individuals per species to range‐wide sampling of diversity now allows for nuanced investigation of the phylogeography of introgression. Analyses by Kishida et al. (2022) show gene flow between Alaskan American black bears ( Ursus americanus ) and both Korean and Japanese populations of Asian black bears ( U. thibetanus ). Further, they show no gene flow between Asian black and brown bears. Fundamental to these results was the use of four taxon D‐ statistics, which placed the polar bear ( U. maritimus ) as the outgroup species. As polar bears are not an outgroup to any of the focal species tested, this violated a main assumption of the D‐ statistic test. Thus, a new analysis of the phylogeography of introgression of Asian black, American black, and brown bears was undertaken, but with the divergent Andean bear ( Tremarctos ornatus ) serving as outgroup. I did not identify introgression between Asian black bear populations and intra‐specific lineages of brown or American black bears. However, an ancient signature of introgression between Asian black and brown bears was observed and affected all intra‐specific lineages of both species. Expanded aDNA resources for these species would aid in explaining the phylogeography of introgression and potential for adaptive introgression among bears.