Abstract
The Karner blue butterfly (KBB),Lycaeides melissa samuelis, is a federally protected taxon whose relationship to the Melissa blue,Lycaeides melissa, has been a point of contention during the 66 years since the KBB was first described. Using a large population-genomic dataset and a model of population divergence with migration, we investigated the relationship between the KBB andL. melissa, as well as the relationship betweenL. melissaand a third taxon,Lycaeides idas. We report that gene flow between the KBB andL. melissais low, and comparable to gene flow betweenL. melissaandL. idas. Considering this population-genetic evidence, we conclude that the KBB is a unique evolutionary lineage that should be recognized asLycaeides samuelis.

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