Genomics confirms surprising ecological divergence and isolation in an endangered butterfly

Phylogeographic patterns in phytophagous organisms are often
contextualized in light of geographic isolation and ecological (host,
habitat) specialization. However, assessing the relative impact of these
phenomena is not straightforward, even in areas where phylogeography is
well-studied, such as the California Floristic Province. Here, we use
genome-wide markers to elucidate population genomic and phylgeographic
patterns for a group of monophytophagous butterflies in southern
California. This group is of high conservation interest because it
includes the El Segundo blue, Euphilotes battoides allyni, one of the
first insects listed under the U.S. Endangered Species Act, and a newly
discovered population putatively assigned to E. b. allyni. Despite using
the same unique host and coastal habitat, our results indicate that the
newly discovered populations are not E. b. allyni and are more closely
related to geographically proximate populations of the E. battoides group
using a different habitat host. Aside from E. b. allyni and the newly
discovered populations, the rest of the group shows only fine-scale
structure and apparently maintains genetic connectivity throughout
southern California, across a vast range of habitats and climates, and on
multiple hosts. Thus, habitat and host specialization did not elicit
genetic isolation in neighboring populations suggesting that: 1) other
phenomena are needed to explain the remarkable and idiosyncratic
divergence of these highly restricted, proximate, taxa, and 2) fine-scale
genomic markers suggest broader implications for understanding the
mechanisms of speciation and reinvestigation of phylogeographic patterns
in regions like the California Floristic Province.