Population genetic structure of a rare high‐elevation black fly, Metacnephia coloradensis , occupying Colorado lake outlet streams

Summary 1. Using a portion of the mitochondrial cytochrome oxidase I gene, we evaluated the population genetic structure of a geographically rare black fly ( Metacnephia coloradensis ) that is a habitat specialist in outlet streams of large, productive, alpine lakes in Colorado, U.S.A. Given its rarity and life history traits that restrict dispersal, we hypothesised that genetic structure would show a signature of allopatric fragmentation associated with climatic warming since Pleistocene glaciations. 2. We tested for genetic isolation by distance (IBD) and applied nested clade analysis (NCA) to ask whether current genetic structure is primarily a consequence of historic fragmentation or if there is evidence of ongoing gene flow. 3. Only four populations were located despite a thorough search of potential sites, and they demonstrated a significant degree of genetic structure (F ST  = 0.17). However, there was some evidence of IBD in a plot of genetic versus geographic distance, and NCA further supported IBD and restricted ongoing gene flow in clades at all nested levels. Compared with a more widespread alpine black fly ( Prosimulium neomacropyga ) in the same region, M. coloradensis demonstrated significantly less population genetic structure. 4. Although these results counterintuitively implicate limited ongoing gene flow driving current population structure, significant IBD may be a signature of historic gene flow, especially if migration–drift equilibrium has not yet been reached since a late‐Pleistocene fragmentation event. Extraordinarily dense local populations probably allowed M. coloradensis to maintain large effective population sizes and minimise genetic drift rates. 5. Despite large local populations, M. coloradensis is vulnerable to continued rapid environmental change because of its limited geographic distribution and high habitat specificity.