Evolutionary Genetics of Flycatchers. II. Differentiation in the Empidonax difficilis Complex

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Abstract
We used starch-gel electrophoresis to assess variability at 41 genetic loci in 208 individuals from 11 breeding populations of the Western Flycatcher (Empidonax difficilis) complex. Genic variability was substantial in most populations and equivalent to levels found in other avian taxa. A sample of E. d. insulicola from Santa Catalina Island, however, showed reduced heterozygosity and an unusually low percentage of polymorphic loci. We attribute this to a bottleneck at the time of the original colonization. Nei's genetic distances among populations of one taxon ranged from D̄ = 0.0003 (in E. d. difficilis) to D̄ = 0.0033 (in E. d. hellmayri). Intertaxon Nei's D̄ ranged from 0.009 (E. d. insulicola vs. E. d. difficilis) and 0.0149 (E. d. difficilis vs. E. d. hellmayri) to 0.0228 (E. d. insulicola vs. E. d. hellmayri). to 0.0228 (E. d. insulicola vs. E. d. hellmayri). F statistics revealed significant population subdivision within the complex. With Slatkin's rare-allele method we estimated the gene-flow parameter, Nm. Mainland populations experience moderately high gene flow (9.62 immigrants/generation). In contrast, Santa Catalina Island receives an estimated 0.093 immigrants/generation, pointing to very low gene flow and essential genetic isolation. Genetic distances yielded phenograms and distance Wagner trees that provide hypotheses for the relationships and phylogenesis of populations in western North America. The lineage leading to modern E. d. difficilis split from that leading to E. flavescens in the mid-Pleistocene at 866,800 yr BP; the ancestors of modern E. d. difficilis diverged from those of present-day E. d. hellmayri at 248,700 yr BP; and the stock leading to modern E. d. insulicola budded from the lineage that became E. d. difficilis in the late Pleistocene, approximately 187,000 yr BP. Empidonax d. difficilis and E. d. hellmayri nest sympatrically and mate assortatively in the Siskiyou region of northern California. Interbreeding has not been demonstrated conclusively, and we regard these taxa as biologic species. In the absence of a test of sympatry, the well-differentiated form E. d. insulicola of the California Channel Islands cannot be proved to be a biologic species. It is clearly a phylogenetic species, however, in the sense of Cracraft.