Genetic variation in the endangered southwestern willow flycatcher

The Southwestern Willow Flycatcher (Empidonax traillii extimus) is an endan gered Neotropical migrant that breeds in isolated remnants of dense riparia n habitat in the southwestern United States. We estimated genetic variation at 20 breeding sites of the Southwestern Willow Flycatcher (290 individual s) using 38 amplified fragment length polymorphisms (AFLPs). Our results su ggest that considerable genetic diversity exists within the subspecies and within local breeding sites. Statistical analyses of genetic variation reve aled only slight, although significant, differentiation among breeding site s (Mantel's r = 0.0705, P < 0.0005; theta = 0.0816, 95% CI = 0.0608 to 0.10 34; Phi(ST) = 0.0458, P < 0.001). UPGMA cluster analysis of the AFLP marker s indicates that extensive gene flow has occurred among breeding sites. No one site stood out as being genetically unique or isolated. Therefore, the small level of genetic structure that we detected may not be biologically s ignificant. Ongoing field studies are consistent with this conclusion. Of t he banded birds that were resighted or recaptured in Arizona during the 199 6 to 1998 breeding seasons, one-third moved between breeding sites and two- thirds were philopatric. Low differentiation may be the result of historica lly high rangewide diversity followed by recent geographic isolation of bre eding sites, although observational data indicate that gene flow is a curre nt phenomenon. Our data suggest that breeding groups of E. t. extimus act a s a metapopulation.