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Background  Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of  Buteo jamaicensis harlani  to other  B. jamaicensis  subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations.    Results  To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor ( Mc1r ) to investigate molecular genetic differentiation among three  B. jamaicensis  subspecies ( B. j. borealis ,  B. j. calurus ,  B. j. harlani ). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between  B. j. harlani  and  B. j. borealis . Differences observed between  B. j. harlani  and  B. j. borealis  in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies,  B. j. borealis  and  B. j. calurus , and estimates of migration rates among all three subspecies were high. No consistent differences were observed in  Mc1r  data between  B. j. harlani  and other  B. jamaicensis  subspecies or between light and dark color morphs within  B. j. calurus , suggesting that  Mc1r  does not play a significant role in  B. jamaicensis  melanism.    Conclusions  These data suggest recent interbreeding and gene flow between  B. j. harlani  and the other  B. jamaicensis  subspecies examined, providing no support for the historical designation of  B. j. harlani  as a distinct species.

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani