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Background  This study was motivated by the observation of unusual mitochondrial haplotype distributions and associated physiological differences between populations of the killifish  Fundulus heteroclitus  distributed along the Atlantic coast of North America. A distinct "northern" haplotype is fixed in all populations north of New Jersey, and does not appear south of New Jersey except in extreme upper-estuary fresh water habitats, and northern individuals are known to be more tolerant of hyposmotic conditions than southern individuals. Complete mitochondrial genomes were sequenced from individuals from northern coastal, southern coastal, and fresh water populations (and from out-groups). Comparative genomics approaches were used to test multiple evolutionary hypotheses proposed to explain among-population genome variation including directional selection and hybridization.    Results  Structure and organization of the  Fundulus  mitochondrial genome is typical of animals, yet subtle differences in substitution patterns exist among populations. No signals of directional selection or hybridization were detected. Mitochondrial genes evolve at variable rates, but all genes exhibit very low dN/dS ratios across all lineages, and the southern population harbors more synonymous polymorphism than other populations.    Conclusion  Evolution of mitochondrial genomes within  Fundulus  is primarily governed by interaction between strong purifying selection and demographic influences, including larger historical population size in the south. Though directional selection and hybridization hypotheses were not supported, adaptive processes may indirectly contribute to partitioning of variation between populations.

Comparative mitochondrial genomics within and among species of killifish