Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences

Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c-myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c-myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (F-ST) based upon mitochondrial data were always higher than nuclear-based F-ST estimates, even after correcting for the expected fourfold lower effective population size (N-e) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the N-e of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c-myc. Nuclear F-ST estimates were approximate to0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of N-e within localities on the order of 10(5). This value is two to three orders of magnitude larger than any previous N-e estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 10(7) years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models.