The population genetic structure of three species of Amazonian rodents (Oligoryzomys microtis, Oryzomys capito, and Mesomys hispidus) is examined for mtDNA sequence haplotypes of the cytochrome b gene by hierarchical analysis of variance and gene flow estimates based on fixation indices (NST) and coalescence methods. Species samples are from the same localities along 1000 km of the Rio Juruá in western Amazonian Brazil, but each species differs in important life history traits such as population size and reproductive rate. Average haplotype differentiation, hierarchical haplotype apportionment, and gene flow estimates are contrasted in discussing the current and past population structure. Two species exhibit isolation by distance patterns wherein gene flow is largely limited to geographically adjacent localities. Mesomys exhibits this pattern throughout its range along the river. More than 75% of haplotype variation is apportioned among localities and regions, and estimates of Nm for pair-wise comparisons are nearly always less than 1. Oligoryzomys shows weak isolation by distance, but only over the largest geographical distances. Nm values for this species are nearly always above 1 and most (about 80%) of haplotype variation is contained within local populations. In contrast, Oryzomys exhibits no genetic structure throughout its entire distribution; Nm values average 17 and nearly 90% of the total haplotype variance is contained within local populations. Although gene flow estimates are high, the pattern of Nm as a function of geographical distance suggests that this species experienced a more recent invasion of the region and is still in genetic disequilibrium under its current demographic conditions.
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