Demographic expansion of parasitic nematodes of livestock based on mitochondrial DNA regions that conflict with the infinite-sites model.

Mitochondrial ND4 sequences of populations of four species of parasitic nematodes of livestock were subjected to demographic analyses. Deviation from selective neutrality was detectable using the frequency spectrum of segregating sites and highly negative neutrality statistics. However, the mitochondrial data sets do not comply with the infinite-sites model that underlies these tests, and as a consequence, it was not established whether these features are solely a result of population expansion, or whether aspects of the molecular evolution of these mitochondrial regions are also involved. Coalescent analyses based on Fu's Fs neutrality test, which incorporated estimates of rate heterogeneity, the transition-transversion ratio and nucleotide bias, as well as analyses that are fairly robust to deviations from the infinite-sites model supported population expansion. Also analyses that do not depend on the infinite-sites model suggested historical population expansion of these nematodes. The very similar time since expansion, the absence of signatures of positive selection in ND4 and the logical association with human demography imply that selective sweeps of mitochondrial variants are less probable, and that expansion is the most likely scenario for the parasitic nematodes of livestock. The methods used to characterize the expansion have different assumptions and emphasize different aspects of expansions. The resulting restrictions on the interpretation of expansions are outlined.