Nested cladistic analysis indicates population fragmentation shapes genetic diversity in a freshwater mussel

Recently developed phylogeographic analyses that incorporate genealogical relationships of alleles offer the exciting prospect of disentangling historical from contemporary events. However, the relative advantages and shortfalls of this approach remain to be studied. We compared the nested cladistic method to the more traditional analysis of variance approach in a study of intraspecific genetic variation in the freshwater mussel, Lampsilis hydiana. We surveyed 257 specimens for nucleotide sequence level variation in a fragment of the mitochondrial 16S rRNA gene. When compared side by side, nested cladistic analysis and analysis of molecular variance (AMOVA) identified fragmentation of Arkansas river populations from remaining populations to the southwest. Nested cladistic analysis identified a second, more recent separation of Ouachita and Upper Saline river populations that was not detected by AMOVA. Differences among analytical methods probably arise from treatment of spatial hierarchical information: hierarchical groups emerge via a parsimony criterion in nested cladistic analysis but must be specified a priori in AMOVA. Both methods identified significant genetic structure among localities within hierarchical groups. Results from AMOVA suggested little gene flow among local populations with an island model. However, inferences about process that gave rise to patterns at this level were not possible in nested cladistic analysis, because an ancestral (interior) haplotype was not observed for a key one-step clade in the parsimony network. Our results suggest that, under some circumstances, nested cladistic analysis has lower power than more traditional analysis of variance to infer processes at the local population level.