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

Recently developed phylogeographic analyses that incorporate genealogical r elationships of alleles offer the exciting prospect of disentangling histor ical from contemporary events. However, the relative advantages and shortfa lls of this approach remain to be studied. Mle compared the nested cladisti c method to the more traditional analysis of variance approach in a study o f intraspecific genetic variation in the freshwater mussel, Lampsilis hydia na. We surveyed 257 specimens for nucleotide sequence level variation in a fragment of the mitochondrial 16S rRNA gene. When compared side by side, ne sted cladistic analysis and analysis of molecular variance (AMOVA) identifi ed fragmentation of Arkansas river populations from remaining populations t o the southwest. Nested cladistic: analysis identified a second, more recen t separation of Ouachita and Upper Saline river populations that was not de tected by AMOVA. Differences among analytical methods probably arise from t reatment of spatial hierarchical information: hierarchical groups emerge vi a a parsimony criterion in nested cladistic analysis but must be specified a prior in AMOVA. Both methods identified significant genetic structure amo ng localities within hierarchical groups. Results from AMOVA suggested litt le gene flow among local populations with an island model. However, inferen ces about process that gave rise to patterns at this level were not possibl e in nested cladistic analysis, because an ancestral (interior) haplotype w as not observed for a key one-step clade in the parsimony network. Our resu lts suggest that, under some circumstances, nested cladistic analysis has l ower power than more traditional analysis of variance to infer processes at the local population level.