Assessment of concordance among genealogical reconstructions from various mtDNA segments in three species of Pacific salmon (genus Oncorhynchus)

Seven segments of mitochondrial DNA (mtDNA), comprising 97% of the mitochon drial genome, were amplified by polymerase chain reaction (PCR) and examine d for restriction site variation using 13 restriction endonucleases in thre e species of Pacific salmon: pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon. The distribution of variability across the s even mtDNA segments differed substantially among species. Little similarity in the distribution of variable restriction sites was found even between t he mitochondrial genomes of the even- and odd-year broodlines of pink salmo n. Significantly different levels of nucleotide diversity were detected amo ng three groups of genes: six NADH-dehydrogenase genes had the highest, two rRNA genes had the lowest; and a group that included genes for ATPase and cytochrome oxidase subunits, the cytochrome b gene, and the control region had intermediate levels of nucleotide diversity. Genealogies of mtDNA haplo types were reconstructed for each species, based on the variation in all mt DNA segments. The contributions of variation within different segments to r esolution of the genealogical trees were compared within each species. With the exception of sockeye salmon, restriction site data from different geno me segments tended to produce rather different trees (and hence rather diff erent genealogies). In the majority of cases, genealogical information in d ifferent segments of mitochondrial genome was additive rather than congruen t. This finding has a relevance to phylogeographic studies of other organis ms and emphasizes the importance of not relying on a limited segment of the mtDNA genome to derive a phylogeographic structure.