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

Abstract

Seven segments of mitochondrial DNA (mtDNA), comprising 97% of the mitochondrial genome, were amplified by polymerase chain reaction (PCR) and examined for restriction site variation using 13 restriction endonucleases in three species of Pacific salmon: pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon. The distribution of variability across the seven mtDNA segments differed substantially among species. Little similarity in the distribution of variable restriction sites was found even between the mitochondrial genomes of the even- and odd-year broodlines of pink salmon. Significantly different levels of nucleotide diversity were detected among 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 haplotypes were reconstructed for each species, based on the variation in all mtDNA segments. The contributions of variation within different segments to resolution of the genealogical trees were compared within each species. With the exception of sockeye salmon, restriction site data from different genome segments tended to produce rather different trees (and hence rather different genealogies). In the majority of cases, genealogical information in different segments of mitochondrial genome was additive rather than congruent. This finding has a relevance to phylogeographic studies of other organisms and emphasizes the importance of not relying on a limited segment of the mtDNA genome to derive a phylogeographic structure.

Mitochondrial DNA diversity and relationships of endemic charrs of the genus Salvelinus from Lake Kronotskoye (Kamchatka Peninsula)

“…The greatest variability of the investigated mtDNA portion in charrs occurred in regions containing genes of the subunits NADH-dehydrogenase-ND1/ND2 and ND5/ND6 (Table 4). These data are in a good agreement with the results obtained for other salmon fish-Oncorhynchus gorbuscha, Oncorhynchus nerka, and Oncorhynchus kusutch (Churikov et al, 2001;Gharrett et al, 2001). The lowest diversity indices among charrs were observed in the regions COI/COII/A8, A8/A6/COIII/ND3, and ND3/ND4L/ ND4 (Table 4).…”

“…The lowest diversity indices among charrs were observed in the regions COI/COII/A8, A8/A6/COIII/ND3, and ND3/ND4L/ ND4 (Table 4). An important feature of salmon fish is the significant differences in the level of variability in homologous mtDNA regions (Churikov et al, 2001). However, analysis of variability usually uses estimates obtained for one or two regions, subjectively selected on the basis of supposed variability level or by extrapolations of results from studies of closely related species.…”

The genetic population structure of lacustrine sockeye salmon, Oncorhynchus nerka, in Japan as the endangered species

“…Anadromous sockeye salmon in south central Alaska and eastern Kamchatka possessed variable sites in the ND5/ND6 mtDNA regions (Churikov et al 2001;Brykov et al 2003). The low genetic variability of the ND5 region used in this study suggests that this region may be of limited use in discriminating among populations of sockeye salmon.…”

The Effect of Reproduction Biotopes on the Genetic Differentiation of Populations of Sockeye Salmon Oncorhynchus nerka

“…A high number of possible alternative associations among haplotypes (loop structures in the network) indicates high homoplasy, i.e., a presumably high rate of reverse and recurrent mutation in mtDNA of the species. The both phylogenetic groups are included in a group revealed earlier in mtDNA analysis for a large region of the sockeye range [15].…”