Mitochondrial DNA analysis of burbot stocks in the Kootenai River Basin of British Columbia, Montana, and Idaho

Differences in mitochondrial haplotype frequency were examined among burbot Lota lota collected from four areas within the Kootenai River Basin of British Columbia, Montana and Idaho. The polymerase chain reaction (PCR) was used to amplify three gene regions of the mitochondrial genome: NADH dehydrogenase subunit 1 (ND1), NADH dehydrogenase subunit 2 (ND2), and NADH dehydrogenase subunits 5 and 6 combined (ND5,6). Amplified DNA was screened for restriction fragment length polymorphisms (RFLPs). Simple haplotypes resulting from RFLPs in a single gene region were combined into composite haplotypes. The distribution of composite haplotypes and their frequencies correspond to areas of the Kootenay River basin above and below a presumptive geographic barrier, Kootenai Falls, Montana, and suggest spatially segregated populations. A test of geographic heterogeneity among haplotype frequency distributions was highly significant (P < 0.001) when a Monte Carlo simulation was used to approximate a chi(2) test. Two populations, one above and one below Kootenai Falls emerged when a neighbor-joining method was used to infer a phylogenetic tree based on estimates of nucleotide divergence between ail pairs of sample locations. These analyses indicate that burbot below Kootenai Falls form a separate genetic group from burbot above the falls and further suggests that Libby Dam, which created Lake Koocanusa, is not an effective barrier segregating burbot above Kootenai Falls. Management implications from these findings are that mitigative efforts in the Kootenai River Basin must address the needs of two genetically divergent burbot stocks, and that a unification of angling regulations for the population downstream of Kootenai Falls in Idaho and British Columbia is warranted.