Mitochondrial DNA analysis of burbot stocks in the Kootenai River Basin ofBritish 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 Bri tish Columbia, Montana and Idaho. The polymerase chain reaction (PCR) was u sed to amplify three gene regions of the mitochondrial genome: NADH dehydro genase subunit 1 (ND1), NADH dehydrogenase subunit 2 (ND2), and NADH dehydr ogenase subunits 5 and 6 combined (ND5,6). Amplified DNA was screened for r estriction fragment length polymorphisms (RFLPs). Simple haplotypes resulti ng from RFLPs in a single gene region were combined into composite haplotyp es. The distribution of composite haplotypes and their frequencies correspo nd to areas of the Kootenay River basin above and below a presumptive geogr aphic barrier, Kootenai Falls, Montana, and suggest spatially segregated po pulations. A test of geographic heterogeneity among haplotype frequency dis tributions 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 inf er a phylogenetic tree based on estimates of nucleotide divergence between ail pairs of sample locations. These analyses indicate that burbot below Ko otenai Falls form a separate genetic group from burbot above the falls and further suggests that Libby Dam, which created Lake Koocanusa, is not an ef fective barrier segregating burbot above Kootenai Falls. Management implica tions from these findings are that mitigative efforts in the Kootenai River Basin must address the needs of two genetically divergent burbot stocks, a nd that a unification of angling regulations for the population downstream of Kootenai Falls in Idaho and British Columbia is warranted.