Disturbance of the indigenous gene pool of the threatened brook lamprey Lethenteron sp. S by intraspecific introgression and habitat fragmentation

Artificial introduction and habitat fragmentation affect the indigenous gene pools of fluvial animals. To investigate the effect of human activities on the genetic population structure of vulnerable brook lamprey Lethenteron sp. S in a single river system, samples from 12 tributaries of the Jinzu River, Japan, were analyzed using mitochondrial and microsatellite DNA markers. Exogenous Lake Biwa (Japan) haplotypes and alleles were detected in lampreys from several Jinzu River tributaries. Since Lake Biwa is the source of the commercial ayu fish Plecoglossus altivelis that is introduced in the Jinzu River, the exogenous Lake Biwa lamprey genotypes in the Jinzu River probably originated from the Lake Biwa lampreys that were unintentionally introduced along with the ayu fish. Bayesian admixture and mitochondrial DNA analyses revealed various genetic disturbance phases of the exogenous genotypes in the Jinzu River, such as the six indigenous populations, four admixed populations with low frequencies (average admixture proportion = 0.02-0.04; exogenous haplotype proportion <0.01), one introgressed population (0.71 and 0.57) and one population almost displaced by exogenous genotypes (0.93 and 0.96). Samples from three tributaries with weirs were genetically differentiated from the others by using pairwise F _ST and Bayesian analyses; the results suggested isolation by the weirs. Reduced mitochondrial DNA diversity was observed in 1 of the 3 samples probably due to reduced population size. These findings indicate that the indigenous lamprey populations in the Jinzu River are seriously affected by introgression with exogenous genotypes via unintentional introduction and habitat fragmentation by weirs.