Genetic identification of native populations of fluvial white-spotted charr Salvelinus leucomaenis in the upper Tone River drainage

Abstract

Stocking of exogenous, hatchery-reared white-spotted charr Salvelinus leucomaenis has been conducted throughout much of their range in Honshu Island, Japan, to increase angling opportunities. Although the native charr populations are thought to have declined because of hybridization with introduced fish, their distribution and genetic status have been uncertain. Fine population structures of charr in the upper Tone River drainage were examined using mitochondrial DNA and microsatellite analyses so as to clarify the presence of native populations. One common mtDNA haplotype was detected in all populations in the Ohashi River and Watarase River, and four and one tributary populations were monomorphic for such haplotypes, respectively. However, several haplotypes, considered to have originated from stocked hatchery fish, were observed in the stocked and the remaining populations. Judging from the genetic integrity over a fine geographic scale, the former were considered as indicative of native populations and the latter as admixtures with hatchery fish. Comparisons of genetic diversity, deviations from the Hardy-Weinberg equilibrium, principal component analysis, and relatedness estimations based on microsatellite DNA can also provide evidence for distinguishing native populations from those influenced by hatchery fish.

Hybridization, Isolation, and Low Genetic Diversity of Kirikuchi Char, the Southernmost Populations of the Genus Salvelinus

“…That is, local populations in A1––A4 and B2‐1 and B4 consisted of homogenous groups (cluster I: A1––A4; cluster II: B2‐1 and B4), whereas the cluster III component was shared among populations from the stocked areas in both drainages (A5, B2‐2, and B3), admixed with cluster I or II. Moreover, the isolation of indigenous populations above barriers as inferred here has been reported in many fluvial salmonid populations in other rivers with intensive stocking of nonnative fishes (e.g., Berrebi et al 2000; Fausch et al 2009; ; Kubota et al 2007).…”

“…The Kirikuchi char populations showed extremely reduced genetic diversity, with fixation of a single mtDNA haplotype in each drainage and lower average H E and A R in microsatellites ( H E == 0.00––0.12; A R == 1.0––1.6) and the MHC gene ( H E == 0.00––0.50; A R == 1.0––2.8) compared with the diversity of native populations in other Japanese mountain rivers. For example, H E was 0.19––0.44 in 10 native landlocked S. leucomaenis pluvius populations based on eight microsatellite loci, seven of which were shared with the populations examined in this study (Kubota et al 2007), and H E was 0.35––0.63 in eight above‐dam S. leucomaenis leucomaenis populations based on five microsatellite loci, four of which were shared with the fish examined this study (Yamamoto et al 2008). This low genetic diversity would have resulted from both historical and recent bottleneck and founder effects.…”

“…Circles with different shading patterns (haplotypes) correspond to the different clades (clades 2‐1 to 2‐4) represented in Figure 1 (see also Yamamoto et al 2004). The numeral in each circle corresponds to the haplotype number in Table 1 and Yamamoto et al (2004, 2008), Kubota et al (2007), and . Haplotypes with asterisks are those detected in the present study; two asterisks denote suspected pure haplotypes of Kirikuchi char S. leucomaenis japonicus .…”

Isolation and characterization of tri‐ and tetra‐repeat microsatellite loci in the white‐spotted charr Salvelinus leucomaenis (Salmonidae)

“…This is of particular relevance because of the supplemental stocking activities. The current evidence suggests accelerated rate of hybridization between wild and hatchery fish within and among subspecies (Kubota et al , ; Kikko et al , ; Sato et al , ). In addition, habitat fragmentation by artificial damming is common on Japanese rivers.…”

Displacement of native white‐spotted charr Salvelinus leucomaenis by non‐native brown trout Salmo trutta after resolution of habitat fragmentation by a migration barrier

“…For stream‐dwelling salmonids, the barriers also protect genetically native populations from interacting ( e.g . hybridization and competition) with stocked hatchery conspecifics (van Houdt et al ., ; Kubota et al ., ). To conserve native populations from these biological invasions, other strategies should be used, such as eradication of non‐native species in combination with barriers, to prepare for the possibility of sudden barrier collapse.…”