Shoichiro Yamamoto

Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream‐dwelling Dolly Varden charr

Isolation by distance is usually tested by the correlation of genetic and geographic distances separating all pairwise populations’ combinations. However, this method can be significantly biased by only a few highly diverged populations and lose the information of individual population. To detect outlier populations and investigate the relative strengths of gene flow and genetic drift for each population, we propose a decomposed pairwise regression analysis. This analysis was applied to the well‐described one‐dimensional stepping‐stone system of stream‐dwelling Dolly Varden charr (Salvelinus malma). When genetic and geographic distances were plotted for all pairs of 17 tributary populations, the correlation was significant but weak (r2 = 0.184). Seven outlier populations were determined based on the systematic bias of the regression residuals, followed by Akaikes information criteria. The best model, 10 populations included, showed a strong pattern of isolation by distance (r2 = 0.758), suggesting equilibrium between gene flow and genetic drift in these populations. Each outlier population was also analysed by plotting pairwise genetic and geographic distances against the 10 nonoutlier populations, and categorized into one of the three patterns: strong genetic drift, genetic drift with a limited gene flow and a high level of gene flow. These classifications were generally consistent with a priori predictions for each population (physical barrier, population size, anthropogenic impacts). Combined the genetic analysis with field observations, Dolly Varden in this river appeared to form a mainland‐island or source‐sink metapopulation structure. The generality of the method will merit many types of spatial genetic analyses.

Effects of habitat fragmentation by damming on salmonid fishes: lessons from white-spotted charr in Japan

Dam construction has serious consequences, and one of the most serious concerns is the fragmentation of riverine ecosystems. We reviewed the influence of habitat fragmentation on white-spotted charr Salvelinus leucomaenis populations. First, habitat fragmentation by damming has serious consequences in terms of alternative life-history strategies. Most fish in dammed-off areas do not migrate to the sea and instead become resident forms. This loss of the anadromous form negatively affects populations through decreased spawning biomass. In addition, the smaller population sizes in dammed-off habitats can negatively affect population dynamics through demographic, environmental, and genetic stochasticity. Therefore, the population viability is reduced in small, dammed-off habitats. White-spotted charr populations also likely experience different selection pressures after damming. Many of these effects of habitat fragmentation due to damming are not immediate but rather occur gradually over several generations. Because most Japanese dams were constructed after 1970, some effects of damming may not yet be obvious.

Evolution, Ecology, and Conservation of Dolly Varden, White spotted Char, and Bull Trout

Abstract We review the ecology and conservation of three lesser-known chars (genus Salvelinus): Dolly Varden (S. malma), white-spotted char (S. leucomaenis), and bull trout (S. confluentus). Dolly Varden is distributed across the northern Pacific Rim and co-occurs with bull trout and white-spotted char at the southern extremes of its range. In contrast, bull trout and white-spotted char are naturally isolated, with the former restricted to North America and the latter distributed in northeastern Asia. Though the range of Dolly Varden overlaps with the two other chars, it is most closely related to Arctic char (S. alpinus), whereas bull trout and white-spotted char are sister taxa. Each species exhibits diverse life histories with respect to demographic characteristics, trophic ecology, and movement. This diversity appears to be tied to environmental variability (e.g., temperature, habitat connectivity), resource availability (e.g., food), and species interactions. Increasingly, these interactions involve ...

Phylogeography of White-Spotted Charr ( Salvelinus leucomaenis ) Inferred from Mitochondrial DNA Sequences

The white-spotted charr (Salvelinus leucomaenis) is a coldwater-adapted fish distributed in far-eastern Asia. To assess phylogeographic patterns of this species over most of its range in the Japanese archipelago and Sakhalin Island, Russia, we examined nucleotide sequences of the mitochondrial DNA (mtDNA) cytochrome b region (557 bp) in 141 individuals from 50 populations. A total of 33 (5.5%) nucleotide positions were polymorphic and defined 29 haplotypes. Phylogenetic analysis assigned the observed haplotypes to four main clades, which were characterized by the idiosyncrasies and discontinuity of geographic distributions. The nested clade analyses revealed that the geographical distribution patterns of some haplotypes and clades were explained by historical event such as past fragmentation. Although substantial genetic differentiation was found among the four main clades, their geographic distributions overlapped extensively in several regions. Since white-spotted charr can potentially use both freshwater and marine environments, coexistence among different lineages can be attributed to secondary contact through range expansion by migratory individuals during multiple glacial periods after interglacial isolation. Finally, our data demonstrate that the current subspecies designation does not reflect the phylogeography of this species based on mtDNA analysis. Hierarchical analysis (AMOVA) also showed that genetic variation was far more pronounced within subspecies than among subspecies (i.e., among discrete regions). These results suggest that each population, rather than each subspecies, must be treated as an evolutionarily significant unit.

INDIRECT CONTRAMENSALISM THROUGH TROPHIC CASCADES BETWEEN TWO OMNIVOROUS FISHES

The impact of trophic cascades on the interspecific relationship between two omnivorous stream fish, ayu (Plecoglossus altivelis altivelis) and Japanese dace (Tribolodon hakonensis), were analyzed in experimental pools. Benthic algae grew on the pool beds, and macroinvertebrates colonized the pools. Ayu predominantly grazed the algae, occasionally forming territories. Japanese dace fed on both benthic algae and invertebrates when ayu were absent, and predominantly on invertebrates when ayu were present. The presence of Japanese dace reduced the number of invertebrates and increased algal biomass (chlorophyll a) through trophic cascades, but the effects of respiration and excretion of dace did not notably increase algal biomass probably because the water continuously pumped into the pools was already nutrient rich. The growth rate of ayu was enhanced in the presence of Japanese dace due to increased algal biomass. In contrast, as the number of ayu increased, the growth rate of Japanese dace was reduced bec...

Phylogeography of the Salmonid Fish, Dolly Varden Salvelinus malma: Multiple Glacial Refugia in the North Pacific Rim

The geographic distribution pattern of mitochondrial DNA (control region) sequence polymorphisms from 73 populations of a salmonid fish, Dolly Varden Salvelinus malma, over most of its range in the North Pacific rim, was examined to assess how its spatial population genetic structure has been molded. The observed 68 haplotypes were grouped into three main lineages, which correspond to western, central, and eastern regions in the North Pacific. The two outlier-haplotype groups gave close agreement with DNA types from two congeneric species, white-spotted charr S. leucomaenis and Arctic charr S. alpinus, respectively. These results suggest that the present-day genetic structure of S. malma reflects historical patterns of isolation and re-colonization, and also historical hybridization with co-distributed species. We also placed the haplotypes of S. malma within our study areas into a pre-existing evolutionary relationship of S. alpinus and S. malma throughout the Northern Hemisphere. Phylogenetic analysis revealed that the Western Lineage S. malma was basal to all other lineages of S. malma and S. alpinus. Our data serve as a biogeographic hypothesis for salmonid fishes that the Sea of Japan and/or Sea of Okhotsk regions represents a place of origin for S. malma and S. alpinus groups currently distributed in circumpolar regions.

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

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 char populations are thought to have declined because of hybridization with introduce 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.

Exposure of a herbivorous fish to 134Cs and 137Cs from the riverbed following the Fukushima disaster

Ayu Plecoglossus altivelis, a herbivorous fish, is an important fishery resource and key component of the foodweb in many Japanese streams. Radionuclide contamination of this species is likely transferred to higher trophic levels, include humans, in the food chain. After the Fukushima accident in March 2011, ayu were exposed to highly contaminated silt while feeding on algae attached to the riverbed stones. To understand the route by which herbivorous fish are exposed to radionuclides, the activity concentrations of sum of (134)Cs and (137)Cs (radiocesium) were analyzed in riverbed samples (algae and silt) and in the internal organs and the muscle of ayu in five river systems in the Fukushima Prefecture between summer 2011 and autumn 2013. Although there was a positive correlation between the radiocesium activity concentrations in the muscle and the internal organs of ayu, the median activity concentration in the muscle was much lower than those in the internal organs. The activity concentrations of radiocesium in the riverbed samples and the internal organs and the muscle of ayu were correlated with contamination levels in soil samples taken from the watershed upstream of the sample sites. The results of the generalized linear mixed models suggest that the activity concentrations in both the internal organs and the muscle of ayu declined over time. Additionally, the activity concentrations in the internal organs were correlated with those in the riverbed samples that were collected around the same time as the ayu. The activity concentrations in the muscle were correlated with ayu body size. Our results suggest that ayu ingest (134)Cs and (137)Cs while grazing silt and algae from the riverbed, and a part of the (134)Cs and (137)Cs is assimilated into the muscle of the fish.

Genetic structure and diversity of Japanese kokanee Oncorhynchus nerka stocks as revealed by microsatellite and mitochondrial DNA markers

Genetic structure and diversity of nine Japanese kokanee (landlocked) Oncorhynchus nerka stocks and anadromous O. nerka from the North Pacific and the Canadian Lake Cultus population were examined using microsatellite and mitochondrial DNA. Sequence analyses of the cytochrome b region of mtDNA for Japanese kokanee O. nerka stocks on Honshu and Hokkaido islands revealed that most Japanese stocks were monomorphic of one major haplotype, which was also dominant in the Lake Cultus population and anadromous O. nerka in the North Pacific. Assignment tests using microsatellite DNA revealed that there was no clear-cut population structure in Japanese kokanee O. nerka stocks.

Prey fish selection by Far Eastern catfish Silurus asotus and largemouth bass Micropterus salmoides

Prey fish selection by Far Eastern catfish and largemouth bass were examined using bluegill, Japanese dace and crucian carp as food fish. In both aquaria (1.2m × 0.45m) and ponds (2.8 m × 1.2 m), bluegill was not preyed on by catfish and bass more than dace and crucian carp. In aquaria, there was no significant difference in the consumption of dace and crucian carp between catfish and bass, but in ponds, catfish preyed on dace and crucian carp more and less than bass, respectively. In the case that only bluegill and catfish were introduced in ponds, catfish consumed 4–15 g of bluegill per day. The introduction of catfish into ponds and lakes for the purpose of eradicating bluegill is considered appropriate for areas with few native fish species.