Itsuro Koizumi

Genetic Differentiation of White-Spotted Charr (Salvelinus leucomaenis) Populations After Habitat Fragmentation: Spatial–Temporal Changes in Gene Frequencies

Freshwater fishes that have been isolated by artificial dams have become models for studying the effects of recent barriers on genetic variation and population differentiation. In this study, we examined the genetic structure of 11 populations of white-spotted charr (Salvelinus leucomaenis) by using polymorphic microsatellite loci. Reduced genetic diversity, expressed as the number of alleles and the expected heterozygosity, was observed in all above-dam relative to below-dam populations. Highly significant genetic differentiation (FST) was found for all pairwise comparisons among populations, with FST-values ranging from 0.023 to 0.639. Both multiple regression analysis and a randomization test revealed that genetic differentiation above and below dams was negatively related to the habitat size of above-dam populations, and was positively related to the time period of isolation. This study is one of the few attempts to predict the population genetic structure of such variable spatial–temporal scales. We conclude that differences in genetic structure above and below dams are related to recent historical population size, whereby sites with a lower effective number of adults are more prone to temporal stochasticity in gene frequencies.

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.

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.

A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England

Salmonid fishes exhibit high levels of population differentiation. In particular, the brown trout (Salmo trutta L.) demonstrates complex within river drainage genetic structure. Increasingly, these patterns can be related to the underlying evolutionary models, of which three scenarios (member‐vagrant hypothesis, metapopulation model and panmixia) facilitate testable predictions for investigations into population structure. We analysed 1225 trout collected from the River Dart, a 75 km long river located in southwest England. Specimens were collected from 22 sample sites across three consecutive summers (2001–2003) and genetic variation was examined at nine microsatellite loci. A hierarchical analysis of molecular variance revealed that negligible genetic variation was attributed among temporal samples. The highest levels of differentiation occurred among samples isolated above barriers to fish movement, and once these samples were removed, a significant effect of isolation‐by‐distance was observed. These results suggest that, at least in the short‐term, ecological events are more important in shaping the population structure of Dart trout than stochastic extinction events, and certainly do not contradict the expectations of a member‐vagrant hypothesis. Furthermore, individual‐level spatial autocorrelation analyses support previous recommendations for the preservation of a number of spawning sites spaced throughout the tributary system to conserve the high levels of genetic variation identified in salmonid species.

Loss of Genetic Diversity Means Loss of Geological Information: The Endangered Japanese Crayfish Exhibits Remarkable Historical Footprints

Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall F ST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events.

The Fishermen Were Right: Experimental Evidence for Tributary Refuge Hypothesis During Floods

Fishermen often anecdotally report an unexpected increase of fish caught in small tributary streams during floods, presumably due to refuge-seeking behavior from the main stem. From a population perspective, this implies the significance of refuge habitats and connectivity for population viability against natural disturbances. Despite the plausibility, however, surprisingly few studies have examined the tributary refuge hypothesis, mainly due to the difficulty in field survey during floods. Here, we made use of a large-scale controlled flood to assess whether fishes move into tributaries during flooding in the main stem. A planned water release from the Satsunai River Dam located on Hokkaido Island in Japan rapidly increased the main stem discharge by more than 20-fold. Before, during, and after flooding censuses in four tributaries provided evidence of the refuge-seeking behavior of fishes from the main stem. For example, more than 10 Dolly Varden char, a salmonid fish, were caught in a tributary during the flood, even though almost no individuals were captured before or after the flood. The fish responded immediately to the flooding, suggesting the need for studies during disturbances. In addition, the likelihood of refuge movements varied among tributaries, suggesting the importance of local environmental differences between tributary and the main stem habitats. This is the first study to experimentally confirm the tributary refuge hypothesis, and underscores the roles of habitat diversity and connectivity during disturbances, even though some habitats are not used during normal conditions.

Spawning Migration of Stream-Dwelling Dolly Varden in Spring-Fed Tributaries of the Shiisorapuchi River, Japan

ABSTRACT During the breeding seasons of 1998–2001, the spawning migration of stream-dwelling Dolly Varden (Salvelinus malma) was investigated in four small spring-fed tributaries of the Shiisorapuchi River, Hokkaido, Japan. From late September to late October, Dolly Varden continuously migrated into these tributaries from the mainstream without any clear peaks. Precipitation was positively correlated (P < 0.05) with the number of migrants in two tributaries, but not in the other two. No clear relationship was observed between the number of migrants and the water temperature for either the mainstream or the tributaries. Nocturnal migration behavior was recognized in one tributary, but it was diurnal in two tributaries, and there was no clear tendency in the other. Body size of migrating Dolly Varden was not correlated with the entry date for either sex. No significant difference in the entry date was observed between males and females for any tributary or for any year. However, the number of males entering a tributary was positively (P < 0.05) correlated with that of females, indicating a synchronous migration of males and females. Because the number of females was not correlated with any environmental factor, we suggest that male Dolly Varden migrate into tributaries following mature females, possibly via pheromonal stimuli.

Seasonal and Diel Activity Patterns of Eight Sympatric Mammals in Northern Japan Revealed by an Intensive Camera-Trap Survey.

The activity patterns of mammals are generally categorized as nocturnal, diurnal, crepuscular (active at twilight), and cathemeral (active throughout the day). These patterns are highly variable across regions and seasons even within the same species. However, quantitative data is still lacking, particularly for sympatric species. We monitored the seasonal and diel activity patterns of terrestrial mammals in Hokkaido, Japan. Through an intensive camera-trap survey a total of 13,279 capture events were recorded from eight mammals over 20,344 camera-trap days, i.e., two years. Diel activity patterns were clearly divided into four categories: diurnal (Eurasian red squirrels), nocturnal (raccoon dogs and raccoons), crepuscular (sika deer and mountain hares), and cathemeral (Japanese martens, red foxes, and brown bears). Some crepuscular and cathemeral mammals shifted activity peaks across seasons. Particularly, sika deer changed peaks from twilight during spring–autumn to day-time in winter, possibly because of thermal constraints. Japanese martens were cathemeral during winter–summer, but nocturnal in autumn. We found no clear indication of predator-prey and competitive interactions, suggesting that animal densities are not very high or temporal niche partitioning is absent among the target species. This long-term camera-trap survey was highly cost-effective and provided one of the most detailed seasonal and diel activity patterns in multiple sympatric mammals under natural conditions.

Long Breeding Season and High Frequency of Multiple Brooding in Great Tits in Northern Japan

The Great Tit Parus major is one of the most intensively studied birds and such studies have contributed greatly to the current understanding of the evolution and ecology of natural populations. However, despite its wide geographic distribution and high variation in life history traits among regions, most ecological studies are concentrated in Europe, and there are relatively few studies elsewhere. We studied the breeding ecology of a Great Tit population in northern Japan and compared their breeding parameters to those described previously for European populations. This population was characterized by a long breeding season, up to four months from May to as late as the end of August (egglaying to fledging), and a high frequency of multiple brooding (≥60%) including two occasions of third broods. In addition, clutch size was large with a mean of over ten, compared to less than eight in European populations at the equivalent latitude. The high productivity of the studied population may be a consequence of the high diversity and abundance of prey items in northern Japan associated with past and present climatic characteristics.