Potential fragmentation and loss of thermal habitats for charrs in the Japanese archipelago due to climatic warming

1. The upper thermal limits of the present distributions of two charr species, Dolly Varden, Salvelinus malma , and white-spotted charr, S. leucomaenis , in streams of the Japanese archipelago were examined using groundwater temperature as an index of thermal condition. The lower limits of the altitudinal distributions of Dolly Varden and white-spotted charr were delineated, respectively, by 8 and 16 °C groundwater isotherms.
2. The potential impact of future climatic warming on the geographical distribution, habitat extent and population fragmentation of each species was predicted at both the full archipelago and individual catchment levels.
3. For Dolly Varden, analysis at the full archipelago level indicated a loss of 27.6, 67.2, 79.6 and 89.6% of the current geographical range, respectively, for a 1, 2, 3 and 4 °C increase in mean annual air temperature. The present distribution area of white-spotted charr would likewise reduce by 4.1, 20.5, 33.8 and 45.6%, respectively.
4. Based on the analyses of three individual catchments, one for Dolly Varden and two for white-spotted charr, the lower habitat boundaries for the two charr species could be expected to rise increasingly to higher elevations in each catchment as warming proceeded. As a consequence, there would be large reductions in mean habitat area, with increasing habitat fragmentation followed by localized extinctions of the two species.     

Redd superimposition by introduced rainbow trout,oncorhynchus mykiss, on native charrs in a japanese stream

Spawning redd superimposition of introduced, spring-spawning rainbow trout,Oncorhynchus mykiss, on native, fall-spawning Dolly varden,Salvelinus malma, and white-spotted charr,S. leucomaenis, were examined in a small stream in Hokkaido, Japan. The stream reaches in which Dolly Varden and white-sported charr redds were observed in fall 1997 greatly overlapped with the reaches in which rainbow trout redds were recorded in spring 1998. Spawning microhabitats were also similar between trout and the two charr species. Thirteen and 3% of Dolly Varden and white-spotted charr redds, respectively, were superimposed by rainbow trout redds. The eggs or alevins in the disturbed charr redds were potentially damaged because charrs were not likely to have emerged from the redds before the superimposition occurred. In sufficiently great abundance, introduced rainbow trout may negatively impact native charr populations by dislodging the latter’s spawning redds.     

Asymmetric competition drives lake use of coexisting salmonids

To what degree are population differences in resource use caused by competition and the occupation of adjacent positions along environmental gradients evidence of competition? Habitat use may be the result of a competitive lottery, or restricted by competition. We tested to what extent population differences in habitat use of two salmonids, cutthroat trout (Oncorhynchus clarki) and Dolly Varden charr (Salvelinus malma) were influenced by interspecific competition. We hypothesized that the depth distribution of Dolly Varden charr would be affected by competition from the more littoral and surface-oriented cutthroat trout, and that the depth distribution of cutthroat trout would be little affected by competition from Dolly Varden charr. Sympatric populations of cutthroat trout and Dolly Varden charr were created by reciprocal transfers of previously allopatric populations in two experimental lakes. We found evidence of asymmetric competition, as Dolly Varden charr were displaced from littoral habitats when sympatric with cutthroat trout, whereas cutthroat trout remained unaffected by the presence of Dolly Varden charr. Evolved differences between the species, and differences between experimental lakes, also contributed to population differences in habitat use, but asymmetric competition remained as the main driver of different depth distributions in sympatry.     

Temperature‐dependent competition between juvenile salmonids in small streams

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Introgressive hybridization between Dolly Varden Salvelinus malma and white‐spotted charr Salvelinus leucomaenis on Hokkaido Island, Japan

Intra‐ and interspecific phylogenetic analysis of Dolly Varden Salvelinus malma and white‐spotted charr Salvelinus leucomaenis throughout Hokkaido Island was conducted using nucleotide sequences of the mitochondrial DNA control region and three nuclear DNA markers [ribosomal DNA (ITS‐1), microsatellite ( u ‐85), SINE ( Fok ‐223)]. A total of 19 mtDNA haplotypes from 271 individuals of Dolly Varden, nine haplotypes from 134 white‐spotted charr were defined, and identified two well‐supported monophyletic clades for each species. Two haplotypes of Dolly Varden, however, were clustered together in the white‐spotted charr clade. Those haplotypes were found only from several rivers in the Shiretoko Peninsula, and a neighbouring river of that region. Analyses of ribosomal DNA and Fok ‐223 loci revealed that both species are characterized by having completely species‐specific diagnostic sequence and fragment patterns. Dolly Varden of the Shiretoko populations are typically allopatric in distribution where white‐spotted charr do not currently occur. In addition, incongruence in genetic relationships between mtDNA and nuclear DNA markers give strong evidence of historical mtDNA introgression between Dolly Varden and white‐spotted charr. Some white‐spotted charr diagnostic alleles in a nuclear microsatellite locus ( u ‐85) were found in some Shiretoko Dolly Varden populations, suggesting that introgressive hybridization might have also occurred in relatively recent contact and potentially ongoing evolutionary event. The present study presents an example of historical hybridization and introgression at the southernmost distribution limits of Dolly Varden.     

Genetic differentiation of three sympatric charr species from genus Salvelinus inferred from PCR-RFLP analysis of mitochondrial DNA

We examined differentiation of three sympatric charr species Dolly Varden charr Salvelinus malma Walbaum, white-spotted charr S. leucomaenis Pallas, and Levanidov charr S. levanidovi Chereshnev, Scopetz, Gudkov. Using restriction fragment length polymorphism analysis (RFLP), three mitochondrial DNA fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified in PCR were compared. The divergence of mtDNA nucleotide sequences between S. levanidovi and S. leucomaenis was about 9.7%, between S. levanidovi and S. malma, 8.7%, and between S. malma and S. laecomaenis, 7.5%. These results indicate genetic isolation of the species examined and support the earlier suggestion on closeness of Levanidov charr to the common ancestor of the genus Salvelinus.     

Evidence for historical introgression along a contact zone between two species of char (Pisces: Salmonidae) in northwestern North America

Phylogeographic analyses can yield valuable insights into the geographic and historical contexts of contact and hybridization between taxa. Two species of char (Salmonidae), Dolly Varden (Salvelinus malma) and bull trout (S. confluentus) have largely parapatric distributions in watersheds of northwestern North America. They are, however, sympatric in several localities and hybridization and some introgression occurs across a broad area of contact. We conducted a comparative phylogenetic analysis of Dolly Varden and bull trout to gain a historical perspective of hybridization between these species and to test for footprints of historical introgression. We resolved two major Dolly Varden mitochondrial DNA (mtDNA) clades (with 1.4-2.2% sequence divergence between haplotypes) that had different geographical distributions. Clade N is distributed across most of the range of Dolly Varden, from southern British Columbia through to the Kuril Islands in Asia. Clade S had a much more limited distribution, from Washington state, at the southern limit of the Dolly Varden range, to the middle of Vancouver Island. The distribution and inferred ages of the mtDNA clades suggested that Dolly Varden survived the Wisconsinan glaciation in a previously unsuspected refuge south of the ice sheet, and that Dolly Varden and bull trout were probably in continuous contact over most of the last 100,000 years. When bull trout were included in the phylogenetic analysis, however, the mtDNA of neither species was monophyletic: Clade S Dolly Varden clustered within the bull trout mtDNA clade. This pattern was discordant with two nuclear phylogenies produced (growth hormone 2 and rRNA internal transcribed sequence 1), in which Dolly Varden and bull trout were reciprocally monophyletic. This discordance between mtDNA- and nDNA-based phylogenies indicates that historical introgression of bull trout mtDNA into Dolly Varden occurred. Percent sequence divergence within these introgressed Dolly Varden (clade S) was 0.2-0.6%, implying that the introgression occurred prior to the most recent glaciation. Our analysis and other evidence of contact between divergent lineages in northwestern North America strongly suggests that the area may be the site of previously unsuspected suture zones of aquatic biotas.     

Differentiation of Salvelinus malma charr and Taranetz Charr Salvelinus taranetzi from PCR-RFLP analysis of mitochondrial DNA

Genetic differentiation of two sympatric charr species, the Dolly Varden charr (Salvelinus malma Walbaum) and the Taranetz charr (S. taranetzi Kaganovski), has been studied. Restriction fragment length polymorphism (RFLP) analysis has been used to compare three mitochondrial DNA (mtDNA) fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified via polymerase chain reaction (PCR). The divergence between S. malma and S. taranetzi inferred from mtDNA nucleotide sequences is 2.8%; between S. leucomaenis and S. taranetzi, 7.1%; and between S. malma and S. leucomaenis, 7.5%. The absence of common haplotypes and the degree of divergence indicate that the Dolly Varden charr and the Taranetz charr are genetically isolated and confirm that S. taranetzi may be regarded as a separate species.     

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.     

Genetic Differentiation of Three Sympatric Charr Species from the Genus SalvelinusInferred from PCR–RFLP Analysis of Mitochondrial DNA

We examined differentiation of three sympatric charr species Dolly Varden charr Salvelinus malmaWalbaum, white-spotted charrS.leucomaenisPallas, and Levanidov charrS. levanidovi Chereshnev, Scopetz, Gudkov. Using restriction fragment length polymorphism analysis (RFLP), three mitochondrial DNA fragments (ND1/ND2, ND5/ND6, and Cytb/D-loop) amplified in PCR were compared. The divergence of mtDNA nucleotide sequences betweenS. levanidovi and S. leucomaenis was about 9.7%, between S. levanidovi and S. malma, 8.7%, and between S. malma andS. laecomaenis, 7.5%. These results indicate genetic isolation of the species examined and support the earlier suggestion on closeness of Levanidov charr to the common ancestor of the genus Salvelinus.     

Intra- and interspecific dominance hierarchies and variation in foraging tactics of two species of stream-dwelling chars

Aggressive interactions, foraging behavior, habitat use and diet were studied in sympatric populations of white-sported char,Salvelinus leucomaenis, and Dolly Varden,Salvelinus malma, in a Japanese mountain stream. Underwater observations on individuals of both species revealed two distinct behavioral regimes: aggressive drift foragers and non-aggressive benthos foragers. Aggressive drift foragers defended partial territories around focal points from which they made forays to capture invertebrates drifting in the water column. Non-aggressive benthos foragers cruised around and beneath cobble in large foraging ranges that overlapped each other. Intra- and interspecific, size-dependent dominance hierarchies were recognized among aggressive drift foragers, whereas non-aggressive benthos foragers showed no such relationships. Terrestrial invertebrates were the most abundant prey in the diets of drift foragers, whereas a very small proportion of the diet of benthos foragers was made up of these taxa. Benthos foragers showed more complex diet composition than drift foragers. These results suggest that non-aggressive benthos foragers may avoid not only interference but also exploitative competition by using alternative foraging tactics. The proportion of drift foragers to benthos foragers among white-spotted char was more than 35 times that among Dolly Varden. The significant difference in the proportion of each species using the two types of foraging strategy results in interspecific food segregation in sympatric populations.     

Effects of forestry on the thermal habitat of Dolly Varden (<Emphasis Type="Italic">Salvelinus malma</Emphasis>)

Forestry activities in riparian areas are known to affect stream communities considerably. Not only do riparian deforestation resulting from agriculture or urbanization developments affect stream communities but extensive commercial plantation and forestry practices can alter stream environments adjacent to remaining, intact or secondary forests. Because forestry often includes the construction of logging roads through the riparian zone, this can directly degrade stream environments. Twelve streams in the Shiretoko Peninsula, Hokkaido were investigated so as to determine the effects of forestry practices on stream temperature, periphyton biomass, grazer (benthic invertebrates) biomass and Dolly Varden (Salvelinus malma Walbaum) biomass. The greater the proportion of planted area in the catchment, the higher the stream temperature. Stream temperature directly affects periphyton biomass and Dolly Varden biomass negatively. Neither stream temperature nor periphyton biomass predicted grazer biomass, whereas a positive correlation was found between grazer biomass and Dolly Varden biomass that forage on invertebrates. The overall results indicated that Dolly Varden in the Shiretoko streams were negatively affected by forestry practices and the resultant stream temperature increases. Without effective future riparian forest management, the complex effects of both riparian disturbance and ongoing global warming could further reduce Dolly Varden populations in the region.     

Ongoing localized extinctions of stream-dwelling white-spotted charr populations in small dammed-off habitats of Hokkaido Island,Japan

Habitat fragmentation caused by damming can greatly reduce the population viability of aquatic organisms, with smaller fragmented populations at higher risk of extinction due to increased demographic, genetic, and environmental stochasticity. However, empirical evidence demonstrating that smaller natural populations are more vulnerable to extinction is limited. We studied the vulnerability to extinction of white-spotted charr (Salvelinus leucomaenis) populations in 30 dammed-off streams in Oshima Peninsula, southwestern Hokkaido Island, Japan, by comparing the incidence of charr populations in streams between 1999 and 2014. Using electrofishing and environmental DNA surveys, we identified three localized extinctions, with the probability of extinction increasing with decreasing watershed area (our surrogate for habitat size). We also found a new population in one dammed-off stream in which white-spotted charr were previously unknown, after installation of a fish ladder, indicating the capacity of white-spotted charr to recolonize reconnected habitat in a short period. Our results suggest that localized extinction of white-spotted charr in small dammed-off streams is ongoing, but that appropriate fish migration corridors can reduce localized extinction risk and increase the probability of species persistence.

     

Evidence for divergence between sympatric stone charr and Dolly Varden along unique environmental gradients in Kamchatka

Here, we describe the biological and ecological differences between partially anadromous Dolly Varden and riverine stone charr distributed in the Kamchatka River middle course. Endemic stone charr, being the ambush predator, is defined by the accelerated growth and prolonged lifespan, robust body, and large mouth, as well as specific marble coloration since an early age. The significant restriction in gene flow between the stone charr and benthos-eating Dolly Varden was supported by an allelic distribution of eight microsatellite loci. Herewith, the identity of mitochondrial DNA control region and intron sequences of growth hormone and metallothionein genes confirms a relatively recent diversification of the groups within the single basin. We suggest the key role of the specific environment for reproduction isolation of stone charr. It occupies coniferous taiga zone with dark-colored water, whereas Dolly Varden spawns uppercourse in the zone of stunted, windblown forest. Conifer litter decomposition products could drive natural selection of stone charr via metabolism acceleration and resistance to toxicants. The metabolic difference could promote piscivory and development of the specific morphological peculiarities of the stone charr. Therefore, we present the first evidence in favor of trophic-based sympatric diversification in a river basin at high latitudes.     

Distribution of two congeneric charrs in streams of Hokkaido Island,Japan: considering multiple factors across scales

Salvelinus leucomaenis (white-spotted charr) and S. malma (Dolly Varden) are distributed throughout Hokkaido Island, Japan, but sites where they occur in sympatry are rare. In general, S. malma inhabit upstream reaches and S. leucomaenis extend downstream to the ocean. Factors influencing their distribution were analyzed at four spatial scales ranging from the whole island to individual stream pools. At the island scale, S. leucomaenis were found in the warmer south-west region and at lower altitudes elsewhere, whereas S. malma were found in the colder north-east and at higher altitudes. At a regional scale, the downstream limit of S. malma and upstream limit of S. leucomaenis shifted to lower altitude from south-west to north-east across the island, coincident with the decrease in temperature. Further analysis showed that transition points from S. leucomaenis or sympatry to S. malma in individual watersheds were closely related to an index of cumulative mean monthly temperatures exceeding 5°C. However, at the scale of a single watershed, the transition occurred at different altitudes, gradients, and temperatures in two tributaries, apparently because stream discharge, habitat, and disturbances from floods interacted with these abiotic factors to limit distribution. The two charr species developed interspecific dominance hierarchies in individual pools, and there was strong complementary density compensation among stream pools that could be explained by interspecific competition but not by differences in habitat. However, patterns at watershed and regional scales suggested that interspecific competition interacts with temperature in complex ways. We conclude that the importance of various abiotic and biotic factors in shaping Hokkaido charr distributions depends on the scale at which they are viewed.     

Microsatellite genetic variation of Asian populations of Dolly Varden char

Genetic variation at eight microsatellite loci was examined in 21 populations of Dolly Varden charrs, Salvelinus malma, representing five geographical regions (Kamchatka Peninsula, Sea of Okhotsk coast, Sea of Japan coast, Sakhalin Island, and Kuril islands). Hierarchical analysis of molecular variance showed that 11% (58% in terms of R-statistics) of the variation was distributed among of northern subspecies of Dolly Varden, Salvelinus malma malma and southern Asian Dolly Varden, S. m. krascheninnikovi while similar values were attributed to the among-regional level within northern Dolly Varden 9% (7%) and southern Asian Dolly Varden 11% (14%). Permutation-based tests indicated a mutational component to genetic differentiation based on allelic size variance and suggested that divergence of the two subspecies had occurred at least 3,000 generations ago. On large spatial scales (within the Asian range of the species), populations clustered according to their geographical location. On smaller scales (within regions and subregions) correlation between genetic and geographic distances was not significant. Northern Dolly Varden has higher allelic diversity and more private alleles than southern subspecies, this probably indicating differences in demographic history.     

Invading rainbow trout usurp a terrestrial prey subsidy from native charr and reduce their growth and abundance

Movements of prey organisms across ecosystem boundaries often subsidize consumer populations in adjacent habitats. Human disturbances such as habitat degradation or non-native species invasions may alter the characteristics or fate of these prey subsidies, but few studies have measured the direct effects of this disruption on the growth and local abundance of predators in recipient habitats. Here we present evidence, obtained from a combined experimental and comparative study in northern Japan, that an invading stream fish usurped the flux of allochthonous prey to a native fish, consequently altering the diet and reducing the growth and abundance of the native species. A large-scale field experiment showed that excluding terrestrial invertebrates that fell into the stream with a mesh greenhouse reduced terrestrial prey in diets of native Dolly Varden charr (Salvelinus malma) by 46–70%, and reduced their growth by 25% over six weeks. However, when nonnative rainbow trout (Oncorhynchus mykiss) were introduced, they monopolized these prey and caused an even greater reduction of terrestrial prey in charr diets of 82–93%, and reduced charr growth by 31% over the same period. Adding both greenhouse and rainbow trout treatments together produced similar results to adding either alone. Results from a comparative field study of six other stream sites in the region corroborated the experimental findings, showing that at invaded sites rainbow trout usurped the terrestrial prey subsidy, causing a more than 75% decrease in the biomass of terrestrial invertebrates in Dolly Varden diets and forcing them to shift their foraging to insects on the stream bottom. Moreover, at sites with even low densities of rainbow trout, biomass of Dolly Varden was more than 75% lower than at sites without rainbow trout. Disruption of resource fluxes between habitats may be a common, but unidentified, consequence of invasions, and an additional mechanism contributing to the loss of native species Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On the Origin of the Lacustrine Charr <Emphasis Type="Italic">Salvelinus alpinus</Emphasis> Complex from the Kolyma and Sea of Okhotsk Basins

Morphological and genetic characteristics are used for the analysis of the origin of charrs from the lakes of the Kolyma basin (Chuk, Gek, Gulyaevskoe-4, Gulyaevskoe-6, and Lenkovoe) and the Sea of Okhotsk basin (Lake Chistoe). In addition to these samples, the fragments of the control region of mitochondrial DNA (CR mtDNA, 550-bp) and exon 2 of recombination activating gene 1 (RAG1, 899-bp) are sequenced in the charrs from lakes Dzhul’etta and Cherechen’ (Kolyma basin) and lakes Elikchanskie, Bol’shoi Mak-Mak, Ueginskoe (Sea of Okhotsk basin), Ulakhan-Silyan-Kyuel’ (Yana River basin) as well as in northern Dolly Varden from the Kamchatka River. The charr from Lake Chistoe is represented by northern Dolly Varden. In the charrs from lakes Chuk, Gek, Gulyaevskoe-4, Gulyaevskoe-6, Lenkovoe, Cherechen’, Elikchanskie, Bol’shoi Mak-Mak, and Ueginskoe, the haplotypes of mtDNA of the Bering group (a haplogroup of northern Dolly Varden) are revealed. Based on the morphological and RAG1 data, populations of charrs from these lakes belong to the Salvelinus alpinus complex. A transfer of mtDNA of northern Dolly Varden to the charrs from the Kolyma and Sea of Okhotsk basins occurred during the last postglacial expansion and subsequent hybridization. Based on the results of morphological and genetic analysis, the charrs from the Kolyma and Sea of Okhotsk basins cannot be unambiguously referred to the phylogenetic groups of Eurasian Arctic charr or Taranets charr. The presence of mtDNA haplotypes of the Arctic group (a haplogroup of Taranets charr) in the populations of lakes Dzhul’etta, Maksi, and Ueginskoe shows a possibility of their belonging to the group of Taranets charr.     

Habitat fragmentation by damming threatens coexistence of stream-dwelling charr and salmon in the Fuji River,Japan

Habitat fragmentation by damming can affect the persistence of single species population and also coexistence of two or more species through intensified competition. This study examined the effects of habitat fragmentation by damming on the coexistence of two stream-dwelling salmonids: the southern form of white-spotted charr (Salvelinus leucomaenis japonicus) and the red-spotted masu salmon (Oncorhynchus masou ishikawae). We examined charr, salmon, and dam distributions in 27 streams of the Fuji River basin, central Japan. In the 1970s, there were streams with five sympatric and 22 allopatric populations (n = 13 for charr, n = 9 for salmon). However, from the 1970s to 2004, 356 impassable dams were constructed in the surveyed streams, and four of the five sympatric streams became allopatric. In the extant sympatric stream, more than 20 dams fragmented habitat. Species distributions were separated by dams (with decreasing altitude) in the following order: extirpation area, charr-dominant area, and salmon-dominant area. Within the uppermost sympatric section (i.e., situated between the dams), salmon congregated in the largest uppermost pool just below the dam; despite these conditions, salmon frequency increased in the downstream direction at the stream scale. The results suggest that habitat fragmentation threatens the coexistence of stream-dwelling charr and salmon at both the basin and stream scales. We believe that exclusion of one species by another is likely in extremely fragmented habitats with minimal gradients and little variation in physical conditions (through reduced stream gradient and increased sand sedimentation caused by damming). In addition, multiple sites of damming ensure that there are no salmonid refuges from the collapse of metapopulation structure. In such fragmented habitats, even small tributaries serve important roles, as they are used mainly by salmonid fry and juveniles. We propose that habitats of native salmonids should be maximized by reconnecting fragmented habitats as part of a broader management plan.     

Metapopulation structure of stream-dwelling Dolly Varden charr inferred from patterns of occurrence in the Sorachi River basin, Hokkaido, Japan

1. We investigated the occurrence (presence or absence) of stream‐dwelling Dolly Varden (Salmonidae: Salvelinus malma) in the 78 tributaries of the Sorachi River system, Hokkaido, Japan to examine evidence for metapopulation structure. 2. We hypothesised (i) that the occurrence of Dolly Varden would be less likely in small tributaries because of the higher extinction risk and (ii) that occurrence would be less likely in isolated tributaries because of reduced rates of dispersal and colonisation. In addition to these two general predictions, we hypothesised (iii) that the occurrence would be more likely in spring‐fed tributaries, because Dolly Varden prefer cold water as present in these systems. 3. When all the tributaries were included in a multiple logistic regression analysis, habitat size and habitat type (spring‐fed versus non‐spring‐fed tributaries) were selected for the best model, whereas isolation was not important. However, when tributaries in the lower Sorachi basin (an area likely influenced by human activities) were excluded from the analysis, the effect of isolation became significant. 4. Our results indicate there is a potential metapopulation structure of the Dolly Varden in the Sorachi River basin. Furthermore, it is possible that metapopulation dynamics follow a clinal pattern. In the upper and middle reaches of the Sorachi River basin, an equilibrium between extinction and colonisation of Dolly Varden populations is a possibility. In the lower portion of the basin, isolation appeared to be less important, and extinction rate may be driving patterns of occurrence toward systematic extinction of local populations. 5. Our results illustrate the possibility of spatial variation in the processes influencing occurrence of Dolly Varden within a single river basin, and the potential influences of habitat alteration on extinction and colonisation processes.