Genetic structure of brown trout, salmo trutta l., at the southern limit of the distribution range of the anadromous form

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.     

Mismatch between fishway operation and timing of fish movements: a risk for cascading effects in partial migration systems

Habitat fragmentation is a growing problem worldwide. Particularly in river systems, numerous dams and weirs hamper the movement of a wide variety of species. With the aim to preserve connectivity for fish, many barriers in river systems are equipped with fishways (also called fish passages or fish ladders). However, few fishways provide full connectivity. Here we hypothesized that restricted seasonal opening times of fishways can importantly reduce their effectiveness by interfering with the timing of fish migration, for both spring‐ and autumn‐spawning species. We empirically tested our hypothesis, and discuss the possible eco‐evolutionary consequences of affected migration timing. We analyzed movements of two salmonid fishes, spring‐spawning European grayling (Thymallus thymallus) and autumn‐spawning brown trout (Salmo trutta), in Norway's two largest river systems. We compared their timing of upstream passage through four fishways collected over 28 years with the timing of fish movements in unfragmented river sections as monitored by radiotelemetry. Confirming our hypothesis, late opening of fishways delayed the migration of European grayling in spring, and early closure of fishways blocked migration for brown trout on their way to spawning locations during late autumn. We show in a theoretical framework how restricted opening times of fishways can induce shifts from migratory to resident behavior in potamodromous partial migration systems, and propose that this can induce density‐dependent effects among fish accumulating in lower regions of rivers. Hence, fragmentation may not only directly affect the migratory individuals in the population, but may also have effects that cascade downstream and alter circumstances for resident fish. Fishway functionality is inadequate if there is a mismatch between natural fish movements and fishway opening times in the same river system, with ecological and possibly evolutionary consequences for fish populations.     

Phylogeography,genetic structure,and conservation of the endangered Caspian brown trout, <Emphasis Type="Italic">Salmo trutta caspius</Emphasis> (Kessler, 1877), from Iran

The Caspian Sea, the largest inland closed water body in the world, has numerous endemic species. The Caspian brown trout (Salmo trutta caspius) is considered as endangered according to IUCN criteria. Information on phylogeography and genetic structure is crucial for appropriate management of genetic resources. In spite of the huge number of studies carried out in the Salmo trutta species complex across its distribution range, very few data are available on these issues for S. trutta within the Caspian Sea. Mitochondrial (mtDNA control region) and nuclear (major ribosomal DNA internal transcribed spacer 1, ITS-1, and ten microsatellite loci) molecular markers were used to study the phylogeography, genetic structure, and current captive breeding strategies for reinforcement of Caspian trout in North Iranian rivers. Our results confirmed the presence of Salmo trutta caspius in this region. Phylogenetic analysis demonstrated its membership to the brown trout Danubian (DA) lineage. Genetic diversity of Caspian brown trout in Iranian Rivers is comparable to the levels usually observed in sustainable anadromous European brown trout populations. Microsatellite data suggested two main clusters connected by gene flow among river basins likely by anadromous fish. No genetic differences were detected between the hatchery sample and the remaining wild populations. While the current hatchery program has not produced detectable genetic changes in the wild populations, conservation strategies prioritizing habitat improvement and recovering natural spawning areas for enhancing wild populations are emphasized.     

Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system

Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and decline worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout (Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia, and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked vs. not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in nonstocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contributes to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long‐term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems.     

Maintenance of a small anadromous subpopulation of brown trout (Salmo trutta L.) by straying

1. Microsatellite and isozyme loci variation were used to study structure and dynamics of a brown trout (Salmo trutta) population heavily affected by damming. The downstream area accessible for spawning was drastically reduced to a stream 1 km long influenced by regulated discharge. 2. Stocking of hatchery‐reared juveniles failed and the population is entirely supported by anadromous adults from neighbouring populations. 3. Temporal genetic stability is reported here. Some punctual between‐river genetic differences are likely because of different contribution from each neighbouring river through years. 4. High anadromy‐mediated gene flow produces a lack of genetic substructure in the region. The role of anadromous brown trout on maintenance of endangered small populations is emphasised.     

Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment

The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

Effects of altered river network connectivity on the distribution of Salmo trutta: Insights from a metapopulation model

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Landscape Genetic Structure of a Streamside Tree Species Euptelea pleiospermum (Eupteleaceae): Contrasting Roles of River Valley and Mountain Ridge

We used landscape genetics and statistical models to test how landscape features influence connectivity or create barriers to dispersal for a mountain riparian tree species, Euptelea pleiospermum. Young leaves from 1078 individuals belonging to 36 populations at elevations of 900–2000 m along upper reaches of four rivers were genotyped using eight nuclear microsatellite markers. We found no evidence for the unidirectional dispersal hypothesis in E. pleiospermum within each river. The linear dispersal pattern along each river valley is mostly consistent with the “classical metapopulaton” model. Mountain ridges separating rivers were genetic barriers for this wind-pollinated tree species with anemochorous seeds, whereas river valleys provided important corridors for dispersal. Gene flow among populations along elevational gradients within each river prevails over gene flow among populations at similar elevations but from different rivers. This pattern of gene flow is likely to promote elevational range shifts of plant populations and to hinder local adaptation along elevational gradients. This study provides a paradigm to determine which of the two strategies (migration or adaptation) will be adopted by mountain riparian plants under climate warming.     

Low stocking incidence in brown trout populations from northwestern Spain monitored by LDH-5* diagnostic marker

Brown trout Salmo trutta is one of the most valuable species inhabiting river drainages in Galicia (northwestern Spain). The influence of man, through overfishing and pollution, is thought to have caused the decline of trout in Galician rivers. To balance the possible population decline, Galician rivers have been stocked extensively with a brown trout stock of German origin during the last 30 years. In this study, the incidence of stocking practices has been investigated by an LDH-5 * genetic marker. A very low number of stocked individuals have been observed within river populations, despite the long period of repopulation. Only eight out of the 44 populations analysed showed a limited number of individuals of hatchery origin. Most stocked individuals detected were 0+ age, and showed a poor condition factor ( K < 1). Environmental factors (muscular stamina and food habits) and genetic factors (different selective conditions in hatchery medium) are invoked to explain the low viability of hatchery fish Observed in this Study.     

Shaping of genetic structure along Pleistocene and modern river systems in the hydrochorous riparian azalea, Rhododendron ripense (Ericaceae)

To determine the effects of hydrochory on the formation of the present range of a species and the spatial distribution of genetic variation, we assessed the rangewide genetic structure of a hydrochorous riparian Japanese species (Rhododendron ripense) using four nuclear microsatellite loci. The patterns of isolation by distance and Bayesian clustering analyses of 33 populations suggested that the present range, characterized by both localized and disjunct distributions across the sea, arose from two contrasting colonization events: (1) primary colonization along two Pleistocene rivers that have been submerged and become partly isolated by marine transgression by 6000 years ago, and (2) additional range expansions from these rivers into unconnected neighboring rivers as a result of river captures. Along the Pleistocene rivers, frequent gene flow by hydrochory resulted in the retention of considerable genetic diversity within each population and genetic homogenization among populations. Within unconnected neighboring rivers, genetic diversity was also retained by the simultaneous redistribution of many individuals as a result of river captures, whereas restricted gene flow within a river resulted in genetic divergence among the river populations. Thus, the evolutionary history of hydrochorous R. ripense appears to have been strongly shaped by both ancient and modern rivers.     

Influence of hydrologic attributes on brown trout recruitment in low-latitude range margins

Factors controlling brown trout Salmo trutta recruitment in Mediterranean areas are largely unknown, despite the relevance this may have for fisheries management. The effect of hydrological variability on survival of young brown trout was studied during seven consecutive years in five resident populations from the southern range of the species distribution. Recruit density at the end of summer varied markedly among year-classes and rivers during the study period. Previous work showed that egg density the previous fall did not account for more than 50% of the observed variation in recruitment density. Thus, we expected that climatic patterns, as determinants of discharge and water temperature, would play a role in the control of young trout abundance. We tested this by analyzing the effects of flow variation and predictability on young trout survival during the spawning to emergence and the summer drought periods. Both hatching and emergence times and length of hatching and emergence periods were similar between years within each river but varied considerably among populations, due to differences in water temperature. Interannual variation in flow attributes during spawning to emergence and summer drought affected juvenile survival in all populations, once the effect of endogenous factors was removed. Survival rate was significantly related to the timing, magnitude and duration of extreme water conditions, and to the rate of change in discharge during hatching and emergence times in most rivers. The magnitude and duration of low flows during summer drought appeared to be a critical factor for survival of young trout. Our findings suggest that density-independent factors, i.e., hydrological variability, play a central role in the population dynamics of brown trout in populations from low-latitude range margins. Reported effects of hydrologic attributes on trout survival are likely to be increasingly important if, as predicted, climate change leads to greater extremes and variability of flow regimes.     

Population structure and genetic diversity of trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) above and below natural and man-made barriers in the Russian River,California

The effects of landscape features on gene flow in threatened and endangered species play an important role in influencing the genetic structure of populations. We examined genetic variation of trout in the species Oncorhynchus mykiss at 22 microsatellite loci from 20 sites in the Russian River basin in central California. We assessed relative patterns of genetic structure and variation in fish from above and below both natural (waterfalls) and man-made (dams) barriers. Additionally, we compared sites sampled in the Russian River with sites from 16 other coastal watersheds in California. Genetic variation among the 20 sites sampled within the Russian River was significantly partitioned into six groups above natural barriers and one group consisting of all below barrier and above dam sites. Although the below-barrier sites showed moderate gene flow, we found some support for sub-population differentiation of individual tributaries in the watershed. Genetic variation at all below-barrier sites was high compared to above-barrier sites. Fish above dams were similar to those from below-barrier sites and had similar levels of genetic diversity, indicating they have not been isolated very long from below-barrier populations. Population samples from above natural barriers were highly divergent, with large F _st values, and had significantly lower genetic diversity, indicating relatively small population sizes. The origins of populations above natural barriers could not be ascertained by comparing microsatellite diversity to other California rivers. Finally, below-barrier sites farther inland were more genetically differentiated from other watersheds than below-barrier sites nearer the river’s mouth.     

Do rivers function as genetic barriers for the plateau wood frog at high elevations?

Using the plateau wood frog Rana kukunoris from the Hengduan Mountains as a model system, we tested whether rivers form significant genetic barriers (the riverine barrier hypothesis) to high elevation amphibians. Samples were collected from eight sites across three major river drainages, the Min, the Dadu and the Yalong Rivers, and the population genetic structure of these frogs was evaluated with data from eight microsatellite DNA loci. A large amount of genetic structure was found, and the pairwise F _ST ranged from 0.022 to 0.508 and a global F _ST was 0.215. Both analysis of molecular variance and isolation by distance analysis suggested that rivers, mountain ridges and geographic distances all contributed significantly to the population structure. However, no single landscape has prominent barrier effect to the plateau wood frog populations. An assignment analysis using the computer program Structure grouped the eight populations into four population clusters, and no single type of landscape can sufficiently explain the clustering. In conclusion, rivers do not appear to be the leading genetic barriers for the plateau wood frog. The strong population genetic structure is likely the consequence of attributes of the species, as opposed to environmental fragmentation, and the barrier effect of the landscapes is largely swamped by the large amount of intrinsic population structure.     

Riverine habitat specificity constrains dispersion in a Neotropical fish (Characidae) along Southern Brazilian drainages

Freshwater fishes often display a marked phylogeographic structure strongly associated with historical and ecological changes in the aquatic environment. Different ecological conditions in the same river drainage may act as permeable barriers to dispersion and gene flow. Previous studies recognized two discrete spatial components for the ichthyofauna in the freshwater coastal drainages of southern Brazil: the lowland fish fauna in the lagoons and the fish fauna of the rivers flowing in the valleys. In order to test if the coastal lagoons may limit the dispersion of a riverine species, we describe the phylogeographic structure among populations of Cyanocharax itaimbe, a species endemic to this region. We analysed 55 specimens characterized for two mitochondrial and one nuclear genes. Sequences were analysed using gene trees and species tree approaches, together with standard population genetics methods. Molecular analyses indicated three evolutionary groups which diverged from each other between an estimated 1,600,000 and 450,000 years before the present. However, two currently isolated river systems share the same evolutionary clade, whereas a single drainage contains two different lineages. Our results indicate strong genetic structure among populations along with generally conserved morphology. The strong genetic structure among populations living in the same drainage system may be explained by ecological differences between lagoons and rivers (or palaeochannels) that act as barriers to dispersion.     

Plitvice Lakes National park harbors ancient,yet endangered diversity of trout (genus Salmo)

National park Plitvice Lakes is the oldest, the largest and the most visited national park in Croatia, well known for its stunning karstic watersheds that supply Plitvice Lakes and exceptionally valuable biodiversity. Lack of knowledge on the taxonomic status, population structure and viability of trout in the Plitvice Lakes National park, as well as the possibility of existence of cryptic diversity, motivated this study which aimed to determine: taxonomic status and phylogenetic relationship of Plitvice Lakes trout with other Salmo species, genetic structure and diversity of their populations, as well as future viability of populations. 150 samples of trout were obtained from 17 localities. Two mitochondrial gene markers, gene for cytochrome b and mitochondrial control region were used in phylogenetic reconstruction, as well as in population genetic investigation. Intraspecific and intrapopulation genetic diversity was described by calculating several measures of genetic polymorphism, while gene flow among populations was estimated as the migration rates and as the number of immigrants per generation. Phylogenetic trees revealed that Plitvice Lakes watershed is inhabited by two evolutionary independent units of the genus Salmo, representing two species, Salmo labrax Pallas, 1814 and Salmo trutta Linnaeus, 1758. Possibly ‘pure’ populations of both species were found alongside several admixed ones in which both species are present. Our data has shown low intraspecific and intrapopulational diversities for Plitvice Lakes trout and restricted gene flow. Small effective sizes of populations and weak interconnections between them, which are most likely a consequence of fragmentation and habitat degradation, accentuating the need for urgent conservation measures.     

Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) differ in their suitability as hosts for the endangered freshwater pearl mussel (Margaritifera margaritifera) in northern Fennoscandian rivers

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The impact of river fragmentation on the population persistence of native and alien mink: an ecological trap for the endangered European mink

The genetic diversity of feral and ranch American mink was studied in order to detect gene flux among rivers, investigate the processes of invasion, and determine the possible effects of river barriers. Tissue samples of 78 feral American mink from 5 different river catchments and 18 ranch mink, collected between 2007 and 2011 in Biscay, northern Spain, were genotyped at 21 microsatellite loci. Lack of genetic differentiation of feral mink among the sites and high differentiation between feral and ranch mink was suggested. These results confirm that the mink population established on Butrón River at the beginning of the 1990s may be the origin of almost all the feral mink population within the study area. Additionally, the occurrence of American and European mink was used to analyse the effect of fragmentation on the population viability. The size and composition of the home range of male European mink was considered to model minimum viable units for presence/absence. Forty-two minimum viable units were randomly distributed among rivers in order to analyse the effect of fragmentation on mink occurrence. Barriers were mapped and classified as slight, moderate or absolute, depending on the effect on mink movement, and were introduced into the models. The presence of European and American mink depended on the non-fragmented main river stretches and the number of tributaries free from barriers. Results showed that fragmented rivers can be temporarily occupied but the likelihood of death means that these areas are only sink patches for mink.     

Gene flow simulations demonstrate resistance of long-lived species to genetic erosion from habitat fragmentation

Habitat fragmentation restricts the movement of individuals across a landscape. In terrestrial and aquatic systems, barriers to movement can modify population and community dynamics at local or regional scales. This study contrasted life history traits related to lifespan with habitat fragmentation to determine impacts on species population genetic structure in the Neuse River Basin, USA. For this, we simulated gene flow among evenly-spaced populations in a river network and tracked individual and population genetics for 200 years. The modeled scenarios represent a full cross between five life history strategies and four riverscapes representing varying degrees of fragmentation. The five life history strategies include species (based on freshwater mussels) with average lifespans ranging from 10 to 50 years and age at maturity from 2 to 6 years. The movement landscapes included a (1) panmictic, (2) stepping-stone landscape allowing movement to only neighboring populations during each dispersal event, (3) partially-fragmented landscape divided by dams currently in the network, and (4) fully-fragmented landscape. Results suggest species with shorter lifespans have higher population genetic structure in fragmented landscapes than species with longer lifespans. Furthermore, species with shorter lifespans in highly fragmented landscapes may be harboring genetic degradation or decline as allele fixation and loss. Although anthropogenic fragmentation of many river systems is only 100–200 years old, the simulation indicates that species can respond genetically in that period of time. Additionally, the time frame of the simulation suggests that genetic impacts of habitat fragmentation in some species present in the Neuse River Basin may not yet be manifesting and restoration activities could be successful.     

No distinct barrier effects of highways and a wide river on the genetic structure of the Alpine newt (<Emphasis Type="Italic">Ichthyosaura alpestris</Emphasis>) in densely settled landscapes

Linear landscape elements such as roads, railways and rivers have been shown to act as barriers to dispersal and gene flow, hence impeding functional connectivity and increasing genetic differentiation between individuals or populations on opposite sides of the barrier. Such putative barriers act through a confluence of mechanisms, including crossing mortality, barrier avoidance and modifications to organisms’ effective dispersal patterns. Small, terrestrial animals such as amphibians are predicted to be vulnerable to the effects of such barriers given their limited locomotive performance and their dependence on spatially distinct breeding habitats. Here, we examined the effects of highways and a wide river on Ichthyosaura alpestris in three regions of northern Switzerland by measuring the genetic differentiation between local populations and describing the spatial genetic structure. Moreover, we estimated effective population sizes as an indicator for the susceptibility of populations to random genetic drift. Based on genetic differentiation, we found evidence to suggest that the highways and river acted as barriers to gene flow for the newt in the study regions, but results were inconsistent when ignoring breeding ponds with low samples sizes. Admixture-based genetic clustering suggested the delineation of the genotypes to rough regional clusters, with only weak structure inferred within these clusters. Thus, results suggest that at present, highways and rivers do not substantially affect the genetic structure of I. alpestris within northern Switzerland in a negative manner. Alternatively, the lack of a distinct genetic structure in regional newt populations may be explained by, e.g., large effective population sizes.