Riverscape Genetics Research Articles

Instream barriers contribute to population isolation of a small‐bodied, benthic, headwater‐specialist fish (Percidae)

AbstractGenetic differentiation in aquatic systems is often driven by geographic distance (isolation by distance) due to the linear and hierarchical distribution of populations, but habitat fragmentation often exacerbates this effect by decreasing population connectivity, leading to isolation by resistance. Stronghold populations of the Kentucky Arrow Darter (Etheostoma spilotum) in the South Fork Kentucky River system within the Daniel Boone National Forest of eastern Kentucky, USA have a high population structure not explained by distance alone. Higher than expected levels of genetic differentiation among proximate populations were hypothesized to be driven by land‐use change, but this was not previously tested. Here we use a riverscape genetics approach to test for the effects of natural landscape features including slope, elevation and stream size, and anthropogenically altered habitat features, including specific conductance (conductivity), culverts and forest cover, on population connectivity and genetic diversity of E. spilotum. We found isolation of populations among all tributary systems and a strong, positive relationship between genetic and geographic distances as expected. However, high conductivity levels due to surface coal mining best explain the population structure observed. We also found signatures of low genetic diversity overall and indicators that culverts may limit upstream movements of E. spilotum. This study provides a novel fine‐scale view of the effects of instream and landscape features on connectivity among, and genetic diversity within populations of an imperilled, small‐bodied, benthic fish.

Using riverscape genetics to investigate the genetic response of two species and their life-history forms to dam removal

Barriers such as hydroelectric dams inhibit migratory pathways essential to many aquatic species, resulting in significant losses of species, their unique life-history forms, and genetic diversity. Understanding the impacts of dam removal to species recovery at these different biological levels is crucial to fully understand the restoration response. We used the removal of two large dams on the Elwha River as an opportunity to characterize how restored connectivity impacts the reestablishment of two fish species, Chinook salmon (Oncorhynchus tshawytscha) and Steelhead/rainbow trout (Oncorhynchus mykiss), and their unique ocean migration return-timing life-history forms. In this study, we employed riverscape genetics to understand how restoration and the environment influence the distribution of neutral and return-timing genetic variation underlying the migratory life-history forms and species at- and between- sampling sites. We genotyped fish sampled over time and space in the Elwha River using Genotyping-in-Thousands by sequencing (GTseq) loci for both species at neutral and putatively adaptive loci in and near the major effect genic region GREB1L/ROCK1 putatively associated with migration timing. We observed little evidence of genetic structure for either species, but a statistically significant increase in early return-timing alleles in upriver O. mykiss population post-dam removal. For O. tshawytscha, at-site genetic variation was shaped by river distance and a combination of environmental habitat differences, while between-site genetic variation was mainly shaped by river distance. For all O. mykiss, at- and between-site genetic variation is primarily explained by river distance. Genetic variation in juvenile and adult Steelhead, respectively, were influenced by at- and between-site environmental and habitat differences. Our study illustrates the power of using genetics to understand the implications of both demography and environment in facilitating the recovery of species and their diverse life-history forms following barrier removal.

Beyond waterfalls and dams: Riverscape genetics of two endemic mountain loaches in the Western Ghats biodiversity hotspot

AbstractRiverscape genetics of fish, though extensively studied in temperate regions, have received limited interest in tropical rivers, especially in montane systems which not only harbour several endemic and threatened species, but are also subjected to extensive habitat modifications. We determine the population genetic structure of two endemic balitorid loaches (Bhavania australis and Travancoria elongata) in response to natural (25 m high waterfall) and artificial (23 m high and 290 m long hydropower dam) barriers in a small mountain riverscape in the Western Ghats Hotspot. Population genetics analysis using mitochondrial cytochrome b gene sequence showed low nucleotide diversity, haplotype diversity and genetic differentiation among populations, for both species, suggesting that barriers did not influence genetic structuring. Though migration analysis also revealed that barriers did not affect movement of the two species through the riverscape, patterns in mutation‐scaled immigration rates and population sizes differed between the two species supporting our observation that they rarely co‐exist in the same habitat, likely as an effect of competitive exclusion. Mismatch distribution and Bayesian skyline plot suggested recent expansion in the populations of B. australis and corresponding population decline in T. elongata in the last 100 years, which probably explains the widespread and abundant distribution of B. australis as opposed to the narrow endemism and rarity of T. elongata. Our results provide novel insights into the ecology of balitorid loaches and their response to riverine barriers in a tropical mountain landscape.

Assessing Genomic Diversity, Connectivity, and Riverscape Genetics Hypotheses in the Endangered Rough Hornsnail, Pleurocera Foremani, Following Habitat Disruption.

The southeastern United States is home to some of the richest biodiversity in the world. Over the last 200 years, however, rapid industrialization and urbanization have threatened many natural areas, including freshwater habitats. River impoundments have also rapidly altered freshwater habitats, often resulting in species extirpation or extinction. The Coosa River in Alabama experienced one of the largest faunal declines in modern history after impoundment, making it an ideal system for studying how invertebrate species are affected by reservoir creation. One such species, the Rough Hornsnail, Pleurocera foremani, is an endangered freshwater snail in the family Pleuroceridae. We sampled all known localities of P. foremani and used 2bRAD-seq to measure genetic diversity. We assessed riverscape genomic patterns across the current range of P. foremani and measured gene flow within and between impoundments. We also investigated the degree to which P. foremani displays an isolation by distance pattern and conforms to broad hypotheses that have been put forth for population genetics of riverine species like the Mighty Headwater Hypothesis that predicts greater genetic diversity in headwater reaches compared with mainstem populations. Like most other freshwater species, a pattern of isolation by distance was observed in P. foremani. We also found that Coosa River dams are a barrier to gene flow, and genetic fragmentation of P. foremani is likely to increase. However, gene flow appeared common within reservoirs and tributaries. Additionally, we found that spatial genetic structure of P. foremani deviates from what is expected under the Mighty Headwaters Hypothesis, adding to a growing body of research suggesting that the majority of genetic diversity in low-dispersing gastropods is found in mainstem populations.

A Novel Quantitative Framework for Riverscape Genetics

Riverscape genetics, which applies concepts in landscape genetics to riverine ecosystems, lack appropriate quantitative methods that address the spatial autocorrelation structure of linear stream networks and account for bidirectional geneflow. To address these challenges, we present a general framework for the design and analysis of riverscape genetic studies. Our framework starts with the estimation of pairwise genetic distance at sample sites and the development of a spatially structured ecological network (SSEN) on which riverscape covariates are measured. We then introduce the novel bidirectional geneflow in riverscapes (BGR) model that uses principles of isolation-by-resistance to quantify the effects of environmental covariates on genetic connectivity, with spatial covariance defined using simultaneous autoregressive models on the SSEN and the generalized Wishart distribution to model pairwise distance matrices arising through a random walk model of geneflow. We highlight the utility of this framework in an analysis of riverscape genetics for brook trout (Salvelinus fontinalis) in north central Pennsylvania, USA. Using the fixation index (FST ) as the measure of genetic distance, we estimated the effects of 12 riverscape covariates on geneflow by evaluating the relative support of eight competing BGR models. We then compared the performance of the top-ranked BGR model to results obtained from comparable analyses using multiple regression on distance matrices (MRM) and the program STRUCTURE. We found that the BGR model had more power to detect covariate effects, particularly for variables that were only partial barriers to geneflow and/or uncommon in the riverscape, making it more informative for assessing patterns of population connectivity and identifying threats to species conservation. This case study highlights the utility of our modeling framework over other quantitative methods in riverscape genetics, particularly the ability to rigorously test hypotheses about factors that influence geneflow and probabilistically estimate the effect of riverscape covariates, including stream flow direction. This framework is flexible across taxa and riverine networks, is easily executable, and provides intuitive results that can be used to investigate the likely outcomes of current and future management scenarios.

Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype.

Understanding the effect of human-induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident European brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We tested the hypotheses of (i) asymmetric gene flow following water current and (ii) an effect of gene flow with the closely related anadromous river lamprey (L. fluviatilis) ecotype on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled from 81 sites upstream and downstream barriers to migration, in 29 western European rivers. Linear modelling revealed a strong positive relationship between genetic diversity and the distance from the river source, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal mediated by water flow. Downstream L. planeri populations in sympatry with L. fluviatilis displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic make-up of upstream L. planeri populations whereas gene flow between ecotypes maintains higher levels of genetic diversity in L. planeri populations sympatric with L. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.

Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given (i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and (ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

A novel quantitative framework for riverscape genetics.

Riverscape genetics, which applies concepts in landscape genetics to riverine ecosystems, lack appropriate quantitative methods that address the spatial autocorrelation structure of linear stream networks and account for bidirectional geneflow. To address these challenges, we present a general framework for the design and analysis of riverscape genetic studies. Our framework starts with the estimation of pairwise genetic distance at sample sites and the development of a spatially structured ecological network (SSEN) on which riverscape covariates are measured. We then introduce the novel bidirectional geneflow in riverscapes (BGR) model that uses principles of isolation-by-resistance to quantify the effects of environmental covariates on genetic connectivity, with spatial covariance defined using simultaneous autoregressive models on the SSEN and the generalized Wishart distribution to model pairwise distance matrices arising through a random walk model of geneflow. We highlight the utility of this framework in an analysis of riverscape genetics for brook trout (Salvelinus fontinalis) in north central Pennsylvania, USA. Using the fixation index (FST ) as the measure of genetic distance, we estimated the effects of 12 riverscape covariates on geneflow by evaluating the relative support of eight competing BGR models. We then compared the performance of the top-ranked BGR model to results obtained from comparable analyses using multiple regression on distance matrices (MRM) and the program STRUCTURE. We found that the BGR model had more power to detect covariate effects, particularly for variables that were only partial barriers to geneflow and/or uncommon in the riverscape, making it more informative for assessing patterns of population connectivity and identifying threats to species conservation. This case study highlights the utility of our modeling framework over other quantitative methods in riverscape genetics, particularly the ability to rigorously test hypotheses about factors that influence geneflow and probabilistically estimate the effect of riverscape covariates, including stream flow direction. This framework is flexible across taxa and riverine networks, is easily executable, and provides intuitive results that can be used to investigate the likely outcomes of current and future management scenarios.

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome-wide SNP data from seven native species.

Since the early Holocene, fish population genetics in the Laurentian Great Lakes have been shaped by the dual influences of habitat structure and post-glacial dispersal. Riverscape genetics theory predicts that longitudinal habitat corridors and unidirectional downstream water-flow drive the downstream accumulation of genetic diversity, whereas post-glacial dispersal theory predicts that fish genetic diversity should decrease with increasing distance from glacial refugia. This study examines populations of seven native fish species codistributed above and below the 58m high Niagara Falls - a hypothesized barrier to gene flow in aquatic species. A better understanding of Niagara Falls' role as a barrier to gene flow and dispersal is needed to identify drivers of Great Lakes genetic diversity and guide strategies to limit exotic species invasions. We used genome-wide SNPs and coalescent models to test whether populations are: (a) genetically distinct, consistent with the Niagara Falls barrier hypothesis; (b) more genetically diverse upstream, consistent with post-glacial expansion theory, or downstream, consistent with the riverscape habitat theory; and (c) have migrated either upstream or downstream past Niagara Falls. We found that genetic diversity is consistently greater below Niagara Falls and the falls are an effective barrier to migration, but two species have probably dispersed upstream past the falls after glacial retreat yet before opening of the Welland Canal. Models restricting migration to after opening of the Welland Canal were generally rejected. These results help explain how river habitat features affect aquatic species' genetic diversity and highlight the need to better understand post-glacial dispersal pathways.

Model-based riverscape genetics: disentangling the roles of local and connectivity factors in shaping spatial genetic patterns of two Amazonian turtles with different dispersal abilities

Genetic patterns are shaped by the interaction of different factors such as distance, barriers, landscape resistance and local environment. The relative importance of these processes may vary for species with different ecological traits. Here we compared two related Amazonian riverine turtle species (Podocnemis erythrocephala and Podocnemis sextuberculata) with distinct dispersal abilities to assess how differently local and connectivity variables influence their genetic patterns. We used a total of 609 genetic samples to estimate mitochondrial (mtDNA) genetic diversity and differentiation for each locality. We applied model selection on models associating genetic diversity to local variables representing hypotheses of climate and primary productivity, water level variation, hunting pressure and downstream increase in genetic diversity. We modeled the relationship of genetic differentiation with connectivity variables representing hypotheses of isolation by distance (IBD), isolation by resistance (IBR) and isolation by barrier (IBB). Model selection for genetic diversity was only important (excluded the null model) for the high-dispersal species (P. sextuberculata), with best models including hypotheses of productivity and hunting pressure. Genetic diversity was higher in more productive sites and in sites with higher concentration of villages (opposed to expected). Although a variable importance testing showed low importance for connectivity models, IBB (Amazon River) and IBR (resistance by current and past climatic suitability and river color) models explained more genetic differentiation turnover than IBD (riverway distance). Models explained a higher percentage of genetic differentiation for the low-dispersal species (P. erythrocephala), with Amazon River as main predictor. We show that, although local variables are often overlooked in riverscape genetics studies, they can influence intrapopulacional genetic diversity of aquatic species, even those with high dispersal ability. By applying a resistance-model framework and by using riverscape genetics factors relevant in basin-wide context, we provide a novel approach to investigate genetic patterns of other aquatic vertebrates in fluvial systems.

Watershed‐level brook trout genetic structuring: Evaluation and application of riverscape genetics models

Abstract Stream connectivity promotes resilience and population viability of aquatic organisms. Landscape genetic approaches, traditionally applied to terrestrial systems, may reveal important watershed‐level dynamics that influence connectivity. Additional validation would improve understanding of how the models perform when gene flow is constrained to dendritic networks. The objectives of this study were to use simulations to assess the utility of landscape genetics analyses in dendritic stream networks and investigate riverscape variables influencing gene flow among brook trout Salvelinus fontinalis populations in headwater streams. We used an individual‐based simulation program to simulate different dispersal scenarios and used combinations of landscape genetic models, model selection methods, and genetic metrics to determine the best combination for riverscape systems. We also sampled brook trout from 76 headwater streams in two watersheds (c. 1,000 km2) in Connecticut, U.S.A. to assess connectivity and riverscape influences on genetic structuring. Gravity models with Bayesian information criterion (BIC) selection were the most accurate (>85%) landscape genetic models that consistently identified the correct simulated gene flow barrier. However, all models performed poorly when unidirectional barriers were simulated without a distance‐based dispersal limitation. Excluding this scenario, model accuracy for the gravity models using BIC selection was >90% across multiple genetic metrics, validating the application of landscape genetic models to riverscape systems. We found highly variable levels of brook trout genetic connectivity (FST range 0.01–0.19) at the watershed level (5–15 river km). Gravity models identified increases in upstream impervious surfaces and decreases in riparian tree canopy cover as riverscape variables associated with increases in genetic differentiation in one watershed, while the other watershed was consistent with an isolation by distance pattern. In this study we used demogenetic (i.e. combined demographic and genetic) simulations to demonstrate the utility of landscape genetics techniques in dendritic river networks. Our empirical genetic study documented gene flow among headwater populations of brook trout at the watershed level and also suggested connectivity can be limited by watershed development. Incorporating the heterogeneity of riverscapes into connectivity‐focused conservation planning is essential to the development of effective restoration actions, and landscape genetics approaches can be useful tools to identify watershed‐level connectivity in stream systems.

The interplay of riverscape features and exotic introgression on the genetic structure of the Mexican golden trout (Oncorhynchus chrysogaster), a simulation approach

AbstractAimWe explored the factors between riverscape features and exotic introgression of cultured rainbow trout (Oncorhynchus mykiss) that drive the current genetic structure in the endemic Mexican golden trout (Oncorhynchus chrysogaster) using a riverscape genetics simulator.LocationSierra Madre Occidental, Northwest Mexico, North America.MethodsWe created a system model for Mexican golden trout to test various scenarios for the effect of riverscape resistance and rainbow trout introgression on the native genetic structure of the Mexican golden trout. Individual genotypes were used to initialize the model and were based upon empirical allele frequencies from three genetically and spatially distinct groups in the study area. The geographical location of the simulated populations was defined using a species distribution model. We included hypotheses for movement of riverine distance and riverscape resistance. We evaluated model performance by conducting population and landscape genetics analyses on the simulation outputs.ResultsThe most plausible scenario included riverscape resistance without introgression, which presented a spatial genetic structure matching the observed riverscape genetic structure and fitting expected general life‐history patterns for high elevation trout streams. In addition, temperature, precipitation, hydrology and topography were the most important variables influencing species occurrence and dispersal.Main conclusionThis work presents one of the first empirically derived simulation studies of introgression. It highlights the importance of considering riverscape resistance (i.e. hydroclimatic and topographical gradient effects) in models of spatial genetic structure and introgression. Moreover, our modelling suggests that what we characterize as riverscape resistance is acting as a boundary against exotic introgression. The results of this study could help to develop management strategies that preserve native gene pools.

Refining and defining riverscape genetics: How rivers influence population genetic structure

AbstractTraditional analysis in population genetics evaluates differences among groups of individuals and, in some cases, considers the effects of distance or potential barriers to gene flow. Genetic variation of organisms in complex landscapes, seascapes, or riverine systems, however, may be shaped by many forces. Recent research has linked habitat heterogeneity and landscape or seascape configuration to genetic structure by integrating methods from landscape ecology, population genetics, and spatial statistics in approaches known as landscape or seascape genetics. However, functional differences between terrestrial or seascapes systems in comparison to riverscape topography (i.e., movement pathways for aquatic obligate species are constrained to river channels) make translating these approaches into freshwater analyses problematic. Studies that may be described as riverscape genetics (RG) have linked temperature, stream gradient, and confluences to genetic variability. Lack of consistency in methodology, however, has made comparisons across species and scales difficult. We provide a perspective on how RG could be used to provide a more comprehensive conceptual and applied understanding of connectivity and dispersal in freshwater systems. We describe four thematic areas of study representing current and future research opportunities and describe a basic workflow for conducting RG analysis. Although numerous methodological challenges remain, a RG approach can enhance our understanding of habitat heterogeneity in shaping gene flow and spatial genetic structure. These characteristics of populations are critical components for interpreting demographic and evolutionary consequences of habitat loss and fragmentation. WIREs Water 2018, 5:e1269. doi: 10.1002/wat2.1269This article is categorized under: Water and Life > Nature of Freshwater Ecosystems Water and Life > Methods Science of Water > Hydrological Processes

Geomorphic influence on intraspecific genetic differentiation and diversity along hyporheic corridors

Abstract The hyporheic zone of rivers potentially acts as a dispersal corridor for groundwater organisms because it provides a spatially continuous interstitial habitat between isolated aquifers. Yet, the degree to which it can facilitate the movement of organisms has been hypothesized to vary in response to change in sediment regime, which determines channel morphology. In this study, we used microsatellite markers to test for a relationship between the genetic structure and diversity of the minute interstitial isopod Proasellus walteri and channel morphology along three nearby hyporheic corridors differing widely in their sediment regime. We predicted that genetic diversity would decrease and genetic structuring would increase as sediment supply‐limited channels would become prominent features in the river corridor. The reason is that such channels have fewer and less suitable sedimentary habitats for migration because they lack large depositional bedforms such as gravel bars. Using genotypic data from seven microsatellite loci for a total of 713 individuals distributed among 25 demes, we found that demes had on average more alleles and were less differentiated in the river showing the most extensive alluvial deposits and shortest length of sediment supply‐limited channels. Population clusters were also of greater size, reaching up to 30 km in length. The longitudinal pattern of genetic differentiation in this sediment‐rich river was best explained by hydrologic distance and the longitudinal pattern of allelic richness was bell‐shaped, as expected under a stepping‐stone model with symmetrical migration. The length of sediment supply‐channels was more important than hydrologic distance in explaining the longitudinal distribution of genetic differentiation in the two other corridors facing a sediment shortage. Allelic richness decreased monotonically upstream in the most sediment‐poor river. This correlates with the expansion further downstream of sediment supply‐limited channels in this river, which is likely to decrease animal movement and hence gene flow among demes. This study provides the first evidence that the degree to which the hyporheic zone facilitates the movement of groundwater organisms varies greatly among rivers of contrasted geomorphology. Extending the application of riverscape genetics across a range of interstitial taxa and geomorphic settings holds much promise for assessing the contribution of the hyporheic zone to the dispersal of groundwater organisms.

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic-spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage.

Fine‐scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation-by-distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50-m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5-2.5 m in height during summer base-flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population-level movement of brook trout was limited in the study headwater stream networks, resulting in the fine-scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by 'riverscape' variables, particularly by physical barriers, waterway distance (i.e. isolation-by-distance) and the presence of tributaries.