Stream Populations Research Articles

On a Lotka–Volterra type competition model from river ecology

We revisit a stream population model which was formulated to study the evolution of passive movement in advective environments and has been discussed by Lou et al. in a homogeneous situation (Lou et al., 2016) and later by Zhou and Zhao, (2018) in a spatially heterogeneous situation but with a restriction that the resource is distributed non-increasingly across space. In this paper, by employing a different and more direct argument, we remove the technical condition imposed in Zhou and Zhao, (2018) and obtain a more general result, which suggests that the outcome of evolution does not depend on the shape of the resource distribution for most situations. Biologically, our main result puts new insights into the understanding of the mechanism behind the evolution of dispersal.

Assessing thermal tolerance of vulnerable alpine stream insects as part of a long-term monitoring project in the Teton Range, Wyoming

Alpine streams are predicted to decline as air temperatures warm and their water sources dry. Stream temperatures are expected to increase as glaciers and permanent snowfields decrease in size. For aquatic insects that are cold-adapted and restricted to small, high elevation streams fed by glaciers or snowfields, warmer water temperatures could be lethal. Conversely, less water in streams may increase the likelihood of insects freezing during winter months. We measured the critical thermal maximum (CTMAX) – the highest non-lethal temperature an insect can survive, and supercooling temperature – the temperature at which an insect freezes, of three alpine stoneflies, Zapada sp., Lednia tetonica and Lednia tumana, collected in Grant Teton and Glacier National Parks. CTMAX and supercooling point varied among species and with stream source (glacier-fed, snowmelt-fed and icy seep) and population (seven populations). Supercooling temperature was lowest in an alpine tarn and highest in glacier- and snowmelt-fed streams. Zapada sp. had the lowest CTMAX of the three species. Stoneflies from icy seeps had lower CTMAX than individuals from glacier- or snowmelt-fed streams. Individuals that likely experience the coldest winter temperatures had the lowest supercooling temperature. Similarly, stoneflies that experienced warmer water temperatures also had higher CTMAX values. Investigating the thermal tolerances of alpine stoneflies allows us to predict how these insects may respond to future climate change scenarios.
 
 Featured photo by Nicole Y-C on Unsplash. https://unsplash.com/photos/9XixVlnUCbk

Response of Brook Trout Biomass to Strategic Wood Additions in the East Branch Nulhegan River Watershed, Vermont

AbstractHistoric logging and log driving have severely degraded fish habitat in many northeastern United States rivers, including the East Branch Nulhegan River, Vermont. To improve the habitat of Brook Trout Salvelinus fontinalis, 43 large woody material structures were constructed using chain saws and grip hoists in the East Branch Nulhegan River and two of its tributaries. The purpose of this study was to assess the effects of these “strategic wood additions” on Brook Trout biomass. Nine pairs of control and treatment sites were electrofished annually for 2 years prior to wood additions and for 4 years afterward. Wood loading increased at treatment sites by 183 to 1,557 pieces/ha, resulting in total wood loadings at these sites ranging from 251 to 1,557 pieces/ha (18 to 66 pieces per 100 m). By the second year of posttreatment sampling, average Brook Trout biomass at treatment sites had approximately tripled. Mean Brook Trout biomass decreased at control sites the first year after wood was added but then rebounded to pretreatment levels, suggesting that added wood contributed to a net increase in Brook Trout abundance in the system and did not simply concentrate fish in favorable habitats. Fisheries managers can consider strategic wood additions as a potential tool for improving Brook Trout habitat and bolstering their populations in streams where the lack of large wood is the most important limiting factor.

Repeatability in boldness and aggression among wild zebrafish (Danio rerio) from two differing predation and flow regimes.

Although flexibility in behavior is adaptive, this flexibility is limited, and the extent of variation and consistency of a trait could depend on the environment. In this study, we investigated repeatability in risk-taking during feeding among individuals and agonistic interactions among dyads of wild zebrafish, Danio rerio, collected from two habitats that differed in predation and flow regimes. We measured boldness as the latency to emerge from a shelter and feed in the presence of predators. We tested this for each individual from the two populations repeatedly across seven trials. We assessed aggression by subjecting size- and sex-matched pairs of fish to dyadic contests repeatedly across seven trials. Individuals from the high-predation stream population were bolder than individuals from the low-predation stagnant water population. Males were bolder than females, and in the low-predation population, larger individuals took greater risks to feed than smaller individuals. The high-predation stream population showed lower inter- and intraindividual variation in boldness than the low-predation stagnant water population. Further, both populations showed significant repeatability in risk-taking during feeding. The high-predation stream habitat fish were more aggressive than low-predation stagnant-water fish. Male dyads from the low-predation stagnant-water population were significantly more aggressive than female dyads. Most fish from the low-predation stagnant water population did not show aggressive behavior, resulting in low between-dyad but high within-dyad variation in aggression. The difference in behavioral responses between the populations and consistency in these traits within individuals is discussed in the light of confounding role of ecological and state-dependent factors. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Genetic structure of lake and stream populations in a Pyrenean amphibian ( Calotriton asper ) reveals evolutionary significant units associated with paedomorphosis

This work was supported by the Biodiversity Conservation Plan of ENDESA, S.A. (ENEL Group) for D.S.; Fonds de la Recherche Scientifique—FNRS under grant numbers J.008.13 and J.0112.16 and Fonds Speciaux de la Recherche (University of Liege) for M.D. (Research Director at F.R.S.–FNRS); and the Marie Curie COFUND Fellowship for N.O. while at the University of Liege. The research and capture permits for newts were issued by Departamento de Agricultura, Ganaderia y Medio Ambiente (Gobierno de Aragon, Spain).

Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio) in the Central European Alpine region.

Ecological speciation and adaptive radiation are key processes shaping northern temperate freshwater fish diversity. Both often involve parapatric differentiation between stream and lake populations and less often, sympatric intralacustrine diversification into habitat- and resource-associated ecotypes. However, few taxa have been studied, calling for studies of others to investigate the generality of these processes. Here, we test for diversification within catchments in freshwater sculpins in a network of peri-Alpine lakes and streams. Using 8047 and 13182 restriction site-associated (RADseq) SNPs, respectively, we identify three deeply divergent phylogeographic lineages associated with different major European drainages. Within the Aare catchment, we observe populations from geographically distant lakes to be genetically more similar to each other than to populations from nearby streams. This pattern is consistent with two distinct colonization waves, rather than by parapatric ecological speciation after a single colonization wave. We further find two distinct depth distribution modes in three lakes of the Aare catchment, one in very shallow and one in very deep water, and significant genomewide differentiation between these in one lake. Sculpins in the Aare catchment appear to represent an early-stage adaptive radiation involving the evolution of a lacustrine lineage distinct from parapatric stream sculpins and the repeated onset of depth-related intralacustrine differentiation.

Projection of invertebrate populations in the headwater streams of a temperate catchment under a changing climate

Climate change places considerable stress on riverine ecosystems by altering flow regimes and increasing water temperature. This study evaluated how water temperature increases under climate change scenarios will affect stream invertebrates in pristine headwater streams. The studied headwater-stream sites were distributed within a temperate catchment of Japan and had similar hydraulic-geographical conditions, but were subject to varying temperature conditions due to altitudinal differences (100 to 850 m). We adopted eight general circulation models (GCMs) to project air temperature under conservative (RCP2.6), intermediate (RCP4.5), and extreme climate scenarios (RCP8.5) during the near (2031–2050) and far (2081–2100) future. Using the water temperature of headwater streams computed by a distributed hydrological-thermal model as a predictor variable, we projected the population density of stream invertebrates in the future scenarios based on generalized linear models. The mean decrease in the temporally averaged population density of Plecoptera was 61.3% among the GCMs, even under RCP2.6 in the near future, whereas density deteriorated even further (90.7%) under RCP8.5 in the far future. Trichoptera density was also projected to greatly deteriorate under RCP8.5 in the far future. We defined taxa that exhibited temperature-sensitive declines under climate change as cold stenotherms and found that most Plecoptera taxa were cold stenotherms in comparison to other orders. Specifically, the taxonomic families that only distribute in Palearctic realm (e.g., Megarcys ochracea and Scopura longa) were selectively assigned, suggesting that Plecoptera family with its restricted distribution in the Palearctic might be a sensitive indicator of climate change. Plecoptera and Trichoptera populations in the headwaters are expected/anticipated to decrease over the considerable geographical range of the catchment, even under the RCP2.6 in the near future. Given headwater invertebrates play important roles in streams, such as contributing to watershed productivity, our results provide useful information for managing streams at the catchment-level.

Change of foraging behavior of cormorants and the effect on river fish

Since the European population of great cormorants (Phalacrocorax carbo sinensis) rapidly increased 30 years ago, Denmark has been one of the core breeding areas for this colonial water bird. Following a 10-year period with stable breeding numbers in Denmark, the population of great cormorants decreased. At the same time, a combination of cold winters and low availability of coastal prey fish apparently triggered birds to seek new foraging areas. Thus, cormorants began to appear in rivers and streams coinciding with an observed massive decline of fish, mainly brown trout (Salmo trutta) and grayling (Thymallus thymallus). In this paper, we present the results from studies using radio-telemetry, PIT-tagging, and traditional fish surveys to estimate the impact of predation in Danish lowland rivers. Recovery of PIT-tags revealed that an estimated 30% of wild trout and 72% of wild grayling tagged in a small river were eaten by cormorants. In another medium-sized river, 79% of radio-tagged adult grayling were removed, presumably by cormorants during winter. Thus, predation from cormorants appears to be at a level that explains the observed collapse of grayling and brown trout populations in many Danish streams.

Brown Trout (Salmo trutta L.) reproduct ion in streams of Onezhskoye Pomorye National Park (Arkhangelsk region)

The surveys were carried out in OnezhskoyePomoryeNational Park, which in 2016 was joined to KenozerskyNational Park(Arkhangelsk Region). Four streams 6 to 13.6 kmlong were surveyed. The occurrence of the Salmo trutta in different areas across the watercourses and the habitat conditions were assessed. Juvenile and adult brown (resident) and sea (anadromous) trout aged 0+ to 6+ were detected. Data on the age composition of the trout are reported, the share of precocious males and the distribution density of juveniles of different age classes were determined for all the surveyed streams. The captures of precocious males and a precocious female confirm the high plasticity of the species in rivers emptying to theWhite Sea, which is manifest in the presence of both resident and sea-going individuals within the same population or reproductive group. The actions required to conserve and enlarge the trout population in streams of the national park include clarification of the timing and conditions of the spawning migration, investigation of the dynamics of the downstream migration of smolts, surveys of their abundance, as well as more intense protection of the watercourses.

Developing a Model to Assess the Potential Impact of TUM Hydropower Turbines on Small River Ecology

Small hydropower is a renewable energy technology that is used for electricity generation worldwide, but still has potential for further development. However, during the installation of small hydropower, the ecological impacts of the power plants need to be thoroughly investigated. In addressing the challenges of energy production and minimizing the environmental impacts of small hydropower installation and operation, this study has applied an ecohydraulic model to investigate river hydrodynamics, hydromorphology, habitat, and the population impacts of small hydropower, and presented the Mum River as a case study. Two scenarios were implemented in this research to simulate the hydrodynamic, sedimentation, habitat, and population status in order to assess the potential effects caused by the TUM plant. At the Mum River, two scenarios were proposed: the TUM plant was not considered in scenario S1, but was considered in scenario S2. The model results for scenario S2 indicated that the habitat was suitable for fish species living in the Mum River, with fish population numbers between 4.6 × 103 and 6.6 × 103. The S2 results indicated that the impacts of the TUM plant were negligible when compared with S1. Although the impact of the TUM plant on the Mum River is relatively large when the discharge is high (19 m3/s), calculations based on stable flow shows that the TUM plant could function well on the river ecosystem when the discharge is low or at normal rates. Therefore, this study shows that the TUM plant would be a good option to meet the needs of energy generation whilst having a minimal impact on river habitats and changes in fish species population in similar small rivers and streams.

Effects of Flow‐Related Variables on Oversummer Survival of Juvenile Coho Salmon in Intermittent Streams

AbstractWhile many studies have established the importance of streamflow as a driver of fish population dynamics, few have examined relationships between survival of juvenile salmonids and flow‐related variables in intermittent streams. With predictions for a higher frequency of drought conditions due to climate change and the associated increasing human demand for water during the dry season, understanding fish–flow relationships is becoming increasingly important for the protection of sensitive aquatic species. To examine the effects of low streamflow on juvenile salmonids rearing in small intermittent streams, we estimated survival and collected environmental data in four coastal California watersheds from 2011 to 2013. We used an individual‐based mark–recapture modeling approach to evaluate the influence of flow‐related variables on oversummer survival of PIT‐tagged juvenile Coho Salmon Oncorhynchus kisutch stocked into eight stream reaches. Survival was positively associated with streamflow magnitude, wetted volume, and dissolved oxygen and negatively associated with days of disconnected surface flow (days of disconnection) and temperature. Days of disconnection best explained survival, though the relationship varied by geomorphic reach type. Survival was lower in alluvial reaches than in bedrock and clay reaches and showed a faster rate of decline with increasing days of disconnection and drought condition. In all reaches, the onset of pool disconnection represented a turning point at which water quality, water quantity, and survival declined. For this reason, we suggest that days of disconnection (or the flow magnitude at which pools become disconnected) is a useful metric for identifying flow‐impaired reaches, informing streamflow protection strategies, and prioritizing streamflow enhancement efforts designed to benefit sensitive salmonid populations in intermittent streams.

A multigear protocol for sampling crayfish assemblages in Gulf of Mexico coastal streams

Identifying an effective protocol for sampling crayfish in streams that vary in habitat and physical/chemical characteristics has proven problematic. We evaluated an active, combined-gear (backpack electrofishing and dipnetting) sampling protocol in 20 Coastal Plain streams in Louisiana. Using generalized linear models and rarefaction curves, we evaluated environmental and gear (separate and combined) effects on crayfish catch-per-unit-effort (CPUE), orbital carapace lengths, sex ratios, frequencies of rare species, and sample richness. Although pooled data from combined gears showed greater total numbers of crayfishes, CPUE, and richness compared to either gear individually, combined gear and backpack electrofisher results differed minimally. Overall, richness was negatively related to specific conductance, indicating potential agricultural influence. Neither crayfish sex ratios, lengths, nor frequencies of rare species differed by gear; however, combining data from both gears ensured crayfish were captured in all study streams, which was not found for electrofishing or dipnetting alone. Species accumulation and rarefaction curves indicated sampling was sufficient for recording crayfish diversity at the scale of the study and that adding streams (versus sites within streams) would be most effective for watershed-scale studies. Our results suggested the combined gear protocol was effective for assessing crayfish population and assemblage characteristics in these Coastal Plain streams.

Mountaintop removal mining alters stream salamander population dynamics

AbstractAimPopulation dynamics are often tightly linked to the condition of the landscape. Focusing on a landscape impacted by mountaintop removal coal mining (MTR), we ask the following questions: (1) How does MTR influence vital rates including occupancy, colonization and persistence probabilities, and conditional abundance of stream salamander species and life stages? (2) Do species and life stages respond similar to MTR mining or is there significant variation among species and life stages?LocationFreshwater and terrestrial habitats in Central Appalachia (South‐eastern Kentucky, USA).MethodsWe conducted salamander counts for three consecutive years in 23 headwater stream reaches in forested or previously mined landscapes. We used a hierarchical, N‐mixture model with dynamic occupancy to calculate species‐ and life stage‐specific occupancy, colonization and persistence rates, and abundance given occupancy. We examined the coefficients of the hierarchical priors to determine population variation among species and life stages.ResultsOver 3 years, reference sites had greater salamander abundances and were occupied at a much higher rate than streams impacted by MTR. At sites impacted by MTR mining, most salamander species and life stages exhibited reduced initial occupancy, colonization rates, persistence rates and conditional abundance relative to reference stream reaches. Furthermore, the rates in MTR sites showed low variance, reinforcing that species and life stages were responding similar to MTR.Main conclusionsSalamander populations in landscapes modified by MTR mining exhibited significantly reduced vital rates compared to reference sites. Yet, similarity in responses across species suggests that management or restoration may benefit the entire salamander assemblage. For example, reforestation could reduce landscape resistance, repair altered hydrologic regimes and allow for higher rates of colonization and persistence in streams impacted by MTR.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

Abstract Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish. As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations. Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence. The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations. Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Characteristics of Capoeta oguzelii, a new species of cyprinid fish from the Ezine Stream, Black Sea basin, Turkey (Teleostei: Cyprinidae)

Four species of Capoeta (C. baliki, C. banarescui, C. sieboldii and C. ekmekciae) have been reported from Black Sea drainages, to date. We recognised an additional species in the Ezine Stream in the Southern Black Sea basin. Based on the analysis of 21 metric and 8 meristic data, we concluded that the Ezine Stream population forms a distinct, unnamed species, which we have described as Capoeta oguzelii sp. n. This species can be distinguished from all other Capoeta species by the following combination of characteristics: small size, presence of only one pair of barbels, absence of a keratinised edge of the lower jaw, a weakly ossified last simple dorsal fin ray, 7–10 gill rakers on the first gill arch and 7½ branched dorsal fin rays.http://www.zoobank.org/urn:lsid:zoobank.org:pub:066CC44A-3806-4DB7-8E88-AD971200E1EE

Relationships between indicators of acid-base chemistry and fish assemblages in streams of the Great Smoky Mountains National Park

The acidity of many streams in the Great Smoky Mountains National Park (GRSM) has increased significantly since pre-industrial (∼1850) times due to the effects of highly acidic atmospheric deposition in poorly buffered watersheds. Extensive stream-monitoring programs since 1993 have shown that fish and macroinvertebrate assemblages have been adversely affected in many streams across the GRSM. Matching chemistry and fishery information collected from 389 surveys performed at 52 stream sites over a 22-year period were assessed using logistic regression analysis to help inform the U.S. Environmental Protection Agency’s assessment of the environmental impacts of emissions of oxides of nitrogen (NOx) and sulfur (SOx). Numerous logistic equations and associated curves were derived that defined the relations between acid neutralizing capacity (ANC) or pH and different levels of community richness, density, and biomass; and density and biomass of brook trout, rainbow trout, and small prey (minnow) populations in streams of the GRSM. The equations and curves describe the status of fish assemblages in the GRSM under contemporary emission levels and deposition loads of nitrogen (N) and sulfur (S) and provide a means to estimate how newly proposed (and various alternative) target deposition loads, which strongly influence stream ANC, might affect key ecological indicators. Several examples using ANC, community richness, and brook trout density are presented to illustrate the steps needed to predict how future changes in stream chemistry (resulting from different target deposition loads of N and S) will affect the probabilities of observing specific levels of selected biological indicators in GRSM streams. The implications of this study to the regulation of NOx and SOx emissions, water quality, and fisheries management in streams of the GRSM are discussed, but also qualified by the fact that specific examples provided need to be further explored before recommendations concerning their use as ecological indicators could be proposed.

Associations of stream geomorphic conditions and prevalence of alternative reproductive tactics among sockeye salmon populations.

In many species, males may exhibit alternative life histories to circumvent the costs of intrasexual competition and female courtship. While the evolution and underlying genetic and physiological mechanisms behind alternative reproductive tactics are well studied, there has been less consideration of the ecological factors that regulate their prevalence. Here, we examine six decades of age composition records from thirty-six populations of sockeye salmon (Oncorhynchus nerka) to quantify associations between spawning habitat characteristics and the prevalence of precocious sneakers known as 'jacks'. Jack prevalence was independent of neutral genetic structure among stream populations, but varied among habitat types and as a function of continuous geomorphic characteristics. Jacks were more common in streams relative to beaches and rivers, and their prevalence was negatively associated with stream width, depth, elevation, slope and area, but positively related to bank cover. Behavioural observations showed that jacks made greater use of banks, wood and shallows than guard males, indicating that their reproductive success depends on the availability of such refuges. Our results emphasize the role of the physical habitat in shaping reproductive tactic frequencies among populations, likely through local adaptation in response to variable fitness expectations under different geomorphic conditions.

Interactions between local population density and limited habitat resources determine movements of juvenile Atlantic salmon

Competition for limited resources and the resulting density-dependent processes are key factors in driving stream salmonid population dynamics. Here we test for the combined effects of density and shelter availability on the movement of juvenile Atlantic salmon (Salmo salar) in a Norwegian river. Individually marked, hatchery-reared salmon juveniles were released at 26 sites along a 2.5 km long stretch and recaptured after 12 months. The spatial variation in shelter availability and density of salmonids was quantified prior to the release. We found no effect of released fish number on the number of marked salmon moving more than 12.5–112.5 m away from their release site. However, the ratio of pre-experiment fish density per shelter was positively related to the number of movers. Thus, fish that were released at sites where the amount of shelter was low relative to the density of the pre-experiment population were more likely to move. These results support the prediction from smaller scale experimental studies that shelter availability may act to determine local carrying capacity in stream-living salmonid populations.

Rainbow trout adaptation to a warmer Patagonia and its potential to increase temperature tolerance in cultured stocks

The viability of rainbow trout Oncorhynchus mykiss (Walbaum, 1792) culture is being challenged progressively by global warming. Previous trials with Australian and Japanese rainbow trout lines suggested that improvements in thermal performance may be possible. Here, we hypothesized that strain-related differences in physiological response to temperature exist between a north Patagonian hatchery stock (CENSALBA), a Neotropical one (Criadero Boca de Río), and a thermal stream (Valcheta) population of wild introduced rainbow trout. This was tested by comparing, at 20°C, the thermal preference, specific metabolic rate, thermal tolerance, growth, and condition on juveniles of the three strains, and on a Valcheta stream male x CENSALBA female F1 cross. Preferred temperature (PT) and loss of equilibrium temperature (LET, a measure of thermal tolerance) of Valcheta stream and F1 were significantly higher than those of CENSALBA, and the average PTs of Valcheta stream and F1 were higher than the 95% confidence interval of available reference data for rainbow trout. These results suggest that the F1, reared under standard hatchery conditions and selected by growth and thermal preference, presents higher thermal preference and higher thermal tolerance than the current CENSALBA hatchery stock. Introduction of this naturally adapted strain to hatchery stocks would likely result in the improvement of their temperature resistance to warmer waters. Current studies on adults of this F1 generation are underway.

Demography and genome divergence of lake and stream populations of an East African cichlid fish.

Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A.burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site-associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A.burtoni. A phylogenetic reconstruction based on genome-wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re-evaluate the independence of replicate lake-stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake-stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake-stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations.