The landscape genetics of yellow perch (Perca flavescens) in a large fluvial ecosystem

Gorges partition diversity within New Zealand flathead Galaxias populations

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.

Reanalysis on Phylogeographic Pattern of Sharpbelly Hemiculter leucisculus (Cyprinidae: Cultrinae) in China: A Review and the Implications for Conservation

Hemiculter leucisclus, as a widely distributed freshwater fish in China, provides an interesting model to explore the impact of drainage evolution and geologic history in the Pleistocene on diversification patterns. We collected the mitochondrial cytochrome b (cytb) gene and the recombination activating gene 2 (RAG2) from 1,070 individuals from 59 sampling locations. Phylogenetic and population genetic approaches were used to describe the phylogeographic pattern and to test how the geological and climatic factors on diversification. The results suggested that there existed four sublineages of the H. leucisclus across six river systems, among which two sublineages, showing strongly indigenous characteristics, are constrained to particular geographical regions in China. The molecular data and ancestral states demonstrated that the H. leucisclus possibly originated from the Pearl River basin during the later Pliocene. The phylogeographic pattern in H. leucisclus appears to have been driven by palaeoenvironmental perturbations rather than anthropogenic translocations. The geographically constrained sublineages A in the middle and lower Pearl River basin and sublineage B in the upper Yangtze River basin deserves special protection.

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.

The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed

Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.

Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin

Understanding the genetic and evolutionary impacts of stocking on wild fish populations has long been of interest as negative consequences such as reduced fitness and loss of genetic diversity are commonly reported outcomes. In an attempt to sustain a fishery, managers implemented nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy), a native species in the Lower St. Lawrence River (Québec, Canada). We investigated the effect of this stocking on population genetic structure and allelic diversity in the St. Lawrence River in addition to tributaries and several stocked inland lakes. Using genotype by sequencing, we genotyped 643 individuals representing 22 locations and combined this information with forward simulations to investigate the genetic consequences of long-term stocking. Individuals native to the St. Lawrence watershed were genetically differentiated from stocking sources and tributaries, and inland lakes were naturally differentiated from the main river. Empirical data and simulations within the St. Lawrence River revealed weak stocking effects on admixture patterns. Our data suggest that the genetic structure associated with stocked fish was diluted into its relatively large effective population size. This interpretation is also consistent with a hypothesis that selection against introgression was in operation and relatively efficient within the large St. Lawrence River system. In contrast, smaller populations from adjacent tributaries and lakes displayed greater stocking-related admixture that resulted in comparatively higher heterozygosity than the St. Lawrence. Finally, individuals from inland lakes that were established by stocking maintained a close affinity with their source populations. This study illustrated a benefit of combining extensive genomic data with forward simulations for improved inference regarding population-level genetic effects of long-term stocking, and its relevance for fishery management decision making.

Cumulative effects of municipal effluent and parasite infection in yellow perch: A field study using high-throughput RNA-sequencing

Multiple metabolic, immune and reproductive effects have been reported in fish residing in effluent-impacted sites. Natural stressors such as parasites also have been shown to impact the responses of organisms to chronic exposure to municipal effluent in the St. Lawrence River (Quebec, Canada). In order to comprehensively evaluate the cumulative impacts of anthropogenic and natural stressors on the health of yellow perch, differential mRNA transcription profiles were examined in juvenile females collected from effluent-impacted and upstream sites with low or high infection levels of the larval trematode Apophallus brevis. Transcriptomics was used to identify biological pathways associated with environmental exposure. In total, 3463 isoforms were differentially transcribed between sites. Patterns reflecting the combined effects of stressors were numerically dominant, with a majority of downregulated transcripts (68%). The differentially expressed transcripts were associated with 27 molecular and cellular functions ranging from cellular development to xenobiotic metabolism and were involved in the development and function of 13 organ systems including hematological, hepatic, nervous, reproductive and endocrine systems. Based on RNA-seq results, sixteen genes were measured by qPCR. Significant differences were observed for six genes in fish exposed to both stressors combined, whereas parasites and effluent individually impacted the transcription of one gene. Lysozyme activity, lipid peroxidation, retinol-binding protein and glucose-6-phosphate dehydrogenase were selected as potential biomarkers of effects to study specific pathways of interest. Lipid peroxidation in perch liver was different between sites, parasite loads, and for combined stressors. Overall, results indicated that juvenile yellow perch responded strongly to combined parasite and effluent exposure, suggesting cumulative effects on immune responses, inflammation and lipid metabolism mediated by retinoid receptors. The present study highlight the importance of using a comprehensive approach combining transcriptomics and endpoints measured at higher levels of biological organization to better understand cumulative risks of contaminants and pathogens in aquatic ecosystems.

RNA-sequencing to assess the health of wild yellow perch (Perca flavescens) populations from the St. Lawrence River, Canada

This study aimed to better understand in situ cumulative effects of anthropogenic stressors on the health of St. Lawrence River (QC, Canada) yellow perch populations using high-throughput transcriptomics and a multi-biological level approach. Fish were collected in the upstream fluvial Lake Saint-François (LSF) with low degree of environmental perturbations; Lake Saint-Louis (LSL) considered having a moderate degree of anthropogenic stressors, and Lake Saint-Pierre (LSP) a sector where the perch population has been severely declining. Morphometric results indicated that fish from the downstream LSP showed lower body condition compared to LSF and LSL. Liver transcriptomic responses were assessed by RNA-sequencing. Two hundred and eighty genes were over-transcribed in LSP perch while 200 genes were under-transcribed compared to LSF and LSL. In LSP fish, genes transcripts related to reproduction, retinol, iron, thyroid hormones, oxidative stress, lipid metabolism and immune functions were among the most abundant suggesting that multiple metabolic and physiological pathways were impacted by environmental stressors at this site. Inhibition of liver superoxide dismutase, catalase and glutathione S-transferase activities were also observed at the cellular level. Overall, identified impacted biological pathways in perch from LSP may help understand the precarious state of this population and identify the factors inhibiting its recovery.

Dam trout: Genetic variability in Oncorhynchus mykiss above and below barriers in three Columbia River systems prior to restoring migrational access

Restoration of access to lost habitat for threatened and endangered fishes above currently impassable dams represents a major undertaking. Biological monitoring is critical to understand the dynamics and success of anadromous recolonization as, in the case of Oncorhynchus mykiss, anadromous steelhead populations are reconnected with their conspecific resident rainbow trout counterparts. We evaluate three river systems in the Lower Columbia River basin: the White Salmon, Sandy, and Lewis rivers that are in the process of removing and/or providing passage around existing human-made barriers in O. mykiss riverine habitat. In these instances, now isolated resident rainbow trout populations will be exposed to competition and/or genetic introgression with steelhead and vice versa. Our genetic analyses of 2,158 fish using 13 DNA microsatellite (mSAT) loci indicated that within each basin anadromous O. mykiss were genetically distinct from and significantly more diverse than their resident above-dam trout counterparts. Above long-standing natural impassable barriers, each of these watersheds also harbors unique rainbow trout gene pools with reduced levels of genetic diversity. Despite frequent releases of non-native steelhead and rainbow trout in each river, hatchery releases do not appear to have had a significant genetic effect on the population structure of O. mykiss in any of these watersheds. Simulation results suggest there is a high likelihood of identifying anadromous x resident individuals in the Lewis and White Salmon rivers, and slightly less so in the Sandy River. These genetic data are a prerequisite for informed monitoring, managing, and conserving the different life history forms during upstream recolonization when sympatry of life history forms of O. mykiss is restored.

Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall F_ST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S F_ST = 0.13; SEQ-N F_ST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.

Riverine fish diversity varies according to geographical isolation and land use modification

Understanding the environmental factors driving species-genetic diversity correlations (SGDCs) is critical for designing appropriate conservation and management strategies to protect biodiversity. Yet, few studies have explored the impact of changing land use patterns on SGDCs specifically in aquatic communities. This study examined patterns of genetic diversity in roach (Rutilus rutilus L.) together with fish species composition across 19 locations in a large river catchment, spanning a gradient in land use. Our findings show significant correlations between some, but not all, species and genetic diversity end points. For example, genetic and species differentiation showed a weak but significant linear relationship across the Thames catchment, but additional diversity measures such as allelic richness and fish population abundance did not. Further examination of patterns in species and genetic diversity indicated that land use intensification has a modest effect on fish diversity compared to the combined influence of geographical isolation and land use intensification. These results indicate that environmental changes in riparian habitats have the potential to amplify shifts in the composition of stream fish communities in poorly connected river stretches. Conservation and management strategies for fish populations should, therefore, focus on enhancing connectivity between river stretches and limit conversion of nearby land to arable or urban use to maintain current levels of biodiversity.

Lipophilic antioxidants and lipid peroxidation in yellow perch subjected to various anthropogenic influences along the St. Lawrence River (QC, Canada)

In Lake Saint-Pierre (LSP), the last great widening of the St. Lawrence River (province of Québec, Canada), the yellow perch has been experiencing a significant decline since the mid-1990s. The combined effect of several stressors (deterioration of habitats appropriate for reproduction and growth, invasive species and poor water quality) seems to exert considerable influence on the yellow perch population in LSP, characterized by low recruitment. To better understand possible stressor effects at the biochemical level, LSP yellow perch were compared with other sites along a gradient of increasing human influences from upstream to downstream along the St. Lawrence River. Morphometry (size, weight, circumference and Fulton's condition factor) and biomarkers associated to the peroxidation of lipids, lipophilic antioxidants (α-tocopherol and carotenoids), along with retinoids (vitamins A1and A2) and proteins were compared between sites at the larval, juvenile and adult stages. Fulton's condition factor was similar between sites for juveniles but was significantly lower in LSP adults, suggesting a weakened physiological condition. In most contaminated sites as LSP, lipid peroxidation tended to be higher in juveniles and adults whereas the lipophilic antioxidant lycopene and proteins content were lower. Retinyl esters were significantly lower for LSP fish compared to other sites, not only in larvae but also in the livers of juveniles and adults. These results are consistent with possible altered metabolism in the retinoid system of LSP yellow perch. The overall results reflect the "pressure" gradient tested, where the yellow perch from the most affected sites located downstream had impaired physiological and biochemical conditions compared to the upstream sectors.

Integrated spatial health assessment of yellow perch (Perca flavescens) populations from the St. Lawrence River, Quebec, Canada) part A: physiological parameters and pathogen assessment

A multi-disciplinary approach was used to evaluate the health of yellow perch (Perca flavescens) in the St. Lawrence River (Quebec, Canada), which is experiencing a severe population decline in the downstream portion of the river. Physiological parameters, liver alterations, trace metal concentrations, parasite prevalence and abundance, stable isotope composition, and the presence/absence of the viral hemorragic septicemia virus (VHSV) were evaluated in perch collected at six sites along the river: Lake St. François, Lake St. Louis (north and south), Beauregard Island, and Lake St. Pierre (north and south). Trace metal concentrations in surface water were higher in Lake St. Louis and downstream of a major urban wastewater treatment plant discharge, indicating that this effluent was a significant source of Cu, As, Ag, Zn, and Cd. Levels of Pb in surface water exceeded thresholds for the protection of aquatic life in Lake St. Louis and were negatively correlated with body condition index in this lake. In Lake St. Pierre, Cu, Ag, and Cd bioaccumulated significantly in perch liver and lower body condition index and greater liver damage were observed compared to upstream sites. Parasite analyses indicated a higher abundance of metacercariae of the trematodes Apophallus brevis and Diplostomum spp. in Lake St. Louis, and VHSV was not detected in the liver of yellow perch for all studied sites. Overall, results suggested that the global health of yellow perch from Lake St. Pierre is lower compared to upstream studied sites, which could contribute to the documented population collapse at this site.

Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment

The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man‐made barriers without fishpasses. The Rhine Falls as the only long‐standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man‐made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.

A salt bath will keep you going? Euryhalinity tests and genetic structure of caridean shrimps from Iberian rivers

We assessed the role of euryhalinity and life-history traits on the population genetic structure of the four main caridean shrimp species from the Iberian Peninsula (Atyaephyra desmarestii, Dugastella valentina, Palaemon varians and Palaemon zariquieyi) able to complete their life cycle in freshwater/oligohaline habitats. Seawater exposure experiments indicated that A. desmarestii, D. valentina and P. zariquieyi are more sensitive to high salinity waters than P. varians and confirm the relationship between osmolality regulation and spatial distribution of species. The limited or no survival in seawater could explain the restricted distributions observed in D. valentina and P. zariquieyi, whereas the current A. desmarestii distribution could be due to either past river dynamics and/or human-mediated water transfers. Conversely, the high tolerance of P. varians to a large salinity range (euryhalinity) could explain its capacity to colonize geographically distant estuaries. In agreement with osmoregulation results, the phylogeography patterns of the cytochrome oxidase 1 (Cox 1) gene fragment revealed significant genetic differentiation among river systems whatever the species considered. Atyidae species presented higher nucleotide diversity levels than Palaemonidae species, while isolation-by-distance patterns were only found for the latter. Our results have important implications for the management and conservation of freshwater species, since the inter-catchment connectivity may affect the speciation processes.

Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems

Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.

Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.

Novel molecular approach demonstrates that turbid river plumes reduce predation mortality on larval fish

Turbidity associated with river plumes is known to affect the search ability of visual predators and thus can drive 'top-down' impacts on prey populations in complex ecosystems; however, traditional quantification of predator-prey relationships (i.e. stomach content analysis) often fails with larval fish due to rapid digestion rates. Herein, we use novel molecular genetic methods to quantify larval yellow perch (YP) in predator stomachs in western Lake Erie to test the hypothesis that turbidity drives variation in larval predation. We characterize predator stomach content DNA to first identify YP DNA (single nucleotide polymorphism) and then quantify larval YP predation (microsatellite allele counting) in two river plumes differing in turbidity. Our results showed elevated larval YP predation in the less turbid river plume, consistent with a top-down impact of turbidity on larval survival. Our analyses highlight novel ecological hypothesis testing using the power of innovative molecular genetic approaches.

Landscape variability explains spatial pattern of population structure of northern pike (Esox lucius) in a large fluvial system

A growing number of studies have been investigating the influence of contemporary environmental factors on population genetic structure, but few have addressed the issue of spatial patterns in the variable intensity of factors influencing the extent of population structure, and particularly so in aquatic ecosystems. In this study, we document the landscape genetics of northern pike (Esox lucius), based on the analysis of nearly 3000 individuals from 40 sampling sites using 22 microsatellites along the Lake Ontario - St. Lawrence River system (750 km) that locally presents diverse degrees of interannual water level variation. Genetic structure was globally very weak (F ST = 0.0208) but spatially variable with mean level of differentiation in the upstream section of the studied area being threefold higher (F ST = 0.0297) than observed in the downstream sector (F ST = 0.0100). Beside interannual water level fluctuation, 19 additional variables were considered and a multiple regression on distance matrices model (R (2)  = 0.6397, P < 0.001) revealed that water masses (b = 0.3617, P < 0.001) and man-made dams (b = 0.4852, P < 0.005) reduced genetic connectivity. Local level of interannual water level stability was positively associated to the extent of genetic differentiation (b = 0.3499, P < 0.05). As water level variation impacts on yearly quality and localization of spawning habitats, our study illustrates how temporal variation in local habitat availability, caused by interannual water level fluctuations, may locally decrease population genetic structure by forcing fish to move over longer distances to find suitable habitat. This study thus represents one of the rare examples of how environmental fluctuations may influence spatial variation in the extent of population genetic structure within a given species.

Restauration des habitats du lac Saint-Pierre : un prérequis au rétablissement de la perchaude

La perchaude (Perca flavescens) du lac Saint-Pierre a connu un déclin majeur à partir du milieu des années 1990. La situation est devenue si critique que le gouvernement du Québec a décrété, en 2012, un moratoire de 5 ans sur les pêches commerciale et sportive. Si la pêche a contribué à cet effondrement, la perchaude a aussi souffert de la détérioration de ses habitats depuis les années 1950. L’analyse de l’utilisation du sol à partir de photographies aériennes, couplée à la modélisation des meilleurs habitats de reproduction dans la zone littorale, indique que 5 000 ha d’habitats printaniers ont été dégradés par plusieurs activités anthropiques. La disparition d’herbiers et la prolifération de cyanobactéries benthiques dans les zones de croissance des jeunes perchaudes, la diminution de la connectivité entre le lac et la zone littorale, l’implantation d’espèces exotiques, l’arrivée d’un nouveau prédateur aviaire et aussi le climat ont contribué à l’échec du recrutement et au déclin de la perchaude. Les constats de détérioration du lac Saint-Pierre indiquent que la situation ne s’améliorera que lorsque les espèces pourront se reproduire et se développer dans un milieu sain, ce qui nécessitera la restauration d’habitats, ainsi que l’amélioration de la qualité de l’eau et de la connectivité entre le lac et la zone littorale.

Connectivity in a pond system influences migration and genetic structure in threespine stickleback

Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least-cost-path and isolation-by-resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation-by-distance) or with landscape connectivity provided by areas prone to flooding (as indicated by Carex sp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (DPS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least-cost-path and isolation-by-resistance than with Euclidean distance, whereas the relative contribution of isolation-by-resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales.

Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico

Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.

Development and characterization of DNA microsatellite primers for buriti (Mauritia flexuosa L.f.)

Mauritia flexuosa L. (Arecaceae) is a palm tree species known as buriti that occurs in the Cerrado biome. It is characteristic of the vereda, a typical ecosystem of central Brazil. In this phytophysiognomy, M. flexuosa and other groups of arboreal-herbaceous species develop in open fields with very humid soils. M. flexuosa can be found in forest borders and is a palm tree with a wide distribution in South America (Brazil, Colombia, Venezuela, French Guyana Ecuador, Peru, and Bolivia). The main objectives of this study were to develop simple sequence repeat marker-enriched libraries and to characterize these loci in buriti palm to facilitate future population studies. A total of 40 sequences derived from the microsatellite-enriched libraries were selected for primer design. The optimization results showed that 9 primer pairs could successfully amplify polymorphic target fragments of the expected sizes. The data also show that the described primers can be used in population genetic studies in M. flexuosa to obtain information that will inform conservation and management strategies.

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.

Genetic population structure of perch Perca fluviatilis along the Swedish coast of the Baltic Sea

In this study, the genetic variation of perch Perca fluviatilis from 18 different sites along the Swedish coast of the Baltic Sea was assessed. There was a relative strong support for isolation by distance and the results suggest an overall departure from panmixia. The level of genetic divergence was moderate (global F(ST) = 0·04) and indications of differences in the population genetic structure between the two major basins (central Baltic Sea and Gulf of Bothnia) in the Baltic Sea were found. There was a higher level of differentiation in the central Baltic Sea compared to the Gulf of Bothnia, and the results suggest that stretches of deep water might act as barriers to gene flow in the species. On the basis of the estimation of genetic patch size, the results corroborate previous mark--recapture studies and suggest that this is a species suitable for local management. In all, the findings of this study emphasize the importance of considering regional differences even when strong isolation by distance characterize the genetic population structure of species.

Landscape genetics: where are we now?

Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Population differentiation in perch Perca fluviatilis: environmental effects on gene flow?

Environmental parameters were used to investigate barriers to gene flow and genetic differentiation in the Eurasian perch (Perca fluviatilis L.) at a small geographical scale in an archipelago system. Significant genetic differentiation was found among locations. Distance per se did not play a major role in the reduction of gene flow. Instead, the largest genetic differences between populations correlated with major changes in environmental conditions, such as temperature at time of spawning. The results show that genetic divergence can arise between populations in habitats thought to be highly connected, and that environmental variables can influence the level of gene flow between populations, including those that are at small spatial scales (tens of kilometres). The importance of a landscape approach when investigating genetic differentiation and defining barriers to gene flow is highlighted.

Habitat continuity and geographic distance predict population genetic differentiation in giant kelp

Isolation by distance (IBD) models are widely used to predict levels of genetic connectivity as a function of Euclidean distance, and although recent studies have used GIS-landscape ecological approaches to improve the predictability of spatial genetic structure, few if any have addressed the effect of habitat continuity on gene flow. Landscape effects on genetic connectivity are even less understood in marine populations, where habitat mapping is particularly challenging. In this study, we model spatial genetic structure of a habitat-structuring species, the giant kelp Macrocystis pyrifera, using highly variable microsatellite markers. GIS mapping was used to characterize habitat continuity and distance between sampling sites along the mainland coast of the Santa Barbara Channel, and their roles as predictors of genetic differentiation were evaluated. Mean dispersal distance (sigma) and effective population size (Ne) were estimated by comparing our IBD slope with those from simulations incorporating habitat continuity and spore dispersal characteristics of the study area. We found an allelic richness of 7-50 alleles/locus, which to our knowledge is the highest reported for macroalgae. The best regression model relating genetic distance to habitat variables included both geographic distance and habitat continuity, which were respectively, positively and negatively related to genetic distance. Our results provide strong support for a dependence of gene flow on both distance and habitat continuity and elucidate the combination of Ne and a that explained genetic differentiation.

Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: a catchment analysis of mitochondrial DNA sequences and nuclear microsatellites

Catchment population structure and divergence patterns of the rainbow darter Etheostoma caeruleum (Percidae: Teleostei), an eastern North American benthic fish, are tested using a landscape genetics approach. Allelic variation at eight nuclear DNA microsatellite loci and two mitochondrial DNA regions [cytochrome (cyt) b gene and control region; 2056 aligned base pairs (bp)] is analysed from 89 individuals and six sites in the Lake Erie catchment (Blanchard, Chagrin, Cuyahoga and Grand Rivers) v. the Ohio River catchment (Big Darby Creek and Little Miami River). Genetic and geographic patterning is assessed using phylogenetic trees, pair-wise F(ST) analogues, AMOVA partitioning, Mantel regression, Bayesian assignment, 3D factorial correspondence and barrier analyses. Results identify 34 cyt b haplotypes, 22 control region haplotypes and 137 microsatellite alleles whose distributions demonstrate marked genetic divergence between populations from the Lake Erie and Ohio River catchments. Etheostoma caeruleum populations in the Lake Erie and Ohio River catchments diverged c. 1.6 mya during the Pleistocene glaciations. Greater genetic separations characterize the Ohio River populations, reflecting their older habitat age and less recent connectivity. Divergence levels within the Lake Erie catchment denote more recent post-glacial origins. Notably, the western Lake Erie Blanchard River population markedly differs from the three central basin tributary samples, which are each genetically distinguishable using microsatellites. Overall relationships among the Lake Erie sites refute a genetic isolation by geographic distance hypothesis. Etheostoma caeruleum populations thus exchange few genes and have low migration among tributaries and catchments.

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.

Genetic structure of Melanotaenia australis at local and regional scales in the east Kimberley, Western Australia

The Kimberley region of Western Australia possesses a poorly studied freshwater fish fauna with high endemism in an aquatic landscape subject to monsoonal floods and dry season isolation. In the first population genetic study of freshwater fish in this region, the authors tested the effects of geographic barriers on genetic structure at multiple spatial scales in east Kimberley populations of the western rainbowfish, Melanotaenia australis, the most widespread and abundant species in the region. Based on allozyme comparisons, hierarchical analysis of F(ST) revealed increasing genetic subdivision with spatial scale. Minimal genetic structure within creeklines demonstrated that wet season dispersal, rather than dry season isolation, determines genetic structure at small scales. At the scale of sub-catchments, a pattern of isolation by distance along creeklines was evident. Genetic subdivision between adjacent river systems was greater between rivers separated by a plateau than by lowlands. This implies greater connectivity of populations in lowland areas and may explain the greater similarity of the east Kimberly freshwater fish fauna with lowlands to the east than with the more rugged regions to the west. Similarly, greater connectivity between lowland populations may account for the on-average larger distribution of lowland Melanotaeniids.