The landscape genetics of syntopic topminnows (Fundulus notatus and F. olivaceus) in a riverine contact zone

The metapopulation dynamics of a species are influenced by the spatial arrangement of preferred habitats across a landscape. Increasing habitat patchiness can result in greater population subdivision, leading to more pronounced population genetic structure. Therefore, even subtle differences in habitat preferences among species could lead to substantial differences in genetic structure. Members of the Fundulus notatus species complex of topminnows include a headwater specialist and a large river specialist with broadly overlapping geographical distributions. Both species are often found in the same drainage systems, but partially isolated by divergent habitat preferences. The purpose of this research was to determine whether distribution along a stream continuum in a contact zone influences population genetic patterns in two species of topminnow (Fundulus olivaceus and Fundulus notatus). Fish were collected in the summers of 2010–2012, and habitat data were collected in summer 2012, within all major tributaries of the Saline River in southern Illinois. In total, 523 fish were genotyped using seven microsatellite loci to assess genetic variation. Species distributions in F. notatus and F. olivaceus were associated with habitat factors that covaried with cumulative drainage area. Populations of F. olivaceus showed a greater level of genetic structure reflected in a significant pattern of isolation by distance, while populations of F. notatus showed no such pattern. Spatial autocorrelation analysis revealed that at an individual level, both species became increasingly divergent with waterway distance. Overall, clear interspecific differences in habitat preferences were translated into measurable but relatively subtle differences in population genetic structure.     

The relationship of environmental factors to spatial and temporal variation of fish assemblages in a floodplain river in Texas, USA

Abstract –  Spatial and temporal variation of species–environment relationships were evaluated for shallow-margin and deep-water fish assemblages in the Brazos River, a large floodplain river in Texas, USA. Total variation among the deep-water assemblages (11 species, 86% turnover across gill net samples) was greater than for shallow-margins (38 species, 64% turnover across seine samples). For both shallow-margin and deep-water assemblages, variation was greater among sites than between winter and summer seasons. Shallow-margin assemblage structure was related to depth, velocity and substrate, whereas for deep-water assemblages river discharge, temperature and velocity were important. Season itself accounted for little of the variation among either shallow (6.7%) or deep-water (2.3%) assemblages. Overall temporal patterns of shallow-margin samples appeared to show responses to juvenile recruitment, spates and migration of coastal fishes, whereas for deep-water samples, patterns related to use of reproductive habitats, juvenile recruitment and seasonal activity levels. Brazos River assemblages were less variable overall in comparison with studies along similar length of reach in headwater streams and wadeable rivers. The residual variation in species distribution (54% for shallow-margin and 67% for deepwater) that was not explained by instream variables and season suggests a greater influence of biotic interactions in rivers, particularly those across the spatially dynamic interface of main channel habitats and shallow river margins.     

Environmental and spatial processes: what controls the functional structure of fish assemblages in tropical rivers and headwater streams?

In this study, we investigated functional structure patterns of tropical headwater and river fish assemblages. We hypothesised that environmental conditions are primarily structuring headwater streams leading to functionally clustered assemblages, whereas processes that favour functional overdispersion would guide river assemblages. For 27 headwater streams and 22 rivers, we used eight functional traits for calculating two functional indexes: mean pairwise distance (MPD) and net relatedness index (NRI). We performed linear regressions between indexes and species richness, a multiple regression between NRI and eight environmental variables and a variation partitioning to disentangle the role of environment and space on NRI. Our findings indicate that fish assemblages of headwaters are structured by environmental conditions as most assemblages in this habitat displayed a tendency to clustering and MPD/NRI were not correlated with species diversity, whereas the opposite pattern was observed for river habitat. Four environmental variables (channel depth, water velocity, dissolved oxygen and turbidity) explain 56% of functional structure variation. These variables seem to function as selective filters in headwaters, whereas channel depth may be determinant for functional overdispersion of river fish assemblages. Components associated with space are also influencing the functional structure. Limitations of species dispersal through space (between both habitat types) appear as a possible cause to this. In this sense, both environmental conditions and processes linked with space are capable of influencing the functional structure of tropical headwater streams and river fish assemblages.     

Lifelong population connectivity between large rivers and their tributaries: A case study of shovelnose sturgeon from the Mississippi and Wisconsin rivers

Fishes that depend on large‐river habitats have declined in many regions due to human alteration of both mainstems and tributaries. Conserving these species is often complicated by their dependence on long‐distance movements to complete their life cycle, but the location of key habitats is difficult to assess across multiple life history stages. Movement of large‐river fishes between mainstems and major tributaries is commonly observed, but the role of these exchanges at the population level is uncertain. We used shovelnose sturgeon (Scaphirhynchus platorynchus) as a case study for assessing the lifelong spatial ecology of large‐river fishes. Fin ray microchemistry data indicate that shovelnose sturgeon from the Mississippi and Wisconsin rivers represent a unified population that relies on connections among multiple large‐river habitats throughout life history. The tributary serves as an important spawning area, but fin ray chemistry data suggest larvae subsequently drift downstream to nursery habitats in the mainstem; an assertion that is supported by extensive field survey data. Our analyses underscore the lifelong importance of connections within river networks for maintaining viable populations of this, and likely other large‐river species that have been documented to use tributary habitats. These findings support a metapopulation perspective on species that depend on large‐river habitats, many of which are now highly altered and fragmented. For shovelnose sturgeon and species with similar life history, protecting or restoring linkages between mainstem rivers and their tributaries should be a conservation priority.     

From regionally predictable to locally complex population structure in a freshwater top predator: river systems are not always the unit of connectivity in Northern Pike Esox lucius

Contemporary genetic diversity is the product of both historical and contemporary forces, such as climatic and geological processes affecting range distribution and continuously moulded by evolutionary forces selection, gene flow and genetic drift. Predatory freshwater fishes, such as Northern Pike Esox lucius, commonly exhibit small population sizes, and several local populations are considered endangered. Pike inhabit diverse habitat types, including lakes, rivers and brackish marine waters, thus spanning from small isolated patches to large open marine systems. However, pike population structure from local to regional scales is relatively poorly described, in spite of its significance to developing conservation measures. We analysed microsatellite variation in a total of 1185 North European pike from 46 samples collected across both local and regional scales, as well as over time, to address two overarching questions: Is pike population structure associated with local and/or regional connectivity patterns, and which factors likely have the main influence on the contemporary distribution of genetic diversity? To answer this, we combined estimators of population diversity and structure to assess evidence of whether populations within (i) habitats, (ii) drainage systems and (iii) geographical regions are closer related than among these ranges, and whether patterns are temporally stable. Contrasting previous predictions that genetic drift obscures signals of postglacial colonisation history, we identified clear regional differences in population genetic signatures, suggesting a major effect of drainage divides on colonisation history and connectivity. However, several populations deviated from the general pattern, showing that local processes may be complex and need to be examined case‐by‐case.     

Genetic diversity and population structure of burbot Lota lota in Germany: Implications for conservation and management

The genetic structure of the gadiform fish species, burbot Lota lota L., was investigated across Germany to derive management options for facilitating the preservation of genetic diversity. Sequence analysis of the mitochondrial control region (n = 244) and microsatellite analysis (n = 861) of specimens from 20 sites revealed genetic structuring between major river basins, and particularly between lake and river habitats. The admixture zone between the Eurasian and West European phylogenetic clades in Lake Constance was confirmed and expanded to include the drainage basins of the rivers Rhine and Schlei/Trave. Haplotype distribution and private haplotypes in single river basins indicated population differentiation and imply that German burbot constituted an important part of the entire species' diversity. The derived genetic structuring has implications for future stocking programmes and the preservation of the adaptive potential of burbot, a guiding species for oligotrophic lakes in Europe.     

Spatiotemporal patterns of fish community composition in Great Lakes drowned river mouths

Freshwater river mouths in large lakes are centres of biological activity, yet little is understood about the spatial and temporal dynamics of fish communities in these systems. In the Laurentian Great Lakes, we sampled littoral fishes over 3 years in six drowned (i.e., protected) river mouths to: (i) quantify spatial (among river mouths) and temporal (among years) variation, (ii) evaluate associations with environmental conditions and (iii) assess spatial patterns of community similarity. We sampled 6787 fish representing 43 species over the course of the study. Multivariate analyses indicated that variation in fish species composition was more strongly partitioned among river mouths than among years. Fish communities across the six river mouths were partitioned into three groups, a pattern we attribute to variability in anthropogenic disturbance and environmental conditions. Canonical correspondence analysis showed that fish species composition was associated with specific conductivity, vegetation cover, turbidity and pH, suggesting species–environment relationships are similar to those shown for Great Lakes coastal wetlands. Finally, we found a negative relationship between geographic distance and community similarity, suggesting that dispersal and/or environmental gradients play a role in shaping these river mouth fish assemblages. We conclude that Great Lakes drowned river mouths can harbour diverse and spatially variable fish assemblages that are driven by a combination of local and regional factors.     

Lack of genetic population structure of slimy sculpin in a large,fragmented lake

Most of what is known about sculpin population structure comes from research in streams; however, slimy sculpins are also a common benthic species in deep lakes. In streams, sculpins are considered to be a relatively inactive species, moving only small distances, and characteristically have high levels of genetic structure. We examined population genetic structure of slimy sculpin (Cottus cognatus) across multiple barriers and over distances up to 227 km in Lake Champlain (USA, Canada) and Lake Ontario (USA, Canada) to determine whether lake populations of sculpin are also highly structured. We predicted that slimy sculpin populations in Lake Champlain would be structured by six causeways as well as by distance, Lake Ontario populations would be structured only by distance, and differences between the lakes would be large relative to within‐lake differences. We examined microsatellite variation among 200 slimy sculpins from Lake Champlain and 48 slimy sculpins from Lake Ontario to evaluate patterns of population connectivity and structure. There was no indication of population substructuring within either lake but sculpin were genetically distinct between lakes. We conclude that there is a single, panmictic population of sculpin present in Lake Champlain and another potentially panmictic population in Lake Ontario, with no indication of genetic isolation by distance. Our results contrast with data from sculpin in streams, suggesting distance and habitat fragmentation exert little influence on population connectivity of benthic fish in lakes.     

Fish species incidence patterns in naturally fragmented Chihuahuan Desert streams

We investigated how stream fragmentation affects local fish species persistence and extinction from three Rio Grande systems (Texas, USA) stream reaches with different levels of natural fragmentation. We examined species–volume (SV) relationships of fish assemblages in 42 pools across the watersheds and predicted greater fragmentation would correspond to an increase in the slope of the SV relationship due to decreased within‐reach rescue effects. In addition, we examined relationships among tributary‐specific nested subset patterns, local habitat features and spatial position of the reaches relative to the Rio Grande mainstem to better understand the importance of local and regional processes on fish species richness patterns in the stream reaches. Slopes of the SV curves did not differ among the stream reaches, but the intercepts of the SV curves were significantly different. These results indicated rescue effects among habitats within a stream reach were not apparent; however, rescue effects from the mainstem largely determined the species richness of a given stream reach. The nested subset patterns in all stream reaches were related to several local environmental factors, and large, deep pools provided important aquatic refugia in all three systems. We suggest declines in mainstem and tributary flows will likely continue to impact local and regional fish assemblage attributes. High flow events are important for dispersal and can reset tributary fish communities for the next extinction‐driven, successional cycle.     

赤水河河源段栖息地现状评价及修复对策探讨

对受损栖息地进行保护与修复是复苏河湖生态环境的重要举措。本文以赤水河河源段为研究区域，综合考虑区域内小水电拆除对鱼类栖息地的影响，依据AHP-熵权法，筛选了金沙鲈鲤、青石爬鮡、圆口铜鱼、岩原鲤、昆明裂腹鱼、长薄鳅六种优先保护鱼类，构建了基于河流地貌特征、水文、水质及鱼类等四方面的河道栖息地健康评价指标体系，建立了多尺度赤水河河源段栖息地综合评价标准。评价结果显示该河段仅30%河道栖息地为较好状况，50%河道栖息地处于一般状况，20%河道栖息地处于较差状况。小水电拆除可以有效恢复鱼类栖息地，但其质量仍需进一步提升，结合对研究区栖息地现状评估结果，可采取河道清理、卵砾石注入、河段平面形态修复等五种修复对策。     

Assessing the consequences of habitat fragmentation for two migratory salmonid fishes

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Seasonal habitat use of alligator gar in a river–floodplain ecosystem at multiple spatial scales

Alligator gar (Atractosteus spatula) populations are declining throughout their range in the United States, even where considered stable. Similar declines in other riverine species are occurring worldwide due to alteration of habitat in river–floodplain systems. Most rivers in the world are highly regulated, resulting in departures from historic hydrology that provides connection to the floodplain habitats used by riverine fishes. Knowledge of the seasonal habitat requirements of alligator gar and similar riverine fishes at a watershed scale is limited, hindering management practices. We used radiotelemetry to monitor movements and habitat use of adult alligator gar (N = 32; 25.0–84.5 kg; 149–224 cm) at macro‐ and microhabitat scales during 2 years of varying hydrology. Fish showed seasonal differences in their use of main channel and floodplain macrohabitats. Floodplain tributaries and their upper reaches were especially important to reproductive ecology. Minimum distance travelled per day varied seasonally. While using the main channel Fourche LaFave River, gar selected low velocity, shallow depth and complex structure along channel margins. The Fourche LaFave River is unique in its connection to floodplain habitats on a relatively predictable basis, with frequent flooding during the spring and summer reproductive period. Our study emphasises the importance of connectivity between the main river channel and floodplain habitats to a floodplain‐obligate riverine species. An intact, heterogeneous riparian zone creates essential microhabitat for the species. Understanding habitat requirements of alligator gar at multiple spatial scales in a river–floodplain system is crucial to management of many other species and river systems.     

Population genetic structure of Atlantic salmon,Salmo salar L., in the River Tamar,southwest England

Abstract Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L., population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment‐specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment‐specific studies of stock abundance. Implications for implementing management actions are considered.     

Conservation genetics of the endangered depressed river mussel,Pseudanodonta complanata,using amplified fragment length polymorphism (AFLP) markers

• 1. Genetic analysis is increasingly recognized as a key tool for understanding demography, and is particularly useful for describing patterns of gene flow between putative populations. Most effort has been directed towards vertebrate systems, where any one study often benefits from marker development in related species. The greater diversity of invertebrate taxa presents a challenge, but amplified fragment length polymorphism (AFLP) markers offer a solution, yielding high levels of polymorphism and no prior knowledge of a species' genome.
• 2. AFLP markers have been used to analyse an unusual metapopulation of an invertebrate, the endangered freshwater mussel, Pseudanodonta complanata, sampled from river systems across the UK. This was done to assess the extent to which individual river systems were genetically isolated from one another.
• 3. The results show patterns of weak genetic differentiation across the UK, with one hydrologically isolated population in the south west showing clear genetic differentiation from the rest of the country. However, the UK population as a whole exhibits significant isolation by distance, particularly when one population subject to fish stocking is removed, this population probably being seeded with mussel glochidia larvae which use fish as vectors. Genetic estimates of inbreeding reveal a complicated pattern in which inbreeding peaks at intermediate densities. High‐density populations may be genetically diverse due to their size, while the lowest density populations may represent transient groups of emigrants from other, larger populations.
• 4. The findings show that limited gene flow does exist between some but not all river systems. The isolation of the south‐west population indicates that dispersal is variable and should not be assumed to be present. Waterways that remain hydrologically isolated may require special attention in conservation programmes as they can harbour genetically distinct populations. The balance between river management activities and conservation priorities therefore needs careful consideration. Copyright © 2010 John Wiley & Sons, Ltd.

     

Temporal segregation in spawning between native Yellowstone cutthroat trout and introduced rainbow trout

Hybridisation with introduced taxa poses a threat to native fish populations. Mechanisms of reproductive isolation can limit or prevent hybridisation between closely related species. Understanding how these mechanisms interact between the same species across geographically distinct occurrences of secondary contact, and how regional factors influence them, can inform our understanding of hybridisation as a threat and management actions to mitigate this threat. We used data collected on adult fish migration timing and approximate emergence timing of subsequent juvenile fish paired with genomic data to assess whether temporal isolation in the timing of spawning exists between Yellowstone cutthroat trout, rainbow trout and hybrids in the North Fork Shoshone River drainage in northwest Wyoming. We found evidence that Yellowstone cutthroat trout spawn, on average, two to four weeks later than rainbow trout and hybrids and two environmental covariates related to water temperature and discharge were associated with differences in spawning migration timing. Despite statistical support for Yellowstone cutthroat trout spawning later, disproportionately high numbers of rainbow trout and hybrids, paired with extended spawning seasons, lead to substantial overlap between all genotypes. Our results provide further evidence of temporal segregation in the timing of spawning as a mechanism of reproductive isolation between closely related species, but substantial spawning overlap suggests temporal segregation alone will not be enough to curtail hybridisation in conservation populations.     

Fishes of the Irrawaddy River: Diversity and conservation

1. Few conservation studies have examined fish communities in entire drainage basins, especially in developing regions such as Southeast Asia, one of the most diverse biomes globally. The aim of this study was to establish conservation projections for the whole of the Irrawaddy River system, based on fish diversity patterns, human impact, and environmental change.
2. The Irrawaddy River is one of the five largest rivers in Southeast Asia. Although it has very high diversity of fish species and species endemism, our understanding of resident fish status remains poor.
3. Based on 1,726 field survey and 1,056 database records, 470 fish species and their distribution patterns (i.e. alpha, beta, threatened species, and endemic species diversities) in sub-basins of the Irrawaddy drainage were identified. Canonical correspondence analysis of diversity and environmental patterns indicated that climatic factors had the largest effect on diversity, compatible with the species–energy theory.
4. Fish conservation priorities of sub-basins were evaluated based on diversity patterns and human impact. The delta and Manipur basin regions were highlighted as areas of focus for future fish diversity conservation, and the importance of connectivity in the Irrawaddy main stem was demonstrated.
5. The results of this study will be valuable for future management of the Irrawaddy basin and as a reference for other river basins when implementing protection strategies for fish diversity. This study also advocates the need for systematic investigations across entire drainage basins and further detailed studies on the ecological conditions of poorly studied river systems.

     

Larval and early juvenile fish dynamics in main channel and backwater lake habitats of the Illinois River ecosystem

The spatial and temporal complexity of large river ecosystems likely promotes biological diversity within riverine larval fish assemblages. However, the focus of most previous riverine studies of larval fish distribution has tended to concentrate mainly on backwater habitats. There has been less focus on the value of the main channel for larval fishes. We sampled two habitats types (three main channel sites and three backwater lakes) along 20 km of the Illinois River ecosystem during 2 years to compare the larval fish distribution along both spatial and environmental gradients between these habitats. Across the 2 years of this study, we found similar trends in the spatial and temporal distribution of larval fish, although there were some differences in densities between years. The relative abundance and size of many of the different fish taxa varied among habitats. Centrarchids, clupeids, poeciliids, cyprinids (excluding common carp) and atherinids were more abundant within backwater lake habitat. In contrast, common carp (Cyprinus carpio), sciaenids, moronids and catostomids were more abundant in main channel habitats. Furthermore, sciaenid and clupeid larvae captured in the backwater lake habitat were larger as the season progressed than those captured in the main channel. Our study suggests that larval fish show habitat specialisation, similar to adults, indicating that both the backwater lakes and the main channel are both important for larval fish and preserving the diversity of the fish assemblages in large floodplain rivers.     

Changes in distance decay relationships after river regulation: similarity among fish assemblages in a large Amazonian river

The construction of large dams has changed natural hydrology of many rivers in South America. Considering that little is known about the reorganisation of nonmigratory fish assemblages following an impoundment, we investigated changes caused by the construction of Lajeado Dam on the spatial distribution of nonmigratory fish along the Tocantins River, a large Amazonian river. In particular, we investigated changes in distance decay of community similarity (initial similarity and halving distance) in periods that preceded and followed the construction of the dam. For this study, we analysed data collected over a four‐year period, including seven sites distributed along the Tocantins River (~270 km). Initial similarity showed high values and little variation over the years. Halving distance, on the other hand, changed considerably after impoundment, showing progressive smaller values. In the first 2 years after impoundment, halving distance decreased by more than half of the initial value, indicating changes in distance decay relationships. An ordination analysis nonmetric multidimensional scaling (NMDS) indicated substantial changes in assemblage structure between pre‐ and postimpoundment periods, especially in sites close to the dam. In addition, after river regulation, we recorded shifts in species abundance across sites, while numerical dominance increased and local richness decreased in sites near the dam. Our results indicate that the dam changed diversity gradients along the river corridor, increasing the distance decay of assemblage similarity. All these findings evidence that nonmigratory fish assemblages are particularly vulnerable to river regulation.     

Consequences of connectivity alteration on riverine fish assemblages: potential opportunities to overcome constraints in applying conventional monitoring designs

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