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38 results for “riverscape”
F I G U R E 3 in Riverscape genetics of the orangethroat darter complex
F I G U R E 3 Orangethroat darter clade collection sites with colored circles corresponding to the proportion of individuals at the site that had predominant assignment to each genetic cluster identified in the STRUCTURE analysis for K=3. Inset shows region boundary between Upper Mississippi River and Ohio River regions.
F I G U R E 7 in Riverscape genetics of the orangethroat darter complex
F I G U R E 7 Principle component analysis (PCA) of Ceasia showing distribution of samples taken from glaciated, unglaciated, or the one basin that had both glaciated and unglaciated sampling sites ("Mix").
F I G U R E 8 in Riverscape genetics of the orangethroat darter complex
F I G U R E 8 FST isolation by distance plots. Segregation of allele frequencies is shown between pairs of basins v. geographic (river/land) distance. (a, b). All basin pairs in this study with comparisons within regions shown in black and between regions in gray for overland distance (a) and river distance (b). (c, d). Within region site comparisons, grouped by regions for overland distance (c) and river distance (d). The Tennessee River and Great Lakes regions were omitted because one basin was sampled in each region.
F I G U R E 1 in Riverscape genetics of the orangethroat darter complex
F I G U R E 1 Approximate collection sites of orangethroat species complex specimens used in this study. Colors indicate species. Numbers and region names correspond to USGS HUC2 watershed designations. Inset shows regional boundary between Upper Mississippi River and Ohio River regions.
F I G U R E 2 in Riverscape genetics of the orangethroat darter complex
F I G U R E 2 Results from STRUCTURE for (a) K = 3 and (b) K = 8. Each color corresponds to a distinct genetic cluster, and each bar represents an individual's assigned ancestry to each cluster. Names above chart correspond to river basin (HUC6). EB—E. burri, EP—E. pulchellum, ES— E. spectabile, and EU—E. uniporum. Glaciated and unglaciated correspond to areas that were/were not covered in ice during the last glacial maximum.
F I G U R E 4 Assigned ancestry plot using AIC criteria determining optimal K in Riverscape genetics of the orangethroat darter complex
F I G U R E 4 Assigned ancestry plot using AIC criteria determining optimal K of 5. Each color corresponds to a distinct genetic cluster, and each bar represents an individual's assigned ancestry to each cluster. Names above chart correspond to river basin (HUC6). EB—E. burri, EP— E. pulchellum, ES—E. spectabile, and EU—E. uniporum. Glaciated and unglaciated correspond to areas that were/were not covered in ice during the last glacial maximum.
F I G U R E 6 in Riverscape genetics of the orangethroat darter complex
F I G U R E 6 Principle component analysis (PCA) of Ceasia. Name indicates the basin where samples were collected.
F I G U R E 5 in Riverscape genetics of the orangethroat darter complex
F I G U R E 5 Cluster assignments at sampling locations under the AIC method and a K=5. Pie graphs represent proportion of individuals at the site assigned to a given cluster. Individuals with less than 85% assigned ancestry in either cluster are shown in gray.
Riverscape heterogeneity in estimated Chinook Salmon emergence phenology and implications for size and growth
<p>Many salmonid-bearing rivers exhibit thermal and hydrologic heterogeneity at multiple spatial and temporal scales, but how this translates into spatiotemporal patterns of fry emergence is poorly understood. Understanding this variability is important because emergence timing determines the biophysical conditions fish first experience (e.g., temperature, flow, food supply), thereby influencing growth opportunities and survival during this critical life stage. We predicted spring Chinook Salmon (<em>Oncorhynchus tshawytscha</em>) emergence phenology across four NE Oregon subbasins over 5-9 years using empirical spawning and temperature data. We then related inter-annual emergence timing estimates to juvenile salmon size and growth rates at consistent sampling locations. There were clear longitudinal patterns of predicted emergence timing in each subbasin: the shape of these patterns was consistent among years, but not among subbasins. In two subbasins emergence occurred progressively later with distance upstream, whereas in the other two subbasins emergence was earliest at upstream sites. Within each year, median emergence dates among sites within each subbasin ranged between 44 and 58 days. This spatial variation was comparable to inter-annual variation, with median emergence dates for a given location in each subbasin ranging between 47 to 74 days among years. Contrary to our expectations, juvenile salmon were not larger in years with earlier emergence, owing to slower spring and summer growth rates compared to years with later emergence. Despite large inter-annual variation in emergence dates, these results suggest that other factors (e.g., stream flow, temperature, density-dependence) were more important than growth duration in determining juvenile salmon growth rates and size among years. We demonstrated considerable spatial and inter-annual variation in emergence phenology within these subbasins. Understanding how this variation translates to spatiotemporal patterns of juvenile salmon habitat use, growth, and survival has important implications for guiding restoration efforts and understanding how climate change may impact these populations.</p>
Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
<p><span>Spatial patterns in genetic variation compared across species provide information about the predictability of genetic diversity of natural populations and areas requiring conservation measures. Due to their remarkable fish diversity, rivers in Neotropical regions are ideal systems to confront theory with observations and would benefit greatly from such approaches given their increasing vulnerability to anthropogenic pressures. We used SNP data from 18 fish species with contrasting life-history traits, co-sampled across 12 sites in the Maroni – a major river system from the Guiana Shield – to compare patterns of intraspecific genetic variation and identify their underlying drivers. Analyses of covariance revealed a decrease in genetic diversity as distance from the river outlet increased for 5 of the 18 species, illustrating a pattern commonly observed in riverscapes for species with low-to-medium dispersal abilities. However, mean within-site genetic diversity was lowest in the two easternmost tributaries of the Upper Maroni and around an urbanized location downstream, indicating the need to address the potential influence of local pressures in these areas, such as goldmining or fishing. Finally, the relative influence of isolation by stream distance, isolation by discontinuous river flow and isolation by spatial heterogeneity in effective size on pairwise genetic differentiation varied across species. Species with similar dispersal and reproductive guilds did not necessarily display shared patterns of population structure. Increasing the knowledge of specific life history traits and ecological requirements of fish species in these remote areas should help further understand factors that influence their current patterns of genetic variation.</span></p>
Genotype and genetic diversity data for: Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value
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Data from: Inferring riverscape dispersal processes from fish biodiversity patterns
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Riverscape genetics of non-native Brook Trout to inform native Cutthroat Trout conservation
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Unnatural selection of salmon life histories in a modified riverscape
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Data from: Assessing short- and long-term anthropogenic threats to a reintroduced fish in a restored urban riverscape
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Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability
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Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish
Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps, and geological faults. The morphological (color pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses, and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within rivers systems and, consequently, the dynamics of gene flow between freshwater lineages/species.
Data from: Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype
<p><span><span>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 </span><span><span>European </span></span><span>brook lamprey (</span><i><span><span>Lampetra planeri</span></span></i><span>) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) a </span><span><span>positive effect of</span></span><span> admixture with the closely related anadromous</span><span><span> river lamprey</span></span><span> (</span><i><span><span>L. fluviatilis</span></span></i><i><span><span>)</span></span></i><span> ecotype on </span><i><span><span>L. planeri</span></span></i><span> genetic diversity. We genotyped 2472 individuals, including 225 </span><i><span><span>L. fluviatilis</span></span></i><span>, sampled </span><span><span>from</span></span><span> 81 sites upstream and downstream barriers to migration, in 29 </span><span><span>western </span></span><span>European rivers. Linear modelling revealed a strong positive relationship between </span><span><span>genetic diversity and</span></span><span> the distance </span><span><span>from </span></span><span><span>the</span></span><span><span> river</span></span><span> 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 </span><span><span>mediated by</span></span><span> water flow. Downstream </span><i><span><span>L. planeri </span></span></i><span>populations in sympatry with </span><i><span><span>L. fluviatilis </span></span></i><span>displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow drive the genetic </span><span><span>make-</span></span><span>up of upstream </span><i><span><span>L. planeri </span></span></i><span>populations</span><i><span> </span></i><span>whereas admixture between ecotypes maintains higher levels of genetic diversity in </span><i><span><span>L. planeri </span></span></i><span>populations</span><i><span> </span></i><span>sympatric</span><i><span> </span></i><span>with </span><i><span><span>L. fluviatilis</span></span></i><span>. 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. </span></span></p>
Data from: Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone
Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection.
Data from: Stream hierarchy defines riverscape genetics of a North American desert fish
Global climate change is apparent within the Arctic and the south-western deserts of North America, with record drought in the latter reflected within 640 000 km2 of the Colorado River Basin. To discern the manner by which natural and anthropogenic drivers have compressed Basin-wide fish biodiversity, and to establish a baseline for future climate effects, the Stream Hierarchy Model (SHM) was employed to juxtapose fluvial topography against molecular diversities of 1092 Bluehead Sucker (Catostomus discobolus). MtDNA revealed three geomorphically defined evolutionarily significant units (ESUs): Bonneville Basin, upper Little Colorado River and the remaining Colorado River Basin. Microsatellite analyses (16 loci) reinforced distinctiveness of the Bonneville Basin and upper Little Colorado River, but subdivided the Colorado River Basin into seven management units (MUs). One represents a cline of three admixed gene pools comprising the mainstem and its lower-gradient tributaries. Six others are not only distinct genetically but also demographically (i.e. migrants/generation <9.7%). Two of these (i.e. Grand Canyon and Canyon de Chelly) are defined by geomorphology, two others (i.e. Fremont-Muddy and San Raphael rivers) are isolated by sharp declivities as they drop precipitously from the west slope into the mainstem Colorado/Green rivers, another represents an isolated impoundment (i.e. Ringdahl Reservoir), while the last corresponds to a recognized subspecies (i.e. Zuni River, NM). Historical legacies of endemic fishes (ESUs) and their evolutionary potential (MUs) are clearly represented in our data, yet their arbiter will be the unrelenting natural and anthropogenic water depletions that will precipitate yet another conservation conflict within this unique but arid region.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.