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155 results for “Range Structure”
Quantifying range structure to inform management in invaded landscapes - Dataset
<p>This data set was collected in Table Mountain National Park, South Africa and comprises count and location data for invasive woody plant species for the genera <em>Acacia</em>, <em>Pinus,</em> and <em>Eucalyptus</em>. The data were collected between 2013 and 2015 and span 10 058 sample plots, uniformly distributed across the protected area. Further details of the dataset are provided in the attached meta-data document.</p>
Data from: Landscape resistance and habitat combine to provide an optimal model of genetic structure and connectivity at the range margin of a small mammal
We evaluated the effect of habitat and landscape characteristics on the population genetic structure of the white-footed mouse. We develop a new approach that uses numerical optimization to define a model that combines site differences and landscape resistance to explain the genetic differentiation between mouse populations inhabiting forest patches in southern Québec. We used ecological distance computed from resistance surfaces with Circuitscape to infer the effect of the landscape matrix on gene flow. We calculated site differences using a site index of habitat characteristics. A model that combined site differences and resistance distances explained a high proportion of the variance in genetic differentiation and outperformed models that used geographical distance alone. Urban and agriculture related land uses were, respectively, the most and the least resistant landscape features influencing gene flow. Our method detected the effect of rivers and highways as highly resistant linear barriers. The density of grass and shrubs on the ground best explained the variation in the site index of habitat characteristics. Our model indicates that movement of white-footed mouse in this region is constrained along routes of low resistance. Our approach can generate models that may improve predictions of future northward range expansion of this small mammal.
Data from: Genetic structure of Pacific trout at the extreme southern end of their native range
Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus Oncorhynchus are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately also facing threats to their continued existence. Previous work has described one endemic species, the Mexican golden trout (O. chrysogaster), and one endemic subspecies, Nelson's trout (O. mykiss nelsoni), in Mexico, but previous work indicated that there is vastly more biodiversity in this group than formally described. Here we conducted a comprehensive genetic analysis of this important group of fishes using novel genetic markers and techniques to elucidate the biodiversity of trout inhabiting northwestern Mexico, examine genetic population structure of Mexican trout and their relationships to other species of Pacific trout, and measure introgression from non-native hatchery rainbow trout. We confirmed substantial genetic diversity and extremely strong genetic differentiation present in the Mexican trout complex, not only between basins but also between some locations within basins, with at least four species-level taxa present. We also revealed significant divergence between Mexican trout and other trout species and found that introgression from non-native rainbow trout is present but limited, and that the genetic integrity of native trout is still maintained in most locations. This information will help to guide effective conservation strategies for this important group of fishes.
Data from: Range-wide population genetic structure of the Caribbean sea fan coral, Gorgonia ventalina
The population structure of benthic marine organisms is of central relevance for the conservation and management of these often threatened species as well as an accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow strong general inferences. Here we describe the range-wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically-modeled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometers, estimated dispersal is low, and populations can be differentiated across distances <2km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks identified in other taxa (e.g. an east/west divide near Puerto Rico) and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). Across the range, diversity was positively correlated with latitude, consistent with a source/sink dynamic driven by ocean currents. High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.
Data from: Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: implications for conservation plans in the Eastern Adriatic Sea
Aim: Understanding how historical and contemporary processes shaped and maintain spatial patterns of genetic diversity is a major goal for conservation biologists. Here, we characterized the pattern of neutral genetic diversity and we inferred underlying processes in the habitat-forming octocoral Paramuricea clavata in the Adriatic Sea, a peculiar phylogeographic region of the Mediterranean Sea. Location: Eastern coast of the Adriatic Sea. Methods: We genotyped seven microsatellites in 454 individuals of P. clavata from 13 populations recolonized after the last glacial maximum (LGM). We estimated the levels of contemporary connectivity and genetic drift and we reconstructed the demographic history of these populations. Results: The pattern of spatial genetic structure resulted from the combination of hierarchical genetic clusters and isolation by distance (IBD). A significant decrease in genetic diversity and an increase of the frequencies of individual alleles likely due to allele surfing from the south to the north of the area were observed as expected after a postglacial sequential recolonization. Based on maximum likelihood analyses, the foundation of these populations was not linked to dramatic change in population size. Main conclusion: Oceanographic barriers to gene flow combined to the restricted dispersal of P. clavata likely maintain the hierarchical structure and the IBD pattern. We suggest that the latitudinal genetic gradient results from a northward 'serial founder events' recolonization. By integrating patterns and processes, we bridge the gap between the evolutionary and the conservation biology of P. clavata, providing management guidelines, which will benefit the associated coralligenous biodiversity.
Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography
Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure, and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analyzed 10 microsatellite loci from over 1,900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation, and management.
Data from: Consequences of multiple mating-system shifts for population and range-wide genetic structure in a coastal dune plant
Evolutionary transitions from outcrossing to selfing can strongly affect the genetic diversity and structure of species at multiple spatial scales. We investigated the genetic consequences of mating system shifts in the North American, Pacific coast dune endemic plant Camissoniopsis cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and six chloroplast (cp) microsatellite (SSR) loci for 38 populations across the species range. As predicted from the expected reduction of effective population size (Ne) caused by selfing, small-flowered, predominantly selfing (SF) populations had much lower nSSR diversity (but not cpSSR) than large flowered, predominantly outcrossing (LF) populations. The reduction of nSSR diversity was greater than expected from the effects of selfing on Ne alone, but could not be accounted for by indirect effects of selfing on population density. Although selfing should reduce gene flow, SF populations were not more genetically differentiated than LF populations. We detected five clusters of nSSR genotypes and three groups of cpSSR haplotypes across the species range consisting of parapatric groups of populations that usually (but not always) differed in mating system, suggesting that selfing may often initiate ecogeographic isolation. However, lineage-wide genetic variation was not lower for selfing clusters, failing to support the hypothesis that selection for reproductive assurance spurred the evolution of selfing in this species. Within three populations where LF and SF plants coexist we detected genetic differentiation among diverged floral phenotypes suggesting that reproductive isolation (probably postzygotic) may help maintain the striking mating system differentiation observed across the range of this species
Data from: Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis
Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis-a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in 2 dimensions over a 50x80 Km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influ ence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs. food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared to the surrounding food-crop plantation populations. Analysis of molecular variance (AMOVA) indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.
Data from: Effects of contemporary shifts of range margins on patterns of genetic structure and mating system in two coastal plant species
Species' geographical ranges are often restricted due to niche limitation resulting in geographical isolation and reduced population size at range margins. Under the 'abundant center' paradigm, static marginal populations are thus expected to show higher genetic differentiation and lower genetic diversity than core populations. Low mate availability may also drive shifts towards higher propensity for selfing in geographically marginal populations. However, these predictions remain to be validated for contemporary range shifts occurring under current environmental change. This study is devoted to bridging this gap and assesses the spatial patterns of genetic structure and mating system across the geographical range of two coastal plant species characterized by contrasting contemporary range dynamics: the receding myrmecochorous Dune pansy (Viola tricolor subsp. curtisii) and the widespread expanding hydrochorous Rock samphire (Crithmum maritimum) Both species exhibited high propensity for selfing, with indications of inbreeding depression acting at early life stages. In Dune pansy, a biogeographical break was observed between core and marginal populations, with trailing-edge populations showing higher levels of genetic differentiation, reduced genetic diversity and higher levels of selfing estimated through progeny arrays. In contrast, genetic structuring was weak in Rock samphire and no clear spatial trends were observed in genetic diversity nor in mating system, likely the result of efficient long-distance seed dispersal by sea-surface currents. Our study highlights that key species differences in life-history traits related to dispersal and/or mate limitation modify the expectations of genetic diversity loss and mating system shift in contemporary range-expanding populations, as compared to historical core populations.
Data from: Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America
Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n=17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.
Data from: Range‐wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum
Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtlegrass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtlegrass has been documented to have long distance dispersal via floating fruits and also extreme clonality and longevity. We hypothesise that across its range, Thalassia testudinum will have very limited regional population structure due to these characteristics and under typical models of population structure would expect to detect high levels of genetic connectivity. There are very few studies of range-wide genetic connectivity documented for seagrasses or other sessile marine species. This study presents a population genetic data set that represents a geographic area exceeding 14,000 km2. Population genetic diversity was evaluated from 32 Thalassia testudinum populations sampled across the Caribbean and Gulf of Mexico. Genotypes were based on nine microsatellites and haplotypes were based on chloroplast DNA sequences. Very limited phylogeographic signal from cpDNA reduced the potential comparative analyses possible. Multiple analytical clustering approaches on population genetic data revealed two significant genetic partitions: 1) The Caribbean, and 2) The Gulf of Mexico. Genetic diversity was high (HE = 0.641) and Isolation by Distance was significant, gene flow and migration estimates across the entire range were however modest, we suggest that the frequency of successful recruitment across the range is uncommon. Thalassia testudinum maintains genetic diversity across its entire distribution range. The genetic split may be explained by genetic drift during recolonsation from refugia following relatively recent reduction in available habitat such as the last glacial maxima.
FIGURE 3 in A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,), including consideration of mitochondrial phylogeographic structuring
FIGURE 3. Female spermathecae, viewed ventrally: A) MY1013 (CASENT9039431) paratype female, Carmel Valley Road (site 18), B) MY1326, Laureles Grade Road (site 13), C) MY374, Jack's Peak County Park (site 12), D) MY955, W of Pinnacles NM (site 8), E) MY3059, Palo Colorado Road (site 15), F) MY4194, Harlan Mtn Road (site 5), G) MY4362, Hidden Valley Road (site 1), H) MY1645, Coalinga Road (site 10), I) MY1642, Lonoak Road (site 11), J) MY829, E of Santa Margarita (site 22), K) MY1010, S of Gorda (site 20), L) MY2671, Kanan Dume Road (site 24). Colored dots correspond to genetic groups of Fig. 5. Site numbers correspond to Table 1 and Fig. 1C. Scale bar = 0.5 mm.
FIGURE 2 in A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,), including consideration of mitochondrial phylogeographic structuring
FIGURE 2. Male holotype, MY999 (CASENT9039430), W of Arroyo Center (site 19): A) carapace and abdomen, viewed dorsally, B) left pedipalp, viewed retrolaterally, C) left leg I, viewed retrolaterally, D) sternum and chelicerae, viewed ventrally, E) palpal bulb, viewed ventrally. Scale bar A–D = 1 mm, E = 0.5 mm.
FIGURE 1. A in A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,), including consideration of mitochondrial phylogeographic structuring
FIGURE 1. A) Adult female Aliatypus coylei (MY4194), Harlan Mountain Road, Gabilan Range, San Benito County; B) Aliatypus trapdoor, Harlan Mountain Road, Gabilan Range, San Benito County; C) Known distribution of Aliatypus coylei. Site numbers correspond to Table 1; some geographically adjacent sites are represented by a single white circle. Regional records of other Aliatypus species as follows: red dots = A. janus, blue dots = A. torridus (records from Coyle 1974, Coye & Icenogle 1994; Satler et al. in review; personal observations). San Luc = Santa Lucia Range, Gab = Gabilan Range, Diablo = Diablo Range.
FIGURE 5. A in A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,), including consideration of mitochondrial phylogeographic structuring
FIGURE 5. A) Majority-rule consensus phylogram resulting from partitioned Bayesian analysis. Aliatypus coylei haplotypes are labeled with specimen number, location abbreviation, and site number (corresponding to Fig. 1). Posterior probability values are shown for both partitioned (above branches) and unpartitioned (below branches) analyses. Samples with morphological images included in Figs 3 and 4 are highlighted. B) Geographic distribution of haplotype groupings. Site numbers correspond to Fig. 1.
FIGURE 4 in A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,), including consideration of mitochondrial phylogeographic structuring
FIGURE 4. Female sternal sigilla, viewed ventrally: A) paratype female, MY1013, Carmel Valley Road (site 18), B) MY374, Jack's Peak County Park (site 12), C) MY2671, Kanan Dume Road (site 24), D) MY4194, Harlan Mtn Road (site 5), E) MY1642, Lonoak Road (site 11) F) MY829, E of Santa Margarita (site 22). Colored dots correspond to genetic groups of Fig. 5. Site numbers correspond to Table 1 and Fig. 1C. Scale bar = 1 mm.
Wide-range viscoelastic compression forces in microfluidics to probe cell-dependent nuclear structural and mechanobiological responses
<p><span>The cell nucleus plays a critical role in mechanosensing and mechanotransduction processes, by adaptive changes of its envelope composition to external biophysical stimuli such as substrate rigidity and tensile forces. Current measurement approaches lack of precise control in stress application on nuclei, thus significantly impairing a complete mechanobiological study of cells. Here, we present a contactless microfluidic approach capable to exert a wide-range of viscoelastic compression forces (10-103 </span>μ<span>N) -as an alternative to adhesion-related techniques- to induce cell-specific mechano-structural and biomolecular changes. We succeed in monitoring substantial nuclear modifications in Lamin A/C expression and coverage, diffusion processes of probing molecules, YAP shuttling, chromatin re-organization and cGAS pathway activation. As a result, high compression forces lead to a nuclear reinforcement (e.g. up to +20% in Lamin A/C coverage) or deconstruction (e.g. down to -45% in Lamin A/C coverage with a 30% reduction of chromatin condensation state parameter) up to cell death. We demonstrate how wide-range compression on suspended cells can be used as a tool to investigate nuclear mechanobiology and to define specific nuclear signatures for cell mechanical phenotyping. </span></p>
Supplementary material 4 from: Boenigk J, Wodniok S, Bock C, Beisser D, Hempel C, Grossmann L, Lange A, Jensen M (2018) Geographic distance and mountain ranges structure freshwater protist communities on a European scalе. Metabarcoding and Metagenomics 2: e21519. https://doi.org/10.3897/mbmg.2.21519
Richness is shown for different elevations. The number of lakes within this elevation range is indicated. While mean richness ranges around 750 OTUs it drops to around 400 OTUs at high elevations. The transition seems to be around or slightly below 1400m.
FIG. 4 in Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge
FIG. 4. Analysis of global structure along the river corridor from the first principal component of the sPCA represented by (A) interpolation of lagged principal scores showing genetic clines and (B) colors indicating individual scores. Coordinates have been deliberately omitted to deter poachers.
FIG. 3 in Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge
FIG. 3. Bubble plot showing the results of two-dimensional local spatial autocorrelation analysis for all Eastern Box Turtles (n ¼ 165) sampled in northwestern Michigan. Circles represent individuals and the size of the circle is proportional to the P-values from permutation testing, with large circles representing individuals that are significantly more related to their five nearest neighbors than expected (P, 0.05) based on a random distribution of genotypes. Figure shows the distribution of five genetic ''hotspots'' in relation to known nesting sites (NS) across the study area. Some distantly sampled individuals are omitted for figure clarity.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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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
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