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2,721 results for “Connectivity”
Data from: Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data
Grey reef sharks (Carcharhinus amblyrhynchos) can be one of the numerically dominant high order predators on pristine coral reefs, yet their numbers have declined even in the highly regulated Australian Great Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine scale genetic connectivity of grey reef sharks is essential for their effective management, but no genetic data are yet available. We investigated grey reef shark genetic structure in the GBR across a 1200 km latitudinal gradient, comparing empirical data with models simulating different levels of migration. The empirical data did not reveal any genetic structuring along the entire latitudinal gradient sampled, suggesting regular widespread dispersal and gene flow of the species throughout most of the GBR. Our simulated datasets indicate that even with substantial migrations (up to 25% of individuals migrating between neighboring reefs) both large scale genetic structure and genotypic spatial autocorrelation at the reef scale were maintained. We suggest that present migration rates therefore exceed this level. These findings have important implications regarding the effectiveness of networks of spatially discontinuous Marine Protected Areas to protect reef sharks.
Data from: On-shelf larval retention limits population connectivity in a coastal broadcast spawner
Broadcast-spawning marine organisms with long pelagic larval duration are often expected to be genetically homogeneous throughout their ranges. When genetic structure is found in such taxa, it may be in the form of chaotic genetic patchiness: i.e. patterns that might seem independent of any underlying environmental variation. The joint analysis of population genetic data and marine environmental data can elucidate factors driving such spatial genetic diversity patterns. Using meso-scale sampling (at a scale of 10s to 100s of km), microsatellite data and advection connectivity simulations, we studied the effect of temperate southern Australian ocean circulation on the genetic structure of the snail Nerita atramentosa. This species has a long pelagic larval duration and is represented as a single metapopulation throughout its ~3000 km range, but even so, we found that its dispersal potential is lower than expected. Connectivity simulations indicate that this is a result of the larvae that remain on the continental shelf (where currents are erratic and often shoreward) returning to the coast in much larger numbers than larvae that become entrained in the region's shelf-edge boundary currents. Our study contributes to the growing evidence that departures from the expectations of panmixia along continuous and environmentally homogeneous coastlines are not limited to low-dispersal species, and it identifies on-shelf larval retention as an important factor limiting dispersal.
Data from: One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan
Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive FIS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise FST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.
Data from: Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, i.e. the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic datasets to investigate the efficiency of an individual-based sampling scheme (ISS) in detecting isolation-by-distance and isolation-by-barrier patterns. Provided that pseudo-replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of inter-individual measures of genotypic dissimilarity may efficiently replace inter-population measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.
Data from: Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic
Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation of Mytilus mussels in the European Arctic. Mytilus edulis was the most abundant species found with a clear genetic split between populations in Greenland and the Eastern Atlantic. Surprisingly, analyses revealed the presence of M. trossulus in high Arctic NW Greenland (77°N) and M. galloprovincialis or their hybrids in SW Greenland, Svalbard and the Pechora Sea. Furthermore, a high degree of hybridization and introgression between species was observed. Our study highlights the importance of distinguishing between congener species, which can display local adaptation and suggests that information on dispersal routes and barriers are essential for accurate predictions of regional susceptibility to range expansions or invasions of boreal species in the Arctic.
Data from: Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum)
Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multi-scale analysis to determine how landscape composition, configuration, and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side-by-side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analyzed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavorable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results, and shows how multi-scale analyses provide insight to scale-dependent processes.
Data from: Mountain metacommunities: climate and spatial connectivity shape ant diversity in a complex landscape
Understanding what drives biodiversity patterns across scales is the central goal of ecology. Both environmental gradients and spatial landscape structure have been found to be important factors influencing species distributions and community composition, and partly reflect the balance of underlying deterministic and stochastic community processes. In some systems, environmental gradients and spatial connectivity are intertwined in that steep environmental gradients serve as boundaries on species movements and impose environment-derived complex spatial structure to metacommunities. Mountainous landscapes are prime examples of this, and recent theory has linked principles of geomorphology, environmental gradients, and spatial structure to make predictions for resulting community patterns. In this context, we examine variation in taxonomic and phylogenetic ant diversity patterns along a geographic transect spanning >5000 m in elevational range in the Hengduan mountains of southern China. We found that environmental gradients dominate variation in both alpha and beta diversity in this landscape, with alpha diversity strongly declining with elevation and beta diversity driven by elevational differences. However, within an elevational band spatial connectivity predicts beta diversity better than geographic distance. Our findings deviate from theoretical predictions in several ways, notably alpha diversity is monotonically declining and within-band beta diversity is invariant with increasing elevation. The discrepancies between theory and observation may be explained by differences in the Hengduan landscape from idealized fluvial landscapes, such as a lack of a mid-elevation peak in connectivity, as well as evolutionary limits on the source pool of species available to populate metacommunities at different elevations. The latter is supported by variation in phylogenetic community structure with elevation. Our results demonstrate the power of conceptual, statistical, and theoretical frameworks that integrate the roles of environment and spatial structure in metacommunities, but that additional work is needed to bridge the gap between abstract theory and real systems.
Data from: High connectivity across the fragmented chemosynthetic ecosystems of the deep Atlantic Equatorial Belt: efficient dispersal mechanisms or questionable endemism?
Chemosynthetic ecosystems are distributed worldwide in fragmented habitats harbouring seemingly highly specialized communities. Yet, shared taxa have been reported from highly distant chemosynthetic communities. These habitats are distributed in distinct biogeographical regions, one of these being the so-called Atlantic Equatorial Belt (AEB). Here, we combined genetic data (COI) from several taxa to assess the possible existence of cryptic or synonymous species and to detect the possible occurrence of contemporary gene flow among populations of chemosynthetic species located on both sides of the Atlantic. Several Evolutionary Significant Units (ESUs) of Alvinocarididae shrimp and Vesicomyidae bivalves were found to be shared across seeps of the AEB. Some were also common to hydrothermal vent communities of the Mid-Atlantic Ridge (MAR), encompassing taxa morphologically described as distinct species or even genera. The hypothesis of current or very recent large-scale gene flow among seeps and vents was supported by microsatellite analysis of the shrimp species Alvinocaris muricola/Alvinocaris markensis across the AEB and MAR. Two nonmutually exclusive hypotheses may explain these findings. The dispersion of larvae or adults following strong deep-sea currents, possibly combined with biochemical cues influencing the duration of larval development and timing of metamorphosis, may result in large-scale effective migration among distant spots scattered on the oceanic seafloor. Alternatively, these results may arise from the prevailing lack of knowledge on the ocean seabed, apart from emblematic ecosystems (chemosynthetic ecosystems, coral reefs or seamounts), where the widespread classification of endemism associated with many chemosynthetic taxa might hide wider distributions in overlooked parts of the deep sea.
Data from: Fractured genetic connectivity threatens a southern California puma (Puma concolor) population
Pumas (Puma concolor; also known as mountain lions and cougars) in southern California live among a burgeoning human population of roughly 20 million people. Yet little is known of the consequences of attendant habitat loss and fragmentation, and human-caused puma mortality to puma population viability and genetic diversity. We examined genetic status of pumas in coastal mountains within the Peninsular Ranges south of Los Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana Mountains are bounded by urbanization to the west, north, and east, and are separated from the eastern Peninsular Ranges to the southeast by a ten lane interstate highway (I-15). We analyzed DNA samples from 97 pumas sampled between 2001 and 2012. Genotypic data for forty-six microsatellite loci revealed that pumas sampled in the Santa Ana Mountains (n = 42) displayed lower genetic diversity than pumas from nearly every other region in California tested (n = 257), including those living in the Peninsular Ranges immediately to the east across I-15 (n = 55). Santa Ana Mountains pumas had high average pairwise relatedness, high individual internal relatedness, a low estimated effective population size, and strong evidence of a bottleneck and isolation from other populations in California. These and ecological findings provide clear evidence that Santa Ana Mountains pumas have been experiencing genetic impacts related to barriers to gene flow, and are a warning signal to wildlife managers and land use planners that mitigation efforts will be needed to stem further genetic and demographic decay in the Santa Ana Mountains puma population.
Data from: Loss of connectivity among island-dwelling Peary caribou following sea ice decline
Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both continental and Peary caribou, even after accounting for the possible effect of sea surface. Sea ice has thus been an effective corridor for Peary caribou, promoting inter-island connectivity and population mixing. Using a time series of remote sensing sea-ice data, we show that landscape resistance in the Canadian Arctic Archipelago has increased by approximately 15% since 1979 and may further increase by 20–77% by 2086 under a high-emission scenario (RCP8.5). Under the persistent increase in greenhouse gas concentrations, reduced connectivity may isolate island-dwelling caribou with potentially significant consequences for population viability.
Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria
An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. In order to test this hypothesis we assessed genetic diversity and structure in populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30 km. Almost all genetic variation was due to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5–10 m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.
Data from: A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii
Seagrass cover has declined in many areas of the world in a trend that has accelerated over the past several decades. This raises concern for both the impact the decline in cover has on coastal ecosystems and the effect it may have on seagrass evolutionary potential, as genotypic and genomic variation is lost. We used 8 microsatellite loci to investigate genetic diversity, structure, and connectivity in the seagrass Halodule wrightii from the Gulf of Mexico (Texas, USA) and western Atlantic (Bermuda). We examined how estimates correlated with changes in H. wrightii abundance and distribution on the Texas Gulf coast over the past 50 yr. Results show that, compared to other species, H. wrightii from this region exhibits variable clonal diversity (R = 0.02-0.81), moderate allelic diversity (mean AR = 4.09), and relatively high heterozygosity (mean He = 0.56). The patterns of genetic diversity and structure, however, do not entirely coincide with either geography or recent historical trends in seagrass distribution in this region. Results from a basin in which seagrasses have recently been expanding were consistent with expectations, as they were for an isolated site near the limit of H. wrightii's range. Results from basins in which seagrasses have been experiencing decline and/or fragmentation, however, were mixed. Genetic structure on the Texas coast was relatively weak and coincided more strongly with tidal range than with geographic barriers or distance. Rapid expansion and the discovery of identical multi-locus genotypes at several sites raises the possibility of migration via drifting vegetative fragments, as the geographic distance among certain multi-locus genotypes cannot be explained by rhizome growth models.
Data from: Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park
Roads can fragment and isolate wildlife populations, which will eventually decrease genetic diversity within populations. Wildlife crossing structures may counteract these impacts, but most crossings are relatively new, and there is little evidence that they facilitate gene flow. We conducted a three-year research project in Banff National Park, Alberta, to evaluate the effectiveness of wildlife crossings to provide genetic connectivity. Our main objective was to determine how the Trans-Canada Highway and crossing structures along it affect gene flow in grizzly (Ursus arctos) and black bears (Ursus americanus). We compared genetic data generated from wildlife crossings with data collected from greater bear populations. We detected a genetic discontinuity at the highway in grizzly bears but not in black bears. We assigned grizzly bears that used crossings to populations north and south of the highway, providing evidence of bidirectional gene flow and genetic admixture. Parentage tests showed that 47% of black bears and 27% of grizzly bears that used crossings successfully bred, including multiple males and females of both species. Differentiating between dispersal and gene flow is difficult, but we documented gene flow by showing migration, reproduction and genetic admixture. We conclude that wildlife crossings allow sufficient gene flow to prevent genetic isolation.
Data from: Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest Gulf of Mexico: population genetics
While there are several areas containing shallow coral habitats in the Gulf of Mexico (GOM), the availability of suitable reef habitat at mesophotic depths (~30–150 m) along the continental shelf margin suggests the potential for ecologically connected coral populations across hundreds of kilometers in the northwest (NW) GOM. The NW GOM includes a relatively high proportion of mesophotic habitats, including salt diapirs in Flower Garden Banks National Marine Sanctuary (FGBNMS), Bright Bank, and McGrail Bank, the latter two being Habitat Areas of Particular Concern (HAPCs). In response to a proposed expansion plan for the sanctuary boundaries to include additional mesophotic banks in the NW GOM, we investigated the genetic connectivity of the depth-generalist coral Montastraea cavernosa, a ubiquitous member of scleractinian communities throughout the Tropical Western Atlantic. Montastraea cavernosa populations in the NW GOM demonstrated strong connectivity with relatively high levels of gene flow and no significant genetic differentiation occurring over banks up to 120 km apart. Historical migration models based on genetic data predicted panmixia of M. cavernosa across the NW GOM. The comparisons between genetic and biophysical models (see Garavelli et al., 2018; associate manuscript) highlight not only the importance of incorporating multiple assessments of connectivity into management schemes, but also the potentially stochastic nature of oceanographic patterns in the NW GOM and their effect on migration estimates among coral habitats. These trends indicate that M. cavernosa populations have remained well-connected in the NW GOM and that coral populations on each bank have likely been receiving larval recruitment through time. Thus, M. cavernosa populations should be managed as a combined unit within the NW GOM, which supports the proposal to expand the NMS boundaries to include mesophotic habitats beyond West and East FGB.
Data from: Population connectivity and phylogeography of a coastal fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current region: evidence of an ancient vicariant event.
Contemporary patterns of genetic diversity and population connectivity within species can be influenced by both historical and contemporary barriers to gene flow. In the marine environment, present day oceanographic features such as currents, fronts and upwelling systems can influence dispersal of eggs/larvae and/juveniles/adults, shaping population substructuring. The Benguela Current system in the southeastern Atlantic is one of the oldest upwelling systems in the world, and provides a unique opportunity to investigate the relative influence of contemporary and historical mechanisms shaping the evolutionary history of warm-temperate fish species. Using the genetic variation in the mitochondrial DNA Control Region and eight nuclear microsatellite DNA loci, we identified the presence of two highly divergent populations in a vagile and warm-temperate fish species, Atractoscion aequidens, across the Benguela region. The geographical distributions of the two populations, on either side of the perennial upwelling cell, suggest a strong correlation between the oceanographic features of the system and the breakdown of gene flow within this species. Genetic divergence (mtDNA φST = 0.902, microsatellite FST = 0.055: probability of genetic homogeneity for either marker = p<0.001), absence of migrants (less than 1% per generation) between populations and coalescent estimates of time since most recent common ancestor suggest that the establishment of the main oceanographic features of the system (2 million years ago), particularly the strengthening and position of the perennial upwelling cell, is the most likely mechanism behind the observed isolation. Concordance between mitochondrial and nuclear genetic markers indicates that isolation and divergence of the northern and southern Benguela populations of A. aequidens occurred deep in the past and has continued to the present day. These findings suggest that the Benguela Current system may constitute an ancient and impermeable barrier to gene flow for warm-temperate fish species.
Data from: Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander
Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.
Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds
Stable isotopes have been used to estimate migratory connectivity in many species. Estimates are often greatly improved when coupled with species distribution models (SDMs), which temper estimates in relation to occurrence. SDMs can be constructed using from point locality data from a variety of sources including extensive monitoring data typically collected by citizen scientists. However, one potential issue with SDM is that these data oven have sampling bias. To avoid this potential bias, an approach using SDMs based on marsh bird monitoring program data collected by citizen scientists and other participants following protocols specifically designed to maximize detections of species of interest at locations representative of the species range. We then used the SDMs to refine isotopic assignments of breeding areas of autumn-migrating and wintering Sora (Porzana carolina), Virginia Rails (Rallus limicola), and Yellow Rails (Coturnicops noveboracensis) based on feathers collected from individuals caught at various locations in the United States from Minnesota south to Louisiana and South Carolina. Sora were assigned to an area that included much of the western U.S. and prairie Canada, covering parts of the Pacific, Central, and Mississippi Flyways. Yellow Rails were assigned to a broad area along Hudson and James Bay in northern Manitoba and Ontario, as well as smaller parts of Quebec, Minnesota, Wisconsin, and Michigan, including parts of the Mississippi and Atlantic Flyways. Virginia Rails were from several discrete areas, including parts of Colorado, New Mexico, the central valley of California, and southern Saskatchewan and Manitoba in the Pacific and Central Flyways. Our study demonstrates extensive data from organized citizen science monitoring programs are especially useful for improving isotopic assignments of migratory connectivity in birds, which can ultimately lead to better informed management decisions and conservation actions.
Database file for Encyclopedia of Finite Graphs: Simple connected graphs, n<=10
<p>This initial release contains all simple connected graphs of order n<=10, and a collection of integer invariants. Up to order n<=6, there is a collection of "special" invariants that are stored in a custom table (see main project for details).</p>
[Dataset] enhanced functional connectivity properties of human brains during in-situ nature experience
<p>Raw data</p> <p>Artifact-free EEG raw data recorded by Emotiv Epoc (sample rate 128/s, 14 channels).</p>
FIGURES 1–5 in The Australia-New Zealand connection re-visited, with two new species of Cartomothrips (Thysanoptera, Phlaeothripinae)
FIGURES 1–5. Cartomothrips species. (1) tofti, pro, meso & metanota, pelta and tergite II. (2) tofti, head of holotype. (3) abrsi, meso & metanota, pelta and tergite II. (4) abrsi, head & pronotum. (5) tofti, female with fustis internally on segment IX. (6) neboissi, male with genital complex internally on segment IX.
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