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193 results for “Population connectivity”
Riparian disturbance restricts connectivity of Appalachian stream salamander populations at the Coweeta Hydrologic Laboratory
Human populations are rapidly expanding and encroaching on previously undisturbed habitats. Stream salamanders in the southern Appalachian Mountains are a diverse and abundant group threatened by rapid exurban development in high-elevation watersheds. Previous research has demonstrated the sensitivity of salamanders to urbanization, but little research exists describing the mechanisms behind population declines and extirpations. Appalachian stream salamanders are adapted to forested streams with dense overstory and little light, yet following urbanization, light gaps associated with land clearing emerge. Light avoidance behaviors may alter movement behaviors of salamanders, fragmenting populations on opposite sides of light gaps. To study the effects on riparian disturbance on salamanders we established 6 experimental sites with canopy gaps ranging from 13m to 85m in stream length and 2 control sites lacking canopy gaps in May of 2010. Animals were collected within these plots, marked, and translocated to the plot on the opposite side of the gap. To establish detection probabilities in the absence of translocation, we established an additional 10m plot in the forest at each site where individuals were captured, marked, and re-released within this area. Recaptured individuals were measured and in some cases re-marked if those individuals had returned to their capture location.
Fig. 4 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 4. Phylogenetic analysis of the subgenus Sophophora and Lissocephala aff. diola Tsacas & Lachaise, 1979. Conventions as for Fig. 3.
Fig. 2 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 2. Percent divergence of the morphospecies DNA barcode from the closest neighbor found in the barcode database.
Fig. 3 in Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon)
Fig. 3. Phylogenetic analysis of the genus Zaprionus and Microdrosophila aff. mamaru (Burla, 1954). This tree is the neighbor-joining tree. The maximum likelihood tree gives the same topology. Nodes with a bootstrap value lower than 50% were merged. Bootstrap values were calculated over 1000 repeats. Above nodes: bootstrap values for maximum likelihood using a GTR + G + I model. Below nodes: bootstrap values for neighbor-joining using the Kimura-2p distance.
Data from: Sporadic genetic connectivity among small insular populations of the rare geoendemic plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)
Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of Caulanthus ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), in order to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g. > 1 km), possibly via zoochory.
Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)
<p>This dataset provides the raw data for the population genetic analyses for the article: "Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)" by Benoit Pujol; Juliette Archambeau; Aurore Bontemps; Mylène Lascoste; Sara Marin; and Alexandre Meunier found in the journal "Botany Letters", Vol 164 pp. 111-119 (DOI: 10.1080/23818107.2017.1310056).</p> <p>Link to journal open access article: http://www.tandfonline.com/doi/pdf/10.1080/23818107.2017.1310056</p> <p>Link to Zenodo article reporsitory: https://zenodo.org/record/801169</p> <p>The datafile includes three data sheets:</p> <p>Data, which contains for each plant : the name of the population, the name of the sampled individual, the subspecies, the latitude of the population, the longitude of the population, the altitudinal elevation of the population in meters, and the microsatellite genotype of each plant. Genotype data is recorded by locus (two columns for the two alleles at one locus). Locus name is found as the title of the column. The record for each allele is its allele size.</p> <p>valleys 1 and valleys 2, which contains the association between populations and valleys following the two scenarios that we analyzed in the paper.</p> <p>Microsatelite loci were developed during previous work: see the following paper for more details: Debout, G., E. Lhuillier, P.-J. Malé, B. Pujol, and C. Thébaud. 2012. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum majus subspecies (Plantaginaceae) using pyrosequencing technology. Conservation Genetics Resources 4:75-79.</p>
Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia
<p><span>Anthropogenic </span>climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in <em>Acropora digitifera</em> across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecasting future genetic offset in random forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming predictions (RCP 2.6), we observed a general pattern of increasing genetic offset with latitude. Under the most extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch in genetic composition, compared to populations in the inshore Kimberley region. The study suggest complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.</p>
Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels"
<p>Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels". </p> <p>migrationmatrix14.txt contains the particle tracking matrix, with the total number of particles that migrated from row i to column j (out of a total of 2217864 particles released per population).</p> <p>mussel_microsat_Genepop.txt contains the microsatellite data for each population in Genepop format.</p>
From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals
<p>Here, we examined the genetic variability in the coral genus <em>Pocillopora</em>, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017b) using species delimitation methods [also named <em>Pocillopora eydouxi/meandrina</em> complex <em>sensu</em> Schmidt-Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three Secondary Species Hypotheses (SSH09a, SSH09b and SSH09c) according to assignment tests using multi-locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP) and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (Structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.</p> <p>This submission contains the genotypes of 2507 individuals from PSH09 for 13 microsatellites.</p>
Fig. 3 in Fig. 3 in Genetic Structure of the Mangrove Killifish Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.
Fig. 3. Haplotype network of the Kryptolebias marmoratus species group. Maps represent the distribution of each group.
Fig. 2 in Fig. 3 in Genetic Structure of the Mangrove Killifish Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.
Fig. 2. Distribution of K. hermaphroditus: Orange star indicates type locality; and Green circles indicate recorded localities for the species (Costa 2011; 2016; Sarmento-Soares et al. 2014; Lira et al. 2015; Berbel-Filho et al. 2016; Guimarães-Costa et al. 2017; Tatarenkov et al. 2017a; This study).
Fig. 1 in Fig. 3 in Genetic Structure of the Mangrove Killifish Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.
Fig. 1. Kryptolebias hermaphroditus from Tutóia, Maranhão State, Delta do Parnaíba, north eastern Brazil; UFRJ12666: A: Hermaphrodite, 35.5 mm SL; B: Male, 20.3 mm SL; C: Male, 28.9 mm SL.
Fig. S4 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. S4. Inbreeding coefficients of each individual. White bars represent individuals from the Northeast and grey bars represent individuals from the Central Catchment Nature Reserve. Error bars represent 95% confidence interval.
Fig. S3 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. S3. Mean inbreeding coefficients of the populations of pigs found in the Northeast and the CCNR (Central Catchment Nature Reserve). Error bars represent 95% confidence interval.
Fig. S2 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. S2. Plot of Delta K from STRUCTURE output showing the Delta K values for the corresponding K values. The higher the Delta K value, the better the genetic structure is explained.
Fig. 4 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. 4. Mean observed heterozygosities of the Northeast population and the Central Catchment Nature Reserve population. Error bars represent 95% confidence intervals of the mean.
Fig. 2. Principal Component Analysis plot showing the 42 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. 2. Principal Component Analysis plot showing the 42 individuals from the Central Catchment Nature Reserve (CCNR) and the Northeast differentiated by sex and age class. Individuals exhibiting genetic admixture are labelled. Percentage variation accounted for by each principal component is indicated in brackets.
Fig. 1 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. 1. Map of Singapore, in relation to Johor (Malaysia), showing various land-use types and the study sites (Central Catchment Nature Reserve, Northeast). Offshore islands Pulau Tekong and Pulau Ubin where pigs are also present are labelled. White stars indicate locations of cage traps.
Fig. S1. Principal Component Analysis plot showing 28 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. S1. Principal Component Analysis plot showing 28 out of 42 individuals from the Central Catchment Nature Reserve (CCNR) and the Northeast with kinship values <0.2. Individuals are differentiated by sex and age class. Individuals exhibiting genetic admixture are labelled. Percentage variation accounted for by each principal component is indicated in brackets.
Fig. 3 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. 3. STRUCTURE plot at K=2. Individuals are labelled according to 1) ID number, 2) sex and 3) age class (A for adult, J for juvenile). Sampling localities are indicated by brackets above the bars.
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