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80 results for “geographical isolation”
Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance
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Figure 7 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 7 BSPs showing NefT (Nef = effective population size; T = generation time) changes over time for P. minor based on Cytb sequences. The upper and lower limits of the blue line represent the 95% confidence intervals of highest posterior densities (HPD) analysis. The solid black line represents median estimates of NefT.
Figure 5 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 5 Matrix of pairwise FST values between 11 P. minor populations based on Cytb sequences. * significant at p < 0.05 by the permutation test, ** extremely significant at p < 0.01 by the permutation test.
Figure 6 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 6 The expected mismatch distributions under a sudden expansion model (solid gray line) and the observed pairwise difference (black bars) of Cytb haplotypes of P. minor.
Figure 4 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 4 Unrooted minimum spanning tree showing the genetic relationships among the Cytb haplotypes of P. minor. Circle sizes are proportional to haplotype frequency. Perpendicular tick marks on the lines joining the haplotypes represent the number of nucleotide substitutions.
Figure 1 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 1 Sampling locations of P. minor. Populations are marked by abbreviations that correspond to Table 1.
Figure 2 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 2 Composition and distribution of 22 Cytb haplotypes in the Chinese and Malaysian populations.
Figure 3 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 3 NJ tree and distribution of Cytb haplotypes among populations for P. minor. Bootstrap supports of > 50 in 1000 replicates are shown.
Data from: Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation
1. In a recent paper, Bradburd et al. (Evolution, 67, 2013, 3258) proposed a model to quantify the relative effect of geographic and environmental distance on genetic differentiation. Here, we enhance this method in several ways. 2. We modify the covariance model so as to fit better with mainstream geostatistical models and avoid mathematically ill-behaved covariance functions. We extend the model – initially implemented only for co-dominant bi-allelic markers such as single nucleotide polymorphisms – to encompass highly polymorphic markers such as microsatellites. We implement and test a model selection procedure that allows users to assess which model (e.g. with or without an environment effect) is most suited. We code all our MCMC algorithms in a mix of compiled languages which allows us to decrease computing time by at least one order of magnitude. We propose an approximate inference and model selection method allowing us to deal with genomic data sets (several hundred thousands loci). 3. We also illustrate the potential of the method by re-analysing three data sets, namely harbour porpoises in Europe, coyotes in California and herrings in the Baltic Sea. 4. The computer program developed here is freely available as an r package called sunder. It takes as input georeferenced allele counts at the individual or population level for co-dominant markers. Program homepage: http://www2.imm.dtu.dk/~gigu/Sunder/.
Data from: Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills
While many conifers produce annually variable seed crops, serotinous species (which hold seeds in cones for multiple years) represent unusually stable food resources for seed predators. Such stability is conducive to residency and potentially population divergence of consumers as exemplified by the Cassia crossbill (Loxia sinesciuris) in North America. We used genotyping-by-sequencing to test whether three Mediterranean subspecies of common crossbills (L. curvirostra) associated with the serotinous Aleppo pine (Pinus halepensis) were more genetically distinct than European crossbills associated with non-serotinous conifers. We assembled a Cassia crossbill draft genome as a reference for mapping GBS reads, and as a first step towards a more contiguous genome assembly. We found clear patterns of genetic divergence for each of the P. halepensis-associated subspecies. Geographic isolation, as promoted by resource stability and residency, is associated with genetic divergence of two of these subspecies. However, geographic isolation cannot account for divergence of L. c. hispana. Instead, resource stability likely contributed to divergence by reducing dispersal and increasing resource competition that may limit breeding by immigrants. In contrast, we found no differentiation among common crossbills associated with less stable resources, and only slight differentiation between common crossbills and parrot crossbills (L. pytyopsittacus). The substantial morphological divergence between common and parrot crossbills has likely originated or been maintained by selection despite gene flow generated by spatiotemporal resource fluctuation. Our results indicate that phenological as well as morphological characteristics of conifers have influenced crossbill diversification, and suggest a possible link between resource stability and population divergence.
Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan
<p>Geographic and environmental isolations of islands and the mainland offer excellent opportunity to investigate colonization and survival dynamics of island populations. We inferred and compared evolutionary processes and the demographic history of <i>Rhododendron tsusiophyllum</i>, in the Izu Islands and the much larger island Honshu, treated here as the mainland, using thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of <i>R. tsusiophyllum</i> and three populations of <i>R. tschonoskii</i> as an outgroup. Phylogenetic relationships and their habitats suggest that <i>R. tsusiophyllum</i> had evolved and migrated from cold north to warm south regions. We detected clear genetic divergence among populations in three regions of Honshu and the Izu Islands, suggesting restricted migration between them due to isolated habitats on mountains even in the mainland. The three regions have different changes in effective population size, especially, genetic diversity and population size of the Izu Islands are small compared to the others. Further, habitats of populations in the Izu Islands are warmer than those in Honshu, suggesting that they have undergone adaptive evolution. Our study provides evidences of montane rather than insular isolation on genetic divergence, survival of populations and significance of adaptive evolution for island populations with small population size and low genetic diversity, despite close proximity to mainland populations.</p>
Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan
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Data from: Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills
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Data from: Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation
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Data from: Geographically distinct patterns of reproductive isolation and hybridisation in two sympatric species of the Jaera albifrons complex (marine isopods)
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Figure 6 in Geographic isolation and human-assisted dispersal in land snails: a Mediterranean story of Helix borealis and its relatives (Gastropoda: Stylommatophora: Helicidae)
Figure 6. Schematic representation of three alternative dating scenarios for the Mediterranean clade. A, a tree calibrated by setting the mean uncorrelated relaxed clock rate to 0.02 substitutions per site per million years; B, C, alternative palaeogeographic calibrations based on the Messinian Salinity Crisis with the associated marine regression. Full black circles mark the nodes used as calibration; in B multiple nodes are marked since the dating scenario assumes all of these splits to occur during the shaded period at the latest. The shaded ranges depict (part of) the uncertainty associated with the calibration: B, the duration of the Messinian Salinity Crisis; C, the time during which the Mid-Aegean Trench formed. Outgroup was removed for plotting.
Figure 3 in Geographic isolation and human-assisted dispersal in land snails: a Mediterranean story of Helix borealis and its relatives (Gastropoda: Stylommatophora: Helicidae)
Figure 3. Phylogeny of the major mitochondrial clades of the Mediterranean clade of Helix inferred from a concatenated alignment of partial mitochondrial COI and 16S gene sequences. A, neighbour-net network; B, maximum likelihood tree. Branch labels in B indicate SH-aLRT support values, standard bootstrap proportions from 1000 pseudoreplicates, and posterior probabilities from a Bayesian analysis, respectively.
Distribution. DR Congo S to N Namibia and N Botswana, and S through Zimbabwe, S Mozambique (approximately S of Zambezi River), NE South Africa (including KwaZulu-Natal), and Swaziland; an isolated population is found in S Gabon. No studies have attempted to distinguish the exact geographical range of R. arundinum from that of the Zambian Reedbuck (R. occidentalis) where the two populations meet. in Bovidae
Distribution. DR Congo S to N Namibia and N Botswana, and S through Zimbabwe, S Mozambique (approximately S of Zambezi River), NE South Africa (including KwaZulu-Natal), and Swaziland; an isolated population is found in S Gabon. No studies have attempted to distinguish the exact geographical range of R. arundinum from that of the Zambian Reedbuck (R. occidentalis) where the two populations meet.
Fig. 2 in Geographical versus ecological isolation of closely related black flies (Diptera: Simuliidae) inferred from phylogeny, geography, and ecology
Fig. 2 Principal components analysis (PCA) of stream variables for four species in Clade I-1 of subgenus Gomphostilbia in Thailand. Factor score 1 (PC-1) explained 33.75 % of the total variation and was related positively to stream width, depth, velocity, pH, and conductivity and negatively to altitude. Factor score 2 (PC-2) explained 26.76 % of the total variation and was positively related to stream width, depth, and velocity and negatively to pH and conductivity. The four taxa of Clade I-1 were separated in environmental space along the two axes
Supplementary Table 1. Isolate code, geographic origin, year, host, phenotypic reaction on four differential wheat lines of Pyrenophora tritici-repentis, PCR reaction and race designation of Ptr isolates in Kazakhstan
<p>Supplementary Table 1. Isolate code, geographic origin, year, host, phenotypic reaction on four differential wheat lines of Pyrenophora tritici-repentis, PCR reaction and race designation of Ptr isolates in Kazakhstan</p>
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