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68 results for “isolation by distance”
SI Figure 2: Compositional differences among bacterial microinvertebrate external and internal microbiomes as well as mats they were isolated from using Bray Curtis distance matrix visualized with a NMDS ordination. Circles indicate each community and stars show centroids of microbiome types for each animal host. All host microbiomes (internal and external) are distinct from mat communities (P<0.05), but external microbiomes are more similar to mats than internal microbiomes are to mats. in External and internal microbiomes of Antarctic nematodes are distinct, but more similar to each other than the surrounding environment
SI Figure 2: Compositional differences among bacterial microinvertebrate external and internal microbiomes as well as mats they were isolated from using Bray Curtis distance matrix visualized with a NMDS ordination. Circles indicate each community and stars show centroids of microbiome types for each animal host. All host microbiomes (internal and external) are distinct from mat communities (P<0.05), but external microbiomes are more similar to mats than internal microbiomes are to mats.
Molecular phylogenetic analyses reveal multiple long-distance dispersal events and extensive cryptic speciation in Nervilia (Orchidaceae), an isolated basal Epidendroid genus
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Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species
PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
<p>Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (<em>Bombus affinis</em>) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of <em>B. affinis</em> from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for <em>B. affinis</em> compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where <em>B. affinis</em> is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.</p>
Isolation-by-distance and genetic parentage analysis provide similar larval dispersal estimates
<p>An R studio project that includes original SNP data files used to quantify dispersal in <em>Elacatinus lori</em> via the isolation-by-distance (IBD) method. Associated R-code used to generate IBD regression slopes, calculate sigma, and construct dispersal kernels. Includes output from NeEstimator, estimating effective population size. </p> <p>Folders 1-3 contain the code/data needed to obtain the slope of the IBD relationship, effective population size, and the standard deviation (sigma) of the dispersal distribution, respectively. Folder 4 contains the R code needed to construct Laplacian dispersal kernels. </p>
Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia)
<p>The marsh fritillary (<i>Euphydryas aurinia</i>) is a critically endangered butterfly species in Denmark known to be particularly vulnerable to habitat fragmentation due to its poor dispersal capacity. We identified and genotyped 318 novel SNP loci across 273 individuals obtained from 10 small and fragmented populations in Denmark using a genotyping-by-sequencing (GBS) approach to investigate its population genetic structure. Our results showed clear genetic substructuring and highly significant population differentiation based on genetic divergence (F<sub>ST</sub>) among the 10 populations. The populations clustered in three overall clusters and due to further substructuring among these, it was possible to clearly distinguish six clusters in total. We found highly significant deviations from Hardy-Weinberg equilibrium due to heterozygote deficiency within every population investigated which indicates substructuring and/or inbreeding (due to mating among closely related individuals). The stringent filtering procedure that we have applied to our genotype quality could have overestimated the heterozygote deficiency and the degree of substructuring of our clusters but is allowing relative comparisons of the genetic parameters among clusters. Genetic divergence increased significantly with geographic distance, suggesting limited gene flow at spatial scales comparable to the dispersal distance of individual butterflies and strong isolation by distance. Altogether, our results clearly indicate that the marsh fritillary populations are genetically isolated. Further, our results highlight that the relevant spatial scale for conservation of rare, low mobile species may be smaller than previously anticipated.</p>
Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans
<p>Wide-ranging species are often polytypic, span geographic dispersal barriers, and experience opportunities for divergence via genetic drift or natural selection. Such conditions can be favorable for speciation and wide-ranging taxa are frequently subdivided into multiple species by modern molecular studies. However, with wide-ranging species, it is important to explicitly test for isolation-by-distance (IBD) which can produce continuous genetic variation that may be misinterpreted as discrete population structure or even distinct species. Here we examine the Green Frog (<em>Rana clamitans</em>), a wide-ranging species of the Aquarana<em> </em>clade distributed across much of North America. Although <em>Rana clamitans</em> is phenotypically variable enough to previously merit description of two subspecies, patterns of genetic diversity remain unclear. Additionally, the broader phylogenetic context for <em>R. clamitans</em> is poorly understood, particularly its relationship with the closely related and IUCN Vulnerable Bog Frog (<em>Rana okaloosae</em>). Using genome-wide ddRAD markers, we largely resolve relationships within Aquarana<em> </em>and unambiguously identify <em>R. okaloosae </em>as the sister lineage to <em>R. clamitans</em>. Within <em>R. clamitans </em>we find two well-supported and geographically divided clades which are identified as distinct species by a widely used genetic species delimitation method, BPP. However, the two clades exhibit low genealogical divergence and population genetic analyses reveal that genetic variation within <em>R. clamitans</em> is best described by a pattern of IBD rather than independently evolving lineages. We conclude that <em>R. clamitans </em>is<em> </em>indeed a single species and the subspecies concept is of limited use. Our analysis emphasizes how existing approaches can erroneously split species characterized by continuous genetic variation and highlights the power of combining population genetic and phylogenetic perspectives to better understand diversity within wide-ranging taxa.</p>
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
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Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans
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Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes
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Using isolation-by-distance to jointly estimate effective population density and dispersal distance: a practical evaluation using bumble bees
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Data from: Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species
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Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia)
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Data from: Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance
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Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback
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Data from: Phylogenetic diversity of two geographically overlapping species in the lichen genus Sticta (Ascomycota: Peltigeraceae): isolation by distance, environment, or fragmentation?
<p><span><b>Aim:</b> To test whether the degree of phylogenetic diversity differs in two congeneric, morphologically similar lichens that are both widespread and with a similar geographical range (Neotropics and Hawaii), but differ in altitudinal and habitat preferences, and whether the two species underwent isolation by distance (IBD), environment (IBE), or fragmentation (IBF).</span></p> <p><span><b>Location:</b> South and Central America, Caribbean, Hawaii, Azores.</span></p> <p><span><b>Taxon:</b> <i>Sticta</i> (Peltigeraceae).</span></p> <p><span><b>Methods:</b> Analysis of 395 specimens across the study area; ITS barcoding marker; maximum likelihood tree reconstruction within a broad taxonomic framework; TCS haplotype networks; Mantel test of genetic vs. geographic, environmental, and fragmentation distances; statistical comparison of BIOclim variables.</span></p> <p><span><b>Results:</b><b> </b><i>Sticta andina</i> exhibited high phenotypic variation and high reticulate phylogenetic diversity across its range, whereas the phenotypically more uniform <i>S. scabrosa</i> contained two main haplotypes, one unique to Hawaii (subsp. <i>hawaiiensis</i>). <i>Sticta andina</i> was restricted to well-preserved andine forests and paramos, habitats fragmented due to disruptive topology, whereas <i>S. scabrosa</i> was found in lowland to lower montane forests in rather exposed microsites, representing a more continuous habitat. These differences were statistically significant for several BIOclim variables. Mantel tests on genetic vs. geographic and environmental distances demonstrated that <i>S. scabrosa</i> followed a pattern of IBD across its full range but not within continental Central and South America. In contrast, <i>S. andina</i> did not exhibit IBD but showed weak, yet significant patterns of IBE at continental level and IBF in the northern Andes.</span></p> <p><b>Main Conclusions:</b> Autecology indirectly drives phylogenetic diversity in the two studied species. In the low altitude species, <i>S. scabrosa</i>, phylogenetic diversity is low and shows no correlation with geographic or environmental distances, except for the differentiation of the Hawaiian subspecies. We attribute this to rapid expansion and effective gene flow between populations across a more or less continuously distributed niche representing partially exposed microsites, including disturbed and anthropogenic vegetation, such as planted trees. In contrast, in the high altitude species, <i>S. andina</i>, phylogenetic diversity is high and correlated with both environmental niche differentiation (IBE) and fragmentation caused by the final Andean uplift (IBF). Therefore, an autoecological preference for high altitudes increases the likelihood for higher phylogenetic diversity.</p>
Data from: Lack of genetic isolation by distance, similar genetic structuring but different demographic histories in a fig-pollinating wasp mutualism
Historical abiotic factors such as climatic oscillations and extreme climatic events as well as biotic factors have shaped the structuring of species' genetic diversity. In obligate species-specific mutualisms, the biogeographic histories of the interacting species are tightly linked. This could be particularly true for nuclear genes in the Ficus-pollinating wasp mutualistic association as the insects disperse pollen from their natal tree. In this study we compare spatial genetic structure of plant and pollinator for the Ficus hirta-Valisia javana association throughout South-East China including Hainan Island, for both nuclear and cytoplasmic markers. We show that dispersal of the insect leads to plant and insect presenting similar signatures of lack of genetic isolation by distance for nuclear genes on the continent over a distance of 1000 km. But we also show that the demographic histories of plant and insect are strikingly different. This is in agreement with extreme climatic events leading to transient regional extinctions of the insects, associated with local survival of the plants. We also evidence genetic differentiation for both wasps and fig-tree between the continent and Hainan Island, although the Qiongzhou Strait is only on average 30 km wide suggesting that geographic isolation by itself has not been sufficient to generate this differentiation. Hence, our results suggest that in highly dispersive mutualistic systems, isolation by dispersal limitation across a geographic barrier could be supplemented by isolation by adaptation, and maybe by coevolution, allowing further genetic divergence. In such systems, species may frequently be composed of a single population.
Data from: Genetic structure of the poplar rust fungus Melampsora larici-populina: Evidence for isolation by distance in Europe and recent founder effects overseas
Dispersal has a great impact on the genetic structure of populations, but remains difficult to estimate by direct measures. In particular, gradual and stochastic dispersal are often difficult to assess and to distinguish, although they have different evolutionary consequences. Plant pathogens, especially rust fungi, are suspected to display both dispersal modes, though on different spatial scales. In this study, we inferred dispersal capacities of the poplar rust fungus Melampsora larici-populina by examining the genetic diversity and structure of 13 populations from eight European and two overseas countries in the Northern hemisphere. M. larici-populina was sampled from both cultivated hybrid poplars and on the wild host, Populus nigra. The populations were analyzed with 11 microsatellite and 8 virulence markers. Although isolates displayed different virulence profiles according to the host plant, neutral markers revealed little population differentiation with respect to the type of host. This suggests an absence of reproductive isolation between populations sampled from cultivated and wild poplars. Conversely, studying the relationship between geographic and genetic structure allowed us to distinguish between isolation by distance (IBD) patterns and long distance dispersal (LDD) events. The European populations exhibited a significant IBD pattern, suggesting a regular and gradual dispersal of the pathogen over this spatial scale. Nonetheless, the genetic differentiation between these populations was low, suggesting an important gene flow on a continental scale. The two overseas populations from Iceland and Canada were shown to result from rare LDD events, and exhibited signatures of strong founder effects. Furthermore, the high genetic differentiation between both populations suggested that these two recent introductions were independent. This study illustrated how the proper use of population genetics methods can enable contrasted dispersal modes to be revealed.
FIG. 5 in Comprehensive Analysis of Salamander Hybridization Suggests a Consistent Relationship between Genetic Distance and Reproductive Isolation across Tetrapods
FIG. 5. Genetic distances between salamanders that hybridize with heteromorphic sex chromosomes (median ¼ 0.109) and salamanders that hybridize without sex chromosomes (median ¼ 0.152). There is no significant difference (P ¼ 0.5293) between salamanders with sex chromosomes and salamanders without sex chromosomes.
FIG. 2 in Comprehensive Analysis of Salamander Hybridization Suggests a Consistent Relationship between Genetic Distance and Reproductive Isolation across Tetrapods
FIG. 2. (A) Histogram of cytochrome b (MT-CYB) genetic distance estimates (HKY85 þ C) between salamanders that hybridize. Graph bin width is 0.0125. (B) Ratio of mitochondrial MT-CYB genetic distance to nuclear recombination activating 1 (RAG1) genetic distance between parental species of salamanders that hybridize on a log scale. The ratio of genetic distance ranged from 0.6 to 162 with the majority of species pairs having a higher mitochondrial genetic distance (median ¼ 21.1).
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OpenNeuro
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