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58 results for “Geographical differentiation”
Data from: Differential predation drives the geographical divergence in multiple traits in aposematic frogs
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Data from: Geographic variation in hybridization and ecological differentiation between three syntopic, morphologically similar species of montane lizards
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Data from: Geographic variation in sex-chromosome differentiation in the common frog (Rana temporaria)
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Differential geographic patterns in song components of male Albert’s lyrebirds
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Strong genetic differentiation on a small geographic scale in the Neotropical rainforest understory tree Paypayrola blanchetiana (Violaceae)
Self-incompatible plants as well as common plant species are expected to be especially vulnerable to the deleterious effects of fragmentation on genetic diversity. Paypayrola blanchetiana (Violaceae) is a common, self-incompatible understory tree in the East Brazilian Atlantic forest. Its autochorous seed dispersal and occurrence in dense, well-separated clusters makes it an interesting model for studies of gene flow and genetic structuring on a small geographic scale. A previous study has found remarkably low fruit set and frequent seed abortions in this species in several populations situated in forest fragments. We tested the hypothesis that P. blanchetiana is affected by inbreeding and loss of genetic diversity in a fragmented landscape. Nine nuclear and three plastid microsatellite loci were genotyped for 285 individuals (149 adult trees and 136 saplings) across seven populations in five forest fragments in a 240 km2 sugarcane-rainforest matrix. We found a low to moderate genetic diversity in nuclear loci of P. blanchetiana, population structuring on a small geographical scale and high levels of inbreeding. Haplotype distributions confirmed that seed dispersal is very limited. There were, however, no signs for lower genetic diversity or higher inbreeding in populations situated in the smallest forest fragments. Furthermore, genetic diversity was not lower in the sapling cohort, which was created in post-fragmentation condition. Therefore, we may be witnessing the genetic consequences of this species biology, rather than immediate effects of fragmentation.
Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.
Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from populations of both species in close proximity to each other and from putative hybrid zones. The species shared all but one SNP polymorphism and on average, allele frequencies differed by only 0.14. However, the species were clearly differentiated using Structure and admixed individuals were primarily identified at putative hybrid zones. PopGraph identified a highly integrated network among all populations but populations of each species and hybrid zones occupied distinct regions in the network. Using either conditional graph distance (cGD) or Fst/(1-Fst) we found significant isolation by distance (IBD) among populations. Within species, IBD was strong, indicating high historic gene flow. IBD extended approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD between the species was very weak and extended only a few km beyond hybrid zones, suggesting little recent gene flow. The extensive sharing of SNP polymorphisms between these species suggests that they are very early in the speciation process while the low signal of IBD suggests that they have largely ceased gene exchange.
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: Geographic structure and adaptive population differentiation in herbivore defense genes in European aspen (Populus tremula L., Salicaceae)
When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation because alternative alleles are favoured in different geographical locations. Here, we study 71 single nucleotide polymorphisms (SNPs) from seven genes associated with inducible defence responses in a sample of Populus tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation, and a principal component analyses conducted on the defence SNPs divides the Swedish population into three distinct clusters. Several defence SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographical variation has been found in genes involved in plant defence against antagonists.
Data from: The geographic mosaic of herbicide resistance evolution in the common morning glory, Ipomoea purpurea: evidence for resistance hotspots and low genetic differentiation across the landscape
Strong human-mediated selection via herbicide application in agroecosystems has repeatedly led to the evolution of resistance in weedy plants. Although resistance can occur among separate populations of a species across the landscape, the spatial scale of resistance in many weeds is often left unexamined. We assessed the potential that resistance to the herbicide glyphosate in the agricultural weed Ipomoea purpurea has evolved independently multiple times across its North American range. We examined both adaptive and neutral genetic variations in 44 populations of I. purpurea by pairing a replicated dose–response greenhouse experiment with SSR genotyping of experimental individuals. We uncovered a mosaic pattern of resistance across the landscape, with some populations exhibiting high-survival postherbicide and other populations showing high death. SSR genotyping revealed little evidence of isolation by distance and very little neutral genetic structure associated with geography. An approximate Bayesian computation (ABC) analysis uncovered evidence for migration and admixture among populations before the widespread use of glyphosate rather than the very recent contemporary gene flow. The pattern of adaptive and neutral genetic variations indicates that resistance in this mixed-mating weed species appears to have evolved in independent hotspots rather than through transmission of resistance alleles across the landscape.
Supplementary material 1 from: Ivković S, Chobanov D, Horvat L, Iorgu IȘ, Hochkirch A (2022) Geographic differentiation in male calling song of Isophya modestior (Orthoptera, Tettigoniidae, Phaneropterinae). ZooKeys 1122: 107-123. https://doi.org/10.3897/zookeys.1122.85721
Table S1
Differential geographical and ecological dynamics allow diversification of morphologically convergent giant bromeliads in the Atlantic Forest
<p>Aim: This paper investigates evolutionary mechanisms that allow morphologically convergent lineages share the same geographical space. We compared the events occurred along the diversification of <i>Karawata</i> and <i>Aechmea</i> subgen. <i>Chevaliera</i> in Atlantic Forest by 1) verifying whether the climatic niches and habitats of <i>Karawata </i>and <i>Aechmea </i>subgen.<i> Chevaliera</i> are similar; 2) testing whether the two groups had the same pattern of colonization in the Atlantic Forest; and 3) evaluating whether they had the same evolutionary dynamics of environmental space occupation. We see the two bomeliad lineages as a model case to understand sympatric diversification in the Atlantic Forest biome.</p> <p>Location: Brazilian Atlantic Forest</p> <p>Taxon: <i>Karawata</i> and <i>Aechmea </i>subgen. <i>Chevaliera</i> (Bromeliaceae: Bromelioideae)</p> <p>Methods: We explored differences in evolutionary dynamics between the lineages analyzing the divergence times, estimating ancestral ranges and habitats, testing niche similarity and evaluating shifts in speciation dynamics.</p> <p>Results: <i>Karawata </i>and <i>A. </i>subgen. <i>Chevaliera </i>most likely originated in the Pliocene and diversified during the Pleistocene. The two clades originated in ombrophilous forests and shared a similar environmental space. However, <i>Karawata </i>and <i>A. </i>subgen. <i>Chevaliera </i>show different dynamics in the occupation of geographical and environmental spaces. Our results suggest that the São Francisco and Jequitinhonha Rivers acted as geographical barriers for <i>Karawata </i>and <i>A. </i>subgen. <i>Chevaliera</i>.</p> <p>Main Conclusions: Differences in spatial and environmental evolutionary dynamics allow the two groups to occupy similar habitats as well as environmental and geographical spaces in the Brazilian Atlantic Forest.</p>
Data from: Geographic structure and adaptive population differentiation in herbivore defense genes in European aspen (Populus tremula L., Salicaceae)
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Differential geographical and ecological dynamics allow diversification of morphologically convergent giant bromeliads in the Atlantic Forest
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Data from: The geographic mosaic of herbicide resistance evolution in the common morning glory, Ipomoea purpurea: evidence for resistance hotspots and low genetic differentiation across the landscape
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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: A novel approach to parasite population genetics: experimental infection reveals geographic differentiation, recombination, and host-mediated population structure in Pasteuria ramosa, a model bacterial parasite of Daphnia
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Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.
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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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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.