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1,467 results for “Genetic structure”
Data from: Genetic structure at three spatial scales is consistent with limited philopatry in Ricord's Rock Iguanas (Cyclura ricordii)
Cyclura ricordii is an endemic iguana from Hispaniola Island and is threatened on the IUCN Red List. The main threats are predation by introduced mammals, habitat destruction, and hunting pressure. The present study focused on two nesting sites from Pedernales Province in the Dominican Republic. The hypothesis that natal philopatry influences dispersal and nest site selection was tested. Monitoring and sampling took place in 2012 and 2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley's K revealed that nests were significantly clustered at multiple scales, when both nesting sites were considered and within each nesting site. This suggests a patchy, non-random distribution of nests within nest sites. Hierarchical AMOVA revealed that nest site aggregations did not explain a significant portion of genetic variation within nesting sites. However, a small but positive correlation between geographic and genetic distance was detected using a Mantel's test. Hence, the relationship between geographic distance and genetic distance among hatchlings within nest sites, while detectable, was not strong enough to have a marked effect on fine scale genetic structure. Spatial and genetic data combined determined that the nesting sites included nesting females from multiple locations, and the hypothesis of 'natal philopatry', was not supported because females nesting in the same cluster were no more closely related to each other than to other females from the same nesting site. These findings imply that nesting aggregations are more likely associated with cryptic habitat variables contributing to optimal nesting conditions.
Data from: Temporal variation in spatial genetic structure during population outbreaks: distinguishing among different potential drivers of spatial synchrony
Spatial synchrony is a common characteristic of spatio-temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, is generally unknown. Distinguishing these mechanisms and their effects on synchrony can help us to better understand spatial population dynamics, design conservation and management strategies, and predict climate change impacts. Population genetic data can be used to tease apart these two processes as the spatio-temporal genetic patterns they create are expected to be different. A challenge, however, is that genetic data are often collected at a single point in time, which may introduce context-specific bias. Spatio-temporal sampling strategies can be used to reduce bias and to improve our characterization of the drivers of spatial synchrony. Using spatio-temporal analyses of genotypic data, our objective was to identify the relative support for these two mechanisms to the spatial synchrony in population dynamics of the irruptive forest insect pest, the spruce budworm (Choristoneura fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by distance and sPCA were used to characterize spatio-temporal genomic variation using 1370 SBW larvae sampled over four years (2012-2015) and genotyped at 3,562 SNP loci. We found evidence of overall weak spatial genetic structure that decreased from 2012 to 2015 and a genetic diversity homogenization among the sites. We also found genetic evidence of a long-distance dispersal event over > 140 km. These results indicate that dispersal is the key mechanism involved in driving population synchrony of the outbreak. Early intervention management strategies that aim to control source populations have the potential to be effective through limiting dispersal. However, the timing of such interventions relative to outbreak progression is likely to influence their probability of success.
Data from: Genetic population structure and variation at phenology-related loci in anadromous Arctic char (Salvelinus alpinus)
The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology-related loci associated with timing of migration and spawning. We contrasted genetic population structure at 53 SNPs versus four phenology-related loci among 15 anadromous Arctic char populations from Western Greenland and three outgroup populations. Among anadromous populations, the time period available for foraging at sea (> 2oC) ranges from a few weeks to several months, motivating two research questions: 1) Is population structure compatible with possibilities for evolutionary rescue of anadromous populations during climate change? 2) Does selection associated with latitude or SST regimes act on phenology-related loci? In Western Greenland, strong isolation-by-distance at SNPs was observed and spatial autocorrelation analysis showed genetic patch size up to 450 km, documenting contingency and gene flow among populations. Outlier tests provided no evidence for selection at phenology-related loci. However, in Western Greenland, mean allele length at OtsClock1b was positively associated with the time of year when SST first exceeded 2oC and negatively associated with duration of the period where SST exceeded 2oC. This is consistent with local adaptation for making full use of the time period available for foraging in the sea. Current adaptation may become maladaptive under climate change, but long-distance connectivity of anadromous populations could redistribute adaptive variation across populations and lead to evolutionary rescue.
Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania
<p>Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically-linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. Elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean FST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean AR = 9.96), heterozygosity (mean µHE = 0.73), and effective population sizes (mean Ne = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.</p>
Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers
Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.
More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast
<p><a name="_Hlk40344892">Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilization should have greater population structure than outcrossed species, however demographic dynamics may affect this scenario. </a>The mangrove killifish clade is composed of the two only known examples of self-fertilising species among vertebrates (<i>Kryptolebias marmoratus </i>and <i>K</i>. <i>hermaphroditus</i>). A third species in this clade, <i>K. ocellatus, </i>inhabits mangrove forests in southeast Brazil, however its mating system and patterns of genetic structure have been rarely explored. Here, we examined the genetic structure and phylogeographic patterns of <i>K</i>. <i>ocellatus</i> along its distribution, using mitochondrial DNA and microsatellites to compare its patterns of genetic structure with the predominantly selfing and often syntopic, <i>K</i>. <i>hermaphroditus.</i> Our results indicate that <i>K</i>. <i>ocellatus</i> reproduces mainly by outcrossing across much of its known range, with no current evidence of selfing, despite being an androdioecious species. Our results also reveal a stronger population subdivision in <i>K</i>. <i>ocellatus </i>compared to <i>K</i>. <i>hermaphroditus</i>, contrary to the theoretical predictions based on reproductive biology of the two species. Our findings indicate that, although morphologically similar, <i>K</i>. <i>ocellatus </i>and <i>K</i>. <i>hermaphroditus</i> had remarkably different evolutionary histories when colonising the same mangrove areas in south-eastern Brazil, with other factors (e. g. time of colonisation, dispersal/establishment capacity) having more profound effects on the current population structuring of those species than differences in mating systems.</p>
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
<p>STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of <span class="Program"><span>STRUCTURE</span></span>-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates, impact the estimation of the optimal number of population clusters <i>K</i><sub>opt</sub> that best describe the observed data. Domestic horses are suited as a test case as there is extensive knowledge of the history of many breeds, extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (<span class="Program"><span>DAPC</span></span>, <span class="Program"><span>FLOCK</span></span>, PCoA and <span class="Program"><span>STRUCTURE</span></span> with different run scenarios) all revealed the general, broad-scale relationships among the breeds that largely reflect known breed histories but diverged largely how they characterized small-scale patterns. <span class="Program"><span>STRUCTURE</span></span> failed to consistently identify <i>K</i><sub>opt</sub> using the most widespread approach, the ΔK method, despite very large numbers of MCMCs (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of<i> K</i>, without assuming a <i>K</i><sub>opt</sub>, was consistent with known breed histories. The over-reliance on <i>K</i><sub>opt</sub> should be replaced by a qualitative description of clustering over increasing <i>K</i>, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.</p>
The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest
<p>Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (<em>Allobates femoralis</em>) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (<em>r</em><sup>2</sup> = 8.4%) and canopy cover (<em>r</em><sup>2</sup> = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure show patterns that are associated with environmental variables also known to predict the density of <em>A. femoralis</em>.</p>
Data from: Genetic structure in Orkney island mice: isolation promotes morphological diversification
<p>Following human occupation, the house mouse has colonized numerous islands, exposing the species to a wide variety of environments. Such a colonization process, involving successive founder events and bottlenecks, may either promote random evolution or facilitate adaptation, making the relative importance of adaptive and stochastic processes in insular evolution difficult to assess.</p> <p>Here, we jointly analyse genetic and morphometric variation in the house mice (<i>Mus musculus domesticus</i>) from the Orkney archipelago. Genetic analyses, based on mitochondrial DNA and microsatellites, revealed considerable genetic structure within the archipelago, suggestive of a high degree of isolation and long-lasting stability of the insular populations. Morphometric analyses, based on a quantification of the shape of the first upper molar, revealed considerable differentiation compared to Western European populations, and significant geographic structure in Orkney, largely congruent with the pattern of genetic divergence. Morphological diversification in Orkney followed a Brownian motion model of evolution, suggesting a primary role for random drift over adaptation to local environments. Substantial structuring of human populations in Orkney has recently been demonstrated, mirroring the situation found here in house mice. This synanthropic species may thus constitute a bio-proxy of human structure and practices even at a very local scale.</p>
Data from: Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers
<p>The small brown planthopper (SBPH)<i><span>, </span></i><i><span>Laodelphax striatellus</span></i> (Fallén) (Hemiptera: Delphacidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively manage this insect pest, we analyzed its genetic variation, genetic structure and population demographic history. We used nine nuclear microsatellite loci to investigate the genetic diversity and population genetic structure of SBPH at 43 sampling sites in China. High levels of genetic diversity and genetic differentiation among most populations were detected. Overall, neighbour-joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed no genetically distinct groups and exhibited an admixed phylogeographic structure in China. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. On the other hand, bottleneck analysis indicated that SBPH populations had not undergone severe bottleneck effects in these regions. This study provides useful data for resolving the genetic relationships and migration patterns of SBPH and thus contribute to developing effective management strategies for this pest.</p>
Genetic structuring in Atlantic haddock contrasts with current management regimes
<div class="WordSection1"> <p><span><span><span><span><span><span><span><span><span><span><span><span>The advent of novel genetic methods has made it possible to investigate population structure and connectivity in mobile marine fish species: knowledge of which is essential to ensure a sustainable fishery. Haddock (<i>Melanogrammus aeglefinus</i>) is a highly exploited marine teleost distributed along the coast and continental shelf on both sides of the North Atlantic Ocean. However, little is known about its population structure. Here, we present the first study using single nucleotide polymorphism markers to assess the genetic population structure of haddock at multiple geographic scales, from the transatlantic to the local (fjord) level. Genotyping 138 SNP loci in 1329 individuals from 19 locations across the North Atlantic revealed three main genetic clusters, consisting of a Northwest Atlantic-, a Northeast Arctic- and a Northeast Atlantic cluster. We also observed a genetically distinct fjord population and a pattern of isolation-by-distance in the Northeast Atlantic. Our results contrast with the current management regime for this species in the Northeast Atlantic, as we found structure within some management areas. The study adds to the growing recognition of population structuring in marine organisms in general, and fishes in particular, and is of clear relevance for management of haddock in the Northeast Atlantic.</span></span></span></span></span></span></span></span></span></span></span></span></p> </div>
Genetic structure and biogeographic history of the Bicknell's Thrush/ Gray-cheeked Thrush species complex
Abstract We examined species limits, admixture, and genetic structure among populations in the Bicknell's Thrush (Catharus bicknelli)–Gray-cheeked Thrush (C. minimus) species complex to establish the geographic and temporal context of speciation in this group, which is a model system in ecology and a high conservation priority. We obtained mitochondrial ND2 sequences from 186 Bicknell's Thrushes, 77 Gray-cheeked Thrushes, and 55 individuals of their closest relative, the Veery (C. fuscescens), and genotyped a subset of individuals (n = 72) at 5,633 anonymous single nucleotide polymorphic (SNP) loci. Between-species sequence divergence was an order of magnitude greater than divergence within each species, divergence was dated to the late Pleistocene (420 kbp) based on Bayesian coalescence estimation, and a coalescent model (IMa) revealed almost no gene flow between species based on ND2. SNP data were consistent with mitochondrial results and revealed low levels of admixture among species (3 of 37 Bicknell's Thrushes, no Gray-cheeked Thrushes, and no Veeries were &gt;2% admixed). Species distribution models projected to the Last Glacial Maximum suggest that Bicknell's Thrush and Gray-cheeked Thrush resided in primarily allopatric refugia in the late Pleistocene, consistent with the genetic data that support reproductive isolation over an extended period of time. Our genetic data suggest that both species underwent demographic expansions, possibly as they expanded out of Pleistocene refugia into their current ranges. We conclude that Bicknell's Thrush and Gray-cheeked Thrush are 2 distinct species-level lineages despite low levels of Gray-cheeked Thrush introgression in Bicknell's Thrushes, and divergence has been maintained by a long history of allopatry in subtly different habitats. Their unique phylogeography among boreal forest birds indicates that either cryptic species breaks in eastern North America are still undiscovered, or another factor, such as divergent natural selection, high migratory connectivity, or interspecific competition, played a role in their divergence.
Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers
<p>The American cockroach (<i>Periplaneta americana</i>) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of <i>P. americana</i>. Our study analyzed 1053 <i>P. americana</i> and other <i>Periplaneta</i> species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of <i>P. americana</i> and 20 haplotypes of the other <i>Periplaneta</i> species accurately identified <i>P. americana</i> with a barcoding threshold of 5.1%. To identify the population genetic structure of <i>P. americana,</i> we investigated <i>wingless</i> gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that <i>P. americana</i> had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of <i>P. americana</i>. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct <i>P. americana</i> haplotype groups, showing four ancient maternal lineages of <i>P. americana</i> in China and the USA.</p>
Genetic structure in populations of Euterpe precatoria Mart. in the Brazilian Amazon
<p><i>Euterpe precatoria</i> is a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource. We need knowledge about its diversity and genetic structure in natural populations. This study aimed to evaluate the influence of geographic distance on genetic structure in the main extractive populations of <i>E. precatoria</i> in the Brazilian Amazon. Leaves from 377 plants were collected in 19 populations located in 16 municipalities in the State of Amazonas and three in the State of Rondônia. Twelve microsatellite loci were used to genotype the plants. The diversity and genetic structure among populations were estimated. The average number of alleles per locus was 5.97. The observed heterozygosity means (<i>H<sub>O</sub></i>) were higher than expected (<i>H<sub>E</sub></i>) at the population level (<i>H<sub>O</sub></i> = 0.72, <i>H<sub>E</sub></i> = 0.66) and fixation index (<i>f</i> = -0.100) was negative. The<i> F<sub>ST</sub></i><sub> </sub>value (0.1820) and the AMOVA results (17.961) showed population structure. The populations were clustered into three groups (K = 3) in Bayesian analysis. The Discriminant Analysis of Principal Components (DAPC) confirmed eight clusters, with the populations close to those identified by the Bayesian analysis. The geographic differentiation was confirmed by the groupings obtained in the analyses by the Structure program and the DACP function. Information related to phenotypic, genetic and environmental characterization of populations is important to guide conservation and management strategies and the formulation of public species management policies in Amazonian.</p>
Fine-scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus
<p>The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, <i><span>Myiopsitta monachus</span></i>, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are often aggregated within nesting trees. We determined patterns of relatedness within compound nests, within nesting trees and between trees. Spatial autocorrelation analyses of pairwise genetic relatedness revealed fine-scale genetic structure with relatives of both sexes spatially clustered within, but not beyond, nesting trees. In addition, males were more related to males sharing their compound nests than to other males occupying the same nesting tree. By contrast, males and females within compound nests were not significantly more closely related than elsewhere in the same tree, and we found no evidence for inbreeding. Adults showed high breeding site fidelity between years despite considerable disturbance of nest sites. Natal dispersal was female-biased, but dispersal distances were relatively short with some natal philopatry observed in both sexes. Sibling coalitions, typically of males, were observed amongst both philopatric and dispersing birds. Our results show significant clustering of kin within compound nests and nesting trees resulting from limited and coordinated natal dispersal, with subsequent breeding site fidelity. The resulting genetic structure has implications for social behaviour in this unusual parrot species.</p>
Data from: Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish
Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the south-western Atlantic and the other along the north-eastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations where found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intra-population genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
Data from: Genetic structure across broad spatial and temporal scales: Rocky Mountain tailed frogs (Ascaphus montanus; Anura: Ascaphidae) in the inland temperate rainforest
Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future changes in the range as a function of changing climate. Genetic structure has a strong spatial signature that is precisely congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we partition populations into 2 clusters (K = 2), and is congruent with refugia areas inferred from our paleorange reconstructions. There is a hierarchical pattern of geographic structure as we permit additional clusters, with populations clustering following mountain ranges. Nevertheless, genetic diversity is the highest in populations at the center of the range and is attenuated in populations closer to the range edges. Similarly, geographic distance is the single best predictor of pairwise genetic differentiation, but connectivity also is an important predictor. At intermediate and local geographic scales, deviations from isolation-by-distance are more apparent, at least in the northern portion of the distribution. These results indicate that both historical and landscape factors are contributing to the genetic structure and diversity of tailed frogs in the Inland Northwest.
Data from: Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the central Great Barrier Reef
The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume–induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70–86% of the total genetic variation. An additional 9–27% of variation was explained by significant differentiation of populations among sites separated by 0.4–13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6–7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.
Data from: Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)
Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations.
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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.