Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
5,538
datasets available to search
ShareScore release 0.9.0
Dataset results
5,538 results for “Population data”
Data from: Harvest-induced phenotypic selection in an island population of moose, Alces alces
Empirical evidence strongly indicates that human exploitation has frequently led to rapid evolutionary changes in wild populations, yet the mechanisms involved are often poorly understood. Here we applied a recently developed demographic framework for analysing selection to data from a 20-year study of a wild population of moose, Alces alces. In this population, a genetic pedigree has been established all the way back to founders. We demonstrate harvest-induced directional selection for delayed birth dates in males and reduced body mass as calf in females. During the study period, birth date was delayed by 0.81 days per year for both sexes, while no significant changes occurred in calf body mass. Quantitative genetic analyses indicated that both traits harboured significant additive genetic variance. These results show that selective harvesting can induce strong selection which oppose natural selection. This may cause evolution of less favourable phenotypes that become maladaptive once harvesting ceases.
Data from: Testing for reproductive interference in the population dynamics of two congeneric species of herbivorous mites
When phylogenetically close, two competing species may reproductively interfere, and thereby affect their population dynamics. We tested for reproductive interference (RI) between two congeneric haplo-diploid spider mites, Tetranychus evansi and Tetranychus urticae, by investigating their interspecific mating and their population dynamics when they competed on the same plants. They are both pests of tomato, but differ in the host plant defences that they suppress or induce. To reduce the effect of plant-mediated interaction, we used a mutant tomato plant lacking jasmonate-mediated anti-herbivore defences in the competition experiment. In addition, to manipulate the effect of RI, we introduced founder females already mated with conspecific males in mild RI treatments or founder, virgin females in strong RI treatments (in either case together with heterospecific and conspecific males). As females show first-male sperm precedence, RI should occur especially in the founder generation under strong RI treatments. We found that T. urticae outcompeted T. evansi in mild, but not in strong RI treatments. Thus, T. evansi interfered reproductively with T. urticae. This result was supported by crossing experiments showing frequent interspecific copulations, strong postmating reproductive isolation and a preference of T. evansi males to mate with T. urticae (instead of conspecific) females, whereas T. urticae males preferred conspecific females. We conclude that interspecific mating comes at a cost due to asymmetric mate preferences of males. Because RI by T. evansi can improve its competitiveness to T. urticae, we propose that RI partly explains why T. evansi became invasive in Europe where T. urticae is endemic.
Data from: Evidence for an association between post-fledging dispersal and microsatellite multilocus heterozygosity in a large population of greater flamingos
Dispersal can be divided into three stages: departure, transience and settlement. Despite the fact that theoretical studies have emphasized the importance of heterozygosity on dispersal strategies, empirical evidence of its effect on different stages of dispersal is lacking. Here, using multi-event capture-mark-recapture models, we show a negative association between microsatellite multilocus heterozygosity (MLH; 10 loci; n = 1023) and post-fledging dispersal propensity for greater flamingos, Phoenicopterus roseus, born in southern France. We propose that the negative effects of inbreeding depression affects competitive ability and therefore more homozygous individuals are more likely to disperse because they are less able to compete within the highly saturated natal site. Finally, a model with the effect of MLH on propensity of post-fledgling dispersers to disperse to the long-distance sites of Africa was equivalent to the null model, suggesting that MLH had low to no effect on dispersal distance. Variations in individual genetic quality thus result in context-dependent heterogeneity in dispersal strategies at each stage of dispersal. Our results have important implications on fitness since sites visited early in life are known to influence site selection later on in life and future survival.
Data from: Strong, nonlinear selection against fluctuating asymmetry in wild populations of a marine fish
Theoretical links between fluctuating asymmetry (FA) and fitness have led many to use FA as a proxy for average fitness. However, studies examining whether asymmetry actually correlates with individual fitness in wild populations are relatively rare and often use simple measures of association (e.g., correlation coefficients). Consequently, the pattern of selection on asymmetry in the wild is seldom clear. We examined selection on FA of pectoral fin morphology in two wild populations of a marine fish (the kelp perch; Brachyistius frenatus). As expected, variance in signed FA in each initial sample was significantly greater than that found in the surviving population, indicating selection against FA. Our estimate of the fitness surface confirmed perfect symmetry as the phenotypic optimum and indicated strong, nonlinear selection against asymmetry. No difference in the form of selection was detected between populations. However, the level of FA in the initial samples varied among populations, leading to an overall difference in the level of selective mortality. Our results suggest that selection on asymmetry in wild populations may be strongly nonlinear, and indicate that the demographic costs of asymmetry may play a substantial role in the dynamics of populations.
Data from: Plant population success across urban ecosystems – a framework to inform biodiversity conservation in cities
1. In a rapidly urbanising world, the ability of plant species to survive and build self-sustaining populations in urban environments is increasingly important for biodiversity conservation. Yet the contribution of cities to biodiversity conservation remains unclear because ecologists have studied biodiversity patterns, largely without considering the population establishment of plants and the ways in which different kinds of urban ecosystems harbour native and endangered plant species. These limitations can mislead conservation policies for cities. 2. To better-understand how urban ecosystems can contribute to biodiversity conservation, we propose a framework that links the population status (casual or established) of plant species with ecosystem novelty and highlights barriers to population establishment in different types of urban ecosystems, from natural remnants to novel ecosystems. 3. To quantify the relative importance of natural remnants vs. human-shaped ecosystems for the conservation of self-sustaining urban plant populations we re-analyse a unique dataset from a metropolitan region in Europe with information on the population status of 1199 plant species. 4. Results demonstrate that urban ecosystems harbour many established native and endangered species although a considerable share (37%) of species of conservation concern are confined to natural remnants. In hybrid and immature novel ecosystems, high species numbers reflect many species with only casual populations. The role of novel ecosystems as habitats for native and endangered plant species increases as novel ecosystems mature. 5. Synthesis and applications. General information about plant species richness in urban environments may mislead conservation policies as different kinds of urban ecosystems can play different roles in harbouring species of conservation concern. Moreover, presence-absence data can mask establishment failures of species. This proposed framework helps to distinguish between casual and established populations of plant species, and highlights barriers to population persistence in urban ecosystems; reflecting different land uses and land use histories over time. Revealing the role of natural remnants vs. hybrid vs. novel ecosystems as habitats for species of conservation concern illustrates opportunities for biodiversity conservation in all urban ecosystems and can support setting priorities for conservation.
Data from: Consistent female preference for rare and unfamiliar male color patterns in wild guppy populations
How genetic variation is maintained in ecologically important traits is a central question in evolutionary biology. Male Trinidadian guppies, Poecilia reticulata, exhibit high genetic variation in color patterns within populations, and field and laboratory studies implicate negative frequency-dependent selection in maintaining this variation. However, behavioral and ecological processes that mediate this selection in natural populations are poorly understood. We evaluated female mate preference in 11 natural guppy populations, including paired populations from high-and low-predation habitats, to determine if this behavior is responsible for negative frequency-dependent selection and to evaluate its prevalence in nature. Females directed significantly more attention to males with rare and unfamiliar color patterns than to males with common patterns. Female attention also increased with the area of male orange coloration, but this preference was independent of the preference for rare and unfamiliar patterns. We also found an overall effect of predation regime; females from high-predation populations directed more attention toward males than those from low-predation populations. Again, however, the habitat-linked preference was statistically independent from the preference for rare and unfamiliar patterns. Because previous research indicates that female attention to males predicts male mating success, we conclude that the prevalence of female preference for males with rare and unfamiliar color patterns across many natural populations supports the hypothesis that female preference is an important process underlying the maintenance of high genetic variation in guppy color patterns.
Data from: Similarity in G matrix structure among natural populations of Arabidopsis lyrata
Understanding the stability of the G matrix in natural populations is fundamental for predicting evolutionary trajectories, yet, the extent of its spatial variation and how this impacts responses to selection remain open questions. With a nested paternal half-sib crossing design and plants grown in a field experiment, we examined differences in the genetic architecture of flowering time, floral display and plant size among four Scandinavian populations of Arabidopsis lyrata. Using a multivariate Bayesian framework, we compared the size, shape and orientation of G matrices and assessed their potential to facilitate or constrain trait evolution. Flowering time, floral display and rosette size varied among populations and significant additive genetic variation within populations indicated potential to evolve in response to selection. Yet, some characters, including flowering start and number of flowers, may not evolve independently because of genetic correlations. Using a multivariate framework, we found few differences in the genetic architecture of traits among populations. G matrices varied mostly in size rather than shape or orientation. Differences in multivariate responses to selection predicted from differences in G were small, suggesting overall matrix similarity and shared constraints to trait evolution among populations.
Data from: Population clustering and clonal structure evidence the relict state of Ulmus minor Mill. in the Balearic Islands
Field elm (Ulmus minor) is a riparian tree that grows in rare, small populations scattered along temporary watercourses in the Balearic Islands, nowadays mostly covered with Mediterranean vegetation. Agriculture and farming on the fertile land along the periodically flooded plains have reduced the elm populations to sparse tree lines along the creek beds. The presence of field elm in this very anthropic landscape has led some authors to consider it as an introduced species in the Balearics. However, pollen data suggest these elms may be the remains of larger populations experiencing continuous population shrinkage during the Holocene, and hence be native to the isles. In this paper, we apply genetic markers to assess whether field elm is or is not indigenous to the Balearic Islands. We compare the genetic variation in nine nuclear microsatellites of six Balearic populations (three in each of the largest islands, Majorca and Minorca) with that of three natural Iberian populations located in two regions, one geologically (Baetic mountains, SE Iberia) and another historically (Catalonia, NE Iberia) related to the islands. Principal coordinates analysis and Bayesian clustering methods reveal a strong genetic differentiation of the Balearic populations from the Iberian ones, and even among islands, which support their native origin. Genotypic variation in the islands is very low and clonal reproduction is very high compared with the mainland, as it is frequently observed in populations of clonal species where sexual reproduction is limited. We discuss the practical implications of these findings for the conservation of elm genetic resources of these findings.
Data from: How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum
The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the maternal parent forms the flesh and the meiospores, while the paternal parent only contributes to the meiospores. We analyzed the genetic diversity of T. melanosporum comparatively in spontaneous forests versus plantations, using SSR polymorphism of 950 samples from South-East France. All populations displayed strong genetic isolation by distance at the metric scale, possibly due to animal dispersal, meiospore persistence in soil, and/or exclusion of unrelated individuals by vegetative incompatibility. High inbreeding was consistently found, suggesting that parents often develop from meiospores produced by the same fruitbody. Unlike maternal genotypes, paternal mycelia contributed to few fruitbodies each, did not persist over years, and were undetectable on tree mycorrhizae. Thus, we postulate that germlings from the soil spore bank act as paternal partners. Paternal genetic diversity and outbreeding were higher in plantations than in spontaneous truffle-grounds, perhaps because truffle growers disperse fruitbodies to maintain inoculation in plantations. However, planted and spontaneous populations were not genetically isolated, so that T. melanosporum illustrates an early step of domestication where genetic structure remains little affected.
Data from: Environmental heterogeneity leads to higher plasticity in dry-edge populations of a semiarid Chilean shrub: insights into climate change responses
1.Interannual variability in climatic conditions should be taken into account in climate change studies in semiarid ecosystems. It may determine differentiation in phenotypic plasticity among populations, with populations experiencing higher environmental heterogeneity showing higher levels of plasticity. 2.The ability of populations to evolve key functional traits and plasticity may determine the survival of plant populations under the drier and more variable climate expected for semiarid ecosystems. 3.Working with populations of the semiarid Chilean shrub Senna candolleana along its entire distribution range, we assessed inter- and intra-population variation in functional traits as well as in their plasticity in response to water availability. We measured morphological and physiological traits related to drought resistance in both field conditions and in a greenhouse experiment, where drought response was evaluated under two water availability treatments. 4.All populations responded plastically, but higher precipitation heterogeneity in dry-edge populations seemed to have selected for more plastic genotypes compared to populations growing at mesic sites and with more homogeneous environmental conditions. 5.Synthesis: Our results suggest adaptive plasticity since higher levels of phenotypic plasticity were positively associated with plant performance. However, we did not find evidence for genetic variation for plasticity within populations. To the extent that phenotypic plasticity may play a key role in future persistence, populations at mesic sites may be more vulnerable to climate change due to their lower plasticity and their current limitations to evolve novel norms of reaction. Conversely, although Senna candolleana populations at the dry-edge are exposed to higher levels of stress, they may be less susceptible to climate change in view of their greater plasticity. We highlight the need to consider population differentiation in both mean traits and their plasticity to model realistic scenarios of species distribution under climate change.
Data from: Habitat explains patterns of population decline for an invasive crayfish
Invasive non-indigenous species are defined by their impacts: they substantially change native communities or ecosystems. Accordingly, invasive species might transform their habitats in ways that eventually become unfavorable to them, causing population declines or even extirpations. Here we use over 40 years of systematically collected data on the abundance of the invasive rusty crayfish Faxonius rusticus from 17 lakes in northern Wisconsin, USA to explore if population declines of this invader are related to the prevalence of rocky habitat, which shelters crayfish from predators and is unchanged by crayfish. We predicted that lakes with rock-dominated substrates would be resistant to F. rusticus population declines, whereas lakes lacking rock-dominated substrates would experience F. rusticus declines due to crayfish destruction of shelter-providing macrophytes. We found that in nearly half (47%) of the study lakes, F. rusticus experienced population declines over the study time period, and these lakes had significantly lower proportions of rock substrate than lakes that did not experience population declines. We recommend that more studies should investigate the potential for invasive species-mediated community or ecosystem feedbacks to eventually contribute to their own population declines.
Data from: A population genetic window into the past and future of the walleye Sander vitreus: Relation to historic walleye and the extinct "blue pike" S. v. "glaucus"
Background: Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– "blue pike" S. v. "glaucus" –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus are evaluated, since some have questioned whether these are related to the "blue pike". Results: Walleye populations are distinguished by significant considerable genetic divergence (mean FST mtDNA=0.32±0.01, μsat=0.13±0.00) and substantial diversity across their range (mean heterozygosity mtDNA=0.53±0.02, μsat=0.68±0.03). Southern populations markedly differ, possessing unique haplotypes and alleles, especially the . The Ohio/New River population that housespossesses the most pronounced divergence and the oldest haplotype. Northerly formerly glaciated populations have greatest diversity in Lake Erie (mean heterozygosity mtDNA=0.79±0.00, μsat=0.72±0.01). Genetic diversity was much less in historic Lake Erie samples from 1923–1949 (mean heterozygosity mtDNA=0.05±0.01, μsat=0.47±0.06) than today. The historic "blue pike" had no unique haplotypes/alleles and there is no evidence that it comprised a separate taxon from walleye. Turquoise mucus walleye also show no genetic differentiation from other sympatric walleye and no correspondence to the "blue pike". Conclusions: Contemporary walleye populations possess high levels of genetic diversity and divergence, despite habitat degradation and exploitation. Genetic and previously published tagging data indicate that natal homing and spawning site philopatry led to population structure. Population patterns were shaped by climate change and drainage connections, with northern ones tracing to post-glacial recolonization. Southerly populations possess unique alleles and may provide an important future genetic reservoir. Allelic frequencies of Lake Erie walleye from ~70–90 years ago significantly differed from today, suggesting population recovery after extensive habitat loss, pollution, and exploitation. The historic "blue pike" was indistinguishable from walleye, indicating that taxonomic designation is not warranted.
Data from: Wind farms affect the occurrence, abundance and population trends of small passerine birds: the case of the Dupont's lark
1.The assessment of the effects of wind farms on bird populations is commonly based on collision fatality records. This could undervalue the effect of wind farms on small-sized birds. We evaluate the effect of wind turbines on occurrence, abundance and population trends of a threatened small passerine species, the Dupont's lark Chersophilus duponti. To our knowledge, this is one of the first studies addressing the effect of wind farms on population trends using time series data from multiple wind farms. 2.We estimated population trends by fitting a switching linear trend model with the software TRIM (Trend & Indices for Monitoring data). We used multiannual data surveys of five populations in the presence of wind farms and nine in their absence (2008–2016 period). Furthermore, we fitted a logistic and a negative binomial regression model to test the effect of wind farm proximity on species occurrence and abundance in 2016, respectively. We incorporated local connectivity and habitat availability estimates in both models as predictors. 3.Results showed a negative trend overall, but that was significantly more regressive in the presence of wind farms: 21.0% versus 5.8% average annual decline in the absence of wind farms. 4.Dupont's lark occurrence and abundance in 2016 were negatively affected by measures of population isolation and positively affected by the distance to wind farms. 5.These results highlight the negative effect of isolation and wind farm proximity on Dupont's lark population parameters. Taking into account the metapopulation structure exhibited by the species in the study area, this work established a 4.5 km threshold distance from wind farms, beyond which Dupont's lark populations should be unaffected. 6.Synthesis and applications. This work highlights the negative impact of wind farms on small-sized birds and provides a 4.5 km threshold distance that should be taken into account in the design of future wind energy projects. Moreover, we suggest an analytical approach based on population trends, species abundance and occurrence variation in relation to wind farms, useful for the assessment of wind farm impacts on small-sized birds.
Data from: Analyses of phenotypic differentiations among South Georgian Diving Petrel (Pelecanoides georgicus) populations reveal an undescribed and highly endangered species from New Zealand
Unresolved taxonomy of threatened species is problematic for conservation as the field relies on species being distinct taxonomic units. Differences in breeding habitat and results from a preliminary molecular analysis indicated that the New Zealand population of the South Georgian Diving Petrel (Pelecanoides georgicus) was a distinct, yet undescribed, species. We measured 11 biometric characters and scored eight plumage characters in 143 live birds and 64 study skins originating from most populations of P. georgicus, to assess their taxonomic relationships. We analysed differences with principal component analyses (PCA), factorial ANOVAs, and Kruskal-Wallis rank sum tests. Results show that individuals from New Zealand differ significantly from P. georgicus from all other populations as following: 1) longer wings, 2) longer outer tail feathers, 3) deeper bills, 4) longer heads, 5) longer tarsi, 6) limited collar extent, 7) greater extent of contrasting scapulars, 8) larger contrasting markings on the secondaries, 9) paler ear coverts, 10) paler collars, and 11) paler flanks. Furthermore, we used a species delimitation test with quantitative phenotypic criteria; results reveal that the New Zealand population of P. georgicus indeed merits species status. We hereby name this new species Pelecanoides whenuahouensis sp. nov. Due to severe reductions in its range and the very low number of remaining birds (~150 individuals limited to a single breeding colony on Codfish Island/Whenua Hou) the species warrants listing as 'Critically Endangered'.
Data from: Distribution and functionality of copy number variation across European cattle populations
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
Data from: Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration, and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98,042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities, and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.
Data from: Adaptive limitations of white spruce populations to drought imply vulnerability to climate change in its western range
A cost-effective climate change adaptation strategy for the forestry sector is to move seed sources to more northern and higher elevation planting sites as part of ongoing reforestation programs. This is meant to match locally adapted populations with anticipated environments, but adaptive traits do not always show population differences suitable to mitigate climate change impacts. For white spruce, drought tolerance is a critical adaptive trait to prevent mortality and productivity losses. Here, we use a 40 year old provenance experiment that has been exposed to severe drought periods in 1999 and 2002 to retrospectively investigate drought response and the adaptive capacity of white spruce populations across their boreal range. Relying on dendrochronological analysis under experimentally controlled environments, we evaluate population differences in resistance, resilience and recovery to these extreme events. Results showed evidence for population differentiation in resistance and recovery parameters, but provenances conformed to approximately the same growth rates under drought conditions and had similar resilience metrics. The lack of populations with better growth rates under drought conditions is contrary to expectations for a wide-ranging species with distinct regional climates. Populations from the wettest environments in the northeastern boreal were surprisingly drought tolerant, suggesting that these populations would readily resist water deficits projected for the 2080s, and supporting the view that northeastern Canada will provide a refugium for boreal species under climate change. The findings also suggest that white spruce is sensitive to growth reductions under climate change in the western boreal. The study highlights that population differentiation in adaptive capacity is species and trait specific, and we provide a counter example for drought tolerance traits, where assisted migration prescriptions may be ineffective to mitigate climate change impacts. For resource managers and policy makers, we provide maps where planning for widespread declines of boreal white spruce forests may be unavoidable.
Data from: Population connectivity and phylogeography of a coastal fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current region: evidence of an ancient vicariant event.
Contemporary patterns of genetic diversity and population connectivity within species can be influenced by both historical and contemporary barriers to gene flow. In the marine environment, present day oceanographic features such as currents, fronts and upwelling systems can influence dispersal of eggs/larvae and/juveniles/adults, shaping population substructuring. The Benguela Current system in the southeastern Atlantic is one of the oldest upwelling systems in the world, and provides a unique opportunity to investigate the relative influence of contemporary and historical mechanisms shaping the evolutionary history of warm-temperate fish species. Using the genetic variation in the mitochondrial DNA Control Region and eight nuclear microsatellite DNA loci, we identified the presence of two highly divergent populations in a vagile and warm-temperate fish species, Atractoscion aequidens, across the Benguela region. The geographical distributions of the two populations, on either side of the perennial upwelling cell, suggest a strong correlation between the oceanographic features of the system and the breakdown of gene flow within this species. Genetic divergence (mtDNA φST = 0.902, microsatellite FST = 0.055: probability of genetic homogeneity for either marker = p<0.001), absence of migrants (less than 1% per generation) between populations and coalescent estimates of time since most recent common ancestor suggest that the establishment of the main oceanographic features of the system (2 million years ago), particularly the strengthening and position of the perennial upwelling cell, is the most likely mechanism behind the observed isolation. Concordance between mitochondrial and nuclear genetic markers indicates that isolation and divergence of the northern and southern Benguela populations of A. aequidens occurred deep in the past and has continued to the present day. These findings suggest that the Benguela Current system may constitute an ancient and impermeable barrier to gene flow for warm-temperate fish species.
Data from: Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments
Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6-week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts ('shuffling') in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs <10-km apart can exhibit substantial differences in their physiological response to thermal stress, which could impact their population dynamics under climate change.
Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysis
The use of procedures for the automated scoring of AFLP fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package RAWGENO to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (Fst). Steps were implemented in R to automatically run the scoring process in RAWGENO for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise Fst values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected Fst values in an only moderate way. At a range of scoring parameters around the default settings of RAWGENO, the number of polymorphic bins as well as pairwise Fst values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.