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502 results for “natural populations”
Data from: Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize
<p>While physiological responses to low-light environments have been studied among corals on mesophotic coral ecosystems worldwide (MCEs; 30–150 m), the mechanisms behind acclimatization and adaptation to depth are not well understood for most coral species. Transcriptomic approaches based on RNA sequencing are useful tools for quantifying gene expression plasticity, particularly in slow-growing species such as scleractinian corals, and for identifying potential functional differences among conspecifics. A tag-based RNA-Seq (Tag-Seq) pipeline was applied to quantify transcriptional variation in natural populations of the scleractinian coral <i>Montastraea cavernosa</i> from mesophotic and shallower environments across five sites in Belize and the Gulf of Mexico: Carrie Bow Cay, West and East Flower Garden Banks, Pulley Ridge, and Dry Tortugas. Regional site location was a stronger driver of gene expression patterns than depth. However, mesophotic corals among all sites shared similar regulation of metabolic and cell growth functional pathways that may represent common physiological responses to environmental conditions at depth. Additionally, in a transplant experiment at West and East Flower Garden Banks, colonies transplanted from mesophotic to shallower habitats diverged from the control mesophotic group over time, indicating depth-regulated plasticity of gene expression. When the shallower depth zone experienced a bleaching event, bleaching severity did not differ significantly between transplants and shallow controls, but gene expression patterns indicated variable regulation of stress responses among depth treatments. Coupled observational and experimental studies of gene expression among mesophotic and shallower <i>M. cavernosa</i> provide insights into the ability of this depth-generalist coral species to persist under varying environmental conditions. </p>
Data from: Divergence of seminal fluid gene expression and function among natural snail populations
Seminal fluid proteins (SFPs) can trigger drastic changes in mating partners, mediating post-mating sexual selection and associated sexual conflict. Also, cross-species comparisons have demonstrated that SFPs evolve rapidly and hint that post-mating sexual selection drives their rapid evolution. In principle, this pattern should be detectable within species as rapid among-population divergence in SFP expression and function. However, given the multiple other factors that could vary among populations, isolating divergence in SFP-mediated effects is not straightforward. Here we attempted to address this gap by combining the power of a common garden design with functional assays involving artificial injection of SFPs in the simultaneously hermaphroditic freshwater snail, Lymnaea stagnalis. We detected among-population divergence in SFP gene expression, suggesting that seminal fluid composition differs among four populations collected in western Europe. Furthermore, by artificially injecting seminal fluid extracted from these field-derived snails into standardized mating partners, we also detected among-population divergence in the strength of post-mating effects induced by seminal fluid. Both egg production and subsequent sperm transfer of partners differed depending on the population origin of seminal fluid, with the response in egg production seemingly closely corresponding to among-population divergence in SFP gene expression. Our results thus lend strong intraspecific support to the notion that SFP expression and function evolve rapidly, and confirm L. stagnalis as an amenable system for studying processes driving SFP evolution.
Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems
<p>If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value - notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and non-crop hosts and between experimental and natural host populations. Here, we used a meta-analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested.</p> <p>We synthesized the results of 102 studies, comprising 2,004 effect sizes representing a diversity of approaches and host-parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ~20% for non-crop hosts and by ~50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.</p>
Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats
Supplementation of wild populations with captive-bred individuals is often ineffective for boosting long-term productivity of wild populations. On the other hand, it remains unknown whether supplementation can act to maintain life-history variation in natural habitats, which is also important for the long-term persistence of populations and species. Partial migration, in which both migratory and resident individuals are maintained in a population, is commonly found across animal taxa. However, human-induced habitat fragmentation continues to cause rapid decline in a migratory phenotype among many natural populations. By using field and hatchery experiments, we here demonstrated that while migrants and residents could be maintained in captive environments, few fish became migrants in natural streams in red-spotted masu salmon Oncorhynchus masou ishikawae. Released captive-bred fish rarely reached the threshold body size necessary to become migrants in natural streams, presumably due to lower growth condition in natural than in captive environments. The decision to migrate is often considered a threshold trait in salmonids and other animal taxa. Our findings highlight the need for supplementation programs to acknowledge environmentally induced changes in life-history decisions for partially migratory species.
Signatures of local adaptation to climate in natural populations of sweet chestnut (Castanea sativa Mill.) from southern Europe
Context: Temperate forest species, such as chestnut (Castanea sativa Mill.), are currently threatened by increasing temperature together with disruption and reduction of precipitation due to climate change. In this context, understanding the adaptation processes of species will help to manage and ensure the conservation of forests. Aims: We studied the relationship between genetic variability and climate variables in natural populations of C. sativa using a landscape genomics approach aimed to identify local adaption processes. Methods: Using five genomic SSRs and eight functional EST-SSRs markers, 268 individuals belonging to ten different natural European chestnut populations distributed in contrasting climatic sites were genotyped. In addition, associations between allelic variation and climatic variables (environmental association analyses approach) were performed using Samada and LFMM. Results: Results highlighted a strong inter-relationship between climate variables and evolutionary processes resulting in adaptive variation. STRUCTURE analysis based on functional markers split the populations in three separate gene pools (K=3), mostly in agreement with the different climatic conditions existing in the studied areas. Divergent spatial patterns of genetic variation between rainy and arid areas were found. We detected a total of 202 associations with climate among 22 different alleles, 9% of which related with the outlier locus FIR059, known to be implicated in regulatory mechanisms during water stress adaptation processes. Conclusions: Landscape genomics analyses revealed a pattern of adaptive variation, where specific climatic variables influenced the frequencies distribution and fixation of several alleles, resulting in local adaptation processes of the populations in the investigated areas. Our findings underline the close inter-relationship existing between climate and genetic variability, and indicate how this approach could provide valuable information for the management of forest species in a rapidly changing environment.
Predation risk shapes the degree of placentation in natural populations of live-bearing fish
<p class="manuscriptABSATZ"><span>The placenta is a complex life-history trait that is ubiquitous across the tree of life. Theory proposes that the placenta evolves in response to high performance-demanding conditions by shifting maternal investment from pre- to post-fertilization, thereby reducing a female's reproductive burden during pregnancy. We test this hypothesis by studying populations of the fish species <i>Poeciliopsis retropinna</i> in Costa Rica. We found substantial variation in the degree of placentation among natural populations associated with predation risk: females from high predation populations had significantly higher degrees of placentation compared to low predation females, while number, size and quality of offspring at birth remained unaffected. Moreover, a higher degree of placentation correlated with a lower reproductive burden and hence likely an improved swimming performance during pregnancy. Our study advances an adaptive explanation for why the placenta evolves by arguing that an increased degree of placentation offers a selective advantage in high predation environments. </span></p>
Figure 1 in Andean bear (Tremarctos ornatus) population density and relative abundance at the buffer zone of the Chingaza National Natural Park, cordillera oriental of the colombian andes
Figure 1. Natural covers map showing camera traps distribution at 9 grids throughout the study area.
Data from: Bayesian quantification of ecological determinants of outcrossing in natural plant populations: computer simulations and the case study of biparental inbreeding in English yew
The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires co-dominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterised by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.
Impacts of environmental heterogeneity on natural selection in a wild bird population
<p>Natural selection has been studied for several decades, resulting in the computation of thousands of selection estimates. Although the importance of environmental conditions on selection has often been suggested, published estimates rarely take into account the effects of environmental heterogeneity on selection patterns. Here, we estimated linear and non‐linear viability selection gradients on morphological traits of 12 days‐old nestlings in a wild population of tree swallows (<i>Tachycineta bicolor</i>) across a large‐scale heterogeneous study system in southern Québec, Canada. We assessed the environmental drivers of nestling survival and evaluated their effects on strength and direction of selection gradients. Separate analyses of environmental variables showed that high temperatures and heavy rainfall caused stronger positive linear selection on morphological traits. Weaker linear selection was also measured in more extensively cultivated areas. Both strength and shape of non‐linear quadratic and correlational components of selection were modified by environmental variables. Considering all environmental variables revealed that precipitation since hatching affected patterns of linear selection on traits, while temperatures since hatching shaped nonlinear selection patterns. Our study underlines the importance of quantifying linear and non‐linear natural selection under various environmental conditions and how the evolutionary response of traits may be affected by ongoing human‐induced environmental changes.</p>
Data from: Endosymbiont diversity in natural populations of Tetranychus mites is rapidly lost under laboratory conditions
<p>Although the diversity of bacterial endosymbionts in arthropods is well documented, whether and how such diversity is maintained remains an open question. We investigated the temporal changes occurring in the prevalence and composition of endosymbionts after transferring natural populations of <i>Tetranychus </i>spider-mites from the field to the laboratory. These populations, belonging to three different <i>Tetranychus </i>species (<i>T. urticae</i>, <i>T. ludeni </i>and <i>T. evansi</i>) carried variable infection frequencies of <i>Wolbachia</i>, <i>Cardinium</i>, and <i>Rickettsia</i>. We report a rapid change of the infection status of these populations after only 6 months of laboratory rearing, with an apparent loss of <i>Rickettsia </i>and <i>Cardinium</i>, while <i>Wolbachia </i>apparently either reached fixation or was lost. We show that <i>Wolbachia </i>had variable effects on host longevity and fecundity, and induced variable levels of cytoplasmic incompatibility (CI) in each fully infected population, despite no sequence divergence in the markers used and full CI rescue between all populations. This suggests that such effects are largely dependent upon the host genotype. Subsequently, we used these data to parameterize a theoretical model for the invasion of CI-inducing symbionts in haplodiploids, which shows that symbiont effects are sufficient to explain their dynamics in the laboratory. This further suggests that symbiont diversity and prevalence in the field are likely maintained by environmental heterogeneity, which is reduced in the laboratory. Overall, this study highlights the lability of endosymbiont infections and draws attention to the limitations of laboratory studies to understand host-symbiont interactions in natural populations.</p>
Data from: Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents
Background: Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating. Results: We provide genome-wide analyses of rapid evolution in two Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation. Conclusions: While the ultimate trajectory of selection in these populations is unknown, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.
Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population
<p>Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (<em>Melospiza melodia</em>) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. Further, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, reshaping the eco-evolutionary implications of immigration.</p>
Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon
<p>The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of geneflow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life-stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of two years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort) . This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.</p>
Populations restored using regional seed are genetically diverse and similar to natural populations in the region
<p>Ecological restoration and plant re-introductions aim to create plant populations that are genetically similar to natural populations to preserve the regional gene pool, yet genetically diverse to allow adaptation to a changing environment. For this purpose, seeds for restoration are increasingly sourced from multiple populations in the target region. However, it has only rarely been tested whether using regional seed indeed leads to genetically diverse restored populations which are genetically similar to natural populations.</p> <p>We used single nucleotide polymorphism (SNP) markers to investigate genetic diversity within and differentiation among populations of <em>Centaurea jacea</em> and <em>Betonica officinalis</em> on restored and natural meadows in the White Carpathians, Czech Republic. The restoration took place 20 years ago using regional seeds propagated from a mix of multiple regional source populations. We included original regional seeds in our analysis to compare the restored populations with their origin (only in <em>C. jacea</em>). Additionally, we analysed conventional seeds without certified origin because these would have constituted a common alternative for restoration seeding in the absence of regional seeds.</p> <p>The differentiation between restored and natural populations (mean pairwise <em>F<sub>ST</sub></em> = 0.018 in <em>Centaurea</em> and 0.021 in <em>Betonica</em>) was similar to the differentiation among natural populations (<em>F<sub>ST</sub></em> = 0.023 and 0.021), and the restored populations were slightly more genetically diverse than the natural populations. In addition, restored populations were relatively similar to their origin, the regional seeds (<em>F<sub>ST</sub></em> = 0.015). In contrast, conventional seeds were strongly differentiated from all regional populations (<em>F<sub>ST</sub></em> = 0.100 and 0.059, in <em>Centaurea</em> and <em>Betonica</em>, respectively) and harboured substantially lower genetic diversity. We also found signs of gene flow via pollen or seed dispersal from natural to restored populations but not <em>vice versa</em>.</p> <p><em>Policy implications</em>. Regionally sourced seeds can produce genetically diverse populations at natural levels of genetic differentiation.</p>
Fitness measures of seed progeny from seven natural populations of Campanula glomerata.
<p>Fitness (rosette diameter in cm) and HL for seed progeny of seven wild populations of <em>Campanula glomerata </em>from southern Belgium and north-eastern France. For details see Van Rossum et al. (2022) in Frontiers in Conservation Science.</p>
Individual multilocus genotypes of adults and seed progeny from eight natural populations of Campanula glomerata
<p>Individual multilocus genotypes based on 15 microsatellite loci of adults and seed progeny from eight natural populations of <em>Campanula glomerata</em>. For more details see Van Rossum et al. (2022) in Frontiers in Conservation Science</p>
From nature reserve to mosaic management: improving matrix survival, not permeability, benefits regional populations under habitat loss and fragmentation
<p>Although matrix improvement in fragmented landscapes is a promising conservation measure, matrix permeability (willingness of an organism to enter the matrix) and movement survival in the matrix are usually aggregated. Consequently, it is unknown which matrix property needs to be improved. It also remains unclear whether matrix upgrading from dispersal passage to providing reproduction opportunities has large conservation benefits and whether there are interactive effects between habitat and matrix management.</p> <p>We examined matrix effects on regional populations across a gradient of habitat loss and fragmentation using simulation experiments that integrated demographic processes and movement modeling based on circuit theory. We separately modified the levels of matrix permeability and movement survival to evaluate their individual effects. We also altered the amount and configuration of not only habitat but also improved matrix to assess their effects on population vital rates (size, survival and density).</p> <p>In binary landscapes comprising habitat and unimproved matrix, matrix movement survival had larger effects on population vital rates than matrix permeability. Increasing movement survival increased vital rates, yet, increasing matrix permeability decreased vital rates. Increased permeability required corresponding increased movement survival to offset potential negative population outcomes.</p> <p>When subsets of the matrix functioning as dispersal passage only (where no reproduction opportunities existed) were improved, increasing matrix permeability but holding movement survival constant reduced all vital rates, especially with increasing habitat fragmentation. In contrast, when movement survival increased, vital rates increased given strong habitat fragmentation. The benefits of upgrading dispersal passage to provide reproduction opportunities for population survival were greatest when habitat amount was moderate. We also found synergetic effects between amounts of habitat and improved matrix, and the benefits of matrix improvement were promoted when improvement was achieved in a spatially aggregated manner.</p> <p><em>Synthesis and applications</em>: Matrix improvement and connectivity modeling aimed at increasing movement survival will likely bring larger conservation benefits than those for improving permeability alone. Buffering and connecting habitat remnants with improved matrix could provide benefits as long as movement survival is increased. Simultaneous implementation of habitat management and matrix improvement would yield synergistic conservation benefits.</p>
Data from: Ecological genetics of Juglans nigra: differences in early growth patterns of natural populations
<p>Many boreal and temperate forest tree species distributed across large geographic ranges are composed of populations adapted to the climate they inhabit. Forestry provenance studies and common gardens provide evidence of local adaptation to climate when associations between fitness traits and the populations' home climates are observed. Most studies that evaluate tree height as a fitness trait do so at a specific point in time. In this study, we elucidate differences in early growth patterns in black walnut (<em>Juglans nigra L.</em>) populations by modeling height growth from seed up to age 11. The data comprise tree height measurements between ages 2 to 11 for 52 natural populations of black walnut collected through its geographic range and planted in one or more of 3 common gardens. We use the Chapman-Richards growth model in a mixed-effects framework and test whether populations differ in growth patterns by incorporating populations' home climate into the model. In addition, we evaluate differences in populations' absolute growth and relative growth based on the fitted model. Models indicated that populations from warmer climates had the highest cumulative growth through time, with differences in average tree height between populations from home climates with a mean annual temperature (MAT) of 13 °C and of 7 °C estimated to be as high as 80% at age 3. Populations from warmer climates were also estimated to have higher and earlier maximum absolute growth rate than populations from colder climates. In addition, populations from warm climates were predicted to have higher relative growth rates at any given tree size. Results indicate that natural selection may shape early growth patterns of populations within a tree species, suggesting that fast early growth rates are likely selected for in relatively mild environments where competition rather than tolerance to environmental stressors becomes the dominant selection pressure.</p>
Sexual coercion in a natural mandrill population
<p>Each prediction (and the test for male aggression ~ rank) corresponds to a differrent table and R script. The legends of the tables are within the corresponding script.</p> <p> </p>
A new theoretical performance landscape for suction feeding reveals adaptive kinematics in a natural population of reef damselfish
<p><span>Understanding how organismal traits determine performance and</span><span>, </span><span>ultimately</span><span>, </span><span>fitness is a fundamental goal of evolutionary ecomorphology. However, multiple traits can interact in non-linear and context-dependent ways to affect performance, hindering efforts to place natural populations with respect to performance peaks or valleys. Here, we used an established mechanistic model of suction-feeding performance (SIFF) derived from hydrodynamic principles to estimate a theoretical performance landscape for zooplankton prey capture. This performance space can be used to predict prey capture performance for any combination of six morphological and kinematic trait values. We then mapped in situ high-speed video observations of suction feeding in a natural population of a coral reef zooplanktivore, Chromis viridis, onto the performance space to estimate the population's location with respect to the topography of the performance landscape. Although the kinematics of the natural population closely matched regions of high performance in the landscape, the population was not located on a performance peak. Individuals were furthest from performance peaks on the peak gape, ram speed and mouth opening speed trait axes. Moreover, we found that the trait combination</span><span>s </span><span>in the observed population were associated with higher performance than expected by chance, suggesting that these combinations are under selection. Our results provide a framework for assessing whether natural populations occupy performance optima.</span></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.