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.
2,603
datasets available to search
ShareScore release 0.9.0
Dataset results
2,603 results for “Ecological data”
Data from: Contemporary ecological interactions improve models of past trait evolution
Despite the fact that natural selection underlies both traits and interactions, evolutionary models often neglect that ecological interactions may, and in many cases do, influence the evolution of traits. Here, we explore the interdependence of ecological interactions and functional traits in the pollination associations of hawkmoths and flowering plants. Specifically, we develop an adaptation of the Ornstein-Uhlenbeck model of trait evolution that allows us to study the influence of plant corolla depth and observed hawkmoth-plant interactions on the evolution of hawkmoth proboscis length. Across diverse modelling scenarios, we find that the inclusion of contemporary interactions can provide a better description of trait evolution than the null expectation. Moreover, we show that the pollination interactions provide more-likely models of hawkmoth trait evolution when interactions are considered at increasingly fine-scale groups of hawkmoths. Finally, we demonstrate how the results of best-fit modelling approaches can implicitly support the association between interactions and trait evolution that our method explicitly examines. In showing that contemporary interactions can provide insight into the historical evolution of hawkmoth proboscis length, we demonstrate the clear utility of incorporating additional ecological information to models designed to study past trait evolution.
Data from: Life history traits and functional processes generate multiple pathways to ecological stability
Stability contributes to the persistence of ecological communities, yet the interactions among different stabilizing forces are poorly understood. We assembled mesocosms with an algal resource and 1-8 different clones of the consumer Daphnia ambigua and tracked algal and Daphnia abundances through time. We then fitted coupled ordinary differential equations (ODEs) to the consumer-resource time series. We show that variation in different components of stability (local stability and the magnitude of population fluctuations) across mesocosms arises through variation in life history traits and the functional processes represented by ODE model parameters. Local stability was enhanced by increased algal growth rate and Daphnia mortality and foraging rate. Population fluctuations were dampened by high Daphnia conversion efficiency and lower interaction strengths, low algal growth rate, high Daphnia death rate, and low Daphnia foraging. These results indicate that 1) stability in consumer-resource systems may arise through the net effect of multiple related stabilizing pathways, and 2) different aspects of stability can vary independently and may respond in opposite directions to the same forces.
Data from: Biotic-drivers of seedling establishment in Neotropical savannas: selective granivory and seedling herbivory by leaf-cutter ants as an ecological filter
Herbivory has been shown to have prominent top-down effects on vegetation in Paleotropical savannas, where consumers of early stages of life history act as demographic bottlenecks. Such impact has been largely ignored in Neotropical savannas, however, despite insect consumption being linked to reduced recruitment of woody species. We hypothesize that Atta leaf-cutter ants – the prevalent herbivores in the Neotropics – alter the establishment of woody plant seedlings in the Brazilian Cerrado by reducing seed availability and seedling survival. We also hypothesize that the demographic effects will be species-specific. To test these hypotheses, we experimentally (i) compared seed removal in areas with and without Atta foraging and (ii) compared the survivorship of seedlings exposed to or protected from Atta foraging. Both experiments were performed with the same common Cerrado species which allowed us to evaluate the potential net effects of consumers at the population and community levels. Overall seed removal rates in sites with Atta foraging were greater than those where ants were absent (59.2% and 39.2% of seeds removed, respectively). There were differences in removal for 10 of the 12 tested species, with per species removal 1.1- to 3.8-fold greater in areas with Atta foraging. On transplanted plants, 45% of seedlings exposed to Atta were attacked, resulting in a survival 7.6% lower than that of protected seedlings. Seedling survival was 11.8–31.5% lower in five species, with the largest differences in survival between treatments during the dry season. Taken together, these results support the hypothesis that consumers can lead to demographic bottlenecks in Neotropical savanna plant species, with effects varying among life-history stages and between species. Synthesis. Granivory by ants has been linked to reduced seedling recruitment of woody species in the Brazilian Cerrado. Our results show that leaf-cutter ants may largely limit early seedling establishment of woody species by reducing seed availability and seedling survival with differential species-specific effects. Atta ants may therefore be acting as an ecological filter, which coupled with potential selectivity in foraging on reproductive life-history stages, may ultimately influence the relative abundance of different species and hence the structure and composition of Cerrado vegetation.
Data from: Ecological speciation by temporal isolation in a population of the stonefly Leuctra hippopus (Plecoptera, Leuctridae)
Stream dwelling invertebrates are ideal candidates for the study of ecological speciation as they are often adapted to particular environmental conditions within a stream and inhabit only certain reaches of a drainage basin, separated by unsuitable habitat. We studied an atypical population of the stonefly Leuctra hippopus at a site in central Norway, the Isterfoss rapids, in relation to three nearby and two remote conspecific populations. Adults of this population emerge about a month earlier than those of nearby populations, live on large boulders emerging from the rapids, and are short-lived. This population also has distinct morphological features and was studied earlier during the period 1975–1990. We reassessed morphological distinctness with new measurements and added several analyses of genetic distinctness based on mitochondrial and nuclear sequence markers, as well as AFLP fingerprinting and SNPs mined from RAD sequences. The Isterfoss population is shown to be most closely related to its geographical neighbors, yet clearly morphologically and genetically distinct and homogeneous. We conclude that this population is in the process of sympatric speciation, with temporal isolation being the most important direct barrier to gene flow. The shift in reproductive season results from the particular temperature and water level regime in the Isterfoss rapids. The distinct adult body shape and loss of flight are hypothesized to be an adaptation to the unusual habitat. Ecological diversification on small spatial and temporal scales is one of the likely causes of the high diversity of aquatic insects.
Data from: Ecological correlates of Himalayan musk deer Moschus leucogaster
Himalayan musk deer (Moschus leucogaster; hereafter musk deer) are endangered as a result of poaching and habitat loss. The species is nocturnal, crepuscular and elusive, making direct observation of habitat use and behavior difficult. However, musk deer establish and repeatedly use the same latrines for defecation. To quantify musk deer habitat correlates, we used observational spatial data based on presence-absence of musk deer latrines, as well as a range of fine spatial-scale ecological covariates. To determine presence-absence of musk deer, we exhaustively searched randomly selected forest trails using a 20-m belt transect in different study sites within the Neshyang Valley in the Annapurna Conservation Area. Subsequently, study sites were classified as habitat or non-habitat for musk deer. A total of 252 plots, 20×20 m were systematically established every 100 m along 51 transects (each ~0.5km long) laid out at different elevations to record a range of ecological habitat variables. We used mixed-effect models and principal component analysis to characterize relationships between deer presence-absence data and habitat variables. We confirmed musk deer use latrines in forests located at higher elevations (3200 - 4200 m) throughout multiple seasons and years. Himalayan birch (Betula utilis) dominated forest, mixed Himalayan fir (Abies spectabilis) and birch forest were preferred over pure Himalayan fir and blue pine (Pinus wallichiana) forest. Greater crown cover and shrub diversity were associated with the presence of musk deer whereas tree height, diameter and diversity were weakly correlated. Topographical attributes including aspect, elevation, distance to water source, and slope were also discriminated by musk deer. Over- and under-story forest management can be used to protect forests likely to have musk deer as predicted by the models to ensure long-term conservation of this rare deer.
Data from: Morphological, ecological and genetic aspects associated with endemism in the Fly Orchid group
The European genus Ophrys (Orchidaceae) is famous for its insect-like floral morphology, an adaptation for a pseudocopulatory pollination strategy involving Hymenoptera males. A large number of endemic Ophrys species have recently been described, especially within the Mediterranean Basin, which is one of the major species diversity hotspots. Subtle morphological variation and specific pollinator dependence are the two main perceptible criteria for describing numerous endemic taxa. However, the degree to which endemics differ genetically remains a challenging question. Additionally, knowledge regarding the factors underlying the emergence of such endemic entities is limited. To achieve new insights regarding speciation processes in Ophrys, we have investigated species boundaries in the Fly Orchid group (Ophrys insectifera sensu lato) by examining morphological, ecological and genetic evidence. Classically, authors have recognized one widespread taxon (O. insectifera) and two endemics (O. aymoninii from France and O. subinsectifera from Spain). Our research has identified clear morphological and ecological factors segregating among these taxa; however, genetic differences were more ambiguous. Insights from cpDNA sequencing and amplified fragment length polymorphisms genotyping indicated a recent diversification in the three extant Fly Orchid species, which may have been further obscured by active migration and admixture across the European continent. Our genetic results still indicate weak but noticeable phylogeographic clustering that partially correlates with the described species. Particularly, we report several isolated haplotypes and genetic clusters in central and southeastern Europe. With regard to the morphological, ecological and genetic aspects, we discuss the endemism status within the Fly Orchid group from evolutionary, taxonomical and conservation perspectives.
Data from: Ecology and signal structure drive the evolution of synchronous displays
Animal synchrony is found in phylogenetically distant animal groups, indicating behavioural adaptations to different selective pressures and in different signaling modalities. A notable example of synchronous display is found in fiddler crabs in that males wave their single enlarged claw during courtship. They present species-specific signals, which are composed of distinctive movement signatures. Given that synchronous waving has been reported for several fiddler crab species, the display pattern could influence the ability of a given species to sufficiently adjust wave timing to allow for synchrony. In this study we quantified the wave displays of fiddler crabs to predict their synchronous behaviour. We combined this information with the group's phylogenetic relationships to trace the evolution of display synchrony in an animal taxon. We found no phylogenetic signal in interspecific variation in predicted wave synchrony, which mirrors the general non-phylogenetic pattern of synchrony across animal taxa. Interestingly, our analyses show that the phenomenon of synchronization stems from the peculiarities of display pattern, mating systems and the complexity of microhabitats. This is the first study to combine mathematical simulations and phylogenetic comparative methods to reveal how ecological factors and the mechanics of animal signals affect the evolution of the synchronous phenomena.
Data from: Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone
Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection.
Data from: Ecological segregation in a small mammal hybrid zone: habitat-specific mating opportunities and selection against hybrids restrict gene flow on a fine spatial scale
The degree to which closely related species interbreed is determined by a complex interaction of ecological, behavioral, and genetic factors. We examine the degree of interbreeding between two woodrat species, Neotoma bryanti and N. lepida, at a sharp ecological transition. We identify the ecological association of each genotypic class, assess the opportunity for mating between these groups, and test whether they have similar patterns of year-to-year persistence on our study site. We find that 13% of individuals have a hybrid signature but that the two parental populations and backcrosses are highly segregated by habitat type and use. Also, we find that adult hybrids are comparable to parental types in terms of year-to-year persistence on our site but that, among juveniles, significantly fewer hybrids reach adulthood on site compared to their purebred counterparts. Our analyses show that this hybrid zone is maintained by occasional nonassortative mating coupled with hybrid fertility, but that these factors are balanced by lower apparent survival of juvenile hybrids and habitat-based preference or selection that limits heterospecific mating while promoting backcrossing to habitat-specific genotypes. This system presents a novel example of the role that sharp resource gradients play in reproductive isolation and the potential for genetic introgression.
Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity
Aim: The International Tree-Ring Data Bank (ITRDB) is the most comprehensive database of tree growth. To evaluate its usefulness and improve its accessibility to the broad scientific community, we aimed to: i) quantify its biases, ii) assess how well it represents global forests, iii) develop tools to identify priority areas to improve its representativity, and iv) make available the corrected database. Location: Worldwide. Time period: Contributed datasets between 1974 and 2017. Major taxa studied: Trees. Methods: We identified and corrected formatting issues in all individual datasets of the ITRDB. We then calculated the representativity of the ITRDB with respect to species, spatial coverage, climatic regions, elevations, need for data update, climatic limitations on growth, vascular plant diversity, and associated animal diversity. We combined these metrics into a global Priority Sampling Index (PSI) to highlight ways to improve ITRDB representativity. Results: Our refined dataset provides access to a network of >52 million growth data points worldwide. We found, however, that the database is dominated by trees from forests with low diversity, in semi-arid climates, coniferous species, and in western North America. Conifers represented 81% of the ITRDB and even in well sampled areas, broadleaves were poorly represented. Our PSI stressed the need to increase the database diversity in terms of broadleaf species and identified poorly represented regions that require scientific attention. Great gains will be made by increasing research and data sharing in African, Asian, and South American forests. Main conclusions: The extensive data and coverage of the ITRDB shows great promise to address macroecological questions. To achieve this, however, we have to overcome the significant gaps in the representativity of the ITRDB. A strategic and organized group effort is required, and we hope the tools and data provided here can guide the efforts to improve this invaluable database.
Data from: Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever
East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.
Data from: Geographic variation in hybridization and ecological differentiation between three syntopic, morphologically similar species of montane lizards
To understand factors shaping species boundaries in closely related taxa, a powerful approach is to compare levels of genetic admixture at multiple points of contact and determine how this relates to intrinsic and extrinsic factors, such as genetic, morphological and ecological differentiation. In the Australian Alps, the threatened alpine bog skink Pseudemoia cryodroma co-occurs with two morphologically and ecologically similar congeners, P. entrecasteauxii and P. pagenstecheri, and all three species are suspected to hybridize. We predicted that the frequency of hybridization should be negatively correlated with genetic divergence, morphological differentiation and microhabitat separation. We tested this hypothesis using a mitochondrial locus, 13 microsatellite loci, morphological and microhabitat data and compared results across three geographically isolated sites. Despite strong genetic structure between species, we detected hybridization between all species pairs, including evidence of backcrossed individuals at the two sites where all three species are syntopic. Hybridization frequencies were not consistently associated with genetic, morphological or ecological differentiation. Furthermore, P. entrecasteauxii and P. pagenstecheri only hybridized at the two sites where they are syntopic with P. cryodroma, but not at the largest site where P. cryodroma was not recorded, suggesting that P. cryodroma may serve as a bridging species. This study reveals the complex dynamics within a three species hybrid zone and provides a baseline for assessing the impact of climate change and anthropogenic habitat modification on future hybridization frequencies.
Data from: Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring
Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal tradeoff between taxonomic resolution and bioassessment quality. Phylogenetic tools may form the bases of new more efficient approaches for biomonitoring if relationships between ecology and phylogeny can be demonstrated. We estimated the ecological optima of 127 diatom species for 19 environmental parameters using count data from 2119 diatom communities sampled during 8 years in eastern France. Using uni- and multivariate analyses, we explored the relationships between freshwater diatom phylogeny and ecology (i.e. the phylogenetic signal). We found a significant phylogenetic signal for many of the ecological optima that were tested, but the strength of the signal varied significantly from one trait to another. Multivariate analysis also showed that the multidimensional ecological niche of diatoms can be strongly related to phylogeny. The presence of clades containing species that exhibit homogeneous ecology suggests that phylogenetic information can be useful for aquatic biomonitoring. This study highlights the presence of significant patterns of ecological optima for freshwater diatoms in relation to their phylogeny. These results suggest the presence of a signal above the species level, which is encouraging for the development of simplified methods for biomonitoring survey.
Data from: Ecological niche modelling for conservation planning of an endemic snail in the verge of becoming a pest in cardamom plantations in the Western Ghats biodiversity hotspot
Conservation managers and policy makers are often confronted with a challenging dilemma of devising suitable strategies to maintain agricultural productivity while conserving endemic species that at the early stages of becoming pests of agricultural crops. Identification of environmental factors conducive to species range expansion for forecasting species distribution patterns will play a central role in devising management strategies to minimize the conflict between the agricultural productivity and biodiversity conservation. Here, we present results of a study that predicts the distribution of Indrella ampulla, a snail endemic to the Western Ghats biodiversity hotspot, which is becoming a pest in cardamom (Ellettaria cardamomum) plantations. We determined the distribution patterns and niche overlap between I. ampulla and Ellettaria cardamomum using maximum entropy (MaxEnt) niche modeling techniques under current and future (2020–2080) climatic scenarios. The results showed that climatic (precipitation of coldest quarter and isothermality) and soil (cation exchange capacity of soil [CEC]) parameters are major factors that determine the distribution of I. ampulla in Western Ghats. The model predicted cardamom cultivation areas in southern Western Ghats are highly sensitive to invasion of I. ampulla under both present and future climatic conditions. While the land area in the central Western Ghats is predicted to become unsuitable for I. ampulla and Ellettaria cardamomum in future, we found 71% of the Western Ghats land area is suitable for Ellettaria cardamomum cultivation and 45% suitable for I. ampulla, with an overlap of 35% between two species. The resulting distribution maps are invaluable for policy makers and conservation managers to design and implement management strategies minimizing the conflicts to sustain agricultural productivity while maintaining biodiversity in the region.
Data from: Ecological opportunity and the evolution of habitat preferences in an arid-zone bird: implications for speciation in a climate-modified landscape
Bioclimatic models are widely used to investigate the impacts of climate change on species distributions. Range shifts are expected to occur as species track their current climate niche yet the potential for exploitation of new ecological opportunities that may arise as ecosystems and communities remodel is rarely considered. Here we show that grasswrens of the Amytornis textilis-modestus complex responded to new ecological opportunities in Australia's arid biome through shifts in habitat preference following the development of chenopod shrublands during the late Plio-Pleistocene. We find evidence of spatially explicit responses to climatically driven landscape changes including changes in niche width and patterns of population growth. Conservation of structural and functional aspects of the ancestral niche appear to have facilitated recent habitat shifts, while demographic responses to late Pleistocene climate change provide evidence for the greater resilience of populations inhabiting the recently evolved chenopod shrubland communities. Similar responses could occur under future climate change in species exposed to novel ecological conditions, or those already occupying spatially heterogeneous landscapes. Mechanistic models that consider structural and functional aspects of the niche along with regional hydro-dynamics may be better predictors of future climate responses in Australia's arid biome than bioclimatic models alone.
Data from: The geographical and institutional distribution of ecological research in the tropics
We reviewed 1333 papers published in Biotropica and the Journal of Tropical Ecology from 1995 to 2004. Only 62 percent of tropical countries were represented in our survey, with 62 percent of the publications based on research conducted in only ten countries. Sixty-two percent of papers had lead authors that were based at institutions outside the country where the research was conducted. Cross-national collaboration was limited, accounting for only 28 percent of papers with multiple authors. To evaluate if our choice of focal journals could have biased our results, we also reviewed 652 papers published in Ecology, Oecologia, Conservation Biology, and Biological Conservation for five randomly selected years from the same time period. While some differences in authorship and the geographic distribution of research existed, the results from these journals generally mirrored patterns observed in the two focal ones—almost 54 percent of publications were based on research conducted in only ten countries, and most studies had lead authors from a developed country. The results of our review suggest that the geographical distribution of research in the tropics is unequal, and that some important regions remain understudied. The results also suggest a need for a greater focus on establishing collaborative relationships with scientists from tropical countries.
Data from: Ecological divergence among colour morphs mediated by changes in spatial network structure associated with disturbance
1. Differences in individual behaviour affect social interactions and contribute to the spatial structuring of animal populations. However, disturbance should also affect spatial networks by altering habitat heterogeneity and resource availability. Variation in resource availability should perturb the frequency and nature of social and ecological interactions within a population by affecting the spatial distribution of individuals. 2. In disturbed habitats where resources are limiting, spatial relationships should reflect behavioural differences among individuals, with higher-quality resources controlled by dominant individuals. In contrast, all individuals may exploit preferred resources in resource-rich habitats. Environmental variation and population reorganisation may also result in variation in morphological, behavioural, and ecological traits, which ultimately affect fitness. 3. We addressed these considerations for male tree lizards (Urosaurus ornatus) at three sites that differ in levels of disturbance. The habitats at these localities differed in the availability of live trees, the preferred microhabitat of U. ornatus. In addition, male U. ornatus exhibit a polymorphism in dewlap colour linked with differences in aggression, which should influence their position in a network and access to resources. We applied a network framework to characterise the spatial organisation of male morphs at each site and quantified male aggressive behaviour in the laboratory. We also compared body size, body condition, number of bite marks, parasite load, and the microhabitat use and diet, of males among the sites. 4. We detected no significant differences in spatial network structure between unburned and infrequently burned sites. However, at a frequently-burned site, the network shifted towards geographically closer, heteromorphic male neighbour associations. Males at this site were also larger, more aggressive, and had more bite marks but fewer parasites than males at the other sites. Moreover, we detected divergence in microhabitat use and diet among the morphs at the frequently-burned site that reflected the shift in spatial network structure and differences in morph behaviour. That is, only more-aggressive morphs usurped trees and consumed prey from higher trophic levels. 5. We conclude that environmental variation may influence animal spatial network structure. Jointly, behavioural and environmental variation may promote despotic social dynamics and ecological divergence in resource-limited habitats.
Data from: Impact of ecological redundancy on the performance of machine learning classifiers in vegetation mapping
Vegetation maps are models of the real vegetation patterns and are considered important tools in conservation and management planning. Maps created through traditional methods can be expensive and time‐consuming, thus, new more efficient approaches are needed. The prediction of vegetation patterns using machine learning shows promise, but many factors may impact on its performance. One important factor is the nature of the vegetation–environment relationship assessed and ecological redundancy. We used two datasets with known ecological redundancy levels (strength of the vegetation–environment relationship) to evaluate the performance of four machine learning (ML) classifiers (classification trees, random forests, support vector machines, and nearest neighbor). These models used climatic and soil variables as environmental predictors with pretreatment of the datasets (principal component analysis and feature selection) and involved three spatial scales. We show that the ML classifiers produced more reliable results in regions where the vegetation–environment relationship is stronger as opposed to regions characterized by redundant vegetation patterns. The pretreatment of datasets and reduction in prediction scale had a substantial influence on the predictive performance of the classifiers. The use of ML classifiers to create potential vegetation maps shows promise as a more efficient way of vegetation modeling. The difference in performance between areas with poorly versus well‐structured vegetation–environment relationships shows that some level of understanding of the ecology of the target region is required prior to their application. Even in areas with poorly structured vegetation–environment relationships, it is possible to improve classifier performance by either pretreating the dataset or reducing the spatial scale of the predictions.
Data from: Novel trophic niches drive variable progress toward ecological speciation within an adaptive radiation of pupfishes
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological, and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation among nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey specialist (durophage), yet the radiation is less than 10,000 years old. Both specialists and an abundant generalist species all coexist in the benthic zone of lakes on San Salvador Island, Bahamas. Based on 13,912 single-nucleotide polymorphisms (SNPs), we found consistent differences in genetic differentiation between each specialist species and the generalist across seven lakes. The scale-eater showed the greatest genetic differentiation and clustered by species across lakes, whereas durophage populations often clustered with sympatric generalist populations, consistent with parallel speciation across lakes. However, we found strong evidence of admixture between durophage populations in different lakes, supporting a single origin of this species and genome-wide introgression with sympatric generalist populations. We conclude that the scale-eater is further along the speciation-with-gene-flow continuum than the durophage and suggest that different adaptive landscapes underlying these two niche environments drive variable progress toward speciation within the same habitat. Our previous measurements of fitness surfaces in these lakes support this conclusion: the scale-eating fitness peak may be more distant than the durophage peak on the complex adaptive landscape driving adaptive radiation.
Data from: Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries
PREMISE OF THE STUDY: Hybrid zones provide 'natural laboratories' for understanding the processes of selection, reinforcement and speciation. We sought to gain insight into the degree of introgression and the extent of ecological/phenotypic intermediacy in the natural hybrid strawberry, Fragaria × ananassa subsp. cuneifolia. METHODS: We used whole plastome sequencing to identify parental species-specific (Fragaria chiloensis and F. virginiana) chloroplast SNPs, and combined the use of these with nuclear microsatellite markers to genetically characterize the hybrid zone. We assessed the potential role of selection in the observed geographic patterns by bioclimatically characterizing the niche of the hybrid populations and phenotypically characterizing hybrid individuals of known genomic constitution. KEY RESULTS: Significant admixture and little overall maternal bias in chloroplast or nuclear genomes suggest a high degree of inter-fertility among the parental and hybrid species and point to a long history of backcrossing and genetic mixing in the hybrid zone. Even though hybrids were phenotypically intermediate to the parental species there was still a discernible fingerprint of the parental genotype within hybrid individuals. Thus, while the pattern of introgression observed suggests geographic limitations to gene flow, it may be reinforced by selection for specific parental traits in the bioclimatically-intermediate habitat occupied by the hybrid. CONCLUSION: This work uncovered the genetic complexity underlying the hybrid zone of the wild relatives of the cultivated strawberry. It lays the foundation for experimental dissection of the causes of genomic introgression and nuclear-cytoplasmic disassociation, and understanding other parts of the Fragaria evolutionary history.
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.