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3,655 results for “Structural data”
Data from: Weak coordination between leaf structure and function among closely related tomato species
Theory predicts that natural selection should favor coordination between leaf physiology, biochemistry and anatomical structure along a functional trait spectrum from fast, resource-acquisitive syndromes to slow, resource-conservative syndromes. However, the coordination hypothesis has rarely been tested at a phylogenetic scale most relevant for understanding rapid adaptation in the recent past or for the prediction of evolutionary trajectories in response to climate change. We used a common garden to examine genetically based coordination between leaf traits across 19 wild and cultivated tomato taxa. We found weak integration between leaf structure (e.g. leaf mass per area) and physiological function (photosynthetic rate, biochemical capacity and CO2 diffusion), even though all were arrayed in the predicted direction along a 'fast–slow' spectrum. This suggests considerable scope for unique trait combinations to evolve in response to new environments or in crop breeding. In particular, we found that partially independent variation in stomatal and mesophyll conductance may allow a plant to improve water-use efficiency without necessarily sacrificing maximum photosynthetic rates. Our study does not imply that functional trait spectra, such as the leaf economics spectrum, are unimportant, but that many important axes of variation within a taxonomic group may be unique and not generalizable to other taxa.
Data from: A metagenetic approach for revealing community structure of marine planktonic copepods
Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.
Data from: Trophic structure modulates community rescue following acidification
Community rescue occurs when a community that experiences a lethal stress persists only through the spread of rare types, either genotypes or species, resistant to the stress. Rescue interacts with trophic structure because a physical stress experienced by a focal assemblage within the community may also be experienced by its predators and prey. In general, trophic structure will facilitate rescue only when a stress has a less severe effect on a focal assemblage than on its predators. In other circumstances, when stress affects prey or has only a weak effect on predators, trophic structure is likely to hamper rescue. We exposed a community of phytoplankton and zooplankton derived from a natural lake to acidification in outdoor mesocosms large enough to support trophically complex communities. Rescue of the phytoplankton from severe acidification was facilitated by prior exposure to sublethal stress, confirming previous results from microcosm experiments. Even communities that have previously been less highly stressed were eventually rescued, however, probably because their zooplankton predators were more sensitive to acidification and became extinct. Our experiment shows how community rescue following severe stress is modulated by the differential effect of the stress relative to trophic level.
Data from: Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs
Life-history characteristics exert a profound influence upon the population structure of many marine organisms. However, relatively few genetic studies have compared direct with indirect-developing species in the same ecosystem or geographic region, and none to our knowledge within an Antarctic setting. To address this issue we have collected novel Amplified Fragment Length Polymorphism (AFLP) data from the direct-developing top shell Margarella antarctica to form a comparison with previously published data for the broadcast-spawning Antarctic limpet Nacella concinna. We scored 270 loci in 240 M. antarctica individuals sampled from five populations spanning the full length of the Antarctic Peninsula. Profound differences were identified in the strength and pattern of population structure between the two species, consistent with gene flow being highly restricted in M. antarctica relative to N. concinna.
Data from: Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single nucleotide polymorphism data
Marine systems have traditionally been thought of as "open" with few barriers to gene flow. In particular, many marine organisms in the Southern Ocean purportedly possess circumpolar distributions that have rarely been well verified. Here, we use the highly abundant and endemic Southern Ocean brittle star Ophionotus victoriae to examine genetic structure and determine whether barriers to gene flow have existed around the Antarctic continent. Ophionotus victoriae possesses feeding planktotrophic larvae with presumed high dispersal capability, but a previous study revealed genetic structure along the Antarctic Peninsula. To test the extent of genetic differentiation within O. victoriae, we sampled from the Ross Sea through the eastern Weddell Sea. Whereas two mitochondrial DNA markers (16S rDNA and COI) were employed to allow comparison to earlier work, a 2b-RAD single-nucleotide polymorphism (SNP) approach allowed sampling of loci across the genome. Mitochondrial data from 414 individuals suggested three major lineages, but 2b-RAD data generated 1,999 biallelic loci that identified four geographically distinct groups from 89 samples. Given the greater resolution by SNP data, O. victoriae can be divided into geographically distinct populations likely representing multiple species. Specific historical scenarios that explain current population structure were examined with approximate Bayesian computation (ABC) analyses. Although the Bransfield Strait region shows high diversity possibly due to mixing, our results suggest that within the recent past, dispersal processes due to strong currents such as the Antarctic Circumpolar Current have not overcome genetic subdivision presumably due to historical isolation, questioning the idea of large open circumpolar populations in the Southern Ocean.
Data from: Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida)
Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within-river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among-drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat-specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.
Data from: Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichthys minckleyi
Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The 'desert cichlid' Herichtys minckleyi is a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco-morphotypes coexist in small spring-fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species Herichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco-morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco-morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages.
Data from: Immediate impact of a hurricane on the structure of a tropical butterfly community
More intense and frequent hurricanes may lead to long-lasting effects to tropical ecosystems. Here we describe the immediate impact on the butterfly community of a lowland forest in Belize, following Hurricane Earl. Species richness and abundance increased post-hurricane, likely driven by convergence of the organisation between the canopy and understory communities.
Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome
A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics.
Data from: Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic
We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.
Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica
Secondary forests constitute a substantial proportion of tropical forestlands. These forests occur on both public and private lands and different underlying environmental variables and management regimes may affect post‐abandonment successional processes and resultant forest structure and biodiversity. We examined whether differences in ownership led to differences in forest structure, tree diversity, and tree species composition across a gradient of soil fertility and forest age. We collected soil samples and surveyed all trees in 82 public and 66 private 0.1‐ha forest plots arrayed across forest age and soil gradients in Guanacaste, Costa Rica. We found that soil fertility appeared to drive the spatial structure of public vs. private ownership; public conservation lands appeared to be non‐randomly located on areas of lower soil fertility. On private lands, areas of crops/pasture appeared to be non‐randomly located on higher soil fertility areas while forests occupied areas of lower soil fertility. We found that forest structure and tree species diversity did not differ significantly between public and private ownership. However, public and private forests differed in tree species composition: 11 percent were more prevalent in public forest and 7 percent were more prevalent in private forest. Swietenia macrophylla, Cedrela odorata, and Astronium graveolens were more prevalent in public forests likely because public forests provide stronger protection for these highly prized timber species. Guazuma ulmifolia was the most abundant tree in private forests likely because this species is widely consumed and dispersed by cattle. Furthermore, some compositional differences appear to result from soil fertility differences due to non‐random placement of public and private land holdings with respect to soil fertility. Land ownership creates a distinctive species composition signature that is likely the result of differences in soil fertility and management between the ownership types. Both biophysical and social variables should be considered to advance understanding of tropical secondary forest structure and biodiversity.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Data from: Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure
Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies infections. Techniques to determine large scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large scale applications. Using blood meal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be extrapolated to metabarcoding diet studies of other animals to couple information on diet and population structure.
Data from: Network-scale effects of invasive species on spatially-structured amphibian populations
<p>Understanding the factors affecting the dynamics of spatially-structured populations (SSP) is a central topic of conservation and landscape ecology. Invasive alien species are increasingly important drivers of the dynamics of native species. However, the impacts of invasives are often assessed at the patch scale, while their effects on SSP dynamics are rarely considered. We used long-term abundance data to test whether the impact of invasive crayfish on subpopulations can also affect the whole SSP dynamics, through their influence on source populations. From 2010 to 2018, we surveyed a network of 58 ponds and recorded the abundance of Italian agile frog clutches, the occurrence of an invasive crayfish, and environmental features. Using Bayesian hierarchical models, we assessed relationships between frog abundance in ponds and a) environmental features; b) connectivity within the SSP; c) occurrence of invasive species at both the patch- and the SSP-levels. If spatial relationships between ponds were overlooked, we did not detect effects of crayfish presence on frog abundance or trends. When we jointly considered habitat, subpopulation, and SSP features, processes acting at all these levels affected frog abundance. At the subpopulation scale, frog abundance in a year was related to habitat features, but was unrelated to crayfish occurrence at that site during the previous year. However, when we considered the SSP level, we found a strong negative relationship between frog abundance in a given site and crayfish frequency in surrounding wetlands during the previous year. Hence, SSP-level analyses can identify effects that would remain unnoticed when focussing on single patches. Invasive species can affect population dynamics even in not invaded patches, through the degradation of subpopulation networks. Patch-scale assessments of the impact of invasive species can thus be insufficient: predicting the long-term interplay between invasive and native populations requires landscape-level approaches accounting for the complexity of spatial interactions.</p>
Data from: Effects of contemporary shifts of range margins on patterns of genetic structure and mating system in two coastal plant species
Species' geographical ranges are often restricted due to niche limitation resulting in geographical isolation and reduced population size at range margins. Under the 'abundant center' paradigm, static marginal populations are thus expected to show higher genetic differentiation and lower genetic diversity than core populations. Low mate availability may also drive shifts towards higher propensity for selfing in geographically marginal populations. However, these predictions remain to be validated for contemporary range shifts occurring under current environmental change. This study is devoted to bridging this gap and assesses the spatial patterns of genetic structure and mating system across the geographical range of two coastal plant species characterized by contrasting contemporary range dynamics: the receding myrmecochorous Dune pansy (Viola tricolor subsp. curtisii) and the widespread expanding hydrochorous Rock samphire (Crithmum maritimum) Both species exhibited high propensity for selfing, with indications of inbreeding depression acting at early life stages. In Dune pansy, a biogeographical break was observed between core and marginal populations, with trailing-edge populations showing higher levels of genetic differentiation, reduced genetic diversity and higher levels of selfing estimated through progeny arrays. In contrast, genetic structuring was weak in Rock samphire and no clear spatial trends were observed in genetic diversity nor in mating system, likely the result of efficient long-distance seed dispersal by sea-surface currents. Our study highlights that key species differences in life-history traits related to dispersal and/or mate limitation modify the expectations of genetic diversity loss and mating system shift in contemporary range-expanding populations, as compared to historical core populations.
Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)
Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data.
Data from: Environmental structure and energetic consequences in groups of young mice
Microenvironments can have considerable physiological consequences for the inhabitants by influencing the movements of individual members. The microenvironment can permit more diverse aggregation patterns or restrict movements to certain dimensions. Here, we tested whether aspects of the microenvironment that influenced aggregation patterns also influenced the energetics of groups of young animals. We tested the effects of enclosure configuration on the group temperature and respiration of infant mice (Mus musculus). We monitored the huddle temperature and respiration of groups in flat, concave and conical enclosures, which varied in shape and available space, and consequently the types of movements they permitted. We found that the amount of available space (or density) had a stronger effect on the group temperature than did the shape of the enclosure or types of permissible movements. We found no evidence that density or shape of the arena strongly affected the respiration rate of the group, with groups showing similar levels of oxygen consumption in all treatments. The lower density enclosures conveyed a considerable metabolic savings to groups in comparison to those tested in a higher density enclosure. These findings show density can have a large effect on the energetics of young mice, and provide insights on how simple features of the environment will influence physiology in a changing world.
Data from: Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change
While the history of taxonomic diversification in open ocean lineages of ray-finned fish and elasmobranchs is increasingly known, the evolution of their roles within the open ocean ecosystem remains poorly understood. To assess the relative importance of these groups through time, we measured the accumulation rate of microfossil fish teeth and elasmobranch dermal denticles (ichthyoliths) in deep-sea sediment cores from the North and South Pacific gyres over the past 85 million years (Myr). We find three distinct and stable open ocean ecosystem structures, each defined by the relative and absolute abundance of elasmobranch and ray-finned fish remains. The Cretaceous Ocean (pre-66 Ma) was characterized by abundant elasmobranch denticles, but low abundances of fish teeth. The Palaeogene Ocean (66–20 Ma), initiated by the Cretaceous/Palaeogene mass extinction, had nearly four times the abundance of fish teeth compared with elasmobranch denticles. This Palaeogene Ocean structure remained stable during the Eocene greenhouse (50 Ma) and the Eocene–Oligocene glaciation (34 Ma), despite large changes in the overall accumulation of both groups during those intervals, suggesting that climate change is not a primary driver of ecosystem structure. Dermal denticles virtually disappeared from open ocean ichthyolith assemblages approximately 20 Ma, while fish tooth accumulation increased dramatically in variability, marking the beginning of the Modern Ocean. Together, these results suggest that open ocean fish community structure is stable on long timescales, independent of total production and climate change. The timing of the abrupt transitions between these states suggests that the transitions may be due to interactions with other, non-preserved pelagic consumer groups.
Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia
The control and eradication of invasive species is a common management strategy to protect or restore native biodiversity. On South Georgia in the Southern Ocean, the brown rat Rattus norvegicus was brought onto the island with the onset of whaling and sealing activity in the 1800s and has had a significant detrimental impact on key bird species of conservation concern. Efforts to eradicate rats from South Georgia using poisoned bait are ongoing. Despite the South Georgia rat eradication programme being the geographically largest and most ambitious eradication initiative to date, its success is facilitated by the potential that rat populations are effectively isolated by glacial barriers. This allows for localized eradication effort at manageable scales, leading to sequential eradication of individual populations with minimal risk of incursion from neighbouring areas. Here, we use the levels of population genetic divergence estimated from 299 single nucleotide polymorphism (SNP) loci and DNA sequence variation across 993 base pairs of the mitochondrial DNA cytochrome B locus to examine whether rat populations from nine glacially isolated areas on South Georgia are genetically distinct and so can be treated as independent eradication units. Bayesian clustering of individuals based on SNP similarity identified seven different genetic groups, which were confirmed using analyses based on pairwise genetic distance estimates and ordination of individuals using principal coordinate analysis. From a management perspective, these seven groups represent individual targets in baiting operations. Two mtDNA haplotypes were resolved across South Georgia, with a distinct geographical separation between the north-western and south-eastern populations. Approximate Bayesian computation (ABC) was used to identify that this divergence was a consequence of two separate historical colonization events. Synthesis and applications. We illustrate that molecular markers are a valuable tool in species management and pest eradication given that the spatial distribution of genetic diversity can: (i) identify demographically and genetically independent populations on which local eradication effort can be focussed, (ii) distinguish between incomplete eradication and immigration in situations where individuals remain after eradication has been attempted and (iii) identify the source of migrants when dispersal occurs over large spatial scales.
Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L. – insights from GWAS and GBS data
<p>Understanding the consequences of exotic diseases on native forests is important to evolutionary ecology and conservation biology because exotic pathogens have drastically altered US eastern deciduous forests. Cornus florida L. (flowering dogwood tree) is one such species facing heavy mortality. Characterizing the genetic structure of C. florida populations and identifying the genetic signature of adaptation to dogwood anthracnose (an exotic pathogen responsible for high mortality) remains vital for conservation efforts. By integrating genetic data from genotype-by-sequencing (GBS) of 289 trees across the host species range and distribution of disease, we evaluated the spatial patterns of genetic variation and population genetic structure of C. florida and compared the pattern to the distribution of dogwood anthracnose. Using GWAS and gradient forest analysis, we identified genetic loci under selection and associated with ecological and diseased regions. The results revealed signals of weak genetic differentiation of three or more subgroups nested within two clusters—explaining up to 2-6% of genetic variation. The groups largely corresponded to the regions within and outside the eastern Hot-Continental ecoregion, which also overlapped with areas within and outside the main distribution of dogwood anthracnose. The fungal sequences contained in the GBS data of sampled trees bolstered visual records of disease at sampled locations and were congruent with the reported range of D. destructiva, suggesting fungal sequences within host genomic data were informative for detecting or predicting disease. The genetic diversity between populations at diseased vs. disease-free sites across the range of C. florida showed no significant difference. We identified 72 SNPs from 68 loci putatively under selection, some of which exhibited abrupt turnover in allele frequencies along the borders of the Hot-Continental ecoregion and the range of dogwood anthracnose. One such candidate SNP was independently identified in two prior studies as a possible L-type lectin-domain containing receptor kinase. While diseased and disease-free areas do not significantly differ in genetic diversity, overall there are slight trends to indicate marginally smaller amounts of genetic diversity in disease-affected areas. Our results were congruent with previous studies that were based on a limited number of genetic markers in revealing high genetic variation and weak population structure in C. florida.</p>
ScienceDex guides
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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.