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.
131
datasets available to search
ShareScore release 0.9.0
Dataset results
131 results for “forest genetics”
Data from: Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae)
Habitat fragmentation and changed land use have seriously reduced population size in many tropical forest tree species. Formerly widespread species with limited gene flow may be particularly vulnerable to the negative genetic effects of forest fragmentation and small population size. Vateriopsis seychellarum (Dipterocarpaceae) is a formerly widespread canopy tree of the Seychelles, but is now reduced to 132 adult individuals distributed in eleven sites. Using ten microsatellite loci, a genetic inventory of all adult trees and a sample of 317 progeny, we demonstrate that despite its restricted range, overall genetic diversity was relatively high (HE: 0.56). The juvenile cohort, however, had significantly lower allelic richness (adults RS: 3.91; juveniles RS: 2.83) and observed heterozygosity than adult trees (adults HO: 0.62; juveniles HO: 0.48). Rare alleles were fewer and kinship between individuals was stronger in juveniles. Significant fine-scale spatial genetic structure was observed in remnant adults, and parentage analysis indicated that more than 90% of sampled progeny disperse <25 m and pollen dispersed <50 m. The molecular data confirmed that two populations were derived entirely from self-fertilized offspring from a single surviving mother tree. These populations produce viable offspring. Despite this extreme genetic bottleneck, self-compatibility may provide V. seychellarum with some resistance to the genetic consequences of habitat fragmentation, at least in the short term. We discuss our findings in the context of other rare and threatened dipterocarp species which are vulnerable to mis-management of genetic resources and population fragmentation.
Data from: Genet dynamics of a regenerating dwarf bamboo population across heterogeneous light environments in a temperate forest understorey
Despite the advantage of plant clonality in patchy environments, studies focusing on genet demography in relation to spatially heterogeneous environments remain scarce. Regeneration of bamboos in forest understoreys after synchronous die-off provides an opportunity for assessing how they come to proliferate across heterogeneous light environments. In a Japanese forest, we examined genet demography of a population of Sasa kurilensis over a 7-year period starting 10 years after die-off, shortly after which some genets began spreading horizontally by rhizomes. The aboveground biomass was estimated and genets were discriminated in 9-m2 plots placed under both canopy gaps and closed canopies. Overall, the results suggest that the survival and spread of more productive genets and the spatial expansion of genets into closed canopies underlie the proliferation of S. kurilensis. Compared to canopy gaps, the recovery rate of biomass was much slower under closed canopies for the first 10 years after the die-off, but became accelerated during the next seven years. Genet survival was greater for more productive genets (with greater initial number of culms), and the spaces occupied by genets that died were often colonized afterward by clonal growth of surviving genets. The number of genets decreased under canopy gaps due to greater mortality, but increased under closed canopies where greater number of genets colonized clonally from outside the plots than genets died. The colonizing genets were more productive (having larger culms) than those originally germinated within the plots, and the contribution of colonizing genets to the biomass was greater under closed canopies. Our study emphasizes the importance of investigating genet dynamics over relevant spatio-temporal scales to reveal processes underlying the success of clonal plants in heterogeneous habitats.
Data from: Applications of random forest feature selection for fine-scale genetic population assignment
Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest, and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP dataset for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than FST-selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each dataset, respectively, a level of accuracy never reached for these species using FST-selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic datasets to improve assignment for management and conservation of exploited populations.
Data from: Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest
Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi-strata capture-recapture models, to infer changes in mobility over time in seven sympatric, forest-dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographic patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post-fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life-history of forest-dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.
Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia
Phylogeographic patterns of trees in topographically subdued, unglaciated landscapes are under-reported, and might reflect population persistence and the influences of environment and distance over historical (~2.6Mya-present) and contemporary (recent generations) time-scales. We examined this hypothesis using genetic analyses of four slowly evolving non-coding chloroplast sequences and 16 nuclear microsatellites in the tree Corymbia calophylla from south-western Australia that has been unglaciated since the Permian (.300-250Mya). We found strong population differentiation for chloroplast DNA and low differentiation for nuclear loci, consistent with higher gene flow by pollen than seed. We identified three divergent chloroplast lineages distributed in central, north and south geographic regions, and diversifying from the early (.3.028Mya), mid- (.0.793Mya) and late- (.0.426Mya) Pleistocene, respectively. Moderate-high nucleotide diversity with population-specific haplotypes supported long-term persistence but diversification of lineages provided evidence of unexpected episodic range expansion. We suggest this pattern reflects environmental influences of climatic oscillations during progressive drying of south-western Australia from the early Pleistocene. Significant tests for isolation by environment for nuclear loci also supported an influence of contemporary environmental (aridity) conditions on genetic structure, but isolation by distance (IBD) was greater. Significant chloroplast and nuclear IBD suggested distance was a major influence on gene flow at both time-scales.
Data from: Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations
Afforestation is a common and widespread management practice throughout the world, yet its implications for the genetic diversity of native populations are still poorly understood. We examined the effect of Aleppo pine (Pinus halepensis) plantations on the genetic composition of nearby conspecific native populations. We focused on two native populations in Israel with different levels of isolation from the surrounding plantations and compared the genetic diversity of naturally established young trees within the native populations with that of local native adults, using nine nuclear microsatellite markers. We found that the genetic composition of the recruits was significantly different from that of local adults in both populations, with allelic frequency changes between generations that could not be ascribed to random drift, but rather to substantial gene flow from the surrounding planted Aleppo pine populations. The more isolated population experienced a lower gene flow level (22%) than the less isolated population (49%). The genetic divergence between native populations at the adult-tree stage (Fst = 0.32) was more than twice as high as that of the young trees naturally established around native adults (Fst = 0.15). Our findings provide evidence for a rapid genetic homogenization process of native populations following the massive planting efforts in the last decades. These findings have important implications for forest management and nature conservation and constitute a warning sign for the risk of translocation of biota for local biodiversity.
Data from: Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect
It is challenging to unravel the history of organisms with highly scattered populations. Such species may have fragmented distributions because extant populations are remnants of a previously more continuous range, or because the species has narrow habitat requirements in combination with good dispersal capacity (naturally or vector borne). The northern pine processionary moth Thaumetopoea pinivora has a scattered distribution with fragmented populations in two separate regions, northern and south-western Europe. The aims of this study were to explore the glacial and postglacial history of T. pinivora, and add to the understanding of its current distribution and level of contemporary gene flow. We surveyed published records of its occurrence and analysed individuals from a representative subset of populations across the range. A 633 bp long fragment of the mtDNA COI gene was sequenced and nine polymorphic microsatellite loci were genotyped. Only nine nucleotide sites were polymorphic in the COI gene and 90% of the individuals from across its whole range shared the same haplotype. The microsatellite diversity gradually declined towards the north, and unique alleles were found in only three of the northern and three of southern sites. Genetic structuring did not indicate complete isolation among regions, but an increase of genetic isolation by geographic distance. Approximate Bayesian model choice suggested recent divergence during the postglacial period, but glacial refugia remain unidentified. The progressive reduction of suitable habitats is suggested to explain the genetic structure of the populations and we suggest that T. pinivora is a cold-tolerant relict species, with situation-dependent dispersal.
Data from: Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics
Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation.
Data from: Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic Forest
Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.
Data from: Effects of fire regime on the population genetics of natural pine stands, in Genetic structure of forest trees in biodiversity hotspots at different spatial scales (Ph.D. thesis).
The recurrence of wildfires is predicted to increase worldwide due to climate change, resulting in severe impacts on biodiversity and ecosystem functioning. We used simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers to examine the effects of fire regime on genetic diversity, demographic history and fine-scale spatial genetic structure (SGS) of Pinus pinaster and P. halepensis, two conifers with similar adaptations to fire in the eastern Iberian Peninsula. Stands growing under high (HiFi) or low (LoFi) frequency of crown fires had similar levels of genetic diversity and similar demographic history, with bottlenecks detected in all stands in both species. HiFi populations were not genetically depleted, suggesting that adaptations such as a diverse canopy seed bank due to serotinous cones, an early age of first flowering and high gene flow buffer against possible reductions of genetic diversity. Significantly stronger SGS at SNPs in HiFi than LoFi stands of P. halepensis suggested fire-related altered dispersal possibly combined with microenvironmental selection in this fire-sensitive "seeder" species. In contrast, SGS at SNP markers was unrelated to fire regime in P. pinaster. This could be a consequence of more pronounced fire-resistance in this species enabling some adults to survive fire, hence causing a lower dependence on post-fire regeneration. Our results highlight that the impact of fire differs in species with similar life-history traits. Therefore, species-specific studies are needed to understand the role of wildfires for the evolution of future forests
Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae)
<p>The Atlantic and Amazon rainforests have a shared but unclear past, with intermittent connections resulting from historical climate change. We investigate these connections by studying the phylogeography and climatic niche of the disjunct distributed frog<em> Lithobates palmipes</em>. We sequenced two fragments of mitochondrial DNA from Atlantic Forest (AtF) and Amazonia (AmF) individuals and evaluated how genetic diversity is distributed in space and whether past demographic changes occurred. Also, we evaluated the existence of past suitable connections between biomes for<em> L. palmipes</em> through ecological niche models (ENM) and tested for niche divergence. The AtF group is nested within the AmF group and closely related to individuals from eastern Amazonia, a pattern recovered in many species that used northeast connection routes. We found evidence of recurrent use of connections in different directions and time during the Pleistocene, resulting in genetic structure between biomes, with no signal of demographic change and evidence of niche divergence across both genetic groups. ENMs indicated suitable areas connecting forests throughout northeastern Brazil during the Pleistocene. Mitochondrial lineages do not match biomes exactly. One lineage is composed of AtF populations and eastern Amazonia individuals. The other is composed of western Amazonia individuals, suggesting an effect of past climatic heterogeneity within the Amazonia forest. This is the first evidence that this route drove genetic and ecological diversity for amphibians recently, a group with habits and ecological requirements different from other vertebrates that have been shown to use this putative corridor.</p>
Supplementary material 1 from: Hermes C, Döpper A, Schaefer MH, Segelbacher G (2016) Effects of forest fragmentation on the morphological and genetic structure of a dispersal-limited, endangered bird species. Nature Conservation 16: 39-58. https://doi.org/10.3897/natureconservation.16.10905
Development of species-specific microsatellite primers : Explanation note: The supplementary material contains a detailed description of the development of a set of 10 microsatellite primers for the Ecuadorian Tapaculo, including primer sequences and gene bank accession numbers.
Growth-defense tradeoffs shape the genetic composition of aspen forests
<p><span><span><span><span><span><span><span><span><span><span><span>All organisms experience fundamental conflicts between divergent metabolic processes. In plants, a pivotal conflict occurs between allocation to growth, which accelerates resource acquisition, and to defense, which protects existing tissue against herbivory. Tradeoffs between growth and defense traits are not universally observed, and a fundamental prediction of plant evolutionary ecology is that context-dependence of these tradeoffs contributes to the maintenance of intraspecific variation in defense. This prediction has rarely been tested, however, and the evolutionary consequences of growth-defense tradeoffs in different environments are poorly understood. Here we show that intraspecific trait tradeoffs interact with competitive environment to drive natural selection of tree genotypes corresponding to their growth-defense phenotypes. Our results show for the first time that a functional trait tradeoff, when coupled with environmental variation, causes real-time divergence in the genetic architecture of forest stands. Specifically, competitive selection for faster growth resulted in dominance by fast-growing tree genotypes that were poorly defended against natural enemies. This outcome is a signature example of eco-evolutionary dynamics: competitive interactions affected microevolutionary trajectories on a timescale relevant to subsequent ecological interactions. Eco-evolutionary drivers of tree growth and defense are thus critical to stand-level trait variation, which structures communities and ecosystems over expansive spatiotemporal scales.</span></span></span></span></span></span></span></span></span></span></span></p>
Population structure and genetic variation of fragmented mountain birch forests in Iceland
<p>Data avilability for the manuscript JOH-2022-096.R2 accepted for application</p>
An evaluation of isolation by distance (IBD) and isolation by resistance (IBR) on genetic structure of the Persian squirrel (Sciurus anomalus) in the Zagros forests of Iran
<p>For conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modelling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.</p>
Data from: Population genetics of Manihot esculenta ssp. flabellifolia gives insight into past distribution of xeric vegetation in a postulated forest refugium area in northern Amazonia
Open the record for dataset details and reuse information.
Data from: The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca)
Open the record for dataset details and reuse information.
Data from: Cryptic diversity and population genetic structure in the rare, endemic, forest-obligate, slender geckos of the Philippines
Open the record for dataset details and reuse information.
Data from: Forest cover mediates genetic connectivity of northwestern cougars
Open the record for dataset details and reuse information.
Data from: Does long distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape
Open the record for dataset details and reuse information.
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.