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.
62
datasets available to search
ShareScore release 0.9.0
Dataset results
62 results for “mixed population”
Mixed population trends inside a California protected area: Evidence from long-term community science monitoring
<p><span>Protected areas are one of the most widespread and accepted conservation interventions, yet their population trends are rarely compared to regional trends to gain insight into their effectiveness. Here, we leverage two long-term community science datasets to demonstrate mixed effects of protected areas on long-term bird population trends. We analyzed 31 years of bird transect data recorded by community volunteers across all major habitats of Stanford University's Jasper Ridge Biological Preserve to determine the population trends for a sample of 66 species. We found that nearly a third of species experienced long-term declines, and on average, all species declined by 12%. Further, we averaged species trends by conservation status and key life history attributes to identify correlates and possible drivers of these trends. Observed increases in some cavity-nesters and declines of scrub-associated species suggest that long-term fire suppression may be a key driver, reshaping bird communities through changes in forest and chaparral structure and composition. Additionally, we compared our results to those of the North American Breeding Bird Survey's Central California Coast region (n = 55 species) to place Jasper Ridge in a broader context. Most species experienced similar directional population trends inside vs. outside of the preserve, and only eight species (14.5%) did better inside this small, protected area. Therefore, we must identify relevant management strategies for declining populations and explicitly consider how existing protected areas target and manage each species. Further, this analysis underscores the importance of local and national community science for revealing nuanced long-term bird population trends.</span></p>
How early does the selfing syndrome arise? Associations between selfing ability and flower size within populations of the mixed mater Collinsia verna
<p>Widespread associations between selfing rate and floral size within and among taxa suggest that these traits may evolve in concert. Does this association develop immediately, because of shared genetic/developmental control, or stepwise with selection shaping the evolution of one trait following the other? If the former, then association ought to appear within and across populations. We explore this fundamental question in three populations of the mixed-mater Collinsia verna where autonomous selfing (AS) ability has been shown to be under selection by the pollination environment. We grew clonal replicates of C. verna in a controlled environment to characterize broad-sense genetic correlations among traits within populations and to assess whether divergence in mating system and floral traits among these populations is consistent with their previously observed selection pressures. As predicted by their respective pollination environments, we demonstrate significant genetic divergence among populations in AS ability. However, patterns of divergence in floral traits (petal, stamen, and style size, stigmatic receptivity, and stigma-anther distance) were not as expected. Within populations, genetic variation in AS appeared largely independent from floral traits, except for a single weak negative association in one population between flower size and AS rate. Together, these results suggest that associations between selfing rate and floral traits across Collinsia species are not reflected at microevolutionary scales. If C. verna were to continue evolving toward the selfing syndrome, floral trait evolution would likely follow stepwise from mating system evolution.</p>
Asymmetric density-dependent competition does not contribute to the maintenance of sex in a mixed population of sexual and asexual Potamopyrgus antipodarum
<p>Asexual reproduction is expected to have a two-fold reproductive advantage over sexual reproduction, owing to the cost of producing males in sexual subpopulations. The persistence of sexual females thus requires an advantage to sexual reproduction, at least periodically. Here we tested the hypothesis that asexual females are more sensitive to limited resources. Under this idea, fluctuations in the availability of resources (<em>per capita</em>) could periodically favor sexual females when resources become limited. We combined sexual and asexual freshwater snails (<em>Potamopyrgus antipodarum</em>) together in nylon mesh enclosures at three different densities in an outdoor mesocosm. After one month, we counted the brood size of fertile female snails. We found that fecundity declined significantly with increasing density. However, sexual females did not produce more offspring than asexual females at any of the experimental densities. Our results thus suggest that the cost of sexual reproduction in <em>P. antipodarum</em> is not ameliorated by periods of intense resource competition.</p>
Differentiation of rhizosphere fungal assemblages by host ploidy level in mixed-ploidy Larrea tridentata populations
<p class="MsoNormal">Polyploidy—whole genome duplication—is common in plants. Studies over the last several decades have documented numerous mixed-ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations is possible by niche differentiation. Specifically, one mechanism facilitating ploidy co-occurrence is microbially-mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush (<em>Larrea tridentata</em>), a dominant desert shrub of the southwestern U.S. and northern Mexico. We sequenced root-associated fungal taxa in soil diploid, autotetraploid, and autohexaploid plants growing in two naturally-occurring mixed-cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a precondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long-term persistence of multiple cytotypes within populations.</p>
Simulating genetic mixing in strongly structured populations of the threatened southern brown bandicoot (Isoodon obesulus)
Open the record for dataset details and reuse information.
Asymmetric density-dependent competition does not contribute to the maintenance of sex in a mixed population of sexual and asexual Potamopyrgus antipodarum
Open the record for dataset details and reuse information.
Mixed population trends inside a California protected area: Evidence from long-term community science monitoring
Open the record for dataset details and reuse information.
Differentiation of rhizosphere fungal assemblages by host ploidy level in mixed-ploidy Larrea tridentata populations
Open the record for dataset details and reuse information.
How early does the selfing syndrome arise? Associations between selfing ability and flower size within populations of the mixed mater Collinsia verna
Open the record for dataset details and reuse information.
Data from: Dynamics of mixed-ploidy populations under demographic and environmental stochasticities
Open the record for dataset details and reuse information.
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
<p><span><span><span><span><span><span><span><span><span><span><span>Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior onBayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effectof the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyze datasets containing both populations and species variation when its computational-efficiency is needed.</span></span></span></span></span></span></span></span></span></span></span></p>
Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure
<p>Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age and that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure, by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Erie's commercial and recreational walleye (<em>Sander vitreus</em>) fisheries and estimate the relative harvest of weakly differentiated stocks. We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks (mean pairwise F<sub>ST</sub> = 0.001) with 95% reassignment accuracy. An outcome not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks supported the majority of the harvest during peak harvest (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in stock-specific harvest existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.</p>
Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata
<p><strong>Premise of the study</strong></p> <p>Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of <em>Larrea tridentata </em>(creosote bush) in the Sonoran Desert, California, USA, where prior work documented ploidy-specific root-associated microbes.</p> <p><strong>Methods</strong></p> <p>We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intra-ploidy vs. inter-ploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants.</p> <p><strong>Key results</strong></p> <p>Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced greater biomass than those grown in soils from further away from plants of a different ploidy. This suggests the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations.</p> <p><strong>Conclusions</strong></p> <p>This is the first evidence, to our knowledge, consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.</p>
Propensity for selfing varies within a population of hermaphroditic snails: coexistence of selfers, outcrossers, and mixed-mating individuals
<p class="MsoNormal">To understand mating-system evolution in self-compatible hermaphrodites, variation in selfing rates is highly relevant. Empirical studies are rarely designed to capture variation between individuals, instead often comparing species and populations. Yet, evolution primarily occurs within populations, rendering among-individual variation essential. </p> <p class="MsoNormal">Observed individual selfing rates depend on the environment (<em>e.g.</em>, differences in mate availability) and individuals' propensity for selfing. We quantified individual variation in selfing propensity in the snail <em>Radix balthica</em> by conducting laboratory mating trials that manipulated mate availability (low <em>vs.</em> moderate) and estimating selfing rates from progeny arrays. We also measured female lifetime fitness. We found substantial among-individual variation in selfing propensity, including pure selfers (32%), pure outcrossers (31%), and mixed-mating individuals that selfed and outcrossed (37%). Experimental levels of mate availability did not significantly affect selfing rates. Selfers had reduced female liftetime fitness.</p> <p class="MsoNormal">Our results show that the propensity for selfing can differ considerably among individuals, with similar proportions of selfers, outcrossers, and mixed maters. As mate availability did not affect selfing, our "moderate" level might still have been too low to prompt selfers to outcross. This and the observed fitness differences also cautiously suggest that investigating the heritability of selfing propensities might be worthwhile in this population.</p>
Disentangling the effects of population mixing and propagule amount in rare plant translocations
Open the record for dataset details and reuse information.
Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure
Open the record for dataset details and reuse information.
Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata
Open the record for dataset details and reuse information.
Genomics-enabled mixed-stock analysis uncovers intraspecific migratory complexity and detects unsampled populations in a harvested fish
Open the record for dataset details and reuse information.
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
Open the record for dataset details and reuse information.
Mixed-stock analysis reveals long-distance movements and few populations with large harvest contributions in lake-migratory brook trout
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.