cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0398053
title: Data from: Grizzly bear response to fine spatial and temporal scale spring snow cover in Western Alberta

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Snow dynamics influence seasonal behaviors of wildlife, such as denning patterns and habitat selection related to the availability of food resources. Under a changing climate, characteristics of the temporal and spatial patterns of snow are predicted to change, and as a result, there is a need to better understand how species interact with snow dynamics. This study examines grizzly bear (Ursus arctos) spring habitat selection and use across western Alberta, Canada. Made possible by newly available fine-scale snow cover data, this research tests a hypothesis that grizzly bears select for locations with less snow cover and areas where snow melts sooner during spring (den emergence to May 31st). Using Integrated Step Selection Analysis, a series of models were built to examine whether snow cover information such as fractional snow covered area and date of snow melt improved models constructed based on previous knowledge of grizzly bear selection during the spring. Comparing four different models fit to 62 individual bear-years, we found that the inclusion of fractional snow covered area improved model fit 60% of the time based on Akaike Information Criterion tallies. Probability of use was then used to evaluate grizzly bear habitat use in response to snow and environmental attributes, including fractional snow covered area, date since snow melt, elevation, and distance to road. Results indicate grizzly bears select for lower elevation, snow-free locations during spring, which has important implications for management of threatened grizzly bear populations in consideration of changing climatic conditions. This study is an example of how fine spatial and temporal scale remote sensing data can be used to improve our understanding of wildlife habitat selection and use in relation to key environmental attributes.
DOI: 10.14288/1.0398057
title: Data from: Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Phenotypic plasticity is thought to facilitate the colonization of novel environments and shape the direction of evolution in colonizing populations. However, the relative prevalence of various predicted patterns of changes in phenotypic plasticity following colonization remain unclear. Here we use a whole-transcriptome approach to characterize patterns of gene expression plasticity in the gills of a freshwater-adapted and a saltwater-adapted ecotype of threespine stickleback (Gasterosteus aculeatus) exposed to a range of salinities. The response of the gill transcriptome to environmental salinity had a large shared component common to both ecotypes (2,159 genes) with significant enrichment of genes involved in transmembrane ion transport and the restructuring of the gill epithelium. This transcriptional response to freshwater acclimation is induced at salinities below two parts per thousand. There was also differentiation in gene expression patterns between ecotypes (2,515 genes), particularly in processes important for changes in the gill structure and permeability. Only 508 genes that differed between ecotypes also responded to salinity and no specific processes were enriched among this gene set, and an even smaller number (87 genes) showed evidence of changes in the extent of the response to salinity acclimation between ecotypes. No pattern of relative expression dominated among these genes, suggesting that neither gains nor losses of plasticity dominated the changes in expression patterns between the ecotypes. These data demonstrate that multiple patterns of changes in gene expression plasticity can occur following colonization of novel habitats.
DOI: 10.14288/1.0398058
title: Data from: Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Conserving tree populations safeguards forests since they represent key elements of the ecosystem. The genetic characteristics underlying the evolutionary success of the tree growth form: high genetic diversity, extensive gene flow and strong species integrity, contribute to their survival in terms of adaptability. However, different biological and landscape contexts challenge these characteristics. This study employs 63 de novo developed microsatellite or SSR (Single Sequence Repeat) markers in different datasets of nine Neotropical Magnolia species. The genetic patterns of these protogynous, insect-pollinated tree species occurring in fragmented, highly-disturbed landscapes were investigated. Datasets containing a total of 340 individuals were tested for their genetic structure and degree of inbreeding. Analyses for genetic structure depicted structuring between species, i.e. strong species integrity. Within the species, all but one population pair were considered moderate to highly differentiated, i.e. no indication of extensive gene flow between populations. No overall correlation was observed between genetic and geographic distance of the pairwise species’ populations. In contrast to the pronounced genetic structure, there was no evidence of inbreeding within the populations, suggesting mechanisms favouring cross pollination and/or selection for more genetically diverse, heterozygous offspring. In conclusion, the data illustrate that the Neotropical Magnolias in the context of a fragmented landscape still have ample gene flow within populations, yet little gene flow between populations.
DOI: 10.14288/1.0398060
title: Data from: A compendium of geochemical information from the Saanich Inlet water column

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Marine oxygen minimum zones (OMZs) are widespread and naturally occurring water column features that constitute ~7% of global ocean volume, but contribute disproportionately to biogeochemical cycling of carbon, nitrogen and climate active trace gases such as nitrous oxide and methane. Climate change compounded by other human activities is causing OMZ expansion. While microbial communities are the primary engines driving biogeochemical cycles in OMZs, our current understanding of microbial community metabolism is hindered by a lack of time-series observations charting responses to changing water column oxygen-deficiency. Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia is a model ecosystem for monitoring microbial community structure, function and dynamics in relation to changing levels of water column oxygen-deficiency extensible to coastal and open ocean OMZs. Here, we present nine years of monthly time series observations in Saanich Inlet encompassing water column chemistry and environmental sequence information. This compendium provides a unique ecological and biogeochemical framework for comparative community analysis and modelling efforts in OMZs throughout the global ocean.
DOI: 10.14288/1.0398061
title: Data from: Population structure of mountain pine beetle symbiont Leptographium longiclavatum and the implication on the multipartite beetle-fungi relationships

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Over 18 million ha of forests have been destroyed in the past decade in Canada by the mountain pine beetle (MPB) and its fungal symbionts. Understanding their population dynamics is critical to improving modeling of beetle epidemics and providing potential clues to predict population expansion. Leptographium longiclavatum and Grosmannia clavigera are fungal symbionts of MPB that aid the beetle to colonize and kill their pine hosts. We investigated the genetic structure and demographic expansion of L. longiclavatum in populations established within the historic distribution range and in the newly colonized regions. We identified three genetic clusters/populations that coincide with independent geographic locations. The genetic profiles of the recently established populations in northern British Columbia (BC) and Alberta suggest that they originated from central and southern BC. Approximate Bayesian Computation supports the scenario that this recent expansion represents an admixture of individuals originating from BC and the Rocky Mountains. Highly significant correlations were found among genetic distance matrices of L. longiclavatum, G. clavigera, and MPB. This highlights the concordance of demographic processes in these interacting organisms sharing a highly specialized niche and supports the hypothesis of long-term multipartite beetle-fungus co-evolutionary history and mutualistic relationships.
DOI: 10.14288/1.0398063
title: Data from: Reproductive losses due to climate change-induced earlier flowering are not the primary threat to plant population viability in a perennial herb

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Despite a global footprint of shifts in flowering phenology in response to climate change, the reproductive consequences of these shifts are poorly understood. Furthermore, it is unknown whether altered flowering times affect plant population viability. 2. We examine whether climate change-induced earlier flowering has consequences for population persistence by incorporating reproductive losses from frost damage (a risk of early flowering) in population models of a subalpine sunflower (Helianthella quinquenervis). Using long-term demographic data for three populations that span the species’ elevation range (8–15 years, depending on the population), we first examine how snowmelt date affects plant vital rates. To verify vital rate responses to snowmelt date experimentally, we manipulate snowmelt date with a snow removal experiment at one population. Finally, we construct stochastic population projection models and Life Table Response Experiments for each population. 3. We find that populations decline (λs &lt; 1) as snowmelt dates become earlier. Frost damage to flower buds, a consequence of climate change-induced earlier flowering, does not contribute strongly to population declines. Instead, we find evidence that negative effects on survival, likely due to increased drought risk during longer growing seasons, drive projected population declines under earlier snowmelt dates. 4. Synthesis. Shifts in flowering phenology are a conspicuous and important aspect of biological responses to climate change, but here we show that the phenology of reproductive events can be unreliable measures of threats to population persistence, even when earlier flowering is associated with substantial reproductive losses. Evidence for shifts in reproductive phenology, along with scarcer evidence that these shifts actually influence reproductive success, are valuable but can paint an incomplete and even misleading picture of plant population responses to climate change.
DOI: 10.14288/1.0398067
title: Data from: Temporal variation favors the evolution of generalists in experimental populations of Drosophila melanogaster

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;In variable environments, selection should favor generalists that maintain fitness across a range of conditions. However, costs of adaptation may generate fitness trade-offs and lead to some compromise between specialization and generalization that maximizes fitness. Here, we evaluate the evolution of specialization and generalization in 20 populations of Drosophila melanogaster experimentally evolved in constant and variable thermal environments for 3 years. We developed genotypes from each population at two temperatures after which we measured fecundity across eight temperatures. We predicted that constant environments would select for thermal specialists and that variable environments would select for thermal generalists. Contrary to our predictions, specialists and generalists did not evolve in constant and spatially variable environments, respectively. However, temporal variation produced a type of generalist that has rarely been considered by theoretical models of developmental plasticity. Specifically, genotypes from the temporally variable selective environment were more fecund across all temperatures than were genotypes from other environments. These patterns suggest certain allelic effects and should inspire new directions for modeling adaptation to fluctuating environments.
DOI: 10.14288/1.0398068
title: Data from: Sockeye salmon repatriation leads to population re-establishment and rapid introgression with native kokanee

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Re-establishing salmonid populations to areas historically occupied has substantial potential for conservation gains, however, such interventions also risk negatively impacting native resident stocks. Here, we assessed the success of the hatchery-assisted reintroduction of anadromous sockeye salmon (Oncorhynchus nerka) into Skaha Lake, British Columbia, Canada, and evaluated the genetic consequences for native kokanee, a freshwater-obligate ecotype, using single nucleotide polymorphism genotypic data collected from reference samples of spawning Okanagan River sockeye and Skaha Lake kokanee pre-sockeye reintroduction, along with annual trawl survey and angler-caught samples obtained over an eight-year period. Significant differentiation was detected between sockeye and kokanee reference samples, with &gt;99% stock assignment. Low proportions of sockeye and hybrids were detected within 2008 and 2010 age-0 trawl samples, however, by 2012, 28% were sockeye, rising to 41% in 2014. The number of hybrids detected rose proportionally with the increase in sockeye, and exhibited an intermediate phenotype. Our results indicate that reintroduction of anadromous sockeye to Skaha Lake is succeeding, with large numbers returning to spawn. However, hybridization with native kokanee is of concern due to the potential for demographic or genetic swamping, with on-going genetic monitoring necessary to assess the long-term effects of introgression and to support interactive fisheries management.
DOI: 10.14288/1.0398069
title: Data from: Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive lifespan

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Seasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian-linked loci. We detected no genetic differences in presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation-by-time as an important evolutionary mechanism underlying seasonal declines in reproductive life span and a need for greater consideration of other mechanisms such as time-dependent, adaptive adjustment of reproductive effort.
DOI: 10.14288/1.0398071
title: Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The relative importance of ecological versus non-ecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages—such as the distinct genetic groups that make up the ranges of many northern species—represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long-toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long-toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non-ecological factors to play a more important role in the maintenance of northern taxa.
DOI: 10.14288/1.0398073
title: Data from: QST FST comparisons with unbalanced half-sib designs

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;QST, a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between QST and FST, but that method is limited to balanced data sets with offspring related as half-sibs through shared fathers. We extend this approach to (1) allow for a model more suitable for some plant populations or breeding designs in which offspring are related through mothers (assuming independent fathers for each offspring; half-sibs by dam), and (2) by explicitly allowing for unbalanced data sets. The resulting approach is made available through the R package QstFstComp.
DOI: 10.14288/1.0398075
title: Data from: Similarities in temperature-dependent gene expression plasticity across time-scales in threespine stickleback (Gasterosteus aculeatus)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Phenotypic plasticity occurs at a variety of time-scales, but little is known about the degree to which plastic responses at different time-scales are associated with similar underlying molecular processes, which is critical for assessing the effects of plasticity on evolutionary trajectories. To address this issue, we identified differential gene expression in response to developmental temperature in the muscle transcriptome of adult threespine stickleback (Gasterosteus aculeatus) exposed to 12, 18, and 24 °C until hatch and then held at 18 °C for nine months, and compared these results to differential gene expression in response to adult thermal acclimation in stickleback developed at 18 °C and then acclimated to 5 and 25 °C as adults. Adult thermal acclimation affected the expression of 7,940 and 7,015 genes in response to cold and warm acclimation, respectively, and 4,851 of these genes responded in both treatments. In contrast, the expression of only 33 and 29 genes were affected by cold and warm development, respectively. The majority of the genes affected by developmental temperature were also affected by adult acclimation temperature. Many genes that were differentially expressed as a result of adult acclimation were associated with previously identified temperature-dependent effects on DNA methylation patterns, suggesting a role of epigenetic mechanisms in regulating gene expression plasticity during acclimation. Taken together, these results demonstrate similarities between the persistent effects of developmental plasticity on gene expression and the effects of adult thermal acclimation, emphasizing the potential for mechanistic links between plasticity acting at these different life stages.
DOI: 10.15468/dl.munvzv
title: Occurrence Download

description: A dataset containing 59318 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ginkgo biloba L."
 ]
}

 The dataset includes 59318 records from 676 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000461-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a5re9e
title: Occurrence Download

description: A dataset containing 28482 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is a344ee9f-f1b7-4761-be2c-58ee6d741395",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 28482 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038175-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xx5wtb
title: Occurrence Download

description: A dataset containing 5806 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sternula lorata"
 ]
}

 The dataset includes 5806 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038176-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/8zhjwb2z54
title: Original Western Blots for Joung et al. A Transcription Factor Atlas of Directed Differentiation

description: Original Western blots for Figure S5R,S and Data S1.3A
DOI: 10.17632/8zhjwb2z54.1
title: Original Western Blots for Joung et al. A Transcription Factor Atlas of Directed Differentiation

description: Original Western blots for Figure S5R,S and Data S1.3A
DOI: 10.15468/dl.fp2hcy
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 "TaxonKey is one of (Podocnemis erythrocephala [GBIF Backbone Taxonomy])"
 ]
}

 The dataset includes 135 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038177-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16923354
title: Reproducibility package for "Learning the Language of Phylogeny with MSA Transformer"

description: Materials (code and data) supporting the analyses reported in "Learning the Language of Phylogeny with MSA Transformer."