cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397683
title: Data from: The evolutionary history of dogs in the Americas

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. Remarkably, the closest detectable extant lineage to pre-contact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8,000 years ago.
DOI: 10.14288/1.0397685
title: Data from: Chlorpyrifos interacts with other agricultural stressors to alter stream communities in laboratory microcosms

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Chlorpyrifos is one of the most widely used agricultural insecticides in the world, but to date there is limited empirical information about its potential to interact with other common agricultural stressors. We conducted a 15-day, community-level microcosm experiment evaluating individual and combined effects of chlorpyrifos, nutrient enrichment, and sedimentation on stream invertebrate communities (abundance, biomass, richness, size structure, composition) and ecosystem processes (primary productivity and leaf decomposition). We found that sedimentation was the most detrimental stressor, with significant negative impacts on most invertebrate community and ecosystem function variables. Even though chlorpyrifos did not cause significant invertebrate mortality in the microcosms, it still altered ecosystem function by lowering leaf decomposition rates, probably through sublethal inhibition of invertebrate shredders. Furthermore, we observed a significant reversal interaction between chlorpyrifos and sediment for small-sized invertebrates collected in gravel (abundance in sediment x insecticide microcosms was 2.4 times lower than predicted by additivity), as well as an antagonistic interaction with nutrients on invertebrate richness in the same microhabitat (richness in nutrient x insecticide microcosms was 1.6 times higher than predicted by additivity). Our results suggest that chlorpyrifos has the potential to alter freshwater ecosystem function and interact non-additively with other common agricultural stressors. These findings are in keeping with a growing body of research highlighting that multiple stressor interactions and ecosystem processes should be considered when evaluating the impacts of organic toxicants on freshwater ecosystems.
DOI: 10.14288/1.0397686
title: Data from: Evolution of haploid selection in predominantly diploid organisms

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Diploid organisms manipulate the extent to which their haploid gametes experience selection. Animals typically produce sperm with a diploid complement of most proteins and RNA, limiting selection on the haploid genotype. Plants, however, exhibit extensive expression in pollen, with actively transcribed haploid genomes. Here we analyze models that track the evolution of genes that modify the strength of haploid selection to predict when evolution intensifies and when it dampens the “selective arena” within which male gametes compete for fertilization. Considering deleterious mutations, evolution leads diploid mothers to strengthen selection among haploid sperm/pollen, because this reduces the mutation load inherited by their diploid offspring. If, however, selection acts in opposite directions in haploids and diploids (“ploidally antagonistic selection”), mothers evolve to reduce haploid selection to avoid selectively amplifying alleles harmful to their offspring. Consequently, with maternal control, selection in the haploid phase either is maximized or reaches an intermediate state, depending on the deleterious mutation rate relative to the extent of ploidally antagonistic selection. By contrast, evolution generally leads diploid fathers to mask mutations in their gametes to the maximum extent possible, whenever masking (e.g., through transcript sharing) increases the average fitness of a father’s gametes. We discuss the implications of this maternal–paternal conflict over the extent of haploid selection and describe empirical studies needed to refine our understanding of haploid selection among seemingly diploid organisms.
DOI: 10.14288/1.0397687
title: Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of a wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha) and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio) and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity [pi]). We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence.
DOI: 10.14288/1.0397689
title: Data from: Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Background: Some clover species, particularly Trifolium subterraneum, have previously been reported to have highly unusual plastomes, relative to closely related legumes, enlarged with many duplications, gene losses and the presence of DNA unique to Trifolium, which may represent horizontal transfer. In order to pinpoint the evolutionary origin of this phenomenon within the genus Trifolium, we sequenced and assembled the plastomes of eight additional Trifolium species widely sampled from across the genus. Results: The Trifolium plastomes fell into two groups: those of Trifolium boissieri, T. strictum and T. glanduliferum (representing subgenus Chronosemium and subg. Trifolium section Paramesus) were tractable, assembled readily and were not unusual in the general context of Fabeae plastomes. The other Trifolium species (“core Trifolium”) proved refractory to assembly mainly because of numerous short duplications. These species form a single clade, which we call the “refractory clade” (comprising subg, Trifolium sections Lupinaster, Trifolium, Trichocephalum, Vesicastrum and Trifoliastrum). The characteristics of the refractory clade are the presence of numerous short duplications and 7-15% longer genomes than the tractable species. Molecular dating estimates that the origin of the most recent common ancestor (MRCA) of the refractory clade is approximately 13.1 million years ago (MYA). This is considerably younger than the estimated MRCA ages of Trifolium (c. 18.6 MYA) andTrifolium subg. Trifolium (16.1 MYA). Conclusions: We conclude that the unusual repetitive plastome type previously characterized in Trifolium subterraneum had a single origin within Trifolium and is characteristic of most (but not all) species of subgenus Trifolium. It appears that an ancestral plastome within Trifolium underwent an evolutionary change resulting in plastomes that either actively promoted, were permissive to, or were unable to control, duplications within the genome. The precise mechanism of this important change in the mode and tempo of plastome evolution deserves further investigation.
DOI: 10.14288/1.0397690
title: Data from: Origins and functional diversification of salinity-responsive Na+, K+ ATPase α1 paralogs in salmonids

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The Salmoniform whole-genome duplication is hypothesized to have facilitated the evolution of anadromy, but little is known about the contribution of paralogs from this event to the physiological performance traits required for anadromy, such as salinity tolerance. Here, we determined when two candidate salinity-responsive paralogs of the Na+, K+ ATPase α subunit (α1a and α1b) evolved and studied their evolutionary trajectories and tissue-specific expression patterns. We found that these paralogs arose during a small scale duplication event prior to the Salmoniform, but after the teleost, whole-genome duplication. The ‘freshwater paralog’ (α1a) is primarily expressed in the gills of Salmoniformes and an unduplicated freshwater sister-species (Esox lucius), and experienced positive selection in the fresh-water ancestor of Salmoniformes and Esociformes. Contrary to our predictions, the ‘saltwater paralog’ (α1b), which is more widely expressed than α1a, did not experience positive selection during the evolution of anadromy in the Coregoninae and Salmonine. To determine if parallel mutations in Na+, K+ ATPase α1 may contribute to salinity tolerance in other fishes, we studied independently evolved salinity-responsive Na+, K+ ATPase α1 paralogs in Anabas testudineus and Oreochromis mossambicus. We found that a quarter of the mutations occurring between salmonid α1a and α1b in functionally important sites also evolved in parallel in at least one of these species. Together, these data argue that paralogs contributing to salinity tolerance evolved prior to the Salmoniform whole-genome duplication and that strong selection and/or functional constraints have led to parallel evolution in salinity-responsive Na+, K+ ATPase α1 paralogs in fishes.
DOI: 10.14288/1.0397691
title: Data from: Responses to simulated winter conditions differ between threespine stickleback ecotypes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Abiotic factors can act as barriers to colonization and drive local adaptation. During colonization, organisms may cope with changes in abiotic factors using existing phenotypic plasticity, but the role of phenotypic plasticity in assisting or hindering the process of local adaptation remains unclear. To address these questions, we explore the role of winter conditions in driving divergence during freshwater colonization and the effects of plasticity on local adaptation in ancestral marine and derived freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We found that freshwater-resident stickleback had greater tolerance of acute exposure to low temperatures than marine stickleback, but these differences were abolished after acclimation to simulated winter conditions (9L:15D photoperiod at 4°C). Plasma chloride levels differed between the ecotypes, but showed a similar degree of plasticity between ecotypes. Gene expression of the epithelial calcium channel (ECaC) differed between ecotypes, with the freshwater ecotype demonstrating substantially greater expression than the marine ecotype, but there was no plasticity in this trait under these conditions in either ecotype. In contrast, growth (assessed as final mass) and the expression of an isoform of the electroneutral Na+/H+ exchanger (NHE3) exhibited substantial change with temperature in the marine ecotype that was not observed in the freshwater ecotype under the conditions tested here, which is consistent with evolution of these traits by a process such as genetic assimilation. These data demonstrate substantial divergence in many of these traits between freshwater and marine stickleback, but also illustrate the complexity of possible relationships between plasticity and local adaptation.
DOI: 10.14288/1.0397693
title: Data from: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most antagonistically with other mutations, a trend we also uncovered through analyses of datasets from other model systems. However, these beneficial mutations interacted multiplicatively (i.e., no epistasis) at the level of enzyme expression. By generating a model that predicts fitness from enzyme levels we could explain the observed sign epistasis as a result of overshooting the optimum defined by a balance between enzyme catalysis benefits and fitness costs. Knowledge of the phenotypic landscape also illuminated that, although the fitness peak was phenotypically far from the ancestral state, it was not genetically distant. Single beneficial mutations jumped straight toward the global optimum rather than being constrained to change the expression phenotypes in the correlated fashion expected by the genetic architecture. Given that adaptation in nature often results from optimizing gene expression, these conclusions can be widely applicable to other organisms and selective conditions. Poor interactions between individually beneficial alleles affecting gene expression may thus compromise the benefit of sex during adaptation and promote genetic differentiation.
DOI: 10.14288/1.0397695
title: Data from: Why less complexity produces better forecasts: an independent data evaluation of kelp habitat models

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Understanding how species are distributed in the environment is increasingly important for natural resource management, particularly for keystone and habitat forming species, and those of conservation concern. Habitat suitability models are fundamental to developing this understanding; however their use in management continues to be limited due to often-vague model objectives and inadequate evaluation methods. Along the Northeast Pacific coast, canopy kelps (Macrocystis pyrifera and Nereocystis luetkeana) provide biogenic habitat and considerable primary production to nearshore ecosystems. We investigated the distribution of these species by examining a series of increasingly complex habitat suitability models ranging from process-based models based on species' ecology to complex Generalised Additive Models applied to purpose-collected survey data. Seeking limits on model complexity, we explored the relationship between model complexity and forecast skill, measured using both cross-validation and independent data evaluation. Our analysis confirmed the importance of predictors used in models of coastal kelp distributions developed elsewhere (i.e., depth, bottom type, bottom slope, and exposure); it also identified additional important factors including salinity, and interactions between exposure and salinity, and slope and tidal energy. Comparative results showed that cross-validation can lead to over-fitting, while independent data evaluation clearly identified the appropriate model complexity for generating habitat forecasts. Our results also illustrate that, depending on the evaluation data, predictions from simpler models can out-perform those from more complex models. Collectively, the insights from evaluating multiple models with multiple data sets contribute to the holistic assessment of model forecast skill. The continued development of methods and metrics for evaluating model forecasts with independent data, and the explicit consideration of model objectives and assumptions, promise to increase the utility of model forecasts to decision makers.
DOI: 10.14288/1.0397696
title: Data from: Ionome and elemental transport kinetics shaped by parallel evolution in threespine stickleback

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here we quantified the suite of elements in individuals (i.e., ionome) and the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony plating is associated with changes in the ionome and nutrient recycling. More broadly, we find that adaptation of marine fish to freshwater conditions shifts the ionomes of natural populations and populations raised in common gardens. In both cases ionomic divergence between populations was primarily driven by differences in trace elements rather than elements typically associated with bone. These findings demonstrate the utility of ecological stoichiometry and the importance of ionome-wide data in understanding eco-evolutionary dynamics.
DOI: 10.14288/1.0397697
title: Data from: High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Background: Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted. Results: A total of 274 candidate miRNAs were identified and 3733 target unigenes were annotated by performing a BLASTX. Through integrated GO and KEGG function annotation, 23 miRNA regulating 131 target genes were identified as lipid metabolism, regulating fatty acid biosynthesis, accumulation and catabolism. We observed one, two, and four miRNAs of lipid metabolism which were specially expressed in C. Meiocarpa, C. oleifera, and the two species collectively, respectively. At 30% moisture contents, C. meiocarpa and C. oleifer produced nine and eight significant differentially expressed miRNAs, respectively, with high fatty acid synthesis and accumulation activities. Across the two species, 12 significant differentially expressed miRNAs were identified at the 50% moisture content. Conclusions: Sequencing of small-RNA revealed the presence of 23 miRNAs regulating lipid metabolism in camellia seed during natural drying and permitted comparative miRNA profiles between C. Meiocarpa and C. oleifera. Furthermore, this study successfully identified the best drying environment at which the quantity and quality of lipid in camellia seed are at its maximum.
DOI: 10.15468/dl.2pj35t
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((88 31,103 31,103 38,88 38,88 31))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera uncia (Schreber, 1775)"
 ]
}

 The dataset includes 20 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004358-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t4kzkv
title: Occurrence Download

description: A dataset containing 213493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hippolais icterina (Vieillot, 1817)",
 "HasCoordinate is true",
 "Year is greater than 1989",
 "Year is less than 2026",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is Absent"
 ]
 }
 },
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 213493 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004349-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4rb9h4
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Kostermansia Soegeng"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004360-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bsqgeh
title: Occurrence Download

description: A dataset containing 313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (India, China, Myanmar, Viet Nam, Cambodia, Indonesia, Nepal, Philippines, Malaysia, Chinese Taipei, Bangladesh, Lao People’s Democratic Republic, Thailand, Bhutan)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Populus nigra L."
 ]
}

 The dataset includes 313 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004359-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ex79ft
title: Occurrence Download

description: A dataset containing 159372 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vitis vinifera L."
 ]
}

 The dataset includes 159372 records from 1050 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004338-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.