cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397803
title: Data from: Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow and natural selection in shaping patterns of population structure

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera (2) isolation-by-distance and (3) natural selection. Introgression was detected only at the margins of the species’ distribution. Isolation-by-distance was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia. We identified a large number of FST outliers. GO analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, while in southern British Columbia heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci.
DOI: 10.14288/1.0397804
title: Data from: Quantifying how constraints limit the diversity of viable routes to adaptation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Convergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.
DOI: 10.14288/1.0397805
title: Data from: Metabolic depression and the evolution of hypoxia tolerance in threespine stickleback, Gasterosteus aculeatus

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Anthropogenic increases in global temperature and agricultural runoff are increasing the prevalence of aquatic hypoxia throughout the world. We investigated the potential for a relatively rapid evolution of hypoxia tolerance using two isolated (for less than 11 000 years) populations of threespine stickleback: one from a lake that experiences long-term hypoxia (Alta Lake, British Columbia) and one from a lake that does not (Trout Lake, British Columbia). Loss-of-equilibrium (LOE) experiments revealed that the Alta Lake stickleback were significantly more tolerant of hypoxia than the Trout Lake stickleback, and calorimetry experiments revealed that the enhanced tolerance of Alta Lake stickleback may be associated with their ability to depress metabolic rate (as indicated by metabolic heat production) by 33% in hypoxia. The two populations showed little variation in their capacities for O2 extraction and anaerobic metabolism. These results reveal that intraspecific variation in hypoxia tolerance can develop over relatively short geological timescales, as can metabolic rate depression, a complex biochemical response that may be favoured in long-term hypoxic environments.
DOI: 10.14288/1.0397806
title: Data from: Complementary and alternative asthma treatments and their association with asthma control: a population-based study

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Objectives: Many patients with asthma spend time and resources consuming complementary and alternative medicines (CAMs). This study explores whether CAM utilization is associated with asthma control and the intake of asthma controller medications. Design: Population-based, prospective cross-sectional study Setting: general population residing in two census areas in the province of British Columbia, Canada. Recruitment was based on random-digit dialing of both landlines and cell phones. Participants: 486 patients with self-reported physician-diagnosis of asthma (mean age 52 years; 67.3% female). Primary and secondary outcome measures: We assessed CAM use over the previous 12 months, level of asthma control as defined by the Global Initiative for Asthma (GINA), and the self-reported intake of controller medications. Multivariate logistic regression was performed to study the relationship between any usage of CAMs (outcome), asthma control and controller medication usage, adjusted for potential confounders. Results: A total of 179 (36.8%) of the sample reported CAM usage in the past 12 months. Breathing exercises (17.7%), herbal medicines (10.1%), and vitamins (9.7%) were the most popular CAMs reported. After adjustment, female sex (OR: 1.66; 95% CI: 1.09-2.52) and uncontrolled asthma( vs. controlled asthma, OR: 2.25, 95% CI: 1.30-3.89) were associated with a higher likelihood of using any CAMs in the past 12 months. Controller medication use was not associated with CAM usage in general and in the subgroups defined by asthma control. Conclusion: Clinicians and policy makers need to be aware of the high prevalence of CAM use in patients with asthma and its association with lack of asthma control.
DOI: 10.14288/1.0397807
title: Data from: Exposure to predators does not lead to the evolution of larger brains in experimental populations of threespine stickleback

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Natural selection is often invoked to explain differences in brain size among vertebrates. However, the particular agents of selection that shape brain size variation remain obscure. Recent studies suggest that predators may select for larger brains because increased cognitive and sensory abilities allow prey to better elude predators. Yet, there is little direct evidence that exposure to predators causes the evolution of larger brains in prey species. We experimentally tested this prediction by exposing families of 1000-2000 F2 hybrid benthic-limnetic threespine stickleback to predators under naturalistic conditions, along with matched controls. After two generations of selection, we found that fish from the predator addition treatment had significantly smaller brains (specifically smaller telencephalons and optic lobes) than fish from the control treatment. After an additional generation of selection, we reared experimental fish in a common environment and found that this difference in brain size was maintained in the offspring of fish from the predator addition treatment. Our results provide direct experimental evidence that (a) predators can indeed drive the evolution of brain size – but not in the fashion commonly expected and (b) that the tools of experimental evolution can be used to the study the evolution of the vertebrate brain.
DOI: 10.14288/1.0397808
title: Data from: A test of hybrid growth disadvantage in wild, free-ranging species pairs of threespine sticklebacks (Gasterosteus aculeatus) and its implications for ecological speciation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ecological speciation is the evolution of reproductive isolation as a direct or indirect consequence of divergent natural selection. Reduced performance of hybrids in nature is thought to be an important process by which natural selection can favour the evolution of assortative mating and drive speciation. Benthic and limnetic sympatric species of threespine stickleback (Gasterosteus aculeatus) are adapted to alternative trophic niches (bottom browsing versus open water planktivory, respectively) and reduced feeding performance of hybrids is thought to have contributed to the evolution of reproductive isolation. We tested this “hybrid-disadvantage hypothesis” by inferring growth rates from otoliths sampled from wild, free-ranging benthic, limnetic, and hybrid sticklebacks from two lakes. There were significant differences in growth rate between lakes, life-history stages, and among years (maximum P = 0.02), as well as interactions between most factors, but not between hybrid and parental species sticklebacks in most comparisons. Our results provide little evidence of a growth disadvantage in hybrid sticklebacks when free-ranging in nature. While trophic ecology per se may contribute less to ecological speciation than envisioned, it may act in concert with other aspects of stickleback biology, such as interactions with parasites, predators, competitors and/or sexual selection, to present strong multifarious selection against hybrids.
DOI: 10.14288/1.0397810
title: Data from: Divergence is focused on few genomic regions early in speciation: incipient speciation of sunflower ecotypes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Early in speciation, when populations are undergoing the transition from local adaptation to incipient species, is when a number of transient, but potentially important, processes appear to be most easily detected. These include signatures of selective sweeps that can point to asymmetry in selection between habitats, divergence hitchhiking and associations of adaptive genes with environments. In a genomic comparison of ecotypes of the prairie sunflower, Helianthus petiolaris, occurring at Great Sand Dunes National Park (Colorado), we found that selective sweeps were mainly restricted to the dune ecotype and that there was variation across the genome in whether proximity to the non-dune population constrained or promoted divergence. The major regions of divergence were few and large between ecotypes, in contrast with an interspecific comparison between H. petiolaris and a sympatric congener, H. annuus. In general, the large regions of divergence observed in the ecotypic comparison swamped locus-specific associations with environmental variables. In both comparisons, regions of high divergence occurred in portions of the genetic map with high marker density, probably reflecting regions of low recombination. The difference in genomic distributions of highly divergent regions between ecotypic and interspecific comparisons highlights the value of studies spanning the spectrum of speciation in related taxa.
DOI: 10.14288/1.0397811
title: Data from: Cognitive function after spinal cord injury: a systematic review

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Objective: To systematically examine the incidence of cognitive impairment in individuals with spinal cord injury (SCI), as well as identify potential contributing and confounding factors. Methods: Studies quantitatively reporting cognitive ability after spinal cord injury were searched electronically via Medline, CINAHL, Embase, and PsycINFO. Manual screening for references within articles was also performed. A total of 2,481 studies were screened and a total of 70 were included in this review, 21 reporting cognitive function after SCI compared to an able-bodied control group and 49 with no able-bodied controls. Studies were analyzed for the incidence of impairment and the interactions with concomitant traumatic brain injury, psychological or somatic complaints, decentralized cardiovascular control, sleep apnea, neurologic level of injury, and age. Results: There is a high volume of evidence reporting substantial cognitive impairment in individuals with SCI. Potential co-contributors include concomitant brain injury, psychological or somatic comorbidities, decentralized cardiovascular control, and sleep apnea. Cognitive functioning was negatively correlated with age. No clear agreement was found for the incidence of cognitive impairment or its association with level of injury. Conclusion: Current evidence suggests that individuals with SCI should be examined and addressed for cognitive impairment. Future studies aimed at identifying potential secondary causative factors should employ stringent controls for co-occurring brain trauma since it appears to be a major contributor and confounder to impaired cognition.
DOI: 10.14288/1.0397812
title: Data from: Group elicitations yield more consistent, yet more uncertain experts in understanding risks to ecosystem services in New Zealand bays

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The elicitation of expert judgment is an important tool for assessment of risks and impacts in environmental management contexts, and especially important as decision-makers face novel challenges where prior empirical research is lacking or insufficient. Evidence-driven elicitation approaches typically involve techniques to derive more accurate probability distributions under fairly specific contexts. Experts are, however, prone to overconfidence in their judgements. Group elicitations with diverse experts can reduce expert overconfidence by allowing cross-examination and reassessment of prior judgements, but groups are also prone to uncritical “groupthink” errors. When the problem context is underspecified the probability that experts commit groupthink errors may increase. This study addresses how structured workshops affect expert variability among and certainty within responses in a New Zealand case study. We find that experts’ risk estimates before and after a workshop differ, and that group elicitations provided greater consistency of estimates, yet also greater uncertainty among experts, when addressing prominent impacts to four different ecosystem services in coastal New Zealand. After group workshops, experts provided more consistent ranking of risks and more consistent best estimates of impact through increased clarity in terminology and dampening of extreme positions, yet probability distributions for impacts widened. The results from this case study suggest that group elicitations have favorable consequences for the quality and uncertainty of risk judgments within and across experts, making group elicitation techniques invaluable tools in contexts of limited data.
DOI: 10.14288/1.0397814
title: Data from: Hummingbirds control hovering flight by stabilizing visual motion

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Relatively little is known about how sensory information is used for controlling flight in birds. A powerful method is to immerse an animal in a dynamic virtual reality environment to examine behavioral responses. Here, we investigated the role of vision during free-flight hovering in hummingbirds to determine how optic flow—image movement across the retina—is used to control body position. We filmed hummingbirds hovering in front of a projection screen with the prediction that projecting moving patterns would disrupt hovering stability but stationary patterns would allow the hummingbird to stabilize position. When hovering in the presence of moving gratings and spirals, hummingbirds lost positional stability and responded to the specific orientation of the moving visual stimulus. There was no loss of stability with stationary versions of the same stimulus patterns. When exposed to a single stimulus many times or to a weakened stimulus that combined a moving spiral with a stationary checkerboard, the response to looming motion declined. However, even minimal visual motion was sufficient to cause a loss of positional stability despite prominent stationary features. Collectively, these experiments demonstrate that hummingbirds control hovering position by stabilizing motions in their visual field. The high sensitivity and persistence of this disruptive response is surprising, given that the hummingbird brain is highly specialized for sensory processing and spatial mapping, providing other potential mechanisms for controlling position.
DOI: 10.14288/1.0397816
title: Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular, or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or sub-functionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.
DOI: 10.14288/1.0397817
title: Data from: Genome-wide admixture and ecological niche modeling reveal the maintenance of species boundaries despite long history of interspecific gene flow

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1.The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. 2.We used ecological niche modeling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P. engelmannii in western North America. 3.Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression, and to identify loci putatively involved in adaptive differences or reproductive barriers between species. 4.Our paleoclimatic modeling suggests these two closely related species have a long history of hybridization and introgression, dating to at least 21,000 years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. 5.20 loci showed evidence of divergent selection, including six loci that were both Fst outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction, and transcription factors.
DOI: 10.14288/1.0397818
title: Data from: Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Background: Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. Results: To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree discordance for nuclear loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for introgression in the concatenated nuclear matrix with Patterson’s D statistics and DFOIL. We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups. Conclusions: Our results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays.
DOI: 10.15468/dl.f7p7p7
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tupaia nicobarica"
 ]
}

 The dataset includes 33 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038087-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.58024/agumdce695a7
title: High-resolution 40Ar/39Ar geochronology of the Koobi Fora Tuff Complex, Turkana Basin: Implications for the hominin bearing strata of the Early Pleistocene (1.6 to 1.4 Ma)

description: Geochemistry and geochronology of the Koobi Fora, Lower Koobi Fora and Karari Blue tuffs of the Omo-Turkana Basin.
DOI: 10.15468/dl.2z2j5j
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ranunculus macropetalus"
 ]
}

 The dataset includes 31 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038089-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13758675
title: Peer-to-Peer Boliviano (BOB) Exchange Data