cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.p7peas
title: Occurrence Download

description: A dataset containing 82624 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Eulophus larvarum (Linnaeus, 1758), Diglyphus chabrias (Walker, 1838), Taphrina robinsoniana Giesenh., Hypoxylon petriniae M.Stadler & J.Fourn., Ramularia alnicola Cooke, Endoclita auratus (Hampson), Endoclita undulifer (Walker, 1869), Agnesiella exigua Huang & Zhang, 2022, Agnesiella glabra Huang & Zhang, 2022, Agnesiella mitrata Huang & Zhang, 2022, Agnesiella lata Huang & Zhang, 2022, Agnesiella tridigitata Huang & Zhang, 2022, Agnesiella longisagittata Huang & Zhang, 2022, Agnesiella gaura Huang & Zhang, 2022, Agnesiella apiculata Huang & Zhang, 2022, Agnesiella eleganta Huang & Zhang, 2022, Agrilus spectabilis Kerremans, 1895, Lambdina fiscellaria fiscellaria, Altica ambiens ambiens, Buprestis fasciata Fabricius, 1787, Buprestis viridisuturalis Nicolay & Weiss, 1918, Chionodes argentipunctella (Ely, 1910), Stigmella confusella (Wood & Walsingham, 1894) Vári, 1944, Stigmella luteella (Stainton, 1857) Beirne, 1945, Stigmella microtheriella (Stainton, 1854) Fletcher et al., 1945, Sabra harpagula (Esper, 1786), Xylena curvimacula Morrison, 1874, Eotetranychus pallidus (Garman, 1940), Tetranycopsis horridus (Canestrini & Fanzago, 1876), Hydriomena ruberata (Freyer), Eupithecia multistrigata (Hulst, 1896), Dysstroma walkerata (Pearsall, 1909), Epione vespertaria (Linnaeus, 1767), Eupithecia perfusca (Hulst, 1898), Eulithis destinata (Möschler, 1860), Euchlaena marginaria (Minot, 1869), Eupithecia fletcherata Taylor, 1907, Eupithecia lachrymosa (Hulst, 1900), Eupithecia maestosa (Hulst, 1896), Eupithecia gelidata Möschler, 1860, Eupithecia anticaria Walker, 1862, Hydriomena pluviata (Guenée), Macaria anataria (Swett, 1913), Protitame matilda (Dyar, 1904), Rheumaptera subhastata (Nolcken, 1870), Caloptilia alnicolella (Chambers, 1875), Caloptilia issikii Kumata, 1982, Neozephyrus japonicus (Murray, 1874), Stigmella continuella (Stainton, 1856) Fletcher et al., 1945, Lyonetia saliciella Busck, 1904)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 82624 records from 413 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012971-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48324/dandi.001346/0.250521.2344
title: Cortical Circuits for the integration of short-latency auditory pathways: Inferior Colliculus retrograde tracing

description: Retrograde tracers were injected in different subdivisions of the mouse inferior colliculus.  Images were taken from the contralateral and ipsilateral cochlear nucleus. The experiments correspond to the data reported in manuscript PMID: 39829930.
DOI: 10.34740/kaggle/dsv/11901778
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.14288/1.0397983
title: Data from: Catch reconstructions reveal that global marine fisheries catches are higher than reported and declining

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Fisheries data assembled by the Food and Agriculture Organization (FAO) suggest that global marine fisheries catches increased to 86 million tonnes in 1996, then slightly declined. Here, using a decade-long multinational ‘catch reconstruction’ project covering the Exclusive Economic Zones of the world’s maritime countries and the High Seas from 1950 to 2010, and accounting for all fisheries, we identify catch trajectories differing considerably from the national data submitted to the FAO. We suggest that catch actually peaked at 130 million tonnes, and has been declining much more strongly since. This decline in reconstructed catches reflects declines in industrial catches and to a smaller extent declining discards, despite industrial fishing having expanded from industrialized countries to the waters of developing countries. The differing trajectories documented here suggest a need for improved monitoring of all fisheries, including often neglected small-scale fisheries, and illegal and other problematic fisheries, as well as discarded bycatch.
DOI: 10.14288/1.0397985
title: Data from: From promise to practice: pairing non-invasive sampling with genomics in conservation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate change-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 nanogram. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.
DOI: 10.14288/1.0397987
title: Data from: Macroevolutionary synthesis of flowering plant sexual systems

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Sexual system is a key determinant of genetic variation and reproductive success, affecting evolution within populations and within clades. Much research in plants has focused on evolutionary transitions away from the most common state of hermaphroditism and toward the rare state of dioecy (separate sexes). Rather than transitions predominantly toward greater sexual differentiation, however, evolution may proceed in the direction of lesser sexual differentiation. We analyzed the macroevolutionary dynamics of sexual system in angiosperm genera that contain both dioecious and non-dioecious species. Our phylogenetic analyses encompass a total of 2145 species from 40 genera. Overall, we found little evidence that rates of sexual system transitions are greater in any direction. Counting the number of inferred state changes revealed a mild prevalence of transitions away from hermaphroditism and away from dioecy, toward states of intermediate sexual differentiation. We identify genera in which future studies of sexual system evolution might be especially productive, and we discuss how integrating genetic or population-level studies of sexual system could improve the power of phylogenetic comparative analyses. Our work adds to the evidence that different selective pressures and constraints act in different groups, helping maintain the variety of sexual systems observed among plants.
DOI: 10.14288/1.0397988
title: Data from: MycoDB, a global database of plant response to mycorrhizal fungi

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.
DOI: 10.14288/1.0397989
title: Data from: Oceanographic drivers of offspring abundance may increase or decrease variance in reproductive success in a temperate marine fish

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;In species that reproduce into uncertain environments, the relationship between mean reproductive success (the abundance of new recruits) and the variance in reproductive success (whether adults contribute disproportionally more offspring) may not be straightforward because of stochastic environmental processes that create high variance in reproductive success among adults. In this study we investigated the relationships between oceanography, reproductive success, and reproductive variance in the black rockfish, Sebastes melanops, a long-lived temperate reef fish with pelagic larvae. We quantified black rockfish recruitment, genetic diversity, and growth rates from otolith microstructure over 5 years (2005-2009) during which oceanographic conditions differed. We used cross-correlations to determine windows of time during which oceanographic variables were significantly correlated with the resulting abundance or genetic diversity of recruits. We found that warmer ocean temperatures were positively correlated with the abundance of recruits, as well as the effective number of breeders. In contrast, the strength of coastal upwelling during settlement was positively correlated with the annual abundance of new recruits, but was negatively correlated with the effective number of breeders. Larval growth rates were explained substantially more by temperature than by upwelling, and suggested that temperature affected survival through growth, while upwelling affected survival through transport. Our results indicated that cold ocean temperatures and intense upwelling caused sweepstakes-like processes to operate on black rockfish populations, despite high abundances of recruits. We propose that a decoupling of the mean and variance in reproductive success may be characteristic of organisms that reproduce into uncertain environments.
DOI: 10.14288/1.0397990
title: Data from: Reversed brain size sexual dimorphism accompanies loss of parental care in white sticklebacks

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Uncovering factors that shape variation in brain morphology remains a major challenge in evolutionary biology. Recently, it has been shown that brain size is positively associated with level of parental care behavior in various taxa. One explanation for this pattern is that the cognitive demands of performing complex parental care may require increased brain size. This idea is known as the parental brain hypothesis (PBH). We set out to test the predictions of this hypothesis in wild populations of threespine stickleback (Gasterosteus aculeatus). These fish are commonly known to exhibit (1) uniparental male care and (2) sexual dimorphism in brain size (males&gt;females). To test the PBH, we took advantage of the existence of closely related populations of stickleback that display variation in parental care behavior: common marine threespine sticklebacks (uniparental male care) and white threespine sticklebacks (no care). To begin, we quantified genetic differentiation among two common populations and three white populations from Nova Scotia. We found overall low differentiation among populations, although FST was increased in between-type comparisons. We then measured the brain weights of males and females from all five populations along with two additional common populations from British Columbia. We found that sexual dimorphism in brain size is reversed in white stickleback populations: males have smaller brains than females. Thus, while several alternatives need to be ruled out, the PBH appears to be a reasonable explanation for sexual dimorphism in brain size in threespine sticklebacks.
DOI: 10.14288/1.0397991
title: Data from: Complex indirect effects of epiphytic bromeliads on the invertebrate food webs of their support tree

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ecosystem engineers are species that affect others through the provision of habitat rather than consumptive resources. The extent to which ecosystem engineers can indirectly affect entire food webs, however, is poorly understood. Epiphytic tank bromeliads (Bromeliaceae) are ecosystem engineers that are common throughout the Neotropics, and are associated with a variety of predatory arthropods. Here, we examine if bromeliads, by increasing predator densities, indirectly benefit their support tree through reduction in herbivorous insects and leaf damage. We observed and manipulated bromeliad densities in Costa Rican orange orchards, and measured impacts on leaf damage and arboreal and bromeliad invertebrate communities in two different seasons. Our results show that bromeliads are associated with predatory and herbivorous invertebrates but not leaf damage. Bromeliads were correlated with increased densities of their associated predators, especially ants and hunting spiders, but we could not confirm a causal link. Associations with bromeliads changed over time, with seasonal shifts interfering with responses to our manipulations. Bromeliads had a reduced association with predators in the dry season. Moreover, a null association between bromeliads and herbivorous invertebrates in the dry season unexpectedly became positive in the wet season. In summary, we have only limited evidence that bromeliads indirectly promote the top-down control of arboreal herbivores; instead, our manipulations suggest that bromeliads increase herbivore densities in the wet season. This research suggests that although bromeliads may act as ecosystem engineers, indirectly influencing the invertebrate food web on support trees, their effects are trophically complex and seasonally dependent.
DOI: 10.14288/1.0397992
title: Data from: Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.
DOI: 10.14288/1.0397993
title: Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of ‘turnover’ of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.
DOI: 10.14288/1.0397994
title: Data from: Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early- and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.
DOI: 10.14288/1.0397995
title: Data from: Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low-oxygen (hypoxia) of the hypoxia tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine if these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O2 tensions chosen to yield a similar level of tissue hypoxia and gene transcription was assessed in the liver over time. There was an effect of time in hypoxia, where the greatest transcriptional change in the silverspotted sculpin occurred between 3 to 24 hours in contrast to the tidepool sculpin where the largest transcriptional change occurred between 24 and 72 hours of hypoxia. A number of genes showed similar hypoxia-induced transcription patterns in both species (e.g. genes associated with glycolysis and apoptosis) suggesting they are involved in a conserved hypoxia response. A large set of genes showed divergent transcriptional patterns in the two species, including fatty acid oxidation and oxidative phosphorylation, suggesting that these biological processes may contribute to explaining variation in hypoxia tolerance in these species. When both species were exposed to a single environmental O2 tension, large transcriptional responses were seen in the hypoxia intolerant silverspotted sculpin while almost no response was observed in the hypoxia tolerant tidepool sculpin. Overall, divergent transcription patterns in response to both magnitude and duration of hypoxia provide insights into the processes that may determine an animal's capacity to tolerate frequent bouts of hypoxia in the wild.
DOI: 10.14288/1.0397996
title: Data from: Environmental stress does not increase the mean strength of selection

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;A common intuition among evolutionary biologists and ecologists is that environmental stress will increase the strength of selection against deleterious alleles and among alternate genotypes. However, the strength of selection is determined by the relative fitness differences among genotypes, and there is no theoretical reason why these differences should be exaggerated as mean fitness decreases. We update a recent review of the empirical results pertaining to environmental stress and the strength of selection and find that there is no overall trend towards increased selection under stress. The majority of past studies measure the strength of selection by quantifying the decrease in fitness imposed by single or multiple mutations in different environments. However, selection rarely acts on one locus independently, and the strength of selection will be determined by variation across the whole genome. We used 20 inbred lines of Drosophila melanogaster to make repeated fitness measurements of the same genotypes in four different environments. This framework allowed us to determine the variation in fitness attributable to genotype across stressful environments and to calculate the opportunity for selection among these genotypes in each stress. While we found significant decreases in mean fitness in our stressful environments, we did not find any significant differences in the strength of selection among any of the four measured environments. Therefore, in agreement with our updated review, we find no evidence for the oft-cited verbal model that stress increases the strength of selection.