cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jq2bvq8bm
title: Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands

description: Ice-free areas are increasing worldwide due to the dramatic glacier
 shrinkage and are undergoing rapid colonization by multiple lifeforms,
 thus representing key environments to study ecosystem development. Soils
 have a complex vertical structure. However, we know little about how
 microbial and animal communities differ across soil depths and development
 stages during the colonization of deglaciated terrains, how these
 differences evolve through time, and whether patterns are consistent among
 different taxonomic groups. Here, we used environmental DNA metabarcoding
 to describe how community diversity and composition of six groups
 (Eukaryota, Bacteria, Mycota, Collembola, Insecta, Oligochaeta) differ
 between surface (0-5 cm) and relatively deep (7.5-20 cm) soils at
 different stages of development across five Alpine glaciers. Taxonomic
 diversity increased with time since glacier retreat and with soil
 evolution; the pattern was consistent across different groups and soil
 depths. For Eukaryota, and particularly Mycota, alpha-diversity was
 generally the highest in soils close to the surface. Time since glacier
 retreat was a more important driver of community composition compared to
 soil depth; for nearly all the taxa, differences in community composition
 between surface and deep soils decreased with time since glacier retreat,
 suggesting that the development of soil and/or of vegetation tends to
 homogenize the first 20 cm of soil through time. Within both Bacteria and
 Mycota, several molecular operational taxonomic units were significant
 indicators of specific depths and/or soil development stages, confirming
 the strong functional variation of microbial communities through time and
 depth. The complexity of community patterns highlights the importance of
 integrating information from multiple taxonomic groups to unravel
 community variation in response to ongoing global changes.
description: Libraries were prepared
 following the MetaFast protocol (Taberlet et al., 2018) and sequenced
 using the MiSeq (Bact02 and Fung02) or HiSeq 2500 (Arth02, Coll01, Euka02,
 Inse01, Olig01, Sper01) Illumina platforms (Illumina, San Diego, CA, USA)
 with a paired-end approach (2 × 250 bp for Bact02 and Fung02, and 2 × 150
 bp for the others markers) at Fasteris (SA, Geneva, Switzerland). For each
 marker, the sequence depth corresponded to 10,000 reads per
 sample.
description: Sequence data have been processed using the
 OBITools software suit (version 1.2.9) then filtered and analyzed in R
 (version 4.0). All scripts to reproduce data processing are provided here
 and described in the "Methods" section of the
 manuscript. See "Data Accessibility" section of the
 manuscript to access raw sequence data.
DOI: 10.5061/dryad.5dv41ns7m
title: Using weather radar to help minimize wind energy impacts on nocturnally migrating birds

description: As wind energy rapidly expands worldwide, information to minimize impacts
 of this development on biodiversity is urgently needed. Here we
 demonstrate how data collected by weather radar networks can inform
 placement and operation of wind facilities to reduce collisions and
 minimize habitat-related impacts for nocturnally migrating birds. We found
 over a third of nocturnal migrants flew through altitudes within the
 rotor-swept zone surrounding the North American Great Lakes, a
 continentally important migration corridor. Migrating birds concentrated
 in terrestrial stopover habitats within 20-km from shorelines, a distance
 well beyond the current guidelines for construction of new land-based
 facilities, and their distributions varied seasonally and at local and
 regional scales, creating predictable opportunities to minimize impacts
 from wind energy development and operation. Networked radar data are
 available across the U.S. and other countries and broad application of
 this approach could provide information critical to bird-friendly
 expansion of this globally important energy source.
DOI: 10.5061/dryad.9w0vt4bhs
title: Sex-specific evolution of brain size, brain structure, and covariation with eye size in Trinidadian killifish

description: Links between contrasting ecological conditions and evolutionary shifts in
 neurosensory components such as brain and eye size are accumulating.
 Whether selection operates differently on these traits between sexes is
 unclear. Trinidadian killifish (Anablepsoides hartii) are located in sites
 with and without predators. Male killifish from sites without predators
 have evolved larger brains and eyes than males from sites with predators.
 These differences in brain size are present early in life but disappear in
 adult size-classes. Here, we evaluated female brain growth allometries to
 determine if females exhibit similar size-specific brain size differences
 between sites that differ in predation intensity. We also quantified brain
 size, structure, and eye size to determine if these structures coevolve in
 a sex-specific manner. We found that female brain growth allometries did
 not differ across populations. Yet, female killifish from sites without
 predators exhibited a larger cerebellum, optic tectum, and dorsal medulla
 early in life (prior to maturation), but such differences disappeared in
 larger size-classes. Females from sites with predators exhibit similar
 patterns in brain growth as males in those sites, therefore shifts in
 brain size and structure are driven by differences between sexes in sites
 without predators. We also found evidence for covariation between brain
 and eye size in both sexes despite different levels of variation in both
 structures, suggesting that these structures may covary to fluctuating
 degrees in sex-specific ways. We conclude that differential investment in
 brain tissue in sites without predators may be linked to varying
 reproductive and cognitive demands across the sexes.
description: Data includes wild-caught and common garden reared specimen.
 Variables are Code - fish ID, River - river of origin, population of
 origin- HP (high predation), RO (Rivulus-only), figh length (mm), ln
 transformed length, fish weight (g), ln transformed weight, brain weight
 (g) and ln transformed brain weight, eye size (mm) and In transformed eye
 size. Telencephalon, dorsal medulla, cerebellum, optic tetcum width (mm)
 and ln transformed widths. Telencephalon, dorsal medulla, cerebellum,
 optic tetcum volume (mm^3) and ln transformed volumes (for wild caught
 only), and overall brain size residuals. Residuals were output from
 regressions between ln-brain and ln-length. For common garden specimen,
 family is included as well as family by population (families designated
 for each population for analysis purposes). See ReadMe
 file.
DOI: 10.5061/dryad.0vt4b8h21
title: Temperature and mating in harvestmen

description: Temperature impacts a wide range of mating behaviours, particularly in
 ectothermic organisms that tend to havebody temperatures similar
 to ambient thermal conditions. Here, we test
 the effects of thermal variation on precopulatory and copulatory behaviour
 in the harvester Leiobunum politum Weed 1889, which
 belongs to the group commonly known as daddy longlegs. We ran single
 choice mating trials across temperatures commonly experienced in the field
 during the mating season (18 - 34 °C) across two years. We tested how
 temperature affected the likelihood to move, attempt to mate, and
 successfully mate, as well as the duration of copulation. Mating was
 highest at low to intermediate temperatures, and the temperature at which
 peak mating rates occurred varied across years. The wide range of
 temperatures across which L. politum are found to mate
 reflect thermal variability in the field and the flexibility in mating
 behaviour in this fascinating animal.
description: Behavioral data collected in 2017 and 2018. 2017 trials were
 video recorded and analyzed for quantitative data. 2018 data set scored
 during the trials.
description: Some trials were excluded due to missing weights. One female was
 missing half her legs. Please contact corresponding author if you wish to
 use the data set.
DOI: 10.5061/dryad.jwstqjqbr
title: Data from: Above- and belowground drivers of intraspecific trait variability across subcontinental gradients for five ubiquitous forest plants in North America

description: Intraspecific trait variability (ITV) provides the material for species
 adaptation to environmental changes. To advance our understanding of how
 ITV can contribute to species adaptation to a wide range of environmental
 conditions, we studied five widespread understory forest species exposed
 to both continental-scale climate gradients, and local soil and
 disturbance gradients. We investigated the environmental drivers of
 between-site leaf and root trait variation, and tested whether higher
 between-site ITV was associated with increased trait sensitivity to
 environmental variation (i.e. environmental fit). We measured
 morphological (specific leaf area: SLA, specific root length: SRL) and
 chemical traits (Leaf and Root N, P, K, Mg, Ca) of five forest understory
 vascular plant species at 78 sites across Canada. A total of 261
 species-by-site combinations spanning ~4300 km were sampled, capturing
 important abiotic and biotic environmental gradients (neighbourhood
 composition, canopy structure, soil conditions, climate). We used
 multivariate and univariate linear mixed models to identify drivers of ITV
 and test the association of between-site ITV with environmental fit.
 Between-site ITV of leaf traits was primarily driven by canopy structure
 and climate. Comparatively, environmental drivers explained only a small
 proportion of variability in root traits: these relationships were
 trait-specific and included soil conditions (Root P), canopy structure
 (Root N) and neighbourhood composition (SRL, Root K). Between-site ITV was
 associated with increased environmental fit only for a minority of traits,
 primarily in response to climate (SLA, Leaf N, SRL). Synthesis. By
 studying how ITV is structured along environmental gradients among species
 adapted to a wide range of conditions, we can begin to understand how
 individual species might respond to environmental change. Our results show
 that generalizable trait-environment relationships occur primarily
 aboveground and only accounted for a small proportion of variability. For
 our group of species with broad ecological niches, variability in traits
 was only rarely associated with higher environmental fit, and primarily
 along climatic gradients. These results point to promising research
 avenues on the various ways in which trait variation can affect species
 performance along different environmental gradients.
DOI: 10.5061/dryad.ghx3ffbr5
title: Data from: Maintenance of local adaptation despite gene flow in a coastal songbird

description: Adaptation to local environments is common in widespread species and the
 basis of ecological speciation. The song sparrow (Melospiza melodia) is a
 widespread, polytypic passerine that occurs in shrubland habitats
 throughout North America. We examined the population structure of two
 parapatric subspecies that inhabit different environments: the Atlantic
 song sparrow (M. m. atlantica), a coastal specialist; and the eastern song
 sparrow (M. m. melodia), a shrubland generalist. These populations lacked
 clear mitochondrial population structure, yet coastal birds formed a
 distinct nuclear genetic cluster. We found weak overall genomic
 differentiation between these subspecies, suggesting either recent
 divergence, extensive gene flow, or a combination thereof. There was a
 steep genetic cline at the transition to coastal habitats, consistent with
 isolation by environment (IBE), not isolation by distance (IBD). A
 phenotype under divergent selection, bill size, varied with the amount of
 coastal ancestry in transitional areas, but larger bill size was
 maintained in coastal habitats regardless of ancestry, further supporting
 a role for selection in the maintenance of these subspecies. Demographic
 modeling suggested a divergence history of limited gene flow followed by
 secondary contact, which has emerged as a common theme in adaptive
 divergence across taxa.
description: Data were generated from genomic DNA of song sparrows
 using restriction-site associated DNA sequencing (RADseq). Libraries were
 prepared following the 3RAD protocol with restriction enzymes
 <em>Nhe</em>I, <em>EcoR</em>I, and
 <em>XBal</em>I. Sequencing was done on an Illumina HiSeq 4000 with paired-end 150bp reads
 at the Duke Center for Genomic and Computational Biology in 2019. Data
 were processed in STACKS using the de novo map approach with
 a catalog set of 45
 individuals and parameters M=4, n=4, and
 m=3. Included are a compressed FASTA of
 the catalog loci and a compressed VCF of genome-wide SNPs after running
 filters (-R 0.8, --max-obs-het 0.7, --write-single-snp) using the STACKS
 <em>populations</em> module (before the application of a MAF
 filter) for all 163 individuals of the final population structure
 dataset. A FASTA file of ND2 sequences, which are
 available on GenBank, is also included. 
description: # Manuscript Title: "Maintenance of local adaptation despite gene
 flow in a coastal songbird" Journal: Evolution Year: 2022 Files:
 **ND2_21Feb2019_Alignment.fasta** FASTA file of ND2 sequences
 **SOSP_RADseq_catalogloci.fa.gz** Compressed FASTA of all catalog RAD-loci
 **SOSP_RADseq_SNPs_NoMAF.vcf.zip** Genome-wide SNPs used for analyses
 Note: Before population structure analyses, SNPs were filtered for a
 minimum minor allele frequency of 5% across the entire sample.
DOI: 10.5061/dryad.7m0cfxpws
title: Data set for behavioural OA experiments with Caribbean Damselfish (Stegastes partitus)

description: The neurobehavioural responses of fish exposed to ocean acidification (OA)
 are variable, possibly due to species-specific differences or involvement
 of multiple neuronal receptors. Here, we investigated behavioural
 responses of bicolor damselfish (Stegastes partitus) to OA and the
 involvement of dopamine receptors. Damselfish were exposed to control (pH
 8.06; CO2 ~400 μatm) or OA (pH 7.73;
 CO2 ~1,000 μatm) seawater for five days, subjected to
 the open field, novel object approach, light/dark, and mirror-aggression
 tests, and returned to their respective aquaria. Two days later, tests
 were repeated upon treatment with the dopamine D1 receptor agonist SKF
 38393. The D1 agonist, but not OA, altered locomotion in the open field
 test and boldness in the novel object approach test. Both the D1 agonist
 and OA increased anxiety-like behaviour in the light/dark test.
description: Video recordings were made with a FireWire 400 Colour Industrial
 Camera with a Tamron CCTV lens (2.8–12mm, f/1.4) Bicolor damselfish
 (Stegastes partitus) were ran through a battery of behavioural tests both
 in the absence and presence of selective D1 receptor agonist SKF 38393.
 Fish were gently netted from their tank and placed into the first test
 (open field). At the end of the test a novel object was added to the
 arena. Fish were then transferred to the light/dark test arena, then
 mirror/aggression test arena for the third and fourth tests, respectively.
 Two days later each fish was individually exposed to SKF 38393 and
 underwent the identical behavioural test battery. EthoVision motion
 tracking software system (v.10, Noldus, Leesburg, VA, USA) was used to
 record and quantify variables in each test.
DOI: 10.15468/dl.2bmjsa
title: Occurrence Download

description: A dataset containing 579 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caenis lactea"
 ]
}

 The dataset includes 579 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003094-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kh189327p
title: Automated, medication-targeted alerts for Acute Kidney Injury – A randomized trial

description: Acute kidney injury is common among hospitalized individuals, particularly
 those exposed to certain medications, and is associated with substantial
 morbidity and mortality. In a pragmatic, open-label, parallel group
 randomized controlled trial (clinicaltrials.gov NCT02771977), we
 investigate whether an automated clinical decision support system affects
 discontinuation rates of potentially nephrotoxic medications and improves
 outcomes in patients with AKI. Participants included 5,060 hospitalized
 adults with AKI and an active order for any of three classes of
 medications of interest: non-steroidal anti-inflammatory drugs,
 renin-angiotensin-aldosterone system inhibitors, or proton pump
 inhibitors. Within 24 hours of randomization, a medication of interest was
 discontinued in 61.1% of the alert group versus 55.9% of the usual care
 group (relative risk 1.08, 1.04–1.14, p=0.0003). The primary outcome – a
 composite of progression of acute kidney injury, dialysis, or death –
 occurred in 585 (23.1%) individuals in the alert group and 639 (25.3%)
 patients in the usual care group (RR 0.92, 0.83–1.01, p=0.09). The
 pre-specified subgroup analysis found a significant benefit of alerting
 among those exposed to proton pump inhibitors but not non-steroidal
 anti-inflammatory drug or renin-angiotensin system inhibitor.
description: Data was collected through electronic medical record abstraction
 in the context of a prospective, randomized clinical trial.
DOI: 10.5061/dryad.vhhmgqnw7
title: Data and code from: The functional form of specialized predation affects whether Janzen-Connell effects can prevent competitive exclusion

description: Janzen-Connell Effects (JCEs), specialized predation of seeds and
 seedlings near conspecific trees, are hypothesized to maintain species
 richness. While previous studies show JCEs can maintain high richness
 relative to neutral communities, recent theoretical work indicates JCEs
 may weakly inhibit competitive exclusion when species exhibit
 inter-specific fitness variation. However, recent models make somewhat
 restrictive assumptions about the functional form of specialized predation
 -- that JCEs occur at a fixed rate when offspring are within a fixed
 distance of a conspecific tree. Using a theoretical model, I show that the
 functional form of JCEs largely impacts their ability to maintain
 coexistence. If predation pressure increases additively with adult tree
 density and decays exponentially with distance, JCEs maintain considerably
 higher species richness than predicted by recent models. Loosely
 parameterizing the model with data from a Panamanian tree community, I
 elucidate the conditions under which JCEs are capable of maintaining high
 species richness.
description: This file contains the simulation outputs that are necessary to
 recreate the figures (figures from the Appendices, mainly). For R code
 that recreates all the figures, see: https://doi.org/10.5281/zenodo.6462743.
DOI: 10.6078/d1vd86
title: The EDA receptor (EDAR) is a candidate gene for lateral plate number variation in stickleback fish

description: Variation in lateral plating in stickleback fish represents a classical
 example of rapid and parallel adaptation in morphology. The underlying
 genetic architecture involves polymorphism at the ectodysplasin-A (EDA)
 gene. However, lateral plate number is influenced by additional loci that
 remain poorly characterized. Here we search for such loci by performing
 genome-wide differentiation mapping based on pooled whole-genome sequence
 data from a European stickleback population variable in the extent of
 lateral plating, while tightly controlling for the phenotypic effect of
 EDA. This suggests a new candidate locus, the EDA receptor (EDAR) gene,
 for which additional support is obtained by individual-level targeted
 Sanger sequencing and by comparing allele frequencies among natural
 populations. Overall, our study illustrates the power of pooled
 whole-genome sequencing for searching phenotypically relevant loci and
 opens opportunities for exploring the population genetics and ecological
 significance of a new candidate locus for stickleback armor evolution.
description: These data were generated to investigate candidate genes for the
 reduction in the lateral plates of stickleback fish (Gasterosteus
 acculeatus). These consist mainly of pool whole-genome single nucleotide
 polymorphism (SNP) data. <br>Individuals were pooled, by plating
 phenotype, controlling for EDA genotype and lateral plate phenotype, and
 all raw whole-genome read data has been deposited in the NCBI SRA library
 (see file SRA_Accession_Info.xlsx for specif codes). Phenotypic data to
 access lateral plate number for the focus population (a stream from
 Constance Lake) is also provided. See methods section in DOI:
 10.1093/g3journal/jkac077 for further details.
description: See README file.
DOI: 10.5061/dryad.wpzgmsbps
title: Data for: Population niche width is driven by within-individual niche expansion and individual specialization in introduced brook trout in mountain lakes

description: The width of a population's resource use niche is determined by
 individual diet breadth (“within-individual component”) and the degree of
 niche partitioning between individuals (“between-individual component”).
 The balance between these two factors affects ecological stability and
 evolutionary trajectories, and may shift as ecological opportunity permits
 broader population niches. Lakes in California’s Sierra Nevada Mountains
 vary in resource diversity for introduced brook trout (Salvelinus
 fontinalis) due to elevation, lake morphometry, and watershed features. We
 compared the relative contributions of within- and between-individual
 niche components to two measures of the dietary niches of thirteen
 populations of brook trout: prey taxonomic composition and prey size
 distribution. For both taxonomic and size diversity of fish diets,
 population niche width was positively related to both the within- and
 between-individual components. For taxonomic diversity, the two components
 increased in parallel, while for size diversity, the between-individual
 component became more important relative to the within-individual
 component in populations with the greatest niche widths. Our results
 support the Niche Variation Hypothesis that populations with broader
 niches are more heterogeneous among individuals and show that individual
 niche width and individual specialization can operate in parallel to
 expand the population niche.
description: Data collected as described in Baker et al. (2022).
 "Population niche width is driven by within-individual niche
 expansion and individual specialization in introduced brook trout in
 mountain lakes."
description: Provided in the README file.