cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6rs23
title: Data from: Using occupancy modeling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species

description: Environmental DNA (eDNA) monitoring approaches promise to greatly improve
 detection of rare, endangered, and invasive species in comparison to
 traditional field approaches. Herein, eDNA approaches and traditional
 seining methods were applied at 29 research locations to compare
 method-specific estimates of detection and occupancy probabilities for
 endangered tidewater goby (Eucyclogobius newberryi). At each location
 multiple paired seine hauls and water samples for eDNA analysis were
 taken, ranging from two to 23 samples per site, depending upon habitat
 size. Analysis using a multi-method occupancy modeling framework indicated
 that the probability of detection using eDNA was nearly double (0.74) the
 rate of detection for seining (0.39). The higher detection rates afforded
 by eDNA allowed determination of tidewater goby occupancy at two locations
 where they have not been previously detected and at one location
 considered to be locally extirpated. Additionally, eDNA concentration was
 positively related to tidewater goby catch per unit effort, suggesting
 eDNA could potentially be used as a proxy for local tidewater goby
 abundance. Compared to traditional field sampling, eDNA provided improved
 occupancy parameter estimates, and can be applied to increase management
 efficiency across a broad spatial range and within a diversity of
 habitats.
description: Sub_sampling_data_eDNA_TWG_occupancyRaw field and lab data for comparative analysis of eDNA to traditional methods for monitoring endangered tidewater goby along California's north coast.Multi-method occupancy analysis input data PRESENCE 7.5Input data for multi-method occupancy analysis using Program Presence 7.5.Hierarchical Occupancy Model R CodeR code for hierarchical occupancy analysis using WinBUGS.Hierarchical Occupancy Model Input DataData input file for hierarchical occupancy analysis using WinBUGS.GLM_DataGeneralized linear model data input for DNA concentration analysis.
DOI: 10.5061/dryad.c553k
title: Data from: Top predators determine how biodiversity is partitioned across time and space

description: Natural ecosystems are shaped along two fundamental axes, space and time,
 but how biodiversity is partitioned along both axes is not well
 understood. Here, we show that the relationship between temporal and
 spatial biodiversity patterns can vary predictably according to habitat
 characteristics. By quantifying seasonal and annual changes in larval
 dragonfly communities across a natural predation gradient we demonstrate
 that variation in the identity of top predator species is associated with
 systematic differences in spatio-temporal β-diversity patterns, leading to
 consistent differences in relative partitioning of biodiversity between
 time and space across habitats. As the size of top predators increased
 (from invertebrates to fish) habitats showed lower species turnover across
 sites and years, but relatively larger seasonal turnover within a site,
 which ultimately shifted the relative partitioning of biodiversity across
 time and space. These results extend community assembly theory by
 identifying common mechanisms that link spatial and temporal patterns of
 β-diversity.
description: Odonata occurrence, pond
 environmental data and locationSheet one: Odonate
 occurrence by location and date matrix. Sheet two: Environmental data for
 ponds. Sheet three: Pond locations by latitude and
 longitude.Data for Top predators
 determine how biodiversity is partitioned across time and
 space.xls
DOI: 10.5061/dryad.ch2pq65h
title: Sex-based population structure of ectoparasites from Neotropical bats

description: The structure and composition of populations may be molded by multiple
 evolutionary and ecological mechanisms, with natural selection affecting
 sex ratios, as well as the distributions of each sex throughout the
 environment. To address sex-based aspects of population structure, I
 evaluated sex ratios, co-occurrence of the sexes, correlations of
 abundance of the sexes, and dispersion of individuals of each sex for each
 of 34 host-ectoparasite associations from Paraguayan bats. Of the 34
 host-ectoparasite associations, 23 exhibited positive co-occurrence, 27
 exhibited positive correlation of abundances, 4 exhibited male sex bias, 1
 exhibited female sex bias, 27 had clumped distributions of males, and 26
 had clumped distributions of females. No associations exhibited negative
 co-occurrence, negative correlation of abundance, or hyper-dispersed males
 or females. There was no evidence for sexual segregation, sex-based niche
 partitioning, or intrasexual selection in any host-ectoparasite
 association. Previously proposed mechanisms (e.g. pre-partum sex bias,
 local mate competition, or mortality from host grooming) fail to explain
 observed patterns of sex bias. For ectoparasites of hosts that occupy
 permanent roost sites, sex-specific behaviour related to reproduction may
 make females more susceptible to off-host predation and less likely to be
 present in samples from bats captured away from the roost.
description: Ischnopsyllidae Number of male and female fleas collected from Paraguayan bats Nycteribiidae Number of male and female nycteribiid bat flies collected from Paraguayan bats Polyctenidae Number of male and female polyctenid bat bugs collected from Paraguayan bats Spinturnicidae Number of male and female spinturnicid mites collected from Paraguayan bats Streblidae Number of male and female streblid bat flies collected from Paraguayan bats
DOI: 10.5061/dryad.j7n42
title: Data from: Predation drives morphological convergence in the Gambusia panuco species group among lotic and lentic habitats

description: Fish morphology is often constrained by a trade-off between optimizing
 steady vs. unsteady swimming performance due to opposing effects of caudal
 peduncle size. Lotic environments tend to select for steady swimming
 performance, leading to smaller caudal peduncles, while predators tend to
 select for unsteady swimming performance, leading to larger caudal
 peduncles. However, it is unclear which aspect of performance should be
 optimized across heterogeneous flow and predation environments and how
 this heterogeneity may affect parallel phenotypic evolution. We
 investigated this question among four Gambusia species in northeastern
 Mexico, specifically the riverine G. panuco, the spring endemics G.
 alvarezi and G. hurtadoi, and a fourth species, G. marshi, found in a
 variety of habitats with varying predation pressure in the Cuatro Ciénegas
 basin and Río Salado de Nadadores. We employed a geometric morphometric
 analysis to examine how body shapes of both male and female fish differ
 among species and habitats and with piscivore presence. We found that
 high-predation and low-predation species diverged morphologically, with G.
 marshi exhibiting a variable, intermediate body shape. Within G. marshi,
 body morphology converged in high-predation environments regardless of
 flow velocity, and fish from high-predation sites had larger relative
 caudal peduncle areas. However, we found that G. marshi from low-predation
 environments diverged in morphology between sub-basins of Cuatro Ciénegas,
 indicating other differences among these basins that merit further study.
 Our results suggest that a morphological trade-off promotes parallel
 evolution of body shape in fishes colonizing high-predation environments
 and that changing predation pressure can strongly impact morphological
 evolution in these species.
description: Female TPS
 fileThis TPS file contains
 the aligned and scaled landmark coordinates for the female specimens used
 in the analyses. This file can be read using TPS software and/or the
 "geomorph" R package (Adams & Otarola-Castillo,
 2013).femaleUANL_scaled.TPSMale TPS fileThis TPS file contains the aligned and scaled landmark coordinates for the male specimens used in our analyses. This file can be read using TPS software and/or the "geomorph" R package (Adams & Otarola-Castillo, 2013).maleUANL_scaled.TPSFemale Specimen DataThis file contains the corresponding information for the specimens in the TPS file including lot number, locality, collection date, predation pressure, habitat type, centroid size, and relative caudal peduncle area.Male Specimen DataThis file contains the corresponding information for the specimens in the TPS file including lot number, locality, collection date, predation pressure, habitat type, centroid size, and relative caudal peduncle area.
DOI: 10.5061/dryad.fm8nv86
title: Data from: Increased developmental density decreases the magnitude of indirect genetic effects expressed during agonistic interactions in an insect

description: The expression of aggression depends not only on the direct genetic
 effects (DGEs) of an individual’s genes on its own behaviour, but also on
 indirect genetic effects (IGEs) caused by heritable phenotypes expressed
 by social partners. IGEs can affect the amount of heritable variance on
 which selection can act. Despite the important roles of IGEs in the
 evolutionary process, it remains largely unknown whether the strength of
 IGEs varies across life stages or competitive regimes. Based on
 manipulations of nymphal densities and &gt;3000 pair-wise aggression
 tests across multiple life stages, we experimentally demonstrate that IGEs
 on aggression are stronger in field crickets (Gryllus bimaculatus) that
 develop at lower densities than in those that develop at higher densities,
 and that these effects persist with age. The existence of
 density-dependent IGEs implies that social interactions strongly determine
 the plastic expression of aggression when competition for resources is
 relaxed. A more competitive (higher-density) rearing environment may fail
 to provide crickets with sufficient resources to develop social cognition
 required for strong IGEs. The contribution of IGEs to evolutionary
 responses was greater at lower densities. Our study thereby demonstrates
 the importance of considering IGEs in density-dependent ecological and
 evolutionary processes.
description: Han_etal_2018_Evolution_datafile
DOI: 10.5061/dryad.c8r03
title: Data from: The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus

description: Genetic drift and selection are ubiquitous evolutionary forces acting to
 shape genetic variation in populations. While their relative importance
 has been well studied in plants and animals, less is known about their
 relative importance in fungal pathogens. Because agro-ecosystems are more
 homogeneous environments than natural ecosystems, stabilizing selection
 may play a stronger role than genetic drift or diversifying selection in
 shaping genetic variation among populations of fungal pathogens in
 agro-ecosystems. We tested this hypothesis by conducting a QST/FST
 analysis using agricultural populations of the barley pathogen
 Rhynchosporium commune. Population divergence for eight quantitative
 traits (QST) was compared with divergence at eight neutral microsatellite
 loci (FST) for 126 pathogen strains originating from nine globally
 distributed field populations to infer the effects of genetic drift and
 types of selection acting on each trait. Our analyses indicated that five
 of the eight traits had QST values significantly lower than FST,
 consistent with stabilizing selection, whereas one trait, growth under
 heat stress (22°C), showed evidence of diversifying selection and local
 adaptation (QST&gt;FST). Estimates of heritability were high for all
 traits (means ranging between 0.55–0.84), and average heritability across
 traits was negatively correlated with microsatellite gene diversity. Some
 trait pairs were genetically correlated and there was significant evidence
 for a trade-off between spore size and spore number, and between
 melanization and growth under benign temperature. Our findings indicate
 that many ecologically and agriculturally important traits are under
 stabilizing selection in R. commune and that high within-population
 genetic variation is maintained for these traits.
description: DRYAD - All traits raw
 data_140912Trait values of
 replicates of 14 isolates of each of nine Rhynchosporium commune
 populations. The eight quantitative traits studied were: growth rate at
 12°C, growth rate at 18°C, growth rate at 22°C, fungicide resistance,
 melanization, spore size, spore number, and virulence.
DOI: 10.15468/dl.rnwfg9
title: Occurrence Download

description: A dataset containing 4677 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "TaxonKey is Aves",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4677 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000624-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hp269
title: Data from: An angiosperm-wide analysis of the correlates of gynodioecy

description: Premise of research. Gynodioecy, a dimorphic sexual system where
 individual plants are either female or hermaphroditic, has been documented
 in ≪1% of plant species. This rarity suggests that gynodioecy can evolve
 and persist only under a restrictive set of conditions. One approach to
 determining these conditions is to identify the phenotypic traits and
 ecological factors that are associated with gynodioecy, as such traits or
 factors may facilitate the evolution and persistence of the sexual system.
 Methodology. We assembled an angiosperm-wide database of gynodioecious
 species and used this database to test whether gynodioecy was associated
 with two phenotypic traits/ecological factors: an herbaceous growth form
 and a temperate geographic distribution. Species-level analyses were used
 to confirm that gynodioecious species are predominately herbaceous and
 temperate. Family-level analyses were then used to test whether the
 presence of herbaceous and temperate species in a lineage was associated
 with the presence of gynodioecious species. Pivotal results. An herbaceous
 growth form and a temperate geographic distribution were significantly
 overrepresented in gynodioecious species relative to their frequency in
 all plant species. Families that contained species with an herbaceous
 growth form and a temperate geographic distribution were significantly
 more likely to also contain gynodioecious species. Conclusions. Gynodioecy
 was associated with an herbaceous growth form and a temperate
 distribution, suggesting that herbaceousness and temperateness can
 facilitate the evolution and/or persistence of gynodioecy. In addition,
 our results suggest that gynodioecy is associated with different
 phenotypic traits/ecological factors than dioecy, a closely related sexual
 system. Consequently, whether gynodioecy is a transitional state in the
 evolution of dioecy may depend on the growth form and geographic
 distribution of the lineage in which it evolves.
description: Angiosperm-wide database
 of gynodioecious speciesA list of gynodioecious
 angiosperm species, indexed by order, family, and subfamily. The citations
 used to identify each species as gynodioecious are included. Synonyms or
 previous latin binomials are noted for some species.Final_May_13_with_families_uploded to dryad.xlsxList of references used to construct gynodioecy databaseA list of the references used to identify angiosperm species as gynodioecious.Database_References_May_13.docx
DOI: 10.5061/dryad.4vb0j
title: Data from: Phylogenetic patterns of codon evolution in the actin-depolymerizing factor/cofilin (adf/cfl) gene family

description: The actin-depolymerizing factor/cofilin (ADF/CFL) gene family encodes a
 diverse group of relatively small proteins. Once known strictly as
 modulators of actin filament dynamics, recent research has demonstrated
 that these proteins are involved in a variety of cellular processes, from
 signal transduction to the cytonuclear trafficking of actin. In both plant
 and animal lineages, expression patterns of paralogs in the ADF/CFL gene
 family vary among tissue types and developmental stages. In this study we
 use computational approaches to investigate the evolutionary forces
 responsible for the diversification of the ADF/CFL gene family. Estimating
 the rate of non-synonymous to synonymous mutations (dN/dS) across
 phylogenetic lineages revealed that the majority of ADF/CFL codon
 positions were under strong purifying selection, with rare episodic events
 of accelerated protein evolution. In both plants and animals these
 instances of accelerated evolution were ADF/CFL subclass specific, and all
 of the sites under selection were located in regions of the protein that
 could serve in new functional roles. We suggest these sites may have been
 important in the functional diversification of ADF/CFL proteins.
description: PlantADFPhyloPlant ADF gene sequence alignment and input file used for phylogenetic analysis in MrBayesAnimalPhyloVertebrate and invertebrate ADF/CFL gene sequence alignment and input file for phylogenetic analysis in MrBayes.PlantADFPhyloNewick output of the MrBayes phylogenetic analysis for the plant ADF gene sequences. This was the newick file that was used for fitmodel analyses.AnimalPhyloNewick output of the MrBayes phylogenetic analysis for the vertebrate and invertebrate ADF/CFL gene sequences. This was the newick file that was used for fitmodel analyses.PlantADFFitmodelPlant ADF sequence file used as input into fitmodel analyses.AnimalFitmodelVertebrate and invertebrate ADF/CFL sequence file used as input into fitmodel analyses.PlantFigure3and4Excel file of the plant ADF fitmodel data set used to produce figures 3 and 4 of the manuscript. Please see associated readme file for more details.AnimalFigure3and4Excel file of the animal ADF/CFL fitmodel data set used to produce figures 3 and 4 of the manuscript. Please see associated readme file for more details.TranslatedOriginalThis is the original alignment, translated to amino acid sequence, that was used for our phylogenetic and fitModeL analyses.TranslatedPRANKThis is the new alignment of the animal CFL/ADF protein variants that was generated using the program PRANK.
DOI: 10.5061/dryad.m2m8f
title: Data from: Does catch and release affect the mating system and individual reproductive success of wild Atlantic salmon (Salmo salar L.)?

description: In this study, we documented the breeding system of a wild population of
 Atlantic salmon (Salmo salar L.) by genetically sampling every returning
 adult and assessed the determinants of individual fitness. We then
 quantified the impacts of catch and release (C&R) on mating and
 reproductive success. Both sexes showed high variance in individual
 reproductive success, and the estimated standardized variance was higher
 for males (2.86) than for females (0.73). We found a weak positive
 relationship between body size and fitness and observed that fitness was
 positively correlated with the number of mates, especially in males.
 Mature male parr sired 44% of the analysed offspring. The impact of
 C&R on the number of offspring was size dependent, as the
 reproductive success of larger fish was more impaired than smaller ones.
 Also, there was an interactive negative effect of water temperature and
 air exposure time on reproductive success of C&R salmon. This
 study improves our understanding of the complex reproductive biology of
 the Atlantic salmon and is the first to investigate the impact of
 C&R on reproductive success. Our study expands the management
 toolbox of appropriate C&R practices that promote conservation of
 salmon populations and limit negative impacts on mating and reproductive
 success.
description: GenotypesC&Ridentity_cervusrepro_anadromous
DOI: 10.5061/dryad.bf4mj
title: Data from: To eat or not to eat: ontogeny of hypothalamic feeding controls and a role for leptin in modulating life history transition in amphibian tadpoles

description: Many animal life histories entail changing feeding ecology, but the
 molecular bases for these transitions are poorly understood. The amphibian
 tadpole is typically a growth and dispersal life history stage. Tadpoles
 are primarily herbivorous, and they capitalize on growth opportunities to
 reach a minimum body size to initiate metamorphosis. During metamorphic
 climax, feeding declines, at which time the gastrointestinal tract
 remodels to accommodate the carnivorous diet of the adult frog. Here we
 show that anorexigenic hypothalamic feeding controls are absent in the
 tadpole, but develop during metamorphosis concurrent with the production
 of the satiety signal leptin. Before metamorphosis there is a large
 increase in leptin mRNA in fat tissue. Leptin receptor mRNA increased
 during metamorphosis in the preoptic area/hypothalamus, the key brain
 region involved with the control of food intake and metabolism. This
 corresponded with an increase in functional leptin receptor, as evidenced
 by induction of socs3 mRNA and phosphorylated STAT3 immunoreactivity, and
 suppression of feeding behavior after injection of recombinant frog
 leptin. Furthermore, we found that immuno-neutralization of leptin in
 tadpoles at metamorphic climax caused them to resume feeding. The absence
 of negative regulation of food intake in the tadpole allows the animal to
 maximize growth prior to metamorphosis. Maturation of leptin-responsive
 neural circuits suppresses feeding during metamorphosis to facilitate
 remodeling of the gastrointestinal tract.
description: Raw data for Bender et
 al.Body morphometry, gene
 expression, histochemistry dataRaw Data for Dryad Bender et
 al.7z
DOI: 10.5281/zenodo.17508285
title: OpenMesh PWS: New York City Personal Weather Station Dataset

description: Personal Weather Station (PWS) observations from 37 stations in the New York City metropolitan area. Data sourced from Weather Underground and formatted to OpenSense-1.0 standard. Part of the OpenMesh dataset for opportunistic urban weather sensing.

Period: October 29, 2023 – July 1, 2024Variables: rainfall_amount, rainfall_rate, temperature, relative_humidity, wind_velocity, wind_direction, air_pressureFormat: NetCDF-4 group
DOI: 10.5281/zenodo.17508286
title: OpenMesh PWS: New York City Personal Weather Station Dataset

description: Personal Weather Station (PWS) observations from 37 stations in the New York City metropolitan area. Data sourced from Weather Underground and formatted to OpenSense-1.0 standard. Part of the OpenMesh dataset for opportunistic urban weather sensing.

Period: October 29, 2023 – July 1, 2024Variables: rainfall_amount, rainfall_rate, temperature, relative_humidity, wind_velocity, wind_direction, air_pressureFormat: NetCDF-4 group