cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.603
title: Data from: A phylogenetic perspective on habitat shifts and diversity in the North American Enallagma damselflies

description: Community ecologists are increasingly aware that the regional history of
 taxon diversification can have an important influence on community
 structure. Likewise, systematists recognize that ecological context can
 have an important influence on the processes of speciation and extinction
 that create patterns of descent. We present a phylogenetic analysis of 33
 species of a North American radiation of damselflies (Zygoptera:
 Coenagrionidae: Enallagma Selys), which have been well-studied
 ecologically, in order to elucidate the evolutionary mechanisms that have
 contributed to differences in diversity between larval habitats (lakes
 with and without fish predators). Analysis of molecular variation in 842
 bp of the mitochondrial cytochrome oxidase I and II subunit and the
 intervening Leu-tRNA and 37 morphological characters resulted in three
 well-defined clades that are only partially congruent with previous
 phylogenetic hypotheses. Molecular and morphological data partitions were
 significantly incongruent. Lack of haplotype monophyly within species and
 small levels of sequence divergence (&lt;1%) between related species
 in 3 of the 4 clades suggests that recent, and parallel, speciation has
 been an important source of community diversity. Reconstruction of habitat
 preference over the phylogeny suggests that the greater species diversity
 in fish-lake habitats is due to the recency of shifts into the
 fishless-lake habit, although a difference in speciation or extinction
 rates between the two habitats is difficult to exclude as an additional
 mechanism.
description: Morphology Data
 SetBrown_morphology.nexusMitochondrial DNA Data SetBrown_mtDNA.nexusCombined Data SetBrown_combined.nexus
DOI: 10.5281/zenodo.18357764
title: WDXX and WDXXR Precipitation Concentration Indices from ERA5 Reanalysis (1980-2024)

description: This dataset contains precipitation concentration indices calculated from ERA5 daily precipitation reanalysis data for the period 1980-2024. The dataset includes two novel types of indices that characterize different aspects of precipitation patterns. The WDXX indices (standard concentration) measure the number of wettest days needed to accumulate a given percentage of annual precipitation (WD25, WD50, WD75), regardless of when these days occur during the year. The WDXXR indices (chronological clustering) measure the number of consecutive days needed to accumulate a given percentage of annual precipitation (WD25R, WD50R, WD75R), considering the temporal sequence of precipitation events. This distinction allows researchers to differentiate between intensity-based concentration (WDXX) and temporal clustering patterns (WDXXR), providing complementary insights into precipitation behavior.

The dataset consists of two NetCDF files: wdxx_1980_2024.nc (56 MB) containing standard concentration indices and wdxxr_1980_2024.nc (90 MB) containing chronological clustering indices. Both files provide global coverage at 0.25° × 0.25° spatial resolution (~28 km at equator) spanning from 90°N to 90°S and 180°W to 180°E, with annual values for the 45-year period from 1980 to 2024. The data are derived from high-quality ERA5 reanalysis precipitation data obtained from the Copernicus Climate Change Service (C3S) Climate Data Store, using a wet day threshold of 1.0 mm/day and concentration curve analysis methodology.

To facilitate reproducibility and ease of use, this package includes comprehensive example Python scripts demonstrating data loading, spatial visualization, temporal analysis, comparison between WDXX and WDXXR indices, and statistical analysis. Sample outputs from these scripts are also provided, showing example visualizations and statistical summaries for land-only analysis. Additionally, a snapshot of all computational codes used to generate these indices is included as github_codes.zip, though users are encouraged to visit the live GitHub repository (https://github.com/SauravBhattarai19/wdxx-precipitation-indices) for the most up-to-date versions of the code, which may contain improvements and bug fixes beyond this Zenodo snapshot.

This dataset is particularly valuable for climate change impact assessment, extreme precipitation pattern analysis, hydrological modeling, water resource management, and climate variability studies. The novel WDXXR indices provide unique insights into how precipitation events cluster temporally, complementing traditional intensity-based metrics and enabling more comprehensive characterization of precipitation regimes. The multi-threshold approach (25%, 50%, 75%) allows researchers to examine precipitation concentration at different accumulation levels, supporting diverse research applications from local-scale water resource planning to global climate trend analysis.
DOI: 10.5281/zenodo.18357763
title: WDXX and WDXXR Precipitation Concentration Indices from ERA5 Reanalysis (1980-2024)

description: This dataset contains precipitation concentration indices calculated from ERA5 daily precipitation reanalysis data for the period 1980-2024. The dataset includes two novel types of indices that characterize different aspects of precipitation patterns. The WDXX indices (standard concentration) measure the number of wettest days needed to accumulate a given percentage of annual precipitation (WD25, WD50, WD75), regardless of when these days occur during the year. The WDXXR indices (chronological clustering) measure the number of consecutive days needed to accumulate a given percentage of annual precipitation (WD25R, WD50R, WD75R), considering the temporal sequence of precipitation events. This distinction allows researchers to differentiate between intensity-based concentration (WDXX) and temporal clustering patterns (WDXXR), providing complementary insights into precipitation behavior.

The dataset consists of two NetCDF files: wdxx_1980_2024.nc (56 MB) containing standard concentration indices and wdxxr_1980_2024.nc (90 MB) containing chronological clustering indices. Both files provide global coverage at 0.25° × 0.25° spatial resolution (~28 km at equator) spanning from 90°N to 90°S and 180°W to 180°E, with annual values for the 45-year period from 1980 to 2024. The data are derived from high-quality ERA5 reanalysis precipitation data obtained from the Copernicus Climate Change Service (C3S) Climate Data Store, using a wet day threshold of 1.0 mm/day and concentration curve analysis methodology.

To facilitate reproducibility and ease of use, this package includes comprehensive example Python scripts demonstrating data loading, spatial visualization, temporal analysis, comparison between WDXX and WDXXR indices, and statistical analysis. Sample outputs from these scripts are also provided, showing example visualizations and statistical summaries for land-only analysis. Additionally, a snapshot of all computational codes used to generate these indices is included as github_codes.zip, though users are encouraged to visit the live GitHub repository (https://github.com/SauravBhattarai19/wdxx-precipitation-indices) for the most up-to-date versions of the code, which may contain improvements and bug fixes beyond this Zenodo snapshot.

This dataset is particularly valuable for climate change impact assessment, extreme precipitation pattern analysis, hydrological modeling, water resource management, and climate variability studies. The novel WDXXR indices provide unique insights into how precipitation events cluster temporally, complementing traditional intensity-based metrics and enabling more comprehensive characterization of precipitation regimes. The multi-threshold approach (25%, 50%, 75%) allows researchers to examine precipitation concentration at different accumulation levels, supporting diverse research applications from local-scale water resource planning to global climate trend analysis.
DOI: 10.5061/dryad.8096
title: Data from: A case-by-case analysis of four imprinted retrogenes

description: Retroposition is a widespread phenomenon resulting in the generation of
 new genes that are initially related to a parent gene via very high coding
 sequence similarity. We examine the evolutionary fate of four retrogenes
 generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5,
 and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of
 parental imprinting. We first provide new data on the age of these
 retrogene insertions. Using codon-based models of sequence evolution, we
 show these retrogenes have diverse evolutionary trajectories, including
 divergence from the parent coding sequence under positive selection
 pressure, purifying selection pressure maintaining parent-retrogene
 similarity, and neutral evolution. Examination of the expression pattern
 of retrogenes shows an atypical, broad pattern across multiple tissues.
 Protein 3D structure modeling reveals that a positively selected residue
 in U2af1-rs1, not shared by its parent, may influence protein
 conformation. Our case-by-case analysis of the evolution of four imprinted
 retrogenes reveals that this interesting class of imprinted genes, while
 similar in regulation and sequence characteristics, follow very varied
 evolutionary paths.
description: Nucleotide_sequences_used_McCole_EvolutionNucleotide sequences for genes used in the study, collected from UCSC, Ensembl genome broswers and the NCBI trace archive. File was created using word and saved as plain text. Abbreviated binomial nomenclature is used for each species, for example H. sapiens for humans.
DOI: 10.5061/dryad.4nb25
title: Data from: Influence of introduction history on genetic variation in introduced populations: a case study of Oregon Chub

description: Population introductions and reintroductions have become a common tool for
 conserving threatened species, but oftentimes introduced populations have
 reduced the genetic diversity compared with the source population they
 were founded from. Population introductions played an important role in
 the recovery of the Oregon Chub Oregonichthys crameri, a small floodplain
 minnow found in western Oregon. Unlike many introduction efforts,
 introduced populations of Oregon Chub were founded using large numbers of
 individuals (hundreds in many cases) and each population had a unique
 introduction history (e.g., number of founders, source populations
 selected, duration of the introduction effort). We used microsatellite
 loci to examine 13 introduced populations and their respective sources to
 evaluate how well the introduction program captured genetic diversity
 present in the wild populations. Genetic variation was reduced by roughly
 25% in one introduced population, and three introduced populations showed
 evidence of a genetic bottleneck due to heterozygote excess. Populations
 introduced from multiple sources had greater genetic diversity than
 populations from a single source. When multiple source populations were
 used, all source populations contributed genetic material to the
 introduced population, though the proportional contribution from each
 source population varied. Using correlation analyses and general linear
 models, we explored the relationship between introduction history
 variables and genetic diversity. Our top-ranked models included genetic
 diversity in the source population, and this variable had the highest
 variable importance weight (0.999), but the number of founders and the
 number of source populations were also important. Overall, the Oregon Chub
 introduction program was highly successful at capturing the genetic
 variation observed in natural populations. Results of this study will be
 useful for planning future population introductions for Oregon Chub and
 other species of conservation concern.
description: Oregon chub
 genotypesIndividual genotypes at
 9 microsatellite loci for Oregon chub from source and introduced
 populations.Chub Microsat Data
 3-11-15.xlsx
DOI: 10.5061/dryad.75ph1
title: Data from: The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster

description: Symbionts and parasites can manipulate their hosts’ reproduction to their
 own benefit, profoundly influencing patterns of mate choice and evolution
 of the host population. Wolbachia is one of the most widespread symbionts
 among arthropods, and one that alters its hosts’ reproduction in diverse
 and dramatic ways. While we are beginning to appreciate how
 Wolbachia's extreme manipulations of host reproduction can influence
 species diversification and reproductive isolation, we understand little
 about how symbionts and Wolbachia, in particular, may affect
 intrapopulation processes of mate choice. We hypothesized that the
 maternally transmitted Wolbachia would increase the attractiveness of its
 female hosts to further its own spread. We therefore tested the effects of
 Wolbachia removal and microbiome disruption on female attractiveness and
 male mate choice among ten isofemale lines of Drosophila melanogaster. We
 found variable effects of general microbiome disruption on female
 attractiveness, with indications that bacteria interact with hosts in a
 line-specific manner to affect female attractiveness. However, we found no
 evidence that Wolbachia influence female attractiveness or male mate
 choice among these lines. Although the endosymbiont Wolbachia can greatly
 alter the reproduction of their hosts in many species, there is no
 indication that they alter mate choice behaviours in D. melanogaster.
description: female
 attractivenessfemale attractiveness
 replicatemale
 choosiness
DOI: 10.5061/dryad.8679
title: Data from: Does morphological variation buffer against extinction? A test using veneroid bivalves from the Plio-Pleistocene of Florida

description: Although morphological variation is known to influence the evolutionary
 fates of species, the relationship between morphological variation and
 survivorship in the face of extinction-inducing perturbations is poorly
 understood. Here, we investigate this relationship for veneroid bivalves
 in association with the Plio-Pleistocene extinction in Florida. Fourteen
 pairs of related species were selected for analysis, with each pair
 including one species that survived the Plio-Pleistocene extinction and
 another that became extinct during the interval. Morphological landmark
 data were acquired for more than 1500 museum specimens, representing 19
 localities that encompass four well-known Plio-Pleistocene units in the
 study region. Procrustes superimposition was applied to each sample, and
 overall multivariate variation was calculated as the mean squared partial
 Procrustes distance between specimens and their mean form. Morphological
 variation was calculated at three geographic scales for each species, and
 differences in variation between survivors and victims were examined
 within each species pair. Results indicate that species surviving the
 Plio-Pleistocene extinction were significantly more variable
 morphologically than victims. Greater morphological variation may promote
 survivorship by directly enhancing species adaptations to changing
 conditions or by permitting the occupation of a larger geographic range.
 Alternatively, high morphological variation and survivorship may both be
 mediated by a third variable, such as large geographic range.
description: Appendix
 1Locality information,
 including locality description and location.Appendix
 2Museum collection
 information for specimens examined in this study.
DOI: 10.5061/dryad.m3d4d
title: Data from: Demography, traits, and vulnerability to urbanization: can we make generalizations?

description: 1. Human-induced land cover change threatens species diversity and
 ecosystem services. The rapid pace of current change makes predicting
 species’ declines imperative, but leaves little time for thorough study of
 all species. One solution is to make generalizations about species’
 vulnerability to urbanization based on traits common among studied species
 in decline. 2. To date, most generalizations about traits associated with
 species’ declines in response to urbanization are based on presence or
 abundance, or detailed studies of a few species. If these generalizations
 broadly reflect responses to urbanization, they should hold across the
 mechanisms driving patterns of abundance, such as survival or
 reproduction. 3. Across 68 bird species in the northeastern USA, we
 investigated how food preference, nest location, habitat preference,
 migration distance, number of broods, clutch size, body mass, and an
 interaction between urbanization and these traits affected survival and
 reproduction. 4. Mass was the strongest predictor of survival, followed by
 number of broods, migration distance, and nest location. Nest location was
 the strongest predictor of reproduction, followed by migration distance.
 No interaction between urbanization and species’ traits affected survival;
 however, differences in response to urbanization among species with
 different food preferences, migration distances, masses, nest locations,
 and number of broods were important in predicting reproduction. 5.
 Synthesis and applications. We found that some traits influenced
 demographic rates even though they were not associated with urbanization;
 identifying differences in species’ baseline demographic rates,
 irrespective of urbanization, is needed to guide management objectives.
 Reproduction, but not survival, was influenced by urbanization, suggesting
 that management in our region of study should target increasing suitable
 nest sites and reducing nest predation. Determining traits associated with
 demographic rates and urbanization across broad geographic extents can
 provide new insights for species’ management, and help guide conservation
 initiatives.
description: BrownGrahamTraitsDataThis file contains the parameter values and covariates used for regression analyses in this paper. Please see the "Data Accessibility" section of the paper for information on obtaining the raw data from which these values were estimated.
DOI: 10.5061/dryad.p7p7p
title: Data from: Coevolution of venom function and venom resistance in a rattlesnake predator and its squirrel prey

description: Measuring local adaptation can provide insights into how coevolution
 occurs between predators and prey. Specifically, theory predicts that
 local adaptation in functionally-matched traits of predators and prey will
 not be detected when coevolution is governed by escalating arms races,
 whereas it will be present when coevolution occurs through an alternate
 mechanism of phenotype matching. Here, we analyze local adaptation in
 venom activity and prey resistance across 12 populations of Northern
 Pacific rattlesnakes and California ground squirrels, an interaction that
 has often been described as an arms race. Assays of venom function and
 squirrel resistance show substantial geographic variation (influenced by
 site elevation) in both venom metalloproteinase activity and resistance
 factor effectiveness. We demonstrate local adaptation in the effectiveness
 of rattlesnake venom to overcoming present squirrel resistance, suggesting
 that phenotype matching plays a role in the coevolution of these molecular
 traits. Further, the predator was the locally adapted antagonist in this
 interaction, arguing that rattlesnakes are evolutionarily ahead of their
 squirrel prey. Phenotype matching needs to be considered as an important
 mechanism influencing coevolution between venomous animals and resistant
 prey.
description: Venom metalloproteinase
 activity and Squirrel InhibitionThis file includes 1440
 rows of snake venom metalloproteinase activity data, where each row is
 defined by a unique combination of of rattlesnake (Crotalus oreganus) and
 a ground squirrel (Otospermophilus beecheyi). Columns include animal
 identification numbers, animal collection site, site elevation, geographic
 distance between snake and squirrel pairings, baseline metalloproteinase
 activity of each snake's venom, and the metalloproteinase activity
 achieved in the presence of ground squirrel blood serum, which contains
 venom inhibitors. This dataset was used to test for local adaptation in
 the interactions between rattlesnake predators and squirrel prey in the
 reference manuscript.SVMP_Dryad.xlsx
DOI: 10.5061/dryad.1647
title: Data from: The cost of sexual signaling in yeast

description: The handicap principle holds that costly sexual signals can reliably
 indicate mate quality. Only individuals of high quality can afford a
 strong signal - the cost of signaling is relatively lower for high quality
 signalers than for low quality signalers. This critical property is
 difficult to test experimentally because the benefit of signaling on
 mating success, and cost of signaling on other components of fitness,
 cannot easily be separated in obligate sexual organisms. We therefore
 studied the facultatively sexual yeast Saccharomyces cerevisiae, which
 produces pheromones to attract potential mates. To precisely measure the
 cost of signaling, the signal was reduced or removed by deleting one or
 both copies of the pheromone-encoding genes and measuring asexual growth
 rate in competition with a wild-type signaler. We manipulated signaler
 quality either by changing the quality of the assay environment or by
 changing the number of deleterious mutations carried. For both types of
 treatment, we found that the cost of signaling decreased as the quality of
 the signaler increased, demonstrating that the yeast pheromone signal has
 the key property required for selection under the handicap principle. We
 found that cells of high genetic quality produce stronger signals than low
 quality cells, verifying that the signal is indeed honest.
description: S3 The cost of signaling
 for signalers in different environmental conditions.S1Asexualfitnessesofweaksignalersandnonsignalersrelativetowildtypesignalers.xlsS1 Asexual fitnesses of weak signalers and non signalers relative to wild type signalersS1Asexualfitnessesofweaksignalersandnonsignalersrelativetowildtypesignalers.xlsS6 The cost of signaling for signalers in different genetic backgroundsS6Thecostofsignalingforsignalersindifferentgeneticbackgrounds.xlsS7 S8 Effects of genetic fitness on signalling strengthS7S8Effectsofgeneticfitnessonsignallingstrength.xls
DOI: 10.5061/dryad.vs7v6
title: Data from: The adaptive significance of provisioning and foraging coordination between breeding partners

description: Sexual conflict over parental care relies on the fundamental assumption
 that parents do not share the cost of their partner’s effort on future
 reproduction. However, this is unlikely to be true whenever partners breed
 together more than once. In that case, individuals should try to optimize
 the cost and benefits for the pair, rather than only for themselves. Here
 we seek to establish whether the synchronization of parents’ provisioning
 visits to the nest could fulfill this function. We conducted a brood-size
 manipulation experiment on wild zebra finches to test whether nest visit
 synchrony was flexible and beneficial for nestlings’ growth, while
 controlling for the confounding effects of pair “quality” and synchrony
 away from the nest during foraging. Using a network of readers to track
 parents at nests and feeding stations, we found that nest visit synchrony
 responded directly to the brood manipulation and increased with brood
 size. Synchrony at the nest and while foraging were correlated, but the
 latter better predicted nestling mass, possibly because it was associated
 with more regular provisioning patterns. Our findings suggest that
 parental coordination could indeed play an important role in partners’
 investment decisions, underpinning the evolution of the most prominent
 mating system in birds.
description: DatasetsMariette&Griffithdaily data set of pair synchrony between day 6 and 14 and mean data set per pair over that period. variable names are as described in the paper. a refrence ID allows to link the two data sets.DatasetsForDryad.xls