cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.be5uy8
title: Occurrence Download

description: A dataset containing 522 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Palorus subdepressus (Wollaston, 1864)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 522 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011027-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15296406
title: Dataset of 1000 axisymmetric positive streamer simulations in air

description: This is the data shown in figure 4 of the paper "Data-driven reduced modeling of streamer discharges in air" by J. Teunissen and A. Malagón-Romero (https://arxiv.org/abs/2501.06093). The following columns are present, see the paper for more details:



sigma_head: line conductivity at streamer head. Unit: A m/MV

R_E: Electrodynamic radius. Unit: mm

v: streamer velocity. Unit: mm/ns

L_E: length of high-field region ahead of streamer. Unit: mm

E_max: maximum electric field strength at streamer head. Unit: MV/m

E_avg: average field between electrode tip and opposite plate. Unit: MV/m
DOI: 10.5281/zenodo.15296407
title: Dataset of 1000 axisymmetric positive streamer simulations in air

description: This is the data shown in figure 4 of the paper "Data-driven reduced modeling of streamer discharges in air" by J. Teunissen and A. Malagón-Romero (https://arxiv.org/abs/2501.06093). The following columns are present, see the paper for more details:



sigma_head: line conductivity at streamer head. Unit: A m/MV

R_E: Electrodynamic radius. Unit: mm

v: streamer velocity. Unit: mm/ns

L_E: length of high-field region ahead of streamer. Unit: mm

E_max: maximum electric field strength at streamer head. Unit: MV/m

E_avg: average field between electrode tip and opposite plate. Unit: MV/m
DOI: 10.14288/1.0397681
title: Data from: Phylogenetic evidence for cladogenetic polyploidization in land plants

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Premise of the study: Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation." Whether polyploidization is associated with the formation of new species ("cladogenesis") or simply occurs over time within a lineage ("anagenesis") has never, however, been assessed systematically. Methods: Here, we tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Key results: Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Conclusions: Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera.
DOI: 10.14288/1.0397694
title: Data from: Evaluating methods for estimating local effective population size with and without migration

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Effective population size is a fundamental parameter in population genetics, evolutionary biology and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed which take advantage of various approaches for inferring Ne. The ability of these methods to accurately estimate Ne, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves Ne estimates.
DOI: 10.14288/1.0397702
title: Data from: Nets versus spraying: a spatial modelling approach reveals indoor residual spraying targets Anopheles mosquito habitats better than mosquito nets in Tanzania

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The global implementation of malaria interventions has averted hundreds of millions of clinical malaria cases in the last decade. This study assesses predicted Anopheles mosquito distributions across the United Republic of Tanzania before large-scale insecticide-treated net (ITN) rollouts and indoor residual spraying (IRS) initiatives to determine whether mosquito net usage by children under the age of five and IRS are targeted to areas where historical evidence indicates mosquitoes thrive. Demographic and Health Surveys data from 2011-2012 and 2015-2016 include detailed measurements of mosquito net and IRS use across Tanzania. Anopheline data are far less intensively collected, but we constructed a Maxent-built baseline mosquito habitat suitability (MHS) map (AUC=0.872) with Tanzanian Anopheles occurrence records from 1999-2003. This MHS model was tested against independently-observed georeferenced Plasmodium falciparum cases from the Malaria Atlas Project, with ~87% of cases from 1999-2003 (n=107) and ~84% of cases from 1985-2012 (n=919) occurring in areas of high predicted suitability for mosquitoes. We compared the validated MHS with subsequent malaria interventions using mixed effects logistic regression. Specifically, we assessed whether Anopheles habitat suitability related to the frequency that ≥1 child in a household reportedly slept under a mosquito net when that intervention later became widely available, and whether IRS was reportedly applied to dwellings over a one-year period. There was no evidence that mosquito net use the night before the survey related to MHS from 2011-2012 and marginally significant evidence (p&lt;0.05) from 2015-2016 (β=1.466, 95% C.I.=0.848-2.103, marginal R2=0.020, respectively). However, the likelihood of IRS treatments rose relatively strongly in the 12 months prior to both surveys (β=13.466, 95% C.I.=10.488-16.456, marginal R2=0.144, and β=6.817, 95% C.I.=5.439-8.303, marginal R2=0.136, respectively). IRS treatments have therefore been targeted more effectively than mosquito nets toward areas where anopheline habitat suitability was previously found to be high.
DOI: 10.14288/1.0397707
title: Data from: Rat aversion to isoflurane versus carbon dioxide

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Some experts suggest that sedation of laboratory rodents with isoflurane before euthanasia with carbon dioxide (CO2) is a humane alternative to euthanasia with CO2 alone, but little research has compared aversion to these agents. Albino rats were tested in a light/dark box where they had the choice between remaining in a dark compartment filling with isoflurane or CO2, or escaping to a lit compartment. Experiment 1 validated the procedure by confirming that rats responded to agent and light intensity. In Experiment 2, 9/16 and 0/16 rats remained in the dark compartment until recumbent when initially exposed to isoflurane and CO2, respectively. In Experiment 3, more rats remained in the dark compartment until recumbent during initial (10/16) versus re-exposure (1/16) to isoflurane. These results indicate that initial exposure to CO2 is more aversive than isoflurane, and that re-exposure to isoflurane is more aversive than initial exposure. We conclude that sedation with isoflurane is a refinement over euthanasia with CO2 alone for rats that have not been previously exposed to inhalant anaesthetics.
DOI: 10.14288/1.0397714
title: Data from: Liking the good guys: amplifying local adaptation via the evolution of condition-dependent mate choice

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Local adaptation can be strengthened through a diversity of mechanisms that reduce gene flow between contrasting environments. Recent work revealed that mate choice could enhance local adaptation when females preferentially mate with locally adapted males and that such female preferences readily evolve, but the opposing effects of recombination, migration, and costs of female preferences remain relatively unexplored. To investigate these effects, we develop a two-patch model with two genes, one influencing an ecological trait and one influencing female preferences, where both male signals and female preferences are allowed to depend on the match between an individual's ecological trait and the local environment (condition). Because trait variation is limited when migration is rare and the benefits of preferential mating are short-lived when migration is frequent, we find that female preferences for males in high condition spread most rapidly with intermediate levels of migration. Surprisingly, we find that preferences for locally adapted males spread fastest with higher recombination rates, which contrasts with earlier studies. This is because a stronger preference allele for locally adapted males can only get uncoupled from maladapted ecological alleles following migration through recombination. The effects of migration and recombination depend strongly on the condition of the males being chosen by females, but only weakly on the condition of the females doing the choosing, except when it comes to the costs of preference. While costs always impede the spread of female preferences for locally adapted males, the impact is substantially lessened if costs are borne primarily by females in poor condition. The abundance of empirical examples of condition-dependent mate choice combined with our theoretical results suggests that the evolution of mate choice could commonly facilitate local adaptation in nature.
DOI: 10.14288/1.0397720
title: Data from: Replicate divergence between and within sounds in a marine fish: the copper rockfish (Sebastes caurinus)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The evolution of population structure in marine organisms and its relevance to conservation has recently received increasing attention. We tested the degree of genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of five replicate sounds on the west coast of Vancouver Island, British Columbia using 17 microsatellite DNA loci. Overall, subdivision (FST) was low (FST = 0.031), but consistently higher between paired coast and head of inlet sites (mean FST = 0.047) compared to among five coast sites (mean FST = -0.001) or among the five head of inlet sites (mean FST = 0.026). Heterozygosity, allelic richness, and estimates of effective population size were also consistently lower in head of inlet sites than in coast sites. Bayesian analysis of population structure identified two genetic groups across all samples, a single genetic group amongst only coast samples, two genetic groups amongst head of inlet samples, and two genetic groups within each sound analysed separately. Head of inlet copper rockfish were also consistently shorter with lower condition factors, and grew more slowly than fish collected from coast sites. Our results implicate coast- head of inlet habitat transitions in driving the evolution of population structure, likely resulting from reduced physical connectivity and selection against immigrants in contrasting environments. Coast sites appear to be well served by existing marine protected areas. By contrast, head of inlet sites may require more specific local conservation measures as they appear to be less well connected to adjacent coast sites as well as to each other.
DOI: 10.14288/1.0397726
title: Data from: Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favour a more annualized life history – grow now rather than save for next year – in environments where severe droughts occur more often. Thus, our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.
DOI: 10.14288/1.0397736
title: Data from: Dietary stress does not strengthen selection against single deleterious mutations in Drosophila melanogaster

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Stress is generally thought to increase the strength of selection, although empirical results are mixed and general conclusions are difficult because data are limited. Here we compare the fitness effects of nine independent recessive mutations in Drosophila melanogaster in a high- and low-dietary-stress environment, estimating the strength of selection on these mutations arising from both a competitive measure of male reproductive success and productivity (female fecundity and the subsequent survival to adulthood of her offspring). The effect of stress on male reproductive success has not been addressed previously for individual loci and is of particular interest with respect to the alignment of natural and sexual selection. Our results do not support the hypothesis that stress increases the efficacy of selection arising from either fitness component. Results concerning the alignment of natural and sexual selection were mixed, although data are limited. In the low-stress environment, selection on mating success and productivity were concordant for five of nine mutations (four out of four when restricted to those with significant or near-significant productivity effects), whereas in the high-stress environment, selection aligned for seven of nine mutations (two out of two when restricted to those having significant productivity effects). General conclusions as to the effects of stress on the strength of selection and the alignment of natural and sexual selection await data from additional mutations, fitness components and stressors.
DOI: 10.14288/1.0397740
title: Data from: Sex uncovered special issue: selective maintenance of recombination between the sex chromosomes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;A hallmark of many sex chromosomes is the dramatically reduced rate of recombination between them in the heterogametic sex (e.g., between the X and Y). Sexually antagonistic selection is thought to be the main selective driver of this reduced recombination, with tighter linkage strengthening the association between alleles favourable to females and the X, as well as alleles favourable to males and the Y. Nevertheless, many sex chromosomes retain substantial levels of recombination over millions of years, and some old sex chromosomes remain homomorphic with few signs of recombination suppression and the chromosomal degradation expected to follow. This paper explores the selective factors that can maintain recombination between the sex chromosomes. Specifically, by analysing the dynamics of genes that modify the rate of recombination, I present results demonstrating that certain forms of selection – all involving overdominance in males – can positively maintain recombination in the pseudo-autosomal region. To understand these cases, one has to revise our standard view of sexual antagonistic selection as involving two partners (males and females) to three partners (the X in females, the X in males, and the Y).
DOI: 10.14288/1.0397751
title: Data from: Resolving the conundrum of inbreeding depression but no inbreeding avoidance: estimating sex-specific selection on inbreeding by song sparrows (Melospiza melodia)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Inbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent ‘inbreeding paradox’. This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long-term pedigree data to estimate phenotypic selection gradients on the degree of inbreeding that female and male song sparrows (Melospiza melodia) expressed by forming socially-persistent breeding pairs with relatives. Fitness was measured as the total numbers of offspring and grand-offspring contributed to the population, and as corresponding expected numbers of identical-by-descent allele copies, thereby accounting for variation in offspring survival, reproduction and relatedness associated with variation in parental inbreeding. Estimated selection gradients on the degree to which individuals paired with relatives were weakly positive in females, but negative in males that formed at least one socially-persistent pairing. However, males that paired had higher mean fitness than males that remained socially unpaired. These analyses suggest that net selection against inbreeding may be weak in both sexes despite strong inbreeding depression, thereby resolving the ‘inbreeding paradox’.
DOI: 10.14288/1.0397757
title: Data from: Calculating the ecological impacts of animal-borne instruments on aquatic organisms

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Animal-borne instruments provide researchers with valuable data to address important questions on wildlife ecology and conservation. However, these devices have known impacts on animal behaviour and energetics. Tags deployed on migrating animals may reduce reproductive output through increased energy demands or cause phenological mismatches of foraging and nesting events. For marine organisms, the only tagging guidelines that exist are based on lift and thrust impacts on birds – concepts that do not translate well to aquatic animals. Herein, we provide guidelines on assessing drag from animal-borne instruments and discuss the ecological impacts on marine organisms. Of particular concern is the effect of drag from instruments to the welfare of the animals and for the applicability of collected data to wild populations. 2. To help understand how drag from electronic tags affects marine animals in the wild, we used marine turtles as model aquatic organisms and conducted wind tunnel experiments to measure the fluid drag of various marine turtle body types with and without commercially available electronic tags (e.g. satellite, TDR, video cameras). We quantified the drag associated with carrying biotelemetry devices of varying frontal area and design (squared or tear drop shaped) and generated contour plots depicting percentage drag increase as a framework for evaluating tag drag by scientists and wildlife managers. Then, using concepts of fluid dynamics, we derived a universal equation estimating drag impacts from instruments across marine taxa. 3. The drag of the marine turtle casts was measured in wind speeds from 2 to 30 m s−1 (Re 3·0 × 104–1·9 × 106), equivalent to 0·1–1·9 m s−1 in seawater. The drag coefficient (CD) of the marine turtles ranged from 0·11 to 0·22, which is typical of other large, air-breathing, marine vertebrates (0·08–0·26). The CD of tags in reference to the turtle casts was 0·91 ± 0·18 and most tags caused minimal additional drag (&lt;5%) to adult animals, but the same devices increased the drag for juveniles significantly (&gt;100%). The sensitivity of aquatic animals to instrument drag is a dynamic relationship between the fluid flow patterns, or CD, and the frontal area ratio of the animal and tag. 4. In this paper, we have outlined methods for quantifying the drag costs from animal-borne instrumentation considering the instrument retention time (time to release from the animal) and the activity of the instrumented animal. With this valuable tool, researchers can quantify the drag costs from animal-borne instrumentation and choose appropriate tags for their intended study organism and question. Reducing drag will ultimately reduce the impact on the instrumented animals and lead to greater biological realism in the collected data.
DOI: 10.14288/1.0397759
title: Data from: Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;PREMISE OF THE STUDY: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we report on the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. METHODS: We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. Where possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. RESULTS: Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. CONCLUSIONS: Transcriptome sequencing using next generation platforms has greatly reduced the cost of genomic studies of non-model organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to quantify the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.