cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qb7t2
title: Data from: Self-reported household impacts of large-scale chemical contamination of the public water supply, Charleston, West Virginia, USA

description: A January 2014 industrial accident contaminated the public water supply of
 approximately 300,000 homes in and near Charleston, West Virginia (USA)
 with low levels of a strongly-smelling substance consisting principally of
 4-methylcyclohexane methanol (MCHM). The ensuing state of emergency closed
 schools and businesses. Hundreds of people sought medical care for
 symptoms they related to the incident. We surveyed 498 households by
 telephone to assess the episode’s health and economic impact as well as
 public perception of risk communication by responsible officials. Thirty
 two percent of households (159/498) reported someone with illness believed
 to be related to the chemical spill, chiefly dermatological or
 gastrointestinal symptoms. Respondents experienced more frequent symptoms
 of psychological distress during and within 30 days of the emergency than
 90 days later. Sixty-seven respondent households (13%) had someone miss
 work because of the crisis, missing a median of 3 days of work. Of 443
 households reporting extra expenses due to the crisis, 46% spent less than
 $100, while 10% spent over $500 (estimated average about $206). More than
 80% (401/485) households learned of the spill the same day it occurred.
 More than 2/3 of households complied fully with “do not use” orders that
 were issued; only 8% reported drinking water against advice. Household
 assessments of official communications varied by source, with local
 officials receiving an average “B” rating, whereas some federal and water
 company communication received a “D” grade. More than 90% of households
 obtained safe water from distribution centers or stores during the
 emergency. We conclude that the spill had major economic impact with
 substantial numbers of individuals reporting incident-related illnesses
 and psychological distress. Authorities were successful supplying
 emergency drinking water, but less so with risk communication.
description: FinalSurveyData_Schade
 et al_PLOS ONEPlease refer to our
 survey questionnaire (uploaded as ReadMe file) which serves as the
 codebook
DOI: 10.5061/dryad.331jq
title: Data from: When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

description: Simulation studies suggest that coalescent-based species-tree methods are
 generally more accurate than concatenated analyses. However, these
 species-tree methods remain impractical for many large datasets. Thus, a
 critical but unresolved issue is when and why concatenated and coalescent
 species-tree estimates will differ. We predict such differences for
 branches in concatenated trees that are short, weakly supported, and have
 conflicting gene trees. We test these predictions in Scincidae, the
 largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa
 and 44 genes for 12 taxa. We support our initial predictions, and suggest
 that simply considering uncertainty in concatenated trees may sometimes
 encompass the differences between these methods. We also found that
 relaxed-clock concatenated trees can be surprisingly similar to the
 species-tree estimate. Remarkably, the coalescent species-tree estimates
 had slightly lower support values when based on many more genes (44 vs.
 10) and a small (∼30%) reduction in taxon sampling. Thus, taxon sampling
 may be more important than gene sampling when applying species-tree
 methods to deep phylogenetic questions. Finally, our coalescent
 species-tree estimates tentatively support division of Scincidae into
 three monophyletic subfamilies, a result otherwise found only in
 concatenated analyses with extensive species sampling.
description: Alignments, MrBayes
 blocks and XML filesContains nexus
 alignments for each of the genes of the 10-gene dataset, as well as a
 concatenated file with associated MrBayes blocks. Also contains .xml files
 for BEAST and *BEAST analyses of the 10-gene and 44-gene
 datasets.For_Dryad.zip
DOI: 10.5281/zenodo.18381977
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Percival Hildebrand Gentle, http://www.wikidata.org/entity/Q106742450. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q106742450
DOI: 10.5061/dryad.64fs5
title: Data from: Introgression in hybrid ants is favored in females but selected against in males

description: Hybridization is not a mere reproductive dead end but has been suggested
 to play a central role in speciation, for example, by introducing adaptive
 genetic variation. Our previous study uncovered a unique consequence of
 hybridization in Formica ants. In a population including two isolated but
 partially introgressed genetic groups, the females have an apparent hybrid
 background, whereas the males do not. This situation results in
 large-scale differences between male and female genomes that are stable
 throughout generations. Here, we compare genotypes from different
 developmental stages to investigate how sex-specific introgression and
 genetic differences between sexes are maintained. We show that strong
 selection rather than sex-dependent transmission maintains the genetic
 differences between sexes. All genotype combinations are produced and
 observed in the eggs of both sexes, but the alleles acquired through
 hybridization disappear from the haploid males during development from egg
 to adult as their frequencies drop toward zero. However, the same
 introgressed alleles increase in frequency and are favored when
 heterozygous in the females. Genotypes eliminated from males most likely
 represent incompatibilities arising from hybridization. Our results show
 an unusual situation of opposite selection, where introgression is favored
 in diploid females but selected against in haploid males. This finding
 suggests that introgressed genomic regions harbor both fitness-enhancing
 and -reducing elements. Our work highlights the complex consequences of
 hybridization and provides a rare opportunity to observe natural selection
 in real time in nature.
description: PARENT_OFFSPRINGDATAHere are genotypes of mother queen, her offspring and their father (spermatheca)POPULATIONDATAHere are microsatellite genotypes from all the individuals collected from the hybrid population during time 1996 - 2011.
DOI: 10.5061/dryad.5hj47mh6
title: Data from: Reductions in prolonged swimming capacity following freshwater colonization in multiple threespine stickleback populations.

description: We compared ancestral anadromous-marine and nonmigratory, stream-resident
 threespine stickleback (Gasterosteus aculeatus) populations to examine the
 outcome of relaxed selection on prolonged swimming performance. We reared
 marine and stream-resident fish from two locations in a common environment
 and found that both stream-resident populations had lower critical
 swimming speeds (Ucrits) than marine populations. F1 hybrids from the two
 locations displayed significant differences in dominance, suggesting that
 the genetic basis for variation in Ucrit differs between locations. To
 determine which traits evolved in conjunction with, and may underlie,
 differences in performance capacity we measured a suite of traits known to
 affect prolonged swimming performance in fishes. While some candidate
 traits did not evolve (standard metabolic rate and two body shape traits),
 multiple morphological (pectoral fin size, shape and four body shape
 measures) and physiological (maximum metabolic rate; MMR) traits evolved
 in the predicted direction in both stream-resident populations. However,
 data from F1 hybrids suggested that only one of these traits (MMR) had
 dominance effects similar to those of Ucrit in both locations. Overall,
 our data suggest that reductions in prolonged swimming performance were
 selected for in non-migratory populations of threespine stickleback, and
 that decreases in MMR may mediate these reductions in performance.
description: R_ScriptR script to re-produce analyses run in Dalziel et al. 2011Fig2_Ucrit_RRaw prolonged swimming speed data (Ucrit) associated with Figure 2Fig3_PecFinSA_RRaw pectoral fin surface area data (residuals of mass and standard length). Figure 3 of Dalziel et al. 2011.PecFinShapelandmarks_UnalignedTPSTPS file of 6 pectoral fin landmarks from Fig.3. Note that these landmarks must be aligned in TpsRelw prior to further analysisFig3_PecFinshape_RRaw data for pectoral fin shape (aligned landmarks), and DFA analysis.Fig4_BodyShape_RCorrected measures of stickleback body shape (see methods) and results of DFA.BodyShape12LandmarksTPS file for use in TmorphGen. Can be used to calculate distances between 12 landmarks from Fig. 4.Fig5_SMR_RRaw standard metabolic rate data.Fig5_MMR_RRaw maximum metabolic rate dataDominanceModelR script for dominance modelDominance_modelUcritdata_RRaw data for testing for differences in dominance among locations (Bonsall and West Creeks)in R.
DOI: 10.25919/pfgk-dg39
title: Long-term project observations for project P456 semester 2025OCTS_12

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. We are now in an exciting regime where a signal detected in our (and other data sets) has the form expected for a gravitational wave background. We, along with the international community, are now working hard to either confirm or deny this result, and to determine the astrophysical origin of this signal. With this proposal, we aim to maintain our pre-eminent position in the field. This is a continuing proposal for which observations of millisecond pulsars (MSPs) will continue to improve bounds on ultra-low-frequency gravitational waves until they are detected with confidence. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected, continued observations will resolve the background origin and individual sources will be identified; advancing the nascent field of gravitational wave astronomy.
DOI: 10.15468/dl.y6j3qu
title: Occurrence Download

description: A dataset containing 14711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Adinetidae, Brachionidae, Gastropodidae, Dicranophoridae, Asplanchnidae, Euchlanidae, Proalidae, Notommatidae, Philodinidae, Collothecidae, Lepadellidae, Conochilidae, Trichocercidae, Epiphanidae, Trochosphaeridae, Flosculariidae, Habrotrochidae, Hexarthridae, Ituridae, Lecanidae, Lindiidae, Mytilinidae, Trichotriidae, Microcodidae, Philodinavidae, Synchaetidae, Testudinellidae, Scaridiidae, Tetrasiphonidae, Centropagidae, Diaptomidae, Cyclopidae, Halicyclopidae, Lernaeidae, Canthocamptidae, Ameiridae, Laophontidae, Phyllognathopodidae, Miraciidae, Ergasilidae, Daphniidae, Moinidae, Bosminidae, Chydoridae, Macrothricidae, Ilyocryptidae, Neothricidae)",
 "Geometry POLYGON ((-181.131592 -37.12775, -187.78141 -33.078885, -189.068184 -33.987495, -186.411552 -37.925243, -192.774353 -44.251839, -195.387383 -46.345032, -192.379532 -48.31083, -188.062592 -45.989329, -183.377609 -41.69727, -180.416107 -38.542795, -181.131592 -37.12775))"
 ]
}

 The dataset includes 14711 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000653-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.51ft1
title: Data from: Testing the terminal investment hypothesis in California oaks

description: The terminal investment hypothesis—which proposes that reproductive
 investment should increase with age-related declines in reproductive
 value—has garnered support in a range of animal species but has not been
 previously examined in long-lived plants, such as trees. We tested this
 hypothesis by comparing relative acorn production and radial growth among
 1,000+ mature individuals of eight species of California oaks (genus
 Quercus) followed for up to 37 years, during which time 70 trees died
 apparently natural deaths. We found no significant differences in the
 radial growth, acorn production, or index of reproductive effort, taking
 into consideration both growth and reproduction among dying trees relative
 to either conspecific trees at the same site that did not die or growth
 and reproduction from earlier years for the focal trees that did
 eventually die. Furthermore, we found no consistent trade-off between
 growth and reproduction among trees that died, nor did dying trees
 significantly alter their relative investment in reproduction even as they
 underwent physical decline. Trees approaching the end of their lives are
 often in poor physical condition but do not appear to differentially
 invest more of their diminished resources in reproduction compared with
 healthy trees.
description: Data for the two main
 analysesThe first sheet has data
 for focal trees followed by data for comparison trees; the second sheet
 has data for growth and reproduction standardized (from 0 to 1), as
 described in the text. Fields are described in the README.xls
 file.Terminvest1.xls
DOI: 10.5061/dryad.3s009
title: Data from: The contribution of spontaneous mutations to thermal sensitivity curve variation in Drosophila serrata

description: Many traits studied in ecology and evolutionary biology change their
 expression in response to a continuously varying environmental factor. One
 well-studied example are thermal performance curves (TPCs); continuous
 reaction norms that describe the relationship between organismal
 performance and temperature and are useful for understanding the
 trade-offs involved in thermal adaptation. We assayed TPCs for locomotor
 activity in a set of 66 spontaneous mutation accumulation lines in the fly
 Drosophila serrata. Factor-analytic modeling of the mutational
 variance-covariance matrix, M, revealed support for three axes of
 mutational variation in males and two in females. These independent axes
 of mutational variance corresponded well to the major axes of TPC
 variation required for different types of thermal adaptation;
 ‘faster-slower’ representing changes in performance largely independent of
 temperature, and the ‘hotter-colder’ and ‘generalist-specialist’ axes,
 representing trade-offs. In contrast to its near-absence from standing
 variance in this species, a ‘faster-slower’ axis, accounted for most
 mutational variance (75% in males and 66% in females) suggesting selection
 may easily fix or remove these types of mutations in outbred populations.
 Axes resembling the ‘hotter-colder’ and ‘generalist-specialist’ modes of
 variation contributed less mutational variance but nonetheless point to an
 appreciable input of new mutations that may contribute to thermal
 adaptation.
description: D. serrata MA lines
 locomotor activity across 6 temperaturesMA
 data.xls
DOI: 10.5061/dryad.7bp65gp
title: Data from: Historical biogeography and temporal diversification in Symphoricarpos (Caprifolieae, Caprifoliaceae, Dipsacales)

description: The major aim of this paper was to investigate temporal diversification
 within Symphoricarpos (Caprifoliaceae, Dipsacales). We used recently
 published molecular sequences, along with fossil data, to examine when
 Symphoricarpos may have arrived in the New World and if current
 distributional patterns can be explained by data based on biogeographic,
 climatological, and geological events. We simultaneously estimated the
 phylogeny and divergence times within Symphoricarpos and related
 Caprifolieae species using BEAST. Based on these phylogenetic and
 divergence time estimations we reconstructed ancestral areas using the
 dispersal-extinction-cladogenesis (DEC) method implemented in Lagrange.
 For Symphoricarpos, our phylogenetic results inferred using BEAST were in
 strong agreement with previous studies, with a well-supported clade
 containing the North American species that was sister to the lone Asian
 species. Our divergence time results suggest that the North American
 species originated in the late Oligocene to mid Miocene (12‐25 million
 years ago) and quickly diversified. The DEC area reconstructions suggest
 that after entering the North American continent from Asia, species of
 Symphoricarpos became widespread across the continent, followed by range
 restrictions to that of what we see today. Although several recent studies
 have argued for the idea of phylogenetic niche conservatism as a general
 explanation for characterizing broad biogeographic patterns, our data
 suggest significant niche evolution within the North American species of
 Symphoricarpos, especially in regard to taxa found in the southwestern
 parts of the USA and Mexico. These observed biome shifts from mesic forest
 habitats to a much drier habitat appear to have happened across a highly
 diverse landscape in which species of Symphoricarpos occur. These results,
 along with results from other plant taxa, support the hypothesis that a
 climate shift in western North America played a role in the assemblage of
 the current flora via migration, as well as in situ adaptation in
 combination with diversification.
description: S10189Aligned nucleotide
 sequences. Data also available in TreeBASE at accession S10189
 . First
 deposited for Bell C. 2010. Towards a Species Level Phylogeny of
 Symphoricarpos (Dipsacales), Based on Nuclear and Chloroplast DNA.
 Systematic Botany, 35(2): 442-450.
 https://doi.org/10.1600/036364410791638351
DOI: 10.5061/dryad.17vs2d34
title: Data from: Rensch's rule in large herbivorous mammals derived from metabolic scaling

description: Rensch’s rule, which states that the magnitude of sexual size dimorphism
 tends to increase with increasing body size, has evolved independently in
 three lineages of large herbivorous mammals: bovids (antelopes), cervids
 (deer), and macropodids (kangaroos). This pattern can be explained by a
 model that combines allometry, life-history theory, and energetics. The
 key features are that female group size increases with increasing body
 size and that males have evolved under sexual selection to grow large
 enough to control these groups of females. The model predicts
 relationships among body size and female group size, male and female age
 at first breeding, death and growth rates, and energy allocation of males
 to produce body mass and weapons. Model predictions are well supported by
 data for these megaherbivores. The model suggests hypotheses for why some
 other sexually dimorphic taxa, such as primates and pinnipeds (seals and
 sea lions), do or do not conform to Rensh’s rule.
description: Dryad
 TableData with sources, on
 adult male and female body mass, female group size, female age of first
 reproduction, and male maturity. Values used in Fig. 2. Adult male and
 female body masses are means, female group sizes are maximum values,
 female AFR data are from Ernest (2003) and ages of male maturity are
 maximum values.
DOI: 10.5061/dryad.rk8df
title: Data from: Evolutionary and ecological implications of trematode parasitism of modern and fossil northern Adriatic bivalves

description: The role of antagonistic organismal interactions in the production of
 long-term macroevolutionary trends has been debated for decades. Some
 evidence seems to suggest that temporal trends in predation frequency
 share a common causative mechanism with genus-level diversity, whereas
 studies on the role of parasites in “shaping” the evolutionary process are
 rare indeed. Digenean trematodes (Phylum Platyhelminthes) infest molluscs
 in at least one stage of their complex life cycle. Trematodes leave
 characteristic oval-shaped pits with raised rims on the interior of their
 bivalve hosts, and these pits are preserved in the fossil record. Here we
 survey 11,785 valves from the Pleistocene– Holocene deposits of the Po
 Plain and from nearby modern coastal environments on the northeast
 Adriatic coast of Italy. Of these, 205 valves exhibited trematode-induced
 pits. Trematodes were selective parasites in terms of host taxonomy and
 host body size. Infestation was restricted to lower
 shoreface/transition-to-platform paleoenvironments. During the Holocene,
 individuals from transgressive systems tracts were significantly more
 likely to be infested than those from highstand systems tracts. Temporal
 trends in infestation frequency cannot be explained as an
 ecological/evolutionary phenomenon (e.g., the hypothesis of escalation);
 instead the trend seems controlled by environmental variation induced by
 glacio-eustatic sea-level changes and inadequate sampling. Because this
 interaction appears to be ephemeral, both temporally and spatially, it is
 not likely that any selective pressure would be continuous over geologic
 time in this region. Furthermore, these results support the hypothesis
 that antagonistic interactions are lower in the northern Adriatic Sea in
 comparison to other midlatitude shallow marine settings.
description: Paleobiology ms 10051
 Huntley and Scarponi Supplementary MaterialModern samples are bulk
 samples collected from the shoreface at the given localities on the
 northern Adriatic coast of Italy. The fossil samples are bulk samples
 collected from cores drilled at three locations in the Po River Plain,
 Italy. Entries under "Taxon" are the genus and species names of
 bivalve (pelecypod) taxa.
DOI: 10.5061/dryad.n31f0t4
title: Data from: Rapid spread of a Wolbachia infection that does not affect host reproduction in Drosophila simulans cage populations

description: Wolbachia endosymbionts that are maternally inherited can spread rapidly
 in host populations through inducing sterility in uninfected females, but
 some Wolbachia infections do not influence host reproduction yet still
 persist. These infections are particularly interesting because they likely
 represent mutualistic endosymbionts, spreading by increasing host fitness.
 Here we document such a spread in the wAu infection of Drosophila
 simulans. By establishing multiple replicate cage populations, we show
 that wAu consistently increased from an intermediate frequency to near
 fixation, representing an estimated fitness advantage of around 20% for
 infected females. The effective population size in the cages was estimated
 from SNP markers to be around a few thousand individuals, precluding large
 effects of genetic drift in the populations. The exact reasons for the
 fitness advantage are unclear but viral protection and nutritional
 benefits are two possibilities.
description: PCR assay
 resultsResults from PCR assays
 of individual fly samples removed from experimental
 cages.Kriesner_Hoffmann_2018_cage_PCR_data1.xlsxKriesner_Hoffmann_2018_stochastic_model1Stochastic model for local dynamics of wAu and wRi infectionPkriesner1_CA5YJANXX_NoIndex_L001_R1.fastq.gz.001ddRAD sequence data Read 1 part 1Pkriesner1_CA5YJANXX_NoIndex_L001_R1.fastq.gz.002ddRAD sequence data Read 1 part 2Pkriesner1_CA5YJANXX_NoIndex_L001_R2.fastq.gz.001ddRAD sequence data Read 2 part 1Pkriesner1_CA5YJANXX_NoIndex_L001_R2.fastq.gz.002ddRAD sequence data Read 2 part 2