cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4v514
title: Data from: Disentangling plastic and genetic changes in body mass of Siberian jays

description: Spatial and temporal phenotypic differentiation in mean body size is of
 commonplace occurrence, but the underlying causes remain often unclear:
 both genetic differentiation in response to selection (or drift) and
 environmentally induced plasticity can create similar phenotypic patterns.
 Studying changes in body mass in Siberian jays (Perisoreus infaustus) over
 three decades, we discovered that mean body mass declined drastically (ca.
 10%) over the first two decades, but increased markedly thereafter back to
 almost the initial level. Quantitative genetic analyses revealed that
 although body mass was heritable (h2 = 0.46), the pronounced temporal
 decrease in body mass was mainly a product of phenotypic plasticity.
 However, a concomitant and statistically significant decrease in predicted
 breeding values suggests a genetic component to this change. The
 subsequent increase in mean body mass was indicated to be entirely due to
 plasticity. Selection on body mass was estimated to be too weak to fully
 account for the observed genetic decline in body mass, but bias in
 selection differential estimates due to environmental covariance between
 body mass and fitness is possible. Hence, the observed body mass changes
 appear to be driven mainly by phenotypic plasticity. Although we were not
 able to identify the ecological driver of the observed plastic changes,
 the results highlight the utility of quantitative genetic approaches in
 disentangling genetic and phenotypic changes in natural populations.
description: Data analysed in Gienapp
 & Merilä J. Evol. Biol.This file contains data
 on individual fitness and life-history, morphometry as well as the
 pedigree that were analysed in Gienapp & Merilä J. Evol. Biol.
 Explanation on data structure is contained withing the file as comments
 marked by '#' directly before the corresponding
 data.Gienapp &
 Merilä_data.txt
DOI: 10.5061/dryad.h1v63
title: Data from: Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

description: As global warming accelerates the melting of Arctic sea ice, polar bears
 (Ursus maritimus) must adapt to a rapidly changing landscape. This process
 will necessarily alter the species distribution together with population
 dynamics and structure. Detailed knowledge of these changes is crucial to
 delineating conservation priorities. Here, we sampled 361 polar bears from
 across the center of the Canadian Arctic Archipelago spanning the Gulf of
 Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites
 and mitochondrial control region sequences to quantify genetic
 differentiation, estimate gene flow, and infer population history. Two
 populations, roughly coincident with GB and MC, are significantly
 differentiated at both nuclear (FST = 0.01) and mitochondrial (ΦST = 0.47;
 FST = 0.29) loci, allowing Bayesian clustering analyses to assign
 individuals to either group. Our data imply that the causes of the
 mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA
 reveals the matrilineal structure dates at least to the Holocene, and is
 common to individuals throughout the species’ range. These mtDNA
 differences probably reflect both genetic drift and historical
 colonization dynamics. In contrast, the differentiation inferred from
 microsatellites is only on the scale of hundreds of years, possibly
 reflecting contemporary impediments to gene flow. Taken together, our data
 suggest that gene flow is insufficient to homogenize the GB and MC
 populations and support the designation of GB and MC as separate polar
 bear conservation units. Our study also provide a striking example of how
 nuclear DNA and mtDNA capture different aspects of a species demographic
 history.
description: Data from Campagna et al
 2013 Ecology and EvolutionMicrosatellite data set
 and all Structure, Geneland, Arlequin and IMa2 input
 files.Data
 from Campagna et al 2013.rar
DOI: 10.15468/dl.wcrq8v
title: Occurrence Download

description: A dataset containing 661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus frigidus"
 ]
}

 The dataset includes 661 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000874-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns11g
title: Data from: Widespread positive but weak assortative mating by diet within stickleback populations

description: Assortative mating – correlation between male and female traits – is
 common within populations and has the potential to promote genetic
 diversity and in some cases speciation. Despite its importance, few
 studies have sought to explain variation in the extent of assortativeness
 across populations. Here, we measure assortative mating based on an
 ecologically important trait, diet as inferred from stable isotopes, in 16
 unmanipulated lake populations of three-spine stickleback. As predicted,
 we find a tendency toward positive assortment on the littoral–pelagic
 axis, although the magnitude is consistently weak. These populations vary
 relatively little in the strength of assortativeness, and what variation
 occurs is not explained by hypothesized drivers including habitat
 cosegregation, the potential for disruptive selection, costs to
 choosiness, and the strength of the relationship between diet and body
 size. Our results support recent findings that most assortative mating is
 positive, while suggesting that new approaches may be required to identify
 the environmental variables that drive the evolution of nonrandom mating
 within populations.
description: Nest Data (Male
 Stickleback and Eggs)Data for male
 stickleback size and isotope values, as well as nest site and habitat, and
 egg isotope values, from 16 lakes in British Columbia.Nest_Data.csvFemale Stickleback and Egg DataFemale stickleback isotopes and egg isotopes from three lakes in British Columbia.Female_Data.csvLake DataLake-level properties used as potential predictors of assortative mating in 16 lakes in British Columbia.Lake_Data.csvR script for analyses and figuresR script including code needed to reproduce all key analyses in the paper, and to reproduce the figures. Comments included where explanation is necessary.Assort_script.R
DOI: 10.5061/dryad.j313j
title: Data from: The reproducibility of research and the misinterpretation of p-values

description: We wish to answer this question: If you observe a ‘significant’ p-value
 after doing a single unbiased experiment, what is the probability that
 your result is a false positive? The weak evidence provided by p-values
 between 0.01 and 0.05 is explored by exact calculations of false positive
 risks. When you observe p = 0.05, the odds in favour of there being a real
 effect (given by the likelihood ratio) are about 3 : 1. This is far weaker
 evidence than the odds of 19 to 1 that might, wrongly, be inferred from
 the p-value. And if you want to limit the false positive risk to 5%, you
 would have to assume that you were 87% sure that there was a real effect
 before the experiment was done. If you observe p = 0.001 in a well-powered
 experiment, it gives a likelihood ratio of almost 100 : 1 odds on there
 being a real effect. That would usually be regarded as conclusive. But the
 false positive risk would still be 8% if the prior probability of a real
 effect were only 0.1. And, in this case, if you wanted to achieve a false
 positive risk of 5% you would need to observe p = 0.00045. It is
 recommended that the terms ‘significant’ and ‘non-significant’ should
 never be used. Rather, p-values should be supplemented by specifying the
 prior probability that would be needed to produce a specified (e.g. 5%)
 false positive risk. It may also be helpful to specify the minimum false
 positive risk associated with the observed p-value. Despite decades of
 warnings, many areas of science still insist on labelling a result of
 p &lt; 0.05 as ‘statistically significant’. This practice must
 contribute to the lack of reproducibility in some areas of science. This
 is before you get to the many other well-known problems, like multiple
 comparisons, lack of randomization and p-hacking. Precise inductive
 inference is impossible and replication is the only way to be sure.
 Science is endangered by statistical misunderstanding, and by senior
 people who impose perverse incentives on scientists.
description: files-paper-2.zipA zip file that contains the six R scripts used in the paper (see ref [44]] and a pdf file with brief instructions for their use (Notes-on-use-of-R-scripts.pdf)
DOI: 10.5061/dryad.36035b9
title: Data from: Regional population structure of the endangered Bridle Shiner (Notropis bifrenatus)

description: In the last 100 years, the Bridle Shiner has declined over significant
 parts of its range. We used mitochondrial and nuclear microsatellite
 markers to investigate population structure of this species. Tissue
 samples were collected from populations in six drainages in PA, NJ, NY and
 CT. One predominant haplotype was observed in the Delaware, Housatonic,
 Passaic, and Raritan specimens. Specimens from the Hudson and St. Lawrence
 drainages had a separate unique haplotype. Microsatellite loci revealed
 low within-population genetic diversity and pairwise population
 comparisons of allelic divergence showed significant genetic differences
 among most drainages. Population structure analysis of microsatellite loci
 recover the same population clusters inferred using mtDNA. Within the
 Delaware drainage, there was significant differentiation among areas
 separated by 128 km. Several alternate scenarios of population divergence
 and population bottlenecks were investigated using approximate Bayesian
 computing. These supported a scenario with a bottleneck occurring in the
 ancestral population of Bridle Shiner followed by recent divergence of
 Northern and Southern drainages.
description: Microsatellite
 datasetMicrosatellite data from
 Notropis bifrenatus populations in Genepop format (7 loci, 180
 individuals). See associated publication for additional information on
 microsatellite loci, primers, and reaction conditions.NOBIF_2pops_7loci.txtND5 and ND6 Nucleotide DataConcatenated partial mitochondrial ND5 and ND6 nucleotide sequences from 177 Notropis binfrenatus individuals in nexus format. See associated publication for primers and reaction conditions.Notropis_ND5_ND6.nex
DOI: 10.5061/dryad.pm4v7
title: Data from: Effects of the early Toarcian Oceanic Anoxic Event on ichthyosaur body size and faunal composition in the Southwest German Basin

description: The Early Jurassic Toarcian Oceanic Anoxic Event is considered one of the
 most dramatic environmental perturbations of the Mesozoic. An elevated
 extinction rate among marine invertebrates accompanied rapid environmental
 changes, but effects on large vertebrates are less understood. We examined
 changes in ichthyosaur body size in the Posidonia Shale of the Southwest
 German Basin spanning the extinction interval to assess how environmental
 changes and biotic crisis among prey species affected large reptiles. We
 report no species-level extinction among the ichthyosaurs coinciding with
 peak invertebrate extinction. Large ichthyosaurs were absent from the
 fauna during the extinction interval, but became more abundant in the
 immediate aftermath. Stenopterygius quadriscissus, the most abundant
 species during the extinction interval, increased in body size after the
 biotic event. Rapid invasion by large taxa occurred immediately following
 the extinction event at the end of the first ammonite zone of the early
 Toarcian. Greater mobility permitting exploitation of ephemeral resources
 and opportunistic feeding behavior may minimize the impacts of
 environmental change on large vertebrates.
description: Specimen list and
 measurement data for Stenopterygius quadriscissus; Plot of lower jaw
 length against stratigraphic occurrence for all specimens of S.
 quadriscissusSupplementary Table
 1.—Specimen list and measurement data for Stenopterygius quadriscissus.
 Note that only approximate geographic provenance is available as these are
 historical finds. All measurements are in millimetres. Specimens for which
 all 6 measurements were not available were included in the lower jaw mean
 length analysis, but not the PCA analysis.; Supplementary Figure 1.—Plot
 of lower jaw length against stratigraphic occurrence for all specimens of
 S. quadriscissus (juveniles included).Maxwell&VincentSI.docx
DOI: 10.5061/dryad.46c39p1
title: Data from: Substantial red wolf genetic ancestry persists in wild canids of southwestern Louisiana

description: Concerns over red wolf (Canis rufus) extinction caused by hybridization
 with coyotes (C. latrans) led to the capture and removal of remnant wild
 wolves from southwestern Louisiana and southeastern Texas, USA, during the
 1970s. Here we show that despite decades of unmitigated hybridization, and
 declaration of endangered red wolves as functionally extinct in the wild,
 red wolf mitochondrial or nuclear DNA ancestry persists in ~55% of
 contemporary wild canids sampled in southwestern Louisiana. Surprisingly,
 one individual had 78–100% red wolf ancestry, which is within the range
 for 75% red wolf, red wolf backcross, or putative red wolf, depending on
 estimation method. Our findings bolster support for designation of red
 wolves as a distinct species, demonstrate a critical need for the United
 States Government to consider adopting an existing but unimplemented
 hybrid policy, and suggest that immediate reassessment of canid management
 and taxonomic designation in southwestern Louisiana may be warranted.
description: Murphy et al. Genotype
 data for scat, hair, tissue samples and samples from gray wolf red wolf
 and dogDatafile contains
 genotypes at 17 microsatellites from hair, fecal and tissue samples from
 Southwestern Louisiana as well as genotypes from gray wolves, red wolves,
 dogs and coyotes from the southeastern United States.
DOI: 10.5061/dryad.6343j
title: Data from: Hill-Robertson interference maintained by red queen dynamics favours the evolution of sex

description: Although it is well established theoretically that selective interference
 among mutations (Hill-Robertson interference) favours meiotic
 recombination, genome-wide mean rates of mutation and strengths of
 selection appear too low to support this as the mechanism favouring
 recombination in nature. A possible solution to this discrepancy between
 theory and observation is that selection is at least intermittently very
 strong due to the antagonistic coevolution between a host and its
 parasites. The Red Queen theory posits that such coevolution generates
 fitness epistasis among loci, which generates negative linkage
 disequilibrium among beneficial mutations, which in turn favours
 recombination. This theory has received only limited support. However, Red
 Queen dynamics without epistasis may provide the ecological conditions
 that maintain strong and frequent selective interference in finite
 populations that indirectly selects for recombination. This hypothesis is
 developed here through the simulation of Red Queen dynamics. This approach
 required the development of a method to calculate the exact frequencies of
 multi-locus haplotypes after recombination. Simulations show that
 recombination is favoured by the moderately weak selection of many loci
 involved in the interaction between a host and its parasites, which
 results in substitution rates that are compatible with empirical
 estimates. The model also reproduces the previously reported rapid
 increase in the rate of outcrossing in Caenorhabditis elegans coevolving
 with a bacterial pathogen.
description: recomb8.f90: Fortran 90
 Code for Main Recursion-Equation ModelFortran 90 code used for
 the simulations reported in Figures 1-7. Compilation of this code requires
 the Intel Math Kernel Library Vector Statistical
 Library.recomb8.f90recomb_individ2.1.f90: Fortran 90 Code for Individual-Based ModelFortran 90 code used for simulations in Figure 8 and used to verify the recursion-equation model (Table S1).recomb_individ2.1.f90recomb2omp3.f90: Fortran 90 Code Used to Calculate Probability of Fixation of Recombination AlleleFortran 90 code used for simulations in Table S5. Compilation of this code requires the Intel Math Kernel Library Vector Statistical Library and an OpenMP library.recomb2omp3.f90
DOI: 10.5061/dryad.c3g48
title: Data from: Ambulatory versus inpatient management of severe nausea and vomiting of pregnancy: a randomized control trial with patient preference arm

description: ABSTRACT Objective To determine whether ambulatory (outpatient, OP)
 treatment of severe nausea and vomiting of pregnancy (NVP) is as effective
 as inpatient (IP) care. Design Non-blinded randomized control trial (RCT)
 with patient preference arm Setting Multi-center Participants Women less
 than 20 weeks pregnant with severe NVP and associated ketonuria Methods
 Women participating in the RCT were randomized via web-based application
 to either ambulatory or IP treatment. Women declining randomisation
 entered the patient preference trial (PPT) arm. Protocols, data collection
 and follow-up were the same for all participants. Main Outcome Measures
 Primary outcome was reduction in Pregnancy Unique Quantification of Emesis
 (PUQE) score at 48 hours. Secondary outcomes were duration of treatment;
 improvement in symptom scores and ketonuria at 48 hours; re-attendances
 within 7 days of discharge; and comparison of symptoms at 7 days post
 discharge Results 152/174 eligible women agreed to participate with 77/152
 (51%) recruited to the RCT and 79/152 (49%) to the PPT. Patients were
 initially compared in 4 groups (randomized IP, randomized OP,
 non-randomized IP and non-randomized OP). Comprehensive cohort analysis of
 participants in the (RCT) and (PPT) did not demonstrate any differences in
 patient demographics or baseline clinical characteristics. Pooled analysis
 of IP versus OP groups showed no difference in reduction in PUQE score at
 48 hours (p=0.86). There was no difference in change in eating score
 (p=0.69), drinking score (p=0.77), wellbeing rating (p=0.64) or reduction
 in ketonuria (p=0.47) at 48 hours, with no difference in duration of index
 treatment episode (p=0.83) or re-attendances within 7 days (p=0.52).
 Conclusions Ambulatory management is an effective alternative to inpatient
 management of severe NVP. The trial also demonstrated that many women
 requiring treatment for HG have a strong preferences regarding treatment
 setting, which needs to be considered by care providers, especially given
 the psychological impact of HG.
description: HIP data NMJ et al
 DryadRaw data for HIP trial.
 For further coding information please contact
 nicola_mitchell_jones@hotmail.com
DOI: 10.5061/dryad.41r54
title: Data from: A multivariate study of differentiating characters between three European species of the genus Lasiochernes Beier, 1932 (Pseudoscorpiones, Chernetidae)

description: Morphological variation in three rarely collected European species of the
 genus Lasiochernes Beier, 1932 is thoroughly examined in the present
 study. Detailed descriptions of previously ignored morphological
 characters of L. cretonatus Henderickx, 1998, L. jonicus (Beier, 1929) and
 L. pilosus (Ellingsen, 1910) are presented. The female of L. cretonatus
 and the nymphs of L. pilosus are described for the first time.
 Multivariate morphometric techniques (principal coordinate analysis and
 discriminant analyses) were employed to confirm morphological
 differentiation of the three Lasiochernes species and to identify the most
 reliable characters for their separation. The usefulness of particular
 body parts for species identification was evaluated. An identification key
 for the females of the Lasiochernes species studied is provided.
 Geographic distribution and habitat preferences of the three species are
 summarized.
description: supplementary material
 1Results of eight
 canonical discriminant analyses (CDA 1–CDA 8, fig. 8) based on
 morphological characters measured/scored on 19 specimens and eight body
 segments of Lasiochernes cretonatus, L. jonicus and L. pilosus. Values of
 the total canonical structure listed in the table express correlations of
 characters with canonical axes (Can 1 and Can 2) in each CDA. Higher total
 canonical structure values are in bold type.Supplementary_file1.pdf
DOI: 10.5061/dryad.n15r5
title: Data from: Oligo-Miocene climate change and mammal body size evolution in the northwest United States a test of Bergmann's Rule

description: Whether or not climate plays a causal role in mammal body-size evolution
 is one of the longest-standing debates in ecology. Bergmann's Rule,
 the longest-standing model addressing this topic, posits that geographic
 body-mass patterns are driven by temperature, whereas subsequent research
 has suggested that other ecological variables, particularly precipitation
 and seasonality, may be the major drivers of body-size evolution. While
 paleoecological data provide a unique and crucial perspective on this
 debate, paleontological tests of Bergmann's rule and its corollaries
 have been scarce. We present a study of body-size evolution in three
 ecologically distinct families of mammal (equids, canids, and sciurids)
 during the Oligo-Miocene of the northwest United States, an ideal natural
 laboratory for such studies because of its rich fossil and paleoclimatic
 records. Body-size trends are different in all three groups, and in no
 case is a significant relationship observed between body size and any
 climatic variable, counter to what has been observed in modern ecosystems.
 We suggest that for most of the Cenozoic, at least in the Northwest, body
 mass has not been driven by any one climatic factor but instead has been
 the product of complex interactions between organisms and their
 environments, though the nature of these interactions varies from taxon to
 taxon. The relationship that exists between climate and body size in many
 groups of modern mammals, therefore, is the exception to the rule and may
 be the product of an exceptionally cool and volatile global climate. As
 anthropogenic global warming continues and ushers in climatic conditions
 more comparable to earlier intervals of the Cenozoic than to the modern
 day, models of corresponding biotic variables such as body size may lose
 predictive power if they do not incorporate paleoecological data.
description: Orcutt &
 Hopkins_SupplementaryRaw body size data
 (based on dental measurements) used in this study. Institutional
 abbreviations for repositories given in text. Measurements were made by
 John Orcutt unless otherwise indicated; some were taken from published
 sources and some were identified and measured by Joshua Samuels (JXS).
 2LPL = second lower premolar length, 3LPL = third lower premolar length,
 4LPL = fourth lower premolar length, 1LML = first lower molar length, 2LML
 = second lower molar length, 3LML = third lower molar length, 2UML =
 second upper molar length; measurements given in
 millimeters.