cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c6b40
title: Data from: Divergent natural selection promotes immigrant inviability at early and late stages of evolutionary divergence

description: Natural selection's role in speciation has been of fundamental
 importance since Darwin first outlined his theory. Recently, work has
 focused on understanding how selection drives trait divergence, and
 subsequently reproductive isolation. ‘Immigrant inviability’, a barrier
 that arises from selection against immigrants in their non-native
 environment, appears to be of particular importance. Although immigrant
 inviability is likely ubiquitous, we know relatively little about how
 selection acts on traits to drive immigrant inviability, and how important
 immigrant inviability is at early-versus-late stages of divergence. We
 present a study evaluating the role of predation in the evolution of
 immigrant inviability in recently-diverged population pairs and a
 well-established species pair of Brachyrhaphis fishes. We evaluate
 performance in a high-predation environment by assessing survival in the
 presence of a predator, and swimming endurance in a low-predation
 environment. We find strong signatures of local adaptation and immigrant
 inviability of roughly the same magnitude both early and late in
 divergence. We find remarkably conserved selection for burst-speed
 swimming (important in predator evasion), and selection for increased size
 in low-predation environments. Our results highlight the consistency with
 which selection acts during speciation, and suggest that similar factors
 might promote initial population differentiation and maintain
 differentiation at late stages of divergence.
description: Brachyrhaphis endurance
 and kinematicsThis file contains
 endurance and kinematics measures for species and populations of
 Brachyrhaphis fishes (Poeciliidae) from different predation
 environments.Brachy_Endurance_EVOLUTION_DRYAD.xlsxBrachyrhaphis burst speed and mesocosmThis file contains the results of a mesocosm experiment with species of Brachyrhaphis fishes (Poeciliidae) from different predation environments. This file also includes burst speed measurements and a measure of relative body shape.Burst_speed_mesocosm_Data_EVOLUTION_DRYAD.xlsx
DOI: 10.5061/dryad.778c9
title: Data from: Genetic impacts of Anacapa deer mice reintroductions following rat eradication

description: The Anacapa deer mouse is an endemic subspecies that inhabits Anacapa
 Island, part of Channel Islands National Park. Anacapa is a chain of three
 small islands (East, Middle and West). In this study, we used
 mitochondrial DNA (mtDNA) cytochrome c oxidase subunit II gene (COII) and
 ten microsatellite loci to evaluate the levels of genetic differentiation
 and variation in ~1400 Anacapa deer mice sampled before and after a black
 rat (Rattus rattus) eradication campaign that included trapping, captive
 holding and reintroduction of deer mice. We also compared levels of
 genetic variation in Anacapa deer mice to those of a nearby mainland
 population. Both mitochondrial and microsatellite analyses indicated
 significant differentiation between Anacapa deer mice and mainland mice,
 and genetic variability of mainland mice was significantly higher than
 Anacapa mice even prior to reintroduction. We also found that East, Middle
 and West Anacapa mice were genetically differentiated from each other, but
 translocation of mice among islands resulted in the East population
 becoming less distinct as a result of management. Levels of heterozygosity
 were similar before and after management. However, numerous private
 alleles in the founder populations were not observed after reintroduction
 and shifts in allele frequencies occurred, indicating that the
 reintroduced populations experienced substantial genetic drift.
 Surprisingly, two mitochondrial haplotypes observed in an earlier study of
 Anacapa deer mice were lost in the 20 years prior to the rat eradication
 program, leaving only a single haplotype in Anacapa deer mice.
description: Ozer2011
DOI: 10.5061/dryad.94rt2
title: Data from: Using virtual reality to estimate aesthetic values of coral reefs

description: Aesthetic value, or beauty, is important to the relationship between
 humans and natural environments and is, therefore, a fundamental
 socioeconomic attribute of conservation alongside other ecosystem
 services. However, beauty is difficult to quantify and is not estimated
 well using traditional approaches to monitoring coral reef aesthetics. To
 improve the estimation of ecosystem aesthetic values, we developed and
 implemented a novel framework used to quantify features of coral reef
 aesthetics based on people’s perceptions of beauty. Three observer groups
 with different experience to reef environments (Marine Scientist,
 Experienced Diver and Citizen) were virtually immersed in Australian’s
 Great Barrier Reef using 360-degree images. Perceptions of beauty and
 observations were used to assess the importance of eight potential
 attributes of reef aesthetic value. Among these, heterogeneity, defined by
 structural complexity and colour diversity, was positively associated with
 coral-reef aesthetic values. There were no group-level differences in the
 way the observer groups perceived reef aesthetics suggesting that past
 experiences with coral reefs do not necessarily influence the perception
 of beauty by the observer. The framework developed here provides a generic
 tool to help identify indicators of aesthetic value applicable to a wide
 variety of natural systems. The ability to estimate aesthetic values
 robustly adds an important dimension to the holistic conservation of the
 Great Barrier Reef, coral reefs worldwide, and other natural ecosystems.
description: Answers of participants
 for reef aesthetic questionsThis data table is
 composed of 523 rows and 33 columns. Each row correspond to an answer and
 associated uncertainty from an observer to an image. Observers are
 differentiated by "RowID" and images by "ImageID".
 Please see the README file describing each columns and Supplementary
 Material of the paper to see the full interview.Answers_from_interviews.csvDemographic information of the observersThis data table describes the demographic information of the observers. Age, gender, frequency of scuba-diving and locations and group of observers are indicated in the table. Please see the README file for the coding.Demographic_information.csv
DOI: 10.5061/dryad.dp0qj
title: Data from: Fractured genetic connectivity threatens a southern California puma (Puma concolor) population

description: Pumas (Puma concolor; also known as mountain lions and cougars) in
 southern California live among a burgeoning human population of roughly 20
 million people. Yet little is known of the consequences of attendant
 habitat loss and fragmentation, and human-caused puma mortality to puma
 population viability and genetic diversity. We examined genetic status of
 pumas in coastal mountains within the Peninsular Ranges south of Los
 Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana
 Mountains are bounded by urbanization to the west, north, and east, and
 are separated from the eastern Peninsular Ranges to the southeast by a ten
 lane interstate highway (I-15). We analyzed DNA samples from 97 pumas
 sampled between 2001 and 2012. Genotypic data for forty-six microsatellite
 loci revealed that pumas sampled in the Santa Ana Mountains (n = 42)
 displayed lower genetic diversity than pumas from nearly every other
 region in California tested (n = 257), including those living in the
 Peninsular Ranges immediately to the east across I-15 (n = 55). Santa Ana
 Mountains pumas had high average pairwise relatedness, high individual
 internal relatedness, a low estimated effective population size, and
 strong evidence of a bottleneck and isolation from other populations in
 California. These and ecological findings provide clear evidence that
 Santa Ana Mountains pumas have been experiencing genetic impacts related
 to barriers to gene flow, and are a warning signal to wildlife managers
 and land use planners that mitigation efforts will be needed to stem
 further genetic and demographic decay in the Santa Ana Mountains puma
 population.
description: Ernest-etal-Genotypes_PLosOne2014README file: Ernest et al. California puma (mountain lion) genetics published in PLOS ONE 2014. Title: Fractured genetic connectivity threatens a southern California puma (Puma concolor) population. Authors: Holly B. Ernest, T. Winston Vickers, Scott A. Morrison, Michael R. Buchalski, Walter M. Boyce. Corresponding author: Holly B. Ernest hbernest-at-ucdavis-dot-edu and hernest-at-uwyo-dot-edu. Data file (tab-delim. text): Ernest-etal-Genotypes_PLosOne2014_FracturedConnecPumasCalif_14Aug2014.txt. File contents: Sample ID #; Population identifier; 3-digit nuclear microsatellite genotypic data (diploid, one allele per column, two columns per locus) for 46 loci (42 for the focal populations of this paper). Locus identifier is listed in the first of the two columns for data of each locus. Data in one row per individual sample.
DOI: 10.5061/dryad.1g71qj2
title: Data from: Measuring agreement among experts in classifying camera images of similar species

description: Camera trapping and solicitation of wildlife images through citizen
 science have become common tools in ecological research. Such studies
 collect many wildlife images for which correct species classification is
 crucial; even low misclassification rates can result in erroneous
 estimation of the geographic range or habitat use of a species,
 potentially hindering conservation or management efforts. However, some
 species are difficult to tell apart, making species classification
 challenging - but the literature on classification agreement rates among
 experts remains sparse. Here, we measure agreement among experts in
 distinguishing between images of two similar congeneric species, bobcats
 (Lynx rufus) and Canada lynx (L. canadensis). We asked experts to classify
 the species in selected images to test whether the season, background
 habitat, time of day, and the visible features of each animal (e.g., face,
 legs, tail) affected agreement among experts about the species in each
 image. Overall, experts had moderate agreement (Fleiss’ kappa = 0.64), but
 experts had varying levels of agreement depending on these image
 characteristics. Most images (71%) had ≥1 expert classification of
 ‘unknown’, and many images (39%) had some experts classify the image as
 ‘bobcat’ while others classified it as ‘lynx’. Further, experts were
 inconsistent even with themselves, changing their classifications of
 numerous images when they were asked to reclassify the same images months
 later. These results suggest that classification of images by a single
 expert is unreliable for similar-looking species. Most of the images did
 obtain a clear majority classification from the experts, although we
 emphasize that even majority classifications may be incorrect. We
 recommend that researchers using wildlife images consult multiple species
 experts to increase confidence in their image classifications of similar
 sympatric species. Still, when the presence of a species with similar
 sympatrics must be conclusive, physical or genetic evidence should be
 required.
description: Image
 classificationsTable shows the list of
 images used in our experiment (image ID), and for each image the trial and
 category that is was used in, the total number of experts that classified
 it as 'bobcat', 'lynx', and 'unknown', and
 the individual classifications of each expert (1 through
 27).
DOI: 10.5061/dryad.jd512
title: Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

description: AIM: Using high-resolution genetic markers on samples gathered from across
 their wide distributional range, we endeavoured to delimit species
 diversity in reef-building Pocillopora corals. They are common,
 ecologically important, and widespread throughout the Indo-Pacific, but
 their phenotypic plasticity in response to environmental conditions and
 their nearly featureless microskeletal structures confound taxonomic
 assignments and limit an understanding of their ecology and evolution.
 LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence
 analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and
 mitochondrial (open reading frame) loci were combined with population
 genetic data (seven microsatellite loci) for Pocillopora samples collected
 throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess
 the evolutionary divergence, reproductive isolation, frequency of
 hybridization and geographical distributions of the genus. RESULTS:
 Between five and eight genetically distinct lineages were identified that
 appear comparable to species with minimal or no hybridization. Colony
 morphology was generally incongruent with genetics across the full range
 of sampling, and the total number of species is apparently consistent with
 lower estimates from competing morphologically based hypotheses (c. seven
 or eight taxa). The most commonly occurring genetic lineages were widely
 distributed and exhibited high dispersal and gene flow, factors that have
 probably minimized allopatric speciation. Uniquely among scleractinian
 genera, this genus contains a monophyletic group of broadcast spawners
 that evolved recently from an ancestral brooder. MAIN CONCLUSIONS: The
 delineation of species diversity guided by genetics fundamentally advances
 our understanding of Pocillopora geographical distributions, ecology and
 evolution. Because traditional diagnostic features of colony and branch
 morphology are proving to be of limited utility, the identification of
 Pocillopora species for future ecological and experimental work should
 rely on genetic characters that will improve research and aid in
 conservation strategies for these and other reef-building corals,
 including the detection of real and mistaken endemic populations.
description: A genetic view of
 Indo-Pacific PocilloporaSample list including
 locations, ORF and ITS2 designations, microsatellite allelic data, and
 structure input filesTo
 Dryad.xlsx
DOI: 10.5061/dryad.33f0n
title: Data from: Individual and group performance suffers from social niche disruption

description: The associated article has been retracted over concerns relating to
 irregularities found in the raw data. Concerns relating to the data can be
 found in the retraction
 notice: https://www.journals.uchicago.edu/doi/abs/10.1086/708066  The social niche specialization hypothesis predicts that animal personalities emerge as a result of individuals occupying different social niches within a group. Here we track individual personality and performance, and collective performance among groups of social spiders where we manipulated the familiarity of the group members. We show that individual personalities, as measured by consistent individual differences in boldness behavior, strengthen with increasing familiarity, and that these personalities can be disrupted by a change in group membership. Changing group membership negatively impacted both individual and group performance. Individuals in less familiar groups lost weight, and these groups were less successful at performing vital collective tasks. These results provide a mechanism for the evolution of stable social groups by demonstrating that social niche re-establishment carries a steep cost to both individuals and groups. Social niche specialization may therefore provide a potential first step on the path towards more organized social systems.
description: Laskowski et al_social
 niche disruption_DATA Individual and colony
 data used in Laskowski et al.   The authors have
 identified biologically unlikely patterns in the original data underlying
 the results reported in the article. The dataset archived with Dryad,
 provided to the other authors by Dr. Jonathan Pruitt, contains an excess
 of exactly duplicated response times, spanning social groups and time
 points and treatments. Hence, the authors have concluded that the data may
 be incorrect and the validity of the results could not be verified, so the
 article has been retracted. <strong>Further use of this data is not
 recommended.</strong>
DOI: 10.5061/dryad.gt524
title: Data from: The effect of sex-biased dispersal on opposite-sexed spatial genetic structure and inbreeding risk

description: Natal sex-biased dispersal has long been thought to reduce the risk of
 inbreeding by spatially separating opposite-sexed kin. Yet, comprehensive
 and quantitative evaluations of this hypothesis are lacking. In this
 study, we quantified the effectiveness of sex-biased dispersal as an
 inbreeding avoidance strategy by combining spatially explicit simulations
 and empirical data. We quantified the extent of kin clustering by
 measuring the degree of spatial autocorrelation among opposite-sexed
 individuals (FM structure). This allowed us to systematically explore how
 the extent of sex-biased dispersal, generational overlap, and mate
 searching distance, influenced both kin clustering, and the resulting
 inbreeding in the absence of complementary inbreeding avoidance
 strategies. Simulations revealed that when sex-biased dispersal was
 limited, positive FM genetic structure developed quickly and increased as
 the mate searching distance decreased or as generational overlap
 increased. Interestingly, complete long-range sex-biased dispersal did not
 prevent the development of FM genetic structure when generations
 overlapped. We found a very strong correlation between FM genetic
 structure and both FIS under random mating, and pedigree-based measures of
 inbreeding. Thus, we show that the detection of FM genetic structure can
 be a strong indicator of inbreeding risk. Empirical data for two species
 with different life history strategies yielded patterns congruent with our
 simulations. Our study illustrates a new application of spatial genetic
 autocorrelation analysis that offers a framework for quantifying the risk
 of inbreeding that is easily extendable to other species. Furthermore, our
 findings provide other researchers with a context for interpreting
 observed patterns of opposite-sexed spatial genetic structure.
description: genotype and spatial
 data for Antechinus agilisColumn 1 = Unique
 Individual ID, Column 2 = the sex of the individuals, Column 3 = the
 region that each individual was assigned to for the spatial genetic
 analysis, Columns 4-29 = microsatellite genotype with the alleles for each
 loci listed in adjacent columns, Columns 30-31 geographic coordinates of
 the individuals averaged over tapping locationsAntechinus
 Data.xlsxgenotype and spatial
 data for Trichosurus cunninghamiColumn 1 = Unique
 Individual ID, Column 2 = the sex of the individuals, Column 3 = year of
 capture, Columns 4-33 = microsatellite genotype with the alleles for each
 loci listed in adjacent columns, Columns 34-35 geographic coordinates of
 the individuals averaged across all trap locations recorded during a two
 year window (centred on the year in question)Possum
 Data.xlsx
DOI: 10.5061/dryad.2n6v4
title: Data from: Can recombinant human thrombomodulin increase survival among patients with severe septic-induced disseminated intravascular coagulation: a single-centre, open-label, randomised controlled trial

description: Objective: To determine whether treatment with recombinant human
 thrombomodulin (rhTM) increases survival among severe septic patients with
 sepsis-induced disseminated intravascular coagulation (DIC) Design:
 Single-center, open-label, randomized controlled trial Setting: Single
 tertiary hospital Participant: 92 severe septic patients with
 sepsis-induced DIC Interventions: Patients with DIC scores ≥4, as defined
 by the Japanese Association of Acute Medicine, were diagnosed with DIC.
 Randomization was performed by the envelope method. The treatment group
 (rhTM group, n = 47) was intravenously treated with rhTM within 24 h of
 admission (day 0), and the control group (n = 45) did not receive any
 anti-coagulants, except in cases of deep venous thrombosis and pulmonary
 embolism. Primary and secondary measurements: Data were collected on days
 0 (admission), 1, 2, 3, 5, 7, and 10. The primary outcome was survival at
 28 and 90 days. The secondary endpoints comprised changes in DIC scores,
 platelet counts, D-dimer, antithrombin III (ATIII), and C-reactive protein
 (CRP) levels, and Sequential Organ Failure Assessment (SOFA) scores. All
 analyses were conducted on an intent-to-treat basis. Main Results: The
 28-day survival rates were 84 and 83% in the control and rhTM groups,
 respectively (p = 0.745, log rank test). The 90-day survival rates were
 73% and 72% in the control and rhTM groups, respectively (p = 0.94, log
 rank test). Meanwhile, the rates of recovery from DIC (&lt;4) were
 significantly higher in the rhTM group than in the control group (p =
 0.001, log rank test). Relative change from baseline of D-dimer levels
 were significantly lower in the rhTM group than in the control group, on
 day 3 and 5. Conclusion: rhTM treatment decreased D-dimer levels and
 facilitated DIC recovery in severe septic patients with sepsis-induced
 DIC. However, the treatment did not improve survival in this cohort.
description: rhTM open
 datarhTM, recombinant human
 thrombomodulin; FDP, fibrin/fibrinogen degradation products; FDP0, FDP
 value ar day 0; delta, Relative change rate from baseline = ([measurement
 day value − day 0 value]/day 0 value); delta FDP1, ([FDP value at day 1−
 day 0 value]/day 0 value); PLT, platelet; Fib, fibrinogen; PT, PTINR,
 prothrombin time ratio, –international normalized ratio; PTperc, PT
 percentage; APTT, partial thromboplastin time; ATIII, antithrombin III;
 TM, thrombomodulin value; SIRS, Systemic inflammatory response syndrome;
 SOFA, sequential organ failure assessment score; SOFA PF, SOFA respiratory
 score; SOFA PL, SOFA coagulation score; SOFA bil, SOFA hepatic dysfunction
 score; SOFA CV, SOFA cardiovascular system score; SOFA GCS, SOFA Glasgow
 Come Scale score; SOFA Cr, SOFA renal dysfunction
 score.coagulation_data_clean_R Open
 data.xlsx