cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7p048mk
title: Data from: Gender differences in peer review outcomes and manuscript impact at six journals of ecology and evolution

description: The productivity and performance of men is generally rated more highly
 than that of women in controlled experiments, suggesting conscious or
 unconscious gender biases in assessment. The degree to which editors and
 reviewers of scholarly journals exhibit gender biases that influence
 outcomes of the peer review process remains uncertain due to substantial
 variation among studies. We test whether gender predicts the outcomes of
 editorial and peer review for &gt;23,000 research manuscripts
 submitted to six journals in ecology and evolution from 2010 to 2015.
 Papers with female and male first authors were equally likely to be sent
 for peer review. However, papers with female first authors obtained, on
 average, slightly worse peer review scores and were more likely to be
 rejected after peer review, though the difference varied among journals.
 These gender differences appear to be partly due to differences in
 authorial roles. Papers for the which the first author deferred
 corresponding authorship to a coauthor (which women do more often than
 men) obtained significantly worse peer review scores and were less likely
 to get positive editorial decisions. Gender differences in corresponding
 authorship explained some of gender differences in peer review scores and
 positive editorial decisions. In contrast to these observations on
 submitted manuscripts, gender differences in peer review outcomes were
 observed in a survey of &gt;12,000 published manuscripts; women
 reported similar rates of rejection (from a prior journal) before eventual
 publication. After publication, papers with female authors were cited less
 often than those with male authors, though the differences are very small
 (~2%). Our data do not allow us to test hypotheses about mechanisms
 underlying the gender discrepancies we observed, but strongly support the
 conclusion that papers authored by women have lower acceptance rates and
 are less well cited than are papers authored by men in ecology.
description: Gender
 outcomes_anonymizedGender, review scores
 and editorial decisions for the first submissions of all standard papers
 (re-submissions and non-standard papers are deleted) submitted to
 Evolution, Functional Ecology (FE), Journal of Applied Ecology (JAPPL),
 Journal of Animal Ecology (JANIM), Journal of Ecology (JECOL) and Methods
 in Ecology and Evolution (MEE) over the period of our study. These data
 allow recreation of nearly all analyses in the published manuscript. Data
 on geographic location of authors is not included to ensure the dataset
 cannot be de-anonymized.
DOI: 10.5061/dryad.r9f25fj
title: Data from: Young but not defenseless: antifungal activity during embryonic development of a social insect

description: Termites live in environments heavily colonized by diverse microbial
 communities, including pathogens. Eggs laid within the nest likely
 experience similar pathogenic pressures as their older nestmates.
 Consequently, they may have also been under selective pressures to be
 immune-competent. Through in vitro experiments, we tested the ontogeny,
 location and strength of embryos’ antifungal activity against the fungus
 Metarhizium brunneum. Extraembryonic washes and intraembryonic components
 were incubated with fungal conidia, which was then scored for viability.
 Fungistatic activity was location- and stage-dependent. Extraembryonic
 washes had relatively weak antifungal activity. Conversely, intraembryonic
 contents were highly antifungal, exhibiting increased potency through
 development. Boiling both embryonic washes and intraembryonic contents
 rescued conidia viability, indicating the antifungal agent(s) is (are)
 likely proteinaceous. Embryonic protein profiles shifted from putative
 vitellogenins in young embryos to multiple proteins in subsequent stages,
 suggesting that the increase in fungistatic activity may be due to the
 expression of endogenous proteins during embryogenesis. This study is the
 first to address embryonic antifungal activity in a hemimetabolous
 eusocial taxon. Our results support the hypothesis that microbes have been
 significant agents of selection, fostering the evolution of antifungal
 properties even in the most immature and supposed, most vulnerable stage
 of development.
description: Total protein and
 Germination ratesThe germination rates,
 Total protein and descriptive information for each embryonic
 sample.Mycosis.xlsxegg volumecontains size measurements for individual eggs (corresponds to descriptive statistics in Figure 1 of the main text)Total proteineggs used in the "egg volume" file were then sorted into samples of 3 eggs and their protein was quantified and compiled into this file.
DOI: 10.5061/dryad.4r0q7m5
title: Data from: Contrasting colonization patterns of black mangrove (Avicennia germinans (L.) L.) gene pools along the Mexican coasts

description: Aim: Historical and geological events can impact the genetic structure of
 species, producing signatures that vary among taxa and gene pools within
 taxa. Such signatures can also be affected by local geography and
 tolerance to environmental conditions. However, disentangling of different
 drivers of population structure is often difficult. In an attempt to do
 so, we surveyed two independent gene pools of the same species that
 followed similar paths of postglacial colonization across contrasting
 landscapes and environmental conditions. We aimed to determine how these
 differences have affected the post-glacial population dynamics of each
 gene pool. Location: The Pacific and Atlantic coasts of Mexico. Taxon:
 Black mangrove, Avicennia germinans (Avicenniaceae). Methods: Using
 microsatellite variation, we estimated the divergence time of black
 mangrove populations through Approximated Bayesian Computation and
 implemented a comparative approach to evaluate different demographic
 hypotheses within and between the coasts. Results: The Pacific and
 Atlantic gene pools diverged long after the rise of the Central American
 Isthmus (Mid-Pleistocene), although occasional transisthmian gene
 exchanges were also inferred. Both coasts showed the characteristic
 isolation by distance (IBD) pattern expected for expanding gene pools.
 However, populations from the Atlantic coast were more genetically diverse
 and admixed than those from the Pacific basin. Both our migration models
 and the climate data gathered suggested a more ancient establishment
 and/or more stable conditions for black mangrove on the Atlantic coast.
 Main conclusions: The Atlantic basin likely bore more favorable climate
 conditions than the Pacific, allowing for the survival of A. germinans
 during the Last Glacial Maximum in situ. Populations from the northern
 Pacific coast became established after the Holocene warming, leading to
 contrasting genetic patterns between the two gene pools. Nevertheless, the
 action of environmental factors in determining the contemporary
 distribution of genetic variation in A. germinans cannot be discarded.
description: Genotypes_Avicenniagerminans Núñez-FarfánGenotypes of 29 natural populations of Avicennia germinans collected along the Pacific and Atlantic coasts of Mexico. The first 544 individuals corresponded to the Atlantic coast. Locus highlighted in yellow contain a high frequency of null alleles
DOI: 10.5061/dryad.rg0n5t5
title: Data from: Prairie plant phenology driven more by temperature than moisture in climate manipulations across a latitudinal gradient in the Pacific Northwest, USA

description: Plant phenology will likely shift with climate change, but how temperature
 and/or moisture regimes will control phenological responses is not well
 understood. This is particularly true in Mediterranean climate ecosystems
 where the warmest temperatures and greatest moisture availability are
 seasonally asynchronous. We examined plant phenological responses at both
 the population and community levels to four climate treatments (control,
 warming, drought, and warming plus additional precipitation) embedded
 within three prairies across a 520 km latitudinal Mediterranean climate
 gradient within the Pacific Northwest, USA. At the population level, we
 monitored flowering and abundances in spring 2017 of eight
 range-restricted focal species planted both within and north of their
 current ranges. At the community level, we used normalized difference
 vegetation index (NDVI) measured from fall 2016 to summer 2018 to estimate
 peak live biomass, senescence, seasonal patterns, and growing season
 length. We found that warming exerted a stronger control than our moisture
 manipulations on phenology at both the population and community levels.
 Warming advanced flowering regardless of whether a species was within or
 beyond its current range. Importantly, many of our focal species had low
 abundances, particularly in the south, suggesting that establishment, in
 addition to phenological shifts, may be a strong constraint on their
 future viability. At the community-level, warming advanced the date of
 peak biomass regardless of site or year. The date of senescence advanced
 regardless of year for the southern and central sites but only in 2018 for
 the northern site. Growing season length contracted due to warming at the
 southern and central sites (~3 weeks) but was unaffected at the northern
 site. Our results emphasize that future temperature changes may exert
 strong influence on the timing of a variety of plant phenological events,
 especially those events that occur when temperature is most limiting, even
 in seasonally water-limited Mediterranean ecosystems.
description: Reed_et_al_2019.zipThis .zip package contains data files for the article: Reed et al. 2019. Prairie plant phenology driven more by temperature than moisture in climate manipulations across a latitudinal gradient in the Pacific Northwest, USA. Ecology and Evolution. Please see the README.txt file for a description of each data file.
DOI: 10.5061/dryad.m8v146p
title: Data from: Pharmacokinetics of morphine in encephalopathic neonates treated with therapeutic hypothermia

description: Objective: Morphine is a commonly used drug in encephalopathic neonates
 treated with therapeutic hypothermia after perinatal asphyxia.
 Pharmacokinetics and optimal dosing of morphine in this population are
 largely unknown. The objective of this study was to describe
 pharmacokinetics of morphine and its metabolites morphine-3-glucuronide
 and morphine-6-glucuronide in encephalopathic neonates treated with
 therapeutic hypothermia and to develop pharmacokinetics based dosing
 guidelines for this population. Study design: Term and near-term
 encephalopathic neonates treated with therapeutic hypothermia and
 receiving morphine were included in two multicenter cohort studies between
 2008-2010 (SHIVER) and 2010-2014 (PharmaCool). Data were collected during
 hypothermia and rewarming, including blood samples for quantification of
 morphine and its metabolites. Parental informed consent was obtained for
 all participants. Results: 244 patients (GA mean (sd) 39.8 (1.6) weeks, BW
 mean (sd) 3,428 (613) g, male 61.5%) were included. Morphine clearance was
 reduced under hypothermia (33.5°C) by 6.89%/°C (95% CI 5.37%/°C –
 8.41%/°C, p&lt;0.001) and metabolite clearance by 4.91%/°C (95% CI
 3.53%/°C – 6.22%/°C, p&lt;0.001) compared to normothermia (36.5°C).
 Simulations showed that a loading dose of 50 μg/kg followed by continuous
 infusion of 5 μg/kg/h resulted in morphine plasma concentrations in the
 desired range (between 10 and 40 μg/L) during hypothermia. Conclusions:
 Clearance of morphine and its metabolites in neonates is affected by
 therapeutic hypothermia. The regimen suggested by the simulations will be
 sufficient in the majority of patients. However, due to the large
 interpatient variability a higher dose might be necessary in individual
 patients to achieve the desired effect.
description: PONE-D-18-26939R2 final
 datasetData concerning morphine
 administration and plasma concentrations f morphine and metabolites in
 neonates during and after therapeutic hypothermia
DOI: 10.5061/dryad.kf0sk11
title: Data from: Phylogeography of Bornean land snails suggests long-distance dispersal as a cause of endemism

description: Aim: Islands are often hotspots of endemism due to their isolation, making
 colonization a rare event, and hence facilitating allopatric speciation.
 Dispersal usually occurs between nearby locations according to a
 stepping-stone model. We aimed to reconstruct colonization and speciation
 processes in an endemic-rich system of land-based islands that does not
 seem to follow the obvious stepping-stone model of dispersal. Location:
 Five land-based habitat archipelagos of limestone outcrops in the
 floodplain of the Kinabatangan River in Sabah, Malaysian Borneo. Methods:
 We studied the phylogeography of three species complexes of endemic land
 snails, using multiple genetic markers. We calculated genetic distances
 between populations, applied BEAST2 to reconstruct phylogenies for each
 taxon, and subsequently reconstructed ancestral ranges using
 ‘BIOGEOBEARS’. Results: We found spatial genetic structure among nearby
 locations to be highly pronounced for each taxon. Genetic correlation was
 present at small spatial scales only, and disappeared at distances of five
 kilometres and above. Most archipelagos have been colonized from within
 the region multiple times over the past three million years, in 78% of
 cases as a result of long-distance dispersal or dispersal from
 non-adjacent limestone outcrops. The flow of the main geographical feature
 within the region, the Kinabatangan River, did not play a role. Main
 conclusions: Phylogeographic structure in these Bornean land snails has
 only partly been determined by small-scale dispersal, where it leads to
 isolation-by-distance, but mostly by long-distance dispersal. Our results
 demonstrate that island endemic taxa only very locally follow a simple
 stepping-stone model, whilst dispersal to non-adjacent islands, and
 especially long-distance dispersal, is most important. This leads to the
 formation of highly localized, isolated “endemic populations” forming the
 onset of a complex radiation of endemic species.
description: Sequence
 alignmentsThese sequence
 alignments have been used in phylogeographical analyses described in the
 paper.Digital Supporting
 Information 1 - Genetic and geographic distance data by
 plotAn R list object
 containing all distance data (PhiST, Jost's D, and geographical
 distances, all plot-by-plot) used in demographic analyses in the
 paper.
DOI: 10.5061/dryad.n6s1dk1
title: Data from: Mating system, reproductive success and sexual selection in bluntnose klipfishes (Clinus cottoides)

description: A critical part of the sexual selection process in animals is the genetic
 mating system. Quantifying mating systems, especially in species with
 cryptic life-histories can be challenging. One approach is to use
 genotypic markers and accurate parentage analysis, along with methods to
 account for bias when sampling natural populations, to calculate sexual
 selection metrics derived from Bateman’s principles. In this study, three
 microsatellites were used to genotype 48 adults (23 female and 25 male)
 and 342 offspring from known mothers of live-bearing bluntnose klipfish.
 Parentage analysis was performed to interpret mating and reproductive
 success for both sexes. Metrics quantified were the opportunity for
 selection (I), the opportunity for sexual selection (Is), absolute (βss)
 and standardised (β’ss) Bateman gradients and the maximum intensity of
 precopulatory sexual selection (s’max). Multiple mating by both sexes were
 revealed by parentage analysis. However, females did not show significant
 Bateman gradients or a significant maximum intensity of precopulatory
 sexual selection (s’max), whereas male sexual selection metrics were all
 significantly greater than zero. These results suggests a polygynandrous
 mating system for this species. There is an opportunity for sexual
 selection to act on males but not females in this population, which is
 evolutionary tied to anisogamy, parental investment and sex-roles.
description: Genotypes Clinus
 cottoides ParentageContains microsatellite
 genotypes of all adults and embryos used for parentage
 analyses
DOI: 10.5061/dryad.j3k19p9
title: Data from: Ancient DNA from mastics solidifies connection between material culture and genetics of Mesolithic hunter-gatherers in Scandinavia

description: The discussion of an early postglacial dual-route colonization of the
 Scandinavian Peninsula is largely based on associating genomic data to an
 early dispersal of lithic technology from the East European Plain.
 However, a direct link between the two has been lacking. We tackle this
 problem by analysing human DNA from birch bark pitch mastics, “chewing
 gums”, from Huseby Klev, a site in western Sweden with eastern lithic
 technology. We generate genome-wide data for three individuals, and show
 their affinity to the Scandinavian hunter-gatherers, more precisely, to
 individuals from postglacial Norway and Sweden. Our samples date to
 9880-9540 calBP, expanding the temporal range of this genetic group as
 well as its distribution. Human DNA from mastics provides a clear
 connection between material culture and genetic data. We also propose that
 DNA from different types of mastics can be used to study environment,
 ecology, and oral microbiome of prehistoric populations.
description: Supplementary_Figures_Kashuba_et_alThis file contains two Supplementary Figures for the paper Kashuba et al., Ancient DNA from chewing gums connects material culture and genetics of Mesolithic hunter-gatherers in Scandinavia.Supplementary_Excel_Tables_Kashuba_et_alThis zipped file contains four different Supplementary Excel Tables (Table 1, 2, 3, 4) for Ancient DNA from chewing gums connects material culture and genetics of Mesolithic hunter-gatherers in Scandinavia.
DOI: 10.5061/dryad.vs0477c
title: Data from: A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

description: Animals vary widely in their ability to regenerate, suggesting that
 regenerative ability has a rich evolutionary history. However, our
 understanding of this history remains limited because regenerative ability
 has only been evaluated in a tiny fraction of species. Available
 comparative regeneration studies have identified losses of regenerative
 ability, yet clear documentation of gains is lacking. We assessed ability
 to regenerate heads and tails either through our own experiments or from
 literature reports for 35 species of Nemertea spanning the diversity of
 the phylum, including representatives of 10 families and all three orders.
 We generated a phylogenetic framework using sequence data to reconstruct
 the evolutionary history of head and tail regenerative ability across the
 phylum and found that all evaluated species can remake a posterior end but
 surprisingly few could regenerate a complete head. Our analysis
 reconstructs a nemertean ancestor unable to regenerate a head and
 indicates independent gains of head regenerative ability in at least four
 separate lineages, with one of these gains taking place as recently as the
 last 10-15 mya. Our study highlights nemerteans as a valuable group for
 studying evolution of regeneration and identifying mechanisms associated
 with repeated gains of regenerative ability.
description: RAxML
 filesCompressed folder
 containing input files (multiple sequence alignment, definitions of
 partitions, constraint trees) and output files for RAxML analyses
 associated to this paper.RAxML.zipMrBayes filesInput (nemerteanMSA.nex) and output files for MrBayes phylogenetic analysis. Bayesian inference from the MSA was run using MrBayes 3.2.6 specifying a GTR model with 4 categories of gamma distributed rate heterogeneity and a proportion of invariant sites. Four heated chains were run for 1,100,000 steps and subsampled every 200 steps; the initial 100,000 steps were discarded as burn-in. We only used Bayesian inference on an unconstrained topology.mrbayes.zipace_nemerteaR script and input character state matrices to reproduce ancestral character estimation analyses.
DOI: 10.5061/dryad.c4q7h62
title: Data from: Plastic changes in brain morphology in relation to learning and environmental enrichment in the guppy (Poecilia reticulata)

description: Despite the common assumption that the brain is mainly malleable to
 surrounding conditions during ontogeny, plastic neural changes can occur
 also in adulthood. One of the driving forces responsible for alterations
 in brain morphology is increasing environmental complexity that may demand
 for enhanced cognitive abilities (e.g. attention, memory and learning).
 However, studies looking at the relationship between brain morphology and
 learning are scarce. Here, we tested the effects of both learning and
 environmental enrichment on neural plasticity in guppies (Poecilia
 reticulata), by means of either a reversal-learning test or a
 spatial-learning test. Given considerable evidence supporting
 environmentally-induced plastic alterations, two separate control groups
 that were not subjected to any cognitive test were included to account for
 potential changes induced by the experimental setup alone. We did not find
 any effect of learning on any of our brain measurements. However, we found
 strong evidence for an environmental effect, where fish given access to
 the spatial-learning environment had larger relative brain size and optic
 tectum size in relation to those exposed to the reversal-learning
 environment. Our results demonstrate the plasticity of the adult brain to
 respond adaptively mainly to environmental conditions, providing support
 for the environmental enhancement theory.
description: Volumes of brain regions
 in female guppiesAll data was collected
 in the lab and analysed using R studio. A list of abbreviations for the
 data can be found on the second spreadsheet of the excel
 file.Fong_et_al_brain_plasticity_data.xlsx