cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b75t4
title: Data from: Combining animal personalities with transcriptomics resolves individual variation within a wild-type zebrafish population and identifies underpinning molecular differences in brain function

description: Resolving phenotype variation within a population in response to
 environmental perturbation is central to understanding biological
 adaptation. Relating meaningful adaptive changes at the level of the
 transcriptome requires the identification of processes that have a
 functional significance for the individual. This remains a major objective
 towards understanding the complex interactions between environmental
 demand and an individual's capacity to respond to such demands. The
 interpretation of such interactions and the significance of biological
 variation between individuals from the same or different populations
 remain a difficult and under-addressed question. Here, we provide evidence
 that variation in gene expression between individuals in a zebrafish
 population can be partially resolved by a priori screening for animal
 personality and accounts for &gt;9% of observed variation in the brain
 transcriptome. Proactive and reactive individuals within a wild-type
 population exhibit consistent behavioural responses over time and context
 that relates to underlying differences in regulated gene networks and
 predicted protein–protein interactions. These differences can be mapped to
 distinct regions of the brain and provide a foundation towards
 understanding the coordination of underpinning adaptive molecular events
 within populations.
description: all behavioural
 dataAll behavioural
 experimental data; consistency studies, risk taking and activity
 experimentsMorphometricsMorphometrics from personality experiments, n=143 individuals, 16 morphometric variables recorded. Data is sourced from wild-type Danio rerio held at the UAB (Universitat Autonoma de Barcelona). Raw data is shown.QPCR DataQPCR validation for Danio rerio mRNA targets: Gadph, FLI-1, Protocadherin, Crx, Opsin, Hox5a, Hox5c, Grk7 and Arrestin.
DOI: 10.5061/dryad.vv840
title: Data from: Complete mitochondrial genome of the poorly known Amur sculpin Mesocottus haitej (Cottoidei: Cottidae)

description: The complete mitochondrial genome sequence of Mesocottus haitej has been
 obtained by the next generation sequencing, which contained 22 tRNA genes,
 13 protein-coding genes, 2 rRNA genes and non-coding control region with
 the total length of 16,527 bp. The gene content, arrangement, codon usage
 and base composition of M. haitej mitogenome have no unusual features that
 distinguish it from most other teleost fishes. According to the result of
 a pilot phylogenetic analysis, the freshwater Mesocottus is a sister
 lineage to the Cottus clade. The new mitogenomic data could provide useful
 information for the further studies on molecular systematics and
 conservation genetics of cottids.
description: mesocottusDATAMATRIXandTREES.xData matrix (NEXUS format) used to estimate the phylogenetic position of Mesocottus. The matrix contains alignment of six complete (Clinocottus analis, Trachidermus fasciatus, Mesocottus haitej, Cottus reinii, C. koreanus and C. hangiongensis) and two partly sequenced (Rheopresbe kazika and Leptocottus armatus) mitogenomes of the Cottidae, as well as the mitogenomes of outgroup taxa – Lycodes toyamensis (Zoarcidae), Anoplopoma fimbria (Anaplopomatidae), Arctoscopus japonicus (Trichodontidae) and Aptocyclus ventricosus (Cyclopteridae). In addition, it contains the final phylogenetic trees.
DOI: 10.5061/dryad.r4ps0
title: Data from: Egg size and the adaptive capacity of early life history traits in Chinook salmon (Oncorhynchus tshawytscha)

description: Offspring traits are greatly influenced by maternal effects and these
 maternal effects may provide an important pathway through which
 populations can adapt to changing thermal environments. We investigated
 the effect of egg size on the among and within population variation in
 early life history traits among introduced Great Lakes Chinook salmon
 (Oncorhynchus tshawytscha) populations under varying thermal conditions.
 We reared Chinook salmon from three populations in a common garden
 hatchery study at 6.5°C, 9.4°C, and 15.2°C, and measured a variety of
 fitness-related traits during development. We found that most of the among
 population variation in early life history traits was explained by egg
 size. However, the contribution of egg size to the among population
 variation decreased with an increase in temperature suggesting that other
 effects, such as genetic, contribute at high temperature. Within
 populations, egg size explained much of the dam variance and maternal
 effect for traits in every temperature, whereas egg size generally had
 little to no influence on the sire variance and heritability. Overall, our
 results demonstrate the significant contribution egg size makes to shaping
 early life history phenotypes among and within populations, and suggests
 that egg size is an important pathway through which offspring phenotypes
 can evolve on contemporary timescales.
description: Early Life History Trait
 DataIncludes data related to
 early life history traits, egg diameter, adult female length, and
 phenotypic divergence rates. A full description of the data files and
 variables can be found in the associated README file.Thorn_EVA_TraitData.zip
DOI: 10.5281/zenodo.18382021
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Erica Heinrichs, http://www.wikidata.org/entity/Q137883458. 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/Q137883458
DOI: 10.5061/dryad.j7090
title: Data from: Independent evolution of the sexes promotes amphibian diversification

description: Classic ecological theory predicts that the evolution of sexual dimorphism
 constrains diversification by limiting morphospace available for
 speciation. Alternatively, sexual selection may lead to the evolution of
 reproductive isolation and increased diversification. We test contrasting
 predictions of these hypotheses by examining the relationship between
 sexual dimorphism and diversification in amphibians. Our analysis shows
 that the evolution of sexual size dimorphism (SSD) is associated with
 increased diversification and speciation, contrary to the ecological
 theory. Further, this result is unlikely to be explained by traditional
 sexual selection models because variation in amphibian SSD is unlikely to
 be driven entirely by sexual selection. We suggest that relaxing a central
 assumption of classic ecological models—that the sexes share a common
 adaptive landscape—leads to the alternative hypothesis that independent
 evolution of the sexes may promote diversification. Once the constraints
 of sexual conflict are relaxed, the sexes can explore morphospace that
 would otherwise be inaccessible. Consistent with this novel hypothesis,
 the evolution of SSD in amphibians is associated with reduced current
 extinction threat status, and an historical reduction in extinction rate.
 Our work reconciles conflicting predictions from ecological and
 evolutionary theory and illustrates that the ability of the sexes to
 evolve independently is associated with a spectacular vertebrate
 radiation.
description: DeLisle&Rowe_DataData set of amphibian body sizes (previously published) as well as Redlist extinction risk and approximate latitudinal midpoint of species ranges, compiled from the IUCN and Amphibiaweb, respectivelyDeLisle&Rowe_ChronogramPyron and Wiens 2011 molecular phylogeny of the Amphibia, dated by penalized maximum likelihood under a strict-clock model with fossil calibration points.
DOI: 10.5061/dryad.95ct6q2c
title: Data from: The imprint of Cenozoic migrations and evolutionary history on the biogeographic gradient of body size in New World mammals

description: Ecology, evolution and historical events all contribute to biogeographic
 patterns, but studies integrating them are scarce. Here we focus on how
 biotic exchanges of mammals during the Late Cenozoic have contributed to
 current geographic body size patterns. We explore differences in the
 environmental correlates and phylogenetic patterning of body size between
 the groups of mammals participating and not participating in past biotic
 exchanges. Both the association of body size with environmental predictors
 and its phylogenetic signal were stronger for groups that immigrated into
 North or South America than for indigenous groups. This pattern, which
 held when extinct clades were included in the analyses, can be interpreted
 based on the length of time that clades have had to diversify and occupy
 niche space. Moreover, we identify a role for historical events such as
 Cenozoic migrations on configuring contemporary mammal body size patterns
 and illustrate where these influences have been strongest for New World
 mammals.
description: Online Appendix G.
 extinct megammamals databaseBody mass estimations
 for species belonging to 61 genera of extinct mammals of the New World.
 Only Pleistocene megafaunal species and genera are considered (≥44 kg)
 since they are known to have selectively been driven extinct. Body size
 values were obtained from Smith et al. (2003), and for unspecific generic
 fossil records an average of the body sizes of the species within was
 used. Latitudinal geographic distribution of extinct species is indicataed
 based on the palaeontological site where collections were registered. Data
 assembled in this database were downloaded from the Paleobiology Database
 (http://paleodb.org/ - url accessed 17 December 2011, using the following
 parameters: taxon name = Mammalia; time intervals = Early to Late
 Pleistocene; continents = North America and South America; include
 occurrences of extant or extinct taxa? = extinct only).Online Appendix A. New
 World mammal speciesTable A1. New World
 mammal species checklist indicating each species body mass. The character
 as GABI allochthon arriving to North America or South America (GABI North
 and GABI South, respectively) and as Eurasian allochthon (Eurasian) is
 also indicated.
DOI: 10.5061/dryad.dj17c
title: Data from: The population demography of Betula maximowicziana, a cool temperate tree species in Japan, in relation to the last glacial period: Its admixture-like genetic structure is the result of simple population splitting not admixing

description: Conservation of the local genetic variation and evolutionary integrity of
 economically and ecologically important trees is a key aspect of studies
 involving forest genetics, and a population demographic history of the
 target species provides valuable information for this purpose. Here, the
 genetic structure of 48 populations of Betula maximowicziana was assessed
 using 12 expressed sequence tag–simple sequence repeat (EST-SSR) markers.
 Genetic diversity was lower in northern populations than southern ones and
 structure analysis revealed three groups: northern and southern clusters
 and an admixed group. Eleven more genomic-SSR loci were added and the
 demographic history of these three groups was inferred by approximate
 Bayesian computation (ABC). The ABC revealed that a simple split scenario
 was much more likely than isolation with admixture, suggesting that the
 admixture-like structure detected in this species was due to ancestral
 polymorphisms. The ABC analysis suggested that the population growth and
 divergence of the three groups occurred 96 800 (95% CI, 20 500–599 000)
 and 28 300 (95% CI, 8700–98 400) years ago, respectively. We need to be
 aware of several sources of uncertainty in the inference such as
 assumptions about the generation time, overlapping of generations,
 confidence intervals of the estimated parameters and the assumed model in
 the ABC. However, the results of the ABC together with the model-based
 maps of reconstructed past species distribution and palaeoecological data
 suggested that the modern genetic structure of B. maximowicziana
 originated prior to the last glacial maximum (LGM) and that some
 populations survived in the northern range even during the LGM.
description: Tsuda_Betulamaximowicziana_genotypesSSR genotypes file of 1416 individuals (12loci) and 441 individuals (23loci). Please see readme file for detail information.
DOI: 10.6073/pasta/44b350d46f371082b2cc98490cf36959
title: Streamflow for Martinelli basin, 1982 - ongoing.

description: This is a summary of discharges from the Martinelli Basin and is
 based on stage records from the outlet channel 30 m below the road
 at the foot of the basin.
DOI: 10.5061/dryad.h3b27
title: Data from: Nature of the coupling between neural drive and force-generating capacity in the human quadriceps muscle

description: The force produced by a muscle depends on both the neural drive it
 receives and several biomechanical factors. When multiple muscles act on a
 single joint the nature of the relationship between the neural drive and
 force-generating capacity of the synergistic muscles is largely unknown.
 This study aimed to determine the relationship between the ratio of neural
 drive and the ratio of muscle force-generating capacity between two
 synergist muscles (vastus lateralis[VL] and medialis[VM]) in humans.
 Twenty-one participants performed isometric knee extensions at 20% and 50%
 of maximal voluntary contractions (MVC). Myoelectric activity (surface
 electromyography [EMG]) provided an index of neural drive. Physiological
 cross-sectional area (PCSA) was estimated from measurements of muscle
 volume (magnetic resonance imaging) and muscle fascicle length (3D
 ultrasound imaging) to represent the muscles’ force-generating capacities.
 Neither PCSA nor neural drive was balanced between VL and VM. There was a
 large (r=0.68) and moderate (r=0.43) correlation between the ratio of
 VL/VM EMG amplitude and the ratio of VL/VM PCSA at 20% and 50% of MVC,
 respectively. This study provides evidence that neural drive is biased by
 muscle force-generating capacity, the greater the force generating
 capacity of VL compared to VM, the stronger bias of drive to the VL.
description: DemographicsThis file contains participant characteristics and demographicsMuscle_ArchitectureThis file contains data of muscle volume (estimated using MRI), fascicle length (estimated using 3-D ultrasound) and PCSA (calculated from muscle volume and fascicle length)Neural_DriveThis file contains data of EMG RMS values measured during the isometric knee extension tasks and normalized to that measured during isometric maximal knee extension.Torque_and_VAThis file contains data measured during the maximal voluntray isometric knee extensions.CorrelationThis file contains the data used to calculate the coefficient of correlation between the ratio of neural drive and the ratio of muscle force-generating capacity between the vastus lateralis (VL) and vastus medialis (VM) muscles
DOI: 10.15468/dl.e2petx
title: Occurrence Download

description: A dataset containing 715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gyps fulvus fulvus"
 ]
}

 The dataset includes 715 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000657-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1vp3j
title: Data from: Reserve size and fragmentation alters community assembly, diversity and dynamics

description: Researchers have disputed whether a single large habitat reserve will
 support more species than many small reserves. However, relatively little
 is known from a theoretical perspective about how reserve size affects
 competitive communities structured by spatial abiotic gradients. We
 investigate how reserve size affects theoretical communities whose
 assembly is governed by dispersal limitation, abiotic niche
 differentiation, and source-sink dynamics. Simulations were conducted with
 varying scales of dispersal across landscapes with variable environmental
 spatial autocorrelation. Landscapes were inhabited by simulated trees with
 seedling and adult stages. For a fixed total area in reserves, we found
 that small reserve systems increased the distance between environments
 dominated by different species, diminishing the effects of source-sink
 dynamics. As reserve size decreased, environmental limitations to
 community assembly became stronger, α-species richness decreased, and
 γ-richness increased. When dispersal occurred across short distances, a
 large reserve strategy caused greater stochastic community variation,
 greater α-richness, and lower γ-richness than in small reserve systems. We
 found that reserve size variation trades off between preserving different
 aspects of natural communities, including α versus γ-diversity. Optimal
 reserve size will depend on the importance of source-sink dynamics and the
 value placed on different characteristics of natural communities.
 Anthropogenic changes to the size and separation of remnant habitats can
 have far reaching effects on community structure and assembly.
description: Community and Landscape
 Dynamic Simulation CodeThis code allows the
 simulation of landscape habitat loss and reserve designation and resulting
 community dynamics, as described in the article. The code relies on R and
 python and includes a 'README' file.LaskyKeittAmNat_SimulationCode.zip
DOI: 10.5061/dryad.7s3m38n
title: Data from: Ocean acidification increases the sensitivity of and variability in physiological responses of an intertidal limpet to thermal stress

description: Understanding physiological responses of organisms to warming and ocean
 acidification is the first step towards predicting the potential
 population- and community-level ecological impacts of these stressors.
 Increasingly, physiological plasticity is being recognized as important
 for organisms to adapt to the changing microclimates. Here, we evaluate
 the importance of physiological plasticity for coping with ocean
 acidification and elevated temperature, and its variability among
 individuals, of the intertidal limpet Cellana toreuma from the same
 population in Xiamen. Limpets were collected from shaded mid-intertidal
 rock surfaces. They were acclimated under combinations of different pCO2
 concentrations (400 and 1000 ppm, corresponding to a pH of 8.1 and 7.8)
 and temperatures (20 and 24 °C) in a short-term period (7 days), with the
 control conditions (20 °C and 400 ppm) representing the average annual
 temperature and present-day pCO2 level at the collection site. Heart rates
 (as a proxy for metabolic performance) and expression of genes encoding
 inducible and constitutive heat-shock proteins (hsp70 and hsc70) at
 different heat-shock temperatures (26, 30, 34, and 38 °C) were measured.
 Hsp70 and Hsc70 play important roles in protecting cells from heat
 stresses, but have different expression patterns, with Hsp70 significantly
 increased in expression during stress and Hsc70 constitutively expressed
 and only mildly induced during stress. Analysis of heart rate showed
 significantly higher temperature coefficients (Q10 rates) for limpets at
 20 °C than at 24 °C and post-acclimation thermal sensitivity of limpets at
 400 ppm was lower than at 1000 ppm. Expression of hsp70 linearly increased
 with the increasing heat-shock temperatures, with the largest slope
 occurring in limpets acclimated under a future scenario (24 °C and
 1000 ppm pCO2). These results suggested that limpets showed increased
 sensitivity and stress response under future conditions. Furthermore, the
 increased variation in physiological response under the future scenario
 indicated that some individuals have higher physiological plasticity to
 cope with these conditions. While short-term acclimation to reduced pH
 seawater decreases the ability of partial individuals against thermal
 stress, physiological plasticity and variability seem to be crucial in
 allowing some intertidal animals to survive in a rapidly changing
 environment.
description: Gene expression
 dataHeart
 ratesMeasured and calculated
 seawater carbonate chemistry variables
DOI: 10.5061/dryad.k7686
title: Data from: Does morphology reflect osteohistology-based ontogeny? A case study of Late Cretaceous pterosaur jaw symphyses from Hungary reveals hidden taxonomic diversity

description: With a single complete mandible and 56 mandibular symphyseal fragments of
 various sizes, the Late Cretaceous Hungarian azhdarchid material has been
 considered one of the most extensive monospecific pterosaur assemblages in
 the world. Representing a broad size range, these elements have been
 thought to demonstrate a developmental series of Bakonydraco galaczi. As
 such, they were ideal to test whether absolute size and/or morphology
 reliably indicate relative ontogenetic stages in this pterosaur.
 Forty-five specimens were selected for multivariate morphometrics and
 classified into four size classes. After acquiring the morphometric data
 set, we thin-sectioned eight symphyses representing all size groups and
 classified them into relative ontogenetic stages based on qualitative
 microstructural inspection prior to quantitative histological analyses.
 Microstructural characters suggestive of developmental state were then
 quantified for intra- and interindividual uni- and multivariate analyses
 to test the correspondence among the results of qualitative and
 quantitative analyses. In contrast to our expectations, histological
 features identified the smallest specimen as an adult and not an early
 juvenile. The substantial size difference between this specimen and other
 adults, along with its distinct microanatomical and histological features,
 implies the presence of at least two pterosaur taxa in this symphysis
 assemblage. This hypothesis is further supported by multivariate
 morphometrics, which separate the smallest symphyses from all other
 specimens that form one continuous group. Although the latter group also
 shows considerable size variability in corresponding ontogenetic stages,
 this suggests developmental plasticity rather than the presence of even
 more taxa, and indicates that symphysis size and morphology are poor
 indicators of skeletal maturity in these animals. Hence, bone histology is
 an important independent test of the assessment of ontogenetic stage using
 size and morphology.
description: Supplementary Table
 1Supplementary Table
 2Supplementary Table
 3Supplementary Table
 4Supplementary Table
 5Supplementary Table
 6Supplementary Table
 7Supplementary Table
 8Supplementary Table
 9