cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r0d2570
title: Data from: High-frequency sampling and piecewise models reshape dispersal kernels of a common reef coral

description: Models of dispersal potential are required to predict connectivity between
 populations of sessile organisms. However, to date, such models do not
 allow for time‐varying rates of acquisition and loss of competence to
 settle and metamorphose, and permit only a limited range of possible
 survivorship curves. We collect high‐resolution observations of coral
 larval survival and metamorphosis, and apply a piecewise modeling approach
 that incorporates a broad range of temporally‐varying rates of mortality
 and loss of competence. Our analysis identified marked changes in
 competence loss and mortality rates, whose timing implicates developmental
 failure and depletion of energy reserves. Asymmetric demographic rates
 suggest more intermediate‐range dispersal, less local retention, and less
 long‐distance dispersal than predicted by previously‐employed
 non‐piecewise models. Because vital rates are likely temporally
 asymmetric, at least for non‐feeding broadcast‐spawned larvae, piecewise
 analysis of demographic rates will likely yield more reliable predictions
 of dispersal potential.
description: TenuisGBR2012longtermsurvivalEmpirical long term survival data for A. Tenuis larvae. "temp" is the temperature that the larvae were raised at, "rep" is the replicate number, "day" is the date the observation was taken, "age (h)" is the larval age (h) at the time of the observation, "age (d)" is the larval age (d) at the time of the observation, "larvae" is the number of larvae at the beginning of the experiment, "surv" is the number of larvae alive at the time of the observation.A.tenuisGBR2012metamorphosisEmpirical metamorphosis data for A. Tenuis larvae. "temp" is the temperature that the larvae were raised at, "date" is the date the observation was taken, "hour" is the hour of the day that the observation was taken, "age (h)" is the larval age (h) at the time of the observation, "age (d)" is the larval age (d) at the time of the observation, "rep" is the replicate number, "larvae" is the number of larvae at the beginning of the experiment, "meta" is the number of larvae that had metamorphosed by the time of the observation, "swimming" is the number of larvae swimming at the time of the observation.Survival model fit R codeThis code fits the best-fitting survival model to the data.survival model code.RCompetence model fit R codeThis code fits the best-fitting competence model to the data.competence model code.R
DOI: 10.5061/dryad.0q2h6tk
title: Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

description: Evolutionary studies are often limited by missing data that are critical
 to understanding the history of selection. Selection experiments, which
 reproduce rapid evolution under controlled conditions, are excellent tools
 to study how genomes evolve under selection. Here we present a genomic
 dissection of the Longshanks selection experiment, in which mice were
 selectively bred over 20 generations for longer tibiae relative to body
 mass, resulting in 13% longer tibiae in two replicates. We synthesized
 evolutionary theory, genome sequences and molecular genetics to understand
 the selection response and found that it involved both polygenic
 adaptation and discrete loci of major effect, with the strongest loci
 tending to be selected in parallel between replicates. We show that
 selection may favor de-repression of bone growth through inactivating two
 limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses
 thus show that it is possible to connect individual base-pair changes to
 the overall selection response.
description: Castro et al - Pedigreed
 Longshanks Phenotypic DataPhenotypic data from the
 Longshanks selection experiment, consisting of the Ctrl and Longshanks
 replicates 1 and 2.
DOI: 10.5061/dryad.63bd5r6
title: Data from: Olfactory receptor repertoire size in dinosaurs

description: The olfactory bulb (OB) ratio is the size of the olfactory bulb relative
 to the cerebral hemisphere, and is used to estimate the proportion of the
 forebrain devoted to smell. In birds, OB ratio correlates with the number
 of olfactory receptor (OR) genes and therefore has been used as a proxy
 for olfactory acuity. By coupling OB ratios with known OR gene repertoires
 in birds, we infer minimum repertoire sizes for extinct taxa, including
 non-avian dinosaurs, using phylogenetic modeling, ancestral state
 reconstruction and comparative genomics. We highlight a shift in the
 scaling of OB ratio to body size along the lineage leading to modern
 birds, demonstrating variable OR repertoires present in different dinosaur
 and crown-bird lineages, with varying factors potentially influencing
 sensory evolution in theropods. We investigate the ancestral sensory space
 available to extinct taxa, highlighting potential adaptations to
 ecological niches. Through combining morphological and genomic data, we
 show that, while genetic information for extinct taxa is forever lost, it
 is potentially feasible to investigate evolutionary trajectories in
 extinct genomes.
description: OR sequence
 dataOR Sequence data for
 Alligator mississippiensis generated using the olfactory receptor
 assignerSequenceData.faAllSupplementaryFiguresAll Supplementary Figures relating to the publicationSupplementary_TablesAll Supplementary tables for this study
DOI: 10.5061/dryad.791n66r
title: Data from: No gains for bigger brains: functional and neuroanatomical consequences of relative brain size in a parasitic wasp

description: Heritable genetic variation in relative brain size can underlie the
 relationship between brain performance and the relative size of the brain.
 We used bidirectional artificial selection to study the consequences of
 genetic variation in relative brain size on brain morphology, cognition
 and longevity in Nasonia vitripennis parasitoid wasps. Our results show a
 robust change in relative brain size after 26 generations of selection and
 6 generations of relaxation. Total average neuropil volume of the brain
 was 16% larger in wasps selected for relatively large brains than in wasps
 selected for relatively small brains, whereas the body length of the
 large-brained wasps was smaller. Furthermore, the relative volume of the
 antennal lobes was larger in wasps with relatively large brains. Relative
 brain size did not influence olfactory memory retention, whereas wasps
 that were selected for larger relative brain size had a shorter longevity,
 which was even further reduced after a learning experience. These effects
 of genetic variation on neuropil composition and memory retention are
 different from previously described effects of phenotypic plasticity in
 absolute brain size. In conclusion, having relatively large brains may be
 costly for N. vitripennis, whereas no cognitive benefits were recorded.
description: Absolute and relative
 volumes of neuropil types in generation 33This file gives the
 absolute volumes in cubic micrometer of all neuropil types, except the
 lamina. A separate sheet gives the volumes relative to the total (except
 lamina) neuropil volume. This data set supports figs 3, 4 and
 5.Brain
 morphology data (gen 33).xlsxMemory data (gen
 33)The raw data supporting
 Fig 6Raw selection
 dataDataset supporting Fig 1
 and 2. For every generation that was used for selection there is a
 separate excel sheet, and every row represents one individual female wasp.
 The rows that have a background color represent the individuals selected
 to produce the next generationSurvival data of wasps
 in generation 40This excel file gives
 time until death in days after emergence, from individuals of the
 selection lines, unselected control lines from the AcymCx and HVRx_2
 strains. These wasps were either naive or trained (=conditioned). This
 dataset supports fig 7.Survival data (gen
 40).xlsx
DOI: 10.5061/dryad.td7sr8s
title: Data from: Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression.

description: Aim: We used genome-scale sampling to assess the phylogeography of a group
 of topminnows in the Fundulus notatus species complex. Two of the species
 have undergone extensive range expansions resulting in broadly overlapping
 distributions, and sympatry within drainages has provided opportunities
 for hybridization and introgression. We assess the timing and pattern of
 range expansion in the context of late-Pleistocene-Holocene drainage
 events, and evaluate the evidence for introgressive hybridization between
 species. Location: Central and southern United States including drainages
 of the Gulf of Mexico Coastal Plain and portions of the Mississippi River
 drainage in and around the Central Highlands. Taxon: Topminnows, Genus
 Fundulus, subgenus Zygonectes - Fundulus notatus, Fundulus olivaceus,
 Fundulus euryzonus Methods: We sampled members of the F. notatus species
 complex throughout their respective ranges, including numerous drainage
 systems where species co-occur. We collected genome-wide Single Nucleotide
 Polymorphisms (SNPs) using the Genotype by Sequencing (GBS) method, and
 subjected data to population genetic analyses to infer the population
 histories of both species, including explicit tests for admixture and
 introgression. The methods employed included STRUCTURE, Principle
 Coordinates Analysis, TreeMix and Approximate Bayesian Computation.
 Results: Genetic data are presented for 749 individuals sampled from 14 F.
 notatus, 20 F. olivaceus, and two F. euryzonus populations. Members of the
 species complex differed in phylogeographic structure, with F. notatus
 exhibiting geographic clusters corresponding to Pleistocene coastal
 drainages, and F. olivaceus comparatively lacking in phylogeographic
 structure. Evidence for interspecific introgression varied by drainage.
 Main Conclusions: Populations of F. notatus and F. olivaceus exhibited
 contrasting patterns of lineage diversity among coastal drainages,
 indicating inter-specific differences in their Pleistocene southern
 refugia. Phylogeographic patterns in both species indicated that range
 expansions into the northern limits of contemporary distributions
 coincided with and continued subsequent to the Last Glacial Maximum. There
 was evidence of introgression between species in some, but not all
 drainages where the species co-occur, in a pattern that is correlated with
 previous estimates of hybridization rates.
description: STRUCTURE file Fundulus
 olivaceus and F. notatusstructure_file_olivaceus_notatus.txtSTRUCTURE file Fundulus notatusstructure_file_notatus_.txtSTRUCTURE file Fundulus olivaceusstructure_file_olivaceus.txtSTRUCTURE file Fundulus olivaceus Ozarksstructure_file_ozark.txtNexus file formatted for SNAPPSNAPP.nexTREEMIX analysis of Fundulus olivaceus and F. notatustreemix2sp.txtTREEMIX analysis of Fundulus olivaceus Ozarks onlytreemixozark.txtDIYABC file for F. notatusDIYABCnot.txtDIYABC file for F. olivaceusDIYABColi.txt
DOI: 10.5061/dryad.3nk236h
title: Data from: Phenology of farmland floral resources reveals seasonal gaps in nectar availability for bumblebees

description: Floral resources are known to be important in regulating wild pollinator
 populations and are therefore an important component of agri‐environment
 and restoration schemes which aim to support pollinators and their
 associated services. However, the phenology of floral resources is often
 overlooked in these schemes – a factor which may be limiting their
 success. Our study characterises and quantifies the phenology of nectar
 resources at the whole‐farm scale on replicate farms in Southwestern UK
 throughout the flowering season. We quantify the corresponding nectar
 demands of a subset of common wild pollinators (bumblebees) to compare
 nectar supply and pollinator demand throughout the year, thereby
 identifying periods of supply‐demand deficit. We record strong seasonal
 fluctuations in farmland nectar supplies, with two main peaks of nectar
 production (May and July) and a considerable ‘June Gap’ in‐between. March
 and August/September are also periods of low nectar availability.
 Comparing the phenology of nectar supply with the phenology of bumblebee
 nectar demand reveals ‘hunger gaps’ during March and much of
 August/September when supply is unlikely to meet demand. Permanent pasture
 and woodland produced the greatest share of farmland nectar because of
 their large area, however linear features such as hedgerows and field
 margins provided the greatest nectar per unit area. 50% of total nectar
 was supplied by just three species (Allium ursinum, Cirsium arvense and
 Trifolium repens), but some less productive species (e.g. Hedera helix and
 Taraxacum agg.) were important in ensuring phenological continuity of
 nectar supply. Synthesis and applications. By comparing the phenology of
 farmland nectar supply with the phenology of pollinator demand, we
 demonstrate that the timing of nectar supply may be as important as total
 nectar production in limiting farmland pollinator populations. Considering
 phenology in the design of agri‐environment or restoration schemes is
 therefore likely to improve their suitability for pollinators. Plant
 species which flower during periods of resource deficit (early spring and
 late summer) should be prioritised in schemes which aim to conserve or
 restore pollinator populations. Maintaining a range of semi‐natural
 habitats with complementary flowering phenologies (e.g. woodland,
 hedgerows and field‐margins) will ensure a more continuous supply of
 nectar on farmland, thereby supporting pollinators for their entire flight
 season.
description: Timberlake et al
 2019_Floral count and nectar production dataExcel datasheet with
 nectar production values per species and floral count records for each
 transect on all farms in 2016 and 2017Timberlake et al_2019_Flowering
 phenology data.xlsx
DOI: 10.5061/dryad.7k1j1j3
title: Data from: Trait identity and functional diversity co-drive response of ecosystem productivity to nitrogen enrichment

description: 1. Exploring the mechanisms underlying the change in ecosystem
 productivity under anthropogenic nitrogen (N) inputs is of fundamental
 ecological interest. It has been proposed that functional traits,
 environmental factors, and species richness are central drivers linking
 ecosystem productivity with environmental change. However, few studies
 have considered the joint effects of functional traits, environmental
 factors, and species richness on ecosystem productivity under increasing N
 inputs. 2. We established a N-manipulation experiment in a Tibetan alpine
 steppe in 2013. Using structural equation models, we assessed the effects
 of N-induced changes in environmental factors, species richness, and trait
 metrics (the mean, variance, skewness and kurtosis of trait distribution)
 on gross ecosystem productivity as well as three resource use efficiencies
 (water, light, and phosphorus (P) use efficiencies), based on measurements
 during the peak growing season in 2016. 3. We found that both light and P
 use efficiencies decreased under N enrichment, largely due to the
 N-induced decline in functional diversity of leaf P concentration.
 However, both gross ecosystem productivity and water use efficiency
 exhibited initial increases and subsequent slight decreases with N
 addition. These nonlinear patterns were closely associated with both the
 increased morphological trait (i.e., mean-leaf area) and decreased
 diversity of leaf P concentration. 4. Synthesis. Our results illustrate
 how N-induced changes in functional traits may have dual effects on
 ecosystem productivity: the stimulating effects of the dominant trait
 identity via increasing canopy light interception vs. the inhibiting
 effect of decreasing trait diversity via declining resource use
 efficiencies. Our results highlight the importance of including functional
 traits in land surface models to improve predictions of the response of
 ecosystem function to N inputs.
description: Responses of ecosystem
 functions, environmental factors, species richness, and functional traits
 to N additionZhang et
 al._Data.xls
DOI: 10.5066/p1ttx78h
title: Fluid inclusion data for fluorite, smoky quartz, and calcite samples from the Bear Lodge alkaline complex, Wyoming

description: This data release is a collection of quantitative and qualitative data for fluid inclusions in samples from the Bear Lodge alkaline complex, Wyoming. The dataset includes:microthermometry, Raman spectroscopy, noble gas spectroscopy, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), and energy dispersive X-ray analyses of fluid inclusions. For spatial context and textural characterization, annotated scans of both sample thin sections, annotated photomicrographs of targeted fluid inclusion areas, cathodoluminescence images, and backscatter electron images of decrepitate mounds are also included.
DOI: 10.5061/dryad.1ht77d7
title: Data from: Taxonomic and functional diversity of the co-flowering community differentially affect Cakile edentula pollination at different spatial scales

description: 1. The number of co-flowering species, floral density and floral trait
 diversity can be major determinants of pollinator-mediated plant-plant
 interactions in a community. However, evaluation of how each one of these
 co-flowering components affects the pollination success of a single focal
 plant species, and how these effects vary at different spatial scales, is
 lacking. 2. Here we evaluated the effects of functional diversity (flower
 morphology and colour), taxonomic diversity (reflecting potential sampling
 effects) and flower density (conspecific and heterospecific), on the
 pollinator environment (i.e. visitation rate and pollinator diversity),
 and pollination success (i.e. pollen load size and number of pollen tubes
 per style) of Cakile edentula (Brassicaceae). We applied structural
 equation models (SEM’s) at the floral-neighbourhood (plot level) and
 community-wide scales to uncover the factors that mediate co-flowering
 community effects on C. edentula pollination success. 3. We found that
 co-flowering community effects at the community level are more important
 than fine-scale floral-neighbourhood differences in mediating plant
 pollination success in our study species. Increasing plant functional
 diversity decreased pollinator visitation rate but increased the diversity
 of pollinator functional groups visiting C. edentula flowers. Taxonomic
 diversity negatively affected pollinator diversity suggesting that other
 unmeasured floral traits may be relevant or that single-species effects
 (sampling effects) may be important. Overall, our results suggest that
 functional floral trait diversity in a community may be the most important
 factor influencing pollination success of species in a community. We also
 found evidence for intra- and interspecific pollinator competition
 mediated by flower density but none of these effects seemed to have a
 significant impact on pollination success. 4. This study is an important
 step towards understanding the complexity of co-flowering community
 effects on the pollination success of individual plant species at multiple
 spatial scales. This study further reveals the potential importance of
 plant functional diversity in a community in helping predict competitive
 and facilitative interactions in co-flowering communities. 5. Synthesis.
 Floral density, taxonomic and functional co-flowering diversity are
 important drivers of pollination success in flowering plants. The effects
 of the co-flowering diversity on the pollination success of plant species
 can largely depend on the spatial scale being studied. Only evaluating the
 outcomes of pollinator-mediated plant-plant interactions at multiple
 stages of the pollination process can lead to a complete understanding of
 their ecological consequences in nature.
description: Cakile edentula
 pollination success and co-flowering environmentAlbor et al. (2019)-Journal of
 Ecology.xlsx
DOI: 10.5061/dryad.bm18c5n
title: Data from: Temperature-induced developmental plasticity in Plodia interpunctella: reproductive behaviour and sperm length.

description: In both plants and animals, male gametogenesis is particularly sensitive
 to heat stress, to the extent that a single hot or cold day can compromise
 crop productivity or population persistence. In animals, heat stress
 during development can impact a male’s ability to secure copulations
 and/or his post-copulatory fertility. Despite such observations,
 relatively few studies have examined the consequences of developmental
 temperature on the reproductive behaviour and physiology of individuals.
 Here we report for the first time the effects of developmental temperature
 on the phenotypic expression of both apyrene and eupyrene sperm and the
 copulatory behaviour of the Indian meal moth, Plodia interpunctella. We
 show that the length of both apyrene and eupyrene sperm decrease with
 increasing developmental temperature and that males are less likely to
 engage in copulation when reared at the highest and lowest temperatures.
 Where copulation occurred, the duration of copula decreased as male
 developmental temperature increased. We argue that identification of the
 mechanisms and consequences of reproductive failure in animals facing heat
 stress will help understand how wild and domesticated populations will
 respond to global climate change. We also contend that such studies will
 help elucidate long-standing evolutionary questions around the maintenance
 of genetic variation in traits highly relevant to fitness and the role of
 phenotypic plasticity in driving the evolution of novel traits.
description: Iossa_et_al_2019_J_Evol_BiolData on Indian meal moth, Plodia interpunctella, eupyrene and apyrene sperm length used in the analyses.