cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd560
title: Data from: Growth and reproduction trade-offs can estimate previous reproductive history in alpine ungulates

description: 1. Life-history theory predicts energy allocation trade-offs between
 traits when resources are limited. If females reduce allocation to growth
 when they reproduce, annual growth could reveal past reproductive effort,
 which would be useful to assess population dynamics and harvest
 sustainability. The potential and accuracy of growth measures for
 predicting reproductive success have rarely been evaluated with
 individuals with known reproductive history. 2. We used long-term
 monitoring of annual growth and reproduction of marked female bighorn
 sheep and mountain goats, two species in which primiparity normally occurs
 well before growth completion, to evaluate growth vs. reproduction
 trade-offs and their potential for predicting reproductive history of
 young females using mixed models and 10-fold block cross-validation. 3. We
 documented a significant reduction in mass gain and horn growth in young
 reproducing females of both species. This trade-off was affected by
 individual differences in energy acquisition and allocation, because
 population density and previous allocation to growth affected the
 trade-off. We then parametrized models to predict individual reproductive
 history of young females based on the growth traits subjected to a
 reproductive trade-off. 4. The accuracy of predictive models ranged from
 85.2% to 91.0% across species and traits, indicating that growth is a good
 predictor of reproductive history. This method is especially useful for
 population management of species with traits that form permanent visible
 yearly annuli because they retain a record of annual growth that allows
 retrospective estimation of reproductive history over multiple years. 5.
 Synthesis and applications. We show that because growth significantly
 decreased in years of allocation to reproduction, annual growth increments
 provide insights on reproductive history of young females. Population or
 temporal differences in reproduction of young females affect demographic
 rates and sustainable harvest. Growth measures of traits that form yearly
 annuli, such as teeth and horns, could be easily obtained at a low cost
 from animals harvested or found dead in multiple species. Thus, predictive
 models of reproductive history based on annual growth could assist
 conservation and management in a broad range of species.
DOI: 10.5061/dryad.tmpg4f4xm
title: Data from: Global patterns of functional trait variation along aridity gradients in bats

description: Aim: Our understanding of the biological strategies employed by species to
 cope with challenges posed by aridity is still limited. Despite being
 sensitive to water loss, bats successfully inhabit a wide range of arid
 lands. We here investigated how functional traits of bat assemblages vary
 along the global aridity gradient to identify traits that favour their
 persistence in arid environments.  Methods: We mapped the
 assemblage-level averages of four key bat traits describing wing
 morphology, echolocation and body size, based on a grid of 100 km
 resolution and a pool of 915 bat species, and modelled them against
 aridity values. To support our results, we conducted analyses also at the
 species level to control for phylogenetic autocorrelation. 
 Results: At the assemblage level, we detected a rise in values of aspect
 ratio, wing loading and forearm length, and a decrease in echolocation
 frequency with increasing aridity. These patterns were consistent with
 trends detected at the species level for all traits.  Main
 conclusions: Our findings show that trait variation in bats is associated
 with the aridity gradient and suggest that greater mobility and larger
 body size are advantageous features in arid environments. Greater mobility
 favours bats ability to track patchy and temporary resources, while the
 reduced surface-to-volume ratio associated with a larger body size is
 likely to reduce water stress by limiting cutaneous evaporation. These
 findings highlight the importance of extending the attention from
 species-specific adaptations to broad scale and multispecies variation in
 traits when investigating the ability of species to withstand arid
 conditions.
description: <strong>Conenna et al. (2021)</strong>
 Functional trait data for echolocating bat species
 (unprocessed); data on statistics of aridity within species geographical
 ranges; data on species distribution over a global grid of 100 by 100 km
 resolution; R code.
DOI: 10.5061/dryad.hx3ffbgd4
title: Identification of common predisposing loci to hematopoietic cancers in four dog breeds

description: Histiocytic sarcoma (HS) is a rare but aggressive cancer in both humans
 and dogs. The spontaneous canine model, which has clinical,
 epidemiological, and histological similarities with human HS and specific
 breed predispositions, provides a unique opportunity to unravel the
 genetic basis of this cancer. In this study, we aimed to identify germline
 risk factors associated with the development of HS in canine-predisposed
 breeds. We used a methodology that combined several genome-wide
 association studies in a multi-breed and multi-cancer approach as well as
 targeted next-generation sequencing, and imputation We combined several
 dog breeds (Bernese mountain dogs, Rottweilers, flat-coated retrievers,
 and golden retrievers), and three hematopoietic cancers (HS, lymphoma, and
 mast cell tumor). Results showed that we not only refined the previously
 identified HS risk CDKN2A locus, but also identified new loci on canine
 chromosomes 2, 5, 14, and 20. Capture and targeted sequencing of specific
 loci suggested the existence of regulatory variants in non-coding regions
 and methylation mechanisms linked to risk haplotypes, which lead to strong
 cancer predisposition in specific dog breeds. We also showed that these
 canine cancer predisposing loci appeared to be due to the additive effect
 of several risk haplotypes involved in other hematopoietic cancers such as
 lymphoma or mast cell tumors as well. This illustrates the pleiotropic
 nature of these canine cancer loci as observed in human oncology, thereby
 reinforcing the interest of predisposed dog breeds to study cancer
 initiation and progression.
description: Samples from cancer-affected and unaffected dogs were collected
 by a network of veterinarians through the Cani-DNA Biological Resource
 Center (http://dog-genetics.genouest.org). DNA samples were genotyped on
 an Illumina 173K SNV Canine HD array and on Affymetrix Axiom Canine
 Genotyping Array Set A and B 1.1M SNV array at Affymetrix, Inc.
DOI: 10.7291/d1xm3b
title: Variation in resting strategies across trophic levels and habitats in mammals

description: Mammals must carefully balance rest with other behaviors that influence
 fitness (e.g., foraging, finding a mate) while minimizing predation risk.
 However, factors influencing resting strategies and the degree to which
 resting strategies are driven by the activities of predators and/or prey
 remain largely unknown. Our goal was to examine how mammalian resting
 strategies varied with trophic level, body mass, and habitat. We reviewed
 findings from 127 publications and classified the resting strategies of
 terrestrial and aquatic mammalian species into three categories: social
 (e.g., resting in groups), temporal (e.g., resting during the day), or
 spatial (e.g., resting in burrows). Temporal strategies were most common
 (54% of cases), but the prevalence of strategies varied with body mass and
 among trophic levels. Specifically, lower trophic levels and smaller
 species such as rodents and lagomorphs used more spatial and social
 resting strategies whereas top predators and larger species used mostly
 temporal resting strategies. Resting strategies also varied among habitat
 types (e.g., rainforest versus grassland) but this was primarily because
 closely related species shared both habitats and resting strategies. Human
 presence also affected resting strategies at all trophic levels but most
 strongly influenced top predators through shifts in rest timing.
 Human-induced behavioral changes in rest patterns cascade to modify
 behaviors across multiple trophic levels. These findings advance our
 fundamental understanding of natural history and ecology in wild animals
 and provide a roadmap for future comparative studies.
DOI: 10.5061/dryad.z08kprrbp
title: Raw data from: Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs

description: Microbial mutualists provide substantial benefits to hosts that feed back
 to enhance fitness of the associated microbes. In many systems, beneficial
 microbes colonize symbiotic organs, specialized host structures that house
 symbionts and mediate resources exchanged between parties. Mutualisms are
 characterized by net benefits exchanged among members of different
 species, however inequalities in the magnitude of these exchanges could
 result in evolutionary conflict, destabilizing the mutualism. We
 investigated joint fitness effects of root nodule formation, the symbiotic
 organ of legumes that house nitrogen-fixing rhizobia in planta. We
 quantified host and symbiont fitness parameters dependent on the number of
 nodules formed using near isogenic Lotus japonicus and Mesorhizobium loti
 mutants, respectively. Empirically estimated fitness functions suggest
 that legume and rhizobia fitness is aligned as the number of nodules
 formed increases from zero until the host optimum is reached, a point
 where aligned fitness interests shift to diverging fitness interests
 between host and symbiont. However, fitness conflict was only inferred
 when analyzing wildtype hosts along with their mutants dysregulated for
 control over nodule formation. These data demonstrate that to avoid
 conflict, hosts must tightly regulate investment into symbiotic organs
 maximizing their benefit to cost ratio of associating with microbes.
description: <strong>Biomass Harvest Data Sheet</strong>
 Host Phenotype data collected at the time of harvest.
 <strong>Culturing Data Sheet</strong>
 Estimated viable rhizobia per nodule. Proportion data and
 corresponding cell estimates are only applicable for coinoculum
 rows. <strong>Histology
 Sheet</strong> Histological measurements of host
 nodules infected with MAFF at 5wpi. Area units are squared
 micrometers. <strong>d15N
 Sheet</strong> Elemental and isotopic analysis
 of leaf tissue for plants harvested at 5wpi.
DOI: 10.5061/dryad.jh9w0vt9q
title: ENIGMA Pediatric msTBI diffusion MRI supplemental data

description: Objective: Our study addressed aims: (1) test the hypothesis that
 moderate-severe TBI in pediatric patients is associated with widespread
 white matter (WM) disruption; (2) test the hypothesis that age and sex
 impact WM organization after injury; and (3) examine associations between
 WM organization and neurobehavioral outcomes. Methods: Data from ten
 previously enrolled, existing cohorts recruited from local hospitals and
 clinics were shared with the ENIGMA (Enhancing NeuroImaging Genetics
 through Meta-Analysis) Pediatric msTBI working group. We conducted a
 coordinated analysis of diffusion MRI (dMRI) data using the ENIGMA dMRI
 processing pipeline. Results: Five hundred and seven children and
 adolescents (244 with complicated mild to severe TBI [msTBI] and 263
 controls) were included. Patients were clustered into three post-injury
 intervals: acute/subacute - &lt;2 months, post-acute - 2-6 months,
 chronic - 6+ months. Outcomes were dMRI metrics and post-injury behavioral
 problems as indexed by the Child Behavior Checklist (CBCL). Our analyses
 revealed altered WM diffusion metrics across multiple tracts and all
 post-injury intervals (effect sizes ranging between d=-0.5 to -1.3).
 Injury severity is a significant contributor to the extent of WM
 alterations but explained less variance in dMRI measures with increasing
 time post-injury. We observed a sex-by-group interaction: females with TBI
 had significantly lower fractional anisotropy in the uncinate fasciculus
 than controls (?=0.043), which coincided with more parent-reported
 behavioral problems (?=-0.0027). Conclusions: WM disruption after msTBI is
 widespread, persistent, and influenced by demographic and clinical
 variables. Future work will test techniques for harmonizing neurocognitive
 data, enabling more advanced analyses to identify symptom clusters and
 clinically-meaningful patient subtypes.
DOI: 10.5061/dryad.sj3tx963r
title: The battle between harvest and natural selection creates small and shy fish

description: Harvest of fish and wildlife, both commercial and recreational, is a
 selective force that can induce evolutionary changes to life-history and
 behaviour. Natural selective forces may create countering selection
 pressures. Assessing natural fitness represents a considerable challenge
 in broadcast spawners. Thus, our understanding of the relative strength of
 natural and fisheries selection is slim. In the field, we compared the
 strength and shape of harvest selection to natural selection on body size
 over four years and behaviour over one year in a natural population of a
 freshwater top predator, the northern pike (Esox lucius). Natural
 selection was approximated by relative reproductive success via
 parent-offspring genetic assignments over four years. Harvest selection
 was measured by comparing individuals susceptible to recreational angling
 with individuals never captured by this gear type. Individual behaviour
 was measured by high-resolution acoustic telemetry. Harvest and natural
 size-selection operated with equal strength but opposing directions, and
 harvest size-selection was consistently negative in all study years.
 Harvest selection also had a substantial behavioural component independent
 of body length, while natural behavioural-selection was not documented,
 suggesting the potential for directional harvest selection favouring
 inactive, timid fish. Simulations of the outcomes of different fishing
 regulations showed that traditional minimum-size based harvest limits are
 unlikely to counteract harvest-selection without being completely
 restrictive. Our study suggests harvest selection may be inevitable and
 recreational fisheries may thus favor small, inactive, shy and
 difficult-to-capture fish. Increasing fractions of shy fish in
 angling-exploited stocks would have consequences for stock assessment and
 all fisheries operating with hook-and-line.
description: Pike sampling was done by angling and electrofishing during
 2007-2010. The pike behavioural data was collected with a high-resolution
 acoustic telemetry system in a small 25-hectare lake in Brandenburg,
 Germany. The parent-offspring assignment was collected using
 microsatellite markers from fin clips of sampled juveniles and parents.
DOI: 10.5061/dryad.tht76hdz1
title: Detecting and removing sample contamination in phylogenomic data: An example and its implications for Cicadidae phylogeny (Insecta: Hemiptera)

description: Contamination of a genetic sample with DNA from one or more non-target
 species is a continuing concern of molecular phylogenetic studies, both
 Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We
 developed an automated pipeline for identifying and excluding likely
 cross-contaminated loci based on detection of bimodal distributions of
 patristic distances across gene trees. When the contamination occurs
 between samples within a dataset, comparisons between a contaminated
 sample and its contaminant taxon will yield bimodal distributions with one
 peak close to zero patristic distance. Here we present an automated
 pipeline for identifying and excluding likely cross-contaminated loci
 based on detection of these bimodal distributions of patristic distances
 between taxa across gene trees. This new method does not rely on a priori
 knowledge of taxon relatedness nor does it determine the process(es) that
 caused the contamination. Exclusion of putatively contaminated loci from a
 dataset generated for the insect family Cicadidae showed that these
 sequences were affecting some topological patterns and branch supports,
 although the effects were sometimes subtle, with some
 contamination-influenced relationships exhibiting strong bootstrap
 support. Long tip branches and outlier values for one anchored
 phylogenomic pipeline statistic (AvgNHomologs) were correlated with the
 presence of contamination. While the AHE markers used here, which target
 hemipteroid taxa, proved effective in resolving deep and shallow level
 Cicadidae relationships in aggregate, individual markers contained
 inadequate phylogenetic signal, in part probably due to short length. The
 cleaned dataset, consisting of 90 genera representing 44 of 56 current
 Cicadidae tribes, and 429 loci, supported three of the four sampled
 Cicadidae subfamilies in concatenated-matrix (IQ-TREE ML) and multispecies
 coalescent-based (ASTRAL-III) species tree analyses, with the fourth
 subfamily weakly supported in the ML trees. No well-supported patterns
 from previous family-level Sanger sequencing studies of Cicadidae
 phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall
 with its current subfamily in the genetic tree, and this genus and its
 tribe Aragualnini is reclassified to Tibicininae following morphological
 re-examination. Only subtle differences were observed in trees after
 removal of loci for which divergent base frequencies were detected.
 Greater success may be achieved by increased taxon sampling and developing
 a probe set targeting a more recent common ancestor and longer loci.
 Searches for contamination are an essential step in phylogenomic analyses
 of all kinds and our pipeline is an effective solution.
DOI: 10.15468/dl.bj5hwj
title: Occurrence Download

description: A dataset containing 14285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Eleusine indica"
 ]
}

 The dataset includes 14285 records from 383 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002739-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0rxwdbrzd
title: Data from two dimensional electronic spectroscopy showing that photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer

description: Raw data from an ultrafast two dimensional electronic spectrometer
 investigating a series of mutants from the Fenna-Matthews Olson
 photosynthetic complex from Chlorobaculum tepidum is included
 here.  This data was analyzed and reduced using the enclosed
 matlab scripts to show that this complex responds to changing oxidation
 conditions by breaking a resonance between a gap between electronic states
 and an attendant vibration within the bacteriochlorophyll molecules.
 Breaking this resonance steers energy differently through the complex and
 enables a photoprotective response that increases quenching of the
 absorbed excitation.  In this regard, using simply the oxidation
 of two cysteine residues, the complex then manipulates this quantum
 mechanical vibronic coupling to redirect energy transfer and protect the
 organism from photooxidative damage. This dataset includes raw and reduced
 data including scripts for fitting trends, time constants, and modelling
 the data using a Redfield model.  This work is being published
 in Higgins et al., "Photosynthesis tunes quantum-mechanical
 mixing of electronic and vibrational states to steer exciton energy
 transfer", PNAS, March 8, 2021.
DOI: 10.5061/dryad.jm63xsj93
title: Synergistic impacts of aggressive species on small birds in a fragmented landscape

description: 1. Attempts to conserve threatened species in fragmented landscapes are
 often challenging because factors such as habitat loss, habitat
 degradation and dominant species interact to reduce threatened species’
 capacity to survive and reproduce. Understanding how threatening and
 mitigating processes interact is critical if conservation measures are to
 be effective. 2. We used data from long-term monitoring of bird
 populations and multivariate latent variable models to quantify how
 Australian woodland birds respond to the presence of the Noisy Miner, a
 despotic species known to exclude other bird species. We then investigated
 the extent to which the presence of other aggressive species exacerbates
 the impacts of the Noisy Miner, and to what extent these impacts can be
 mitigated by dense midstorey plantings. 3. We found strong synergies
 between the Noisy Miner and two other aggressive species (Grey Butcherbird
 and Pied Butcherbird), despite weak effects of butcherbirds in isolation.
 4. The impacts of aggressive birds are most pronounced for small-bodied
 species; but these impacts are lessened in the presence of high midstorey
 cover. 5. Synthesis and applications. Accounting for interactions reveals
 that revegetation may be capable of improving conservation outcomes even
 when the proximate cause of species declines (i.e. exclusion or predation
 by aggressive bird species) cannot be managed directly.
description: This dataset consists of 1520 observations of 36 bird species
 at 220 locations. They are presented as three inputs necessary to run a
 latent variable model as implemented in the R package
 'boral'. Species observations ('species.csv') are
 presence/absence (0/1). Site data ('sites.csv') show percentage
 overstorey and midstorey cover as taken from field surveys; percentage
 cover of native vegetation in a 500m buffer around each site from remote
 sensing; the year of observation; and whether the Noisy Miner or either of
 the Grey or Pied Butcherbirds were seen on that occasion. Trait data
 ('traits.csv') show log body mass and are taken from the
 scientific literature. Data have been grouped from 6 observations per year
 (3 plots x 2 observers) for this analysis.
description: Observations that contain missing values have been removed. Prior
 to analysis all percentage cover variables were log(x + 1)-transformed and
 scaled to a mean of zero and a standard deviation of one. The variables
 'year' and 'log body mass' were also scaled but not
 log-transformed.