cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5c5372c
title: Data from: Differences in mitochondrial efficiency explain individual variation in growth performance

description: The physiological causes of intraspecific differences in fitness
 components such as growth rate are currently a source of debate. It has
 been suggested that differences in energy metabolism may drive variation
 in growth, but it remains unclear whether covariation between growth rates
 and energy metabolism is (i) a result of certain individuals acquiring and
 consequently allocating more resources to growth, and/or is (ii)
 determined by variation in the efficiency with which those resources are
 transformed into growth. Studies of individually-housed animals under
 standardized nutritional conditions can help shed light on this debate.
 Here we quantify individual variation in metabolic efficiency in terms of
 the amount of ATP generated per molecule of oxygen consumed by liver and
 muscle mitochondria, and examine its effects both on the rate of protein
 synthesis within these tissues and on the rate of whole-body growth of
 individually-fed juvenile brown trout (Salmo trutta) receiving either a
 high or low food ration. As expected, fish on the high ration on average
 gained more in body mass and protein content than those maintained on the
 low ration. Yet, growth performance varied more than 10-fold amongst
 individuals on the same ration, resulting in some fish on low rations
 growing faster than others on the high ration. This variation in growth
 for a given ration was related to individual differences in mitochondrial
 properties: a high whole-body growth performance was associated with high
 mitochondrial efficiency of ATP production in the liver. Our results show
 for the first time that among-individual variation in the efficiency with
 which substrates are converted into ATP can help explain marked variation
 in growth performance, independent of food intake. This study highlights
 the existence of inter-individual differences in mitochondrial efficiency
 and its potential importance in explaining intraspecific variation in
 whole animal performance.
description: RSPB-2019-1466_Data
DOI: 10.5061/dryad.q3d8c77
title: Data from: Rapid plastic breeding response to rain matches peak prey abundance in a tropical savannah bird

description: 1. Changes in climate are shifting the timing of life cycle events in the
 natural world. Compared to northern-temperate areas, these effects are
 relatively poorly understood in tropical and southern regions, where there
 is limited information on how timing of breeding and food availability are
 affected by climatic factors, and where patterns of breeding activity are
 more unpredictable within and between years. 2. Combining a new
 statistical modelling approach with 5 years of continuous individual-based
 monitoring of a monsoonal tropical insectivorous bird, we quantified (i)
 the proximate climatic drivers at two trophic levels: timing of breeding
 and abundance of arthropod prey; (ii) the effect of climate variation on
 reproductive output and (iii) the role of individual plasticity. 3.
 Rainfall was identified as the main determinant of phenology at both
 trophic levels. Throughout the year, likelihood of egg laying increased
 very rapidly in response to even small amounts of rain during the
 preceding 0-3 weeks. Adult body mass and male sperm storage also increased
 rapidly after rain, suggesting high breeding preparedness. Additionally,
 females were flexible, since they were more likely to nest if their
 previous attempt was longer ago and unsuccessful. Arthropod abundance also
 increased after rainfall, but more slowly, with a peak around 10 weeks.
 Therefore, the peak food availability coincided with the presence of
 dependent fledglings. 4. Fitness benefits of nesting after more rain
 appeared to be linked to offspring quantity rather than quality: nest
 attempts following higher rainfall produced larger clutches, but showed no
 improvement in nestling mass or relative fledging success. The response of
 clutch size to rainfall was plastic, since repeated sampling showed that
 individual females laid larger clutches after more rain, possibly mediated
 by improved body mass. 5. Rapid, individually flexible breeding in
 response to rainfall and slower increase in arthropod abundance also as a
 response to rainfall, might buffer insectivorous species living in
 tropical seasonal environments from climate-change induced phenological
 trophic mismatches.
description: DATA_Rapid plastic
 breeding response to rain matches peak prey abundance for
 JAE_DRYADData for Rapid plastic
 breeding response to rain matches peak prey abundanceDATA_rainfall and purple c
 fairy wrens for JAE_DRYAD.xlsx
DOI: 10.5061/dryad.6054537
title: Data from: Accounting for long-term directional trends on year-to-year synchrony in species fluctuations

description: What determines the stability of communities under environmental
 fluctuations remains one of the most debated questions in ecology.
 Scholars generally agree that the similarity in year-to-year fluctuations
 between species is an important determinant of this stability. Concordant
 fluctuations in species abundances through time (synchrony) decrease
 stability while discordance in fluctuations (anti-synchrony) should
 stabilize communities. Researchers have interpreted the community-wide
 degree of synchrony in temporal fluctuations as the outcome of different
 processes. However, existing synchrony measures depend not only on
 year-to-year species fluctuations, but also on long-term directional
 trends in species composition, for example due to land-use or climate
 change. The neglected effect of directional trends in species composition
 could cause an increase in synchrony that is not due to year-to-year
 fluctuations, as species that simultaneously increase (or decrease) in
 abundance over time will appear correlated, even if they fluctuate
 discordantly from year to year. The opposite pattern is also conceivable,
 where different species show contrasting trends in their abundances, thus
 overestimating year-to-year anti-synchrony. Therefore, trends in species
 composition may limit our understanding of potential ecological mechanisms
 behind synchrony between species. We propose two easily implementable
 solutions, with corresponding R functions, for testing and accounting for
 the effect of trends in species composition on overall synchrony. The
 first approach is based on computing synchrony over the residuals of
 fitted species trends over time. The second approach, applicable to
 already existing indices, is based on three-terms local variance, i.e.
 computing variance over three-years-long, movable windows. We demonstrate
 these methods using simulations and data from real plant communities under
 long-term directional changes, discussing when one approach can be
 preferred. We show that accounting for long-term temporal trends is both
 necessary and that separation of effect of trends and year-to-year
 fluctuation provides a better understanding of ecological mechanisms and
 their connections with ecological theory.
description: Temporal changes in
 species composition for demonstration of asynchrony and
 trendThe zip archive file
 contains six files, all in the txt format. The technical details are in
 the read_me.txt, the five remaining files contain species composition
 sampled repeatedly in permanent plots.LepsetalEcography2019Data.zip
DOI: 10.5061/dryad.0fs2vn4
title: Data from: Population-scale treatment informs solutions for control of environmentally transmitted wildlife disease

description: 1. Long-term pathogen control or eradication in wildlife is rare and
 represents a major challenge in conservation. Control is particularly
 difficult for environmentally transmitted pathogens, including some of the
 most conservation-critical wildlife diseases. 2. We undertook a treatment
 program aimed at population-scale eradication of the environmentally
 transmitted Sarcoptes scabiei mite (causative agent of sarcoptic mange)
 during an epizootic in bare-nosed wombats (Vombatus ursinus). Field trial
 results were used to parameterize a mechanistic host-disease model that
 explicitly described indirect-transmission, host behaviour, and viable
 disease intervention methods. 3. Model analysis shows that elimination of
 S. scabiei in the wild is most sensitive to the success of treatment
 delivery, and duration of the program. In addition, we found the frequency
 that wombats switch burrows was an important positive driver of mite
 persistence. 4. Synthesis and applications: This research emphasises the
 utility of applying model-guided management techniques in order to achieve
 practical solutions in the field. Our approach and findings have
 applicability to other species affected by S. scabiei (e.g., wolves, red
 foxes, Spanish ibex, and American black bear), as well as other
 conservation-critical systems involving environmental transmission (e.g.,
 bat white-nose syndrome and amphibian chytridiomycosis).
description: Weekly burrow flap
 activationWeekly status (activated
 or not) of each burrow during the treatment regime at Narawntapu national
 Park.BurrowFlapWeekly.csvWeekly wombat observations during surveysWeekly observations during survey days (on average, two survey days per week). State refers to disease state: infected, recovered, or total number of wombats observed.Dryad-Martin-WombatMangeCounts.csvBurrow switching modelR markdown file for the burrow switching model.RSPB-2018-2512-BurrowSwitching.RmdHost disease modelR markdown of the host-disease model used to infer management changes.RSPB-2018-2512-ManagementChanges.Rmd
DOI: 10.5061/dryad.5h3r278
title: Data from: Anticipating arrival: tackling the national challenges associated with the redistribution of biodiversity driven by climate change

description: 1. The redistribution of species in response to climate change is expected
 to significantly challenge environmental management and conservation
 efforts around the globe. To date, we have had restricted understanding of
 the benefits and risks that species redistribution may pose to individual
 countries, and a limited appreciation of the variability in current
 opportunities for developing effective monitoring approaches that build on
 existing national frameworks. 2. To assess the present level of
 ecological, economical and societal risks and opportunities associated
 with new arrivals driven by changes in climatic conditions, we conducted a
 review of the available information on climate driven changes in animal
 species (both terrestrial and marine) composition and distribution in the
 United Kingdom over the past ten years (2008-2018). 3. We found evidence
 that at least 55 species have colonised new locations in the country due
 to climate change in past decade, with 22 of them suspected to impact
 positively or negatively the receiving ecosystems and/or nearby human
 communities. Ten of these 55 species were identified thanks to social
 media. 4. Synthesis and applications. Our work identifies pressing
 monitoring gaps relevant to the management of species on the move and
 discusses the potential for social media to help address current
 information needs. It also calls for more theoretical work to enable the
 quick identification of species likely to be problematic (or beneficial)
 and locations likely to experience significant ecological and societal
 impacts from biodiversity’s redistribution under a changing climate.
description: Species on the move
 occurrencesThis dataset provides
 information on the location of occurrences of UK species known to be
 outside of their distribution ranges.Case_NewPresence.xlsx
DOI: 10.5061/dryad.3pn57h0
title: Data from: Female-biased gape and body-size dimorphism in the New World watersnakes (tribe: Thamnophiini) oppose predictions from Rensch’s Rule

description: Sexual size dimorphism (SSD) is ubiquitous across animals with female bias
 most prominent in snakes and other ectothermic organisms. To understand
 how SSD evolves across species, Rensch’s Rule predicts that in taxa where
 males are larger, SSD increases with body size. In contrast, where females
 are larger, SSD decreases with body size. While this rule holds for many
 taxa, it may be ambiguous for others, particularly ectothermic
 vertebrates. Importantly, this rule suggests that the outcomes of SSD over
 phylogenetic time scales depends on the direction of dimorphism predicated
 on the difference in reproductive efforts between males and females. Here
 we examine SSD in the context of Rensch’s Rule in Thamnophiini, the garter
 and waternsakes, a prominent group composing the North American snake
 biota. Using a dated phylogeny, measurements of gape, body and tail size,
 we show that these snakes do not follow Rensch’s Rule, but rather
 female-biased SSD increases with body size. We in turn find that this
 allometry is most pronounced with gape and is correlated with both neonate
 and litter size, suggesting that acquiring prey of increased size may be
 directly related to fecundity selection. These changes in SSD are not
 constrained to any particular clade; we find no evidence of phylogenetic
 shifts in those traits showing SSD. We suggest several ways forward to
 better understand the anatomical units of selection for SSD and modularity
description: Supporting_Information_Data_S1_Thamnophiini_Final_Morph_DataMorphological Data RawSupporting_Information_Data_S2_Thamnophiini_Tree_TotalPhylogeny of Thamnophiini from McVay et al. 2015Supporting_Information_Data_S3_Morph_data_totalAll morphological data summarized with referencesSupporting_Information_Data_S4_Morph_data_for_RData for importation and processing in R.Supporting_Information_Table_S1_SMA_StatisticsSMA and OLS regression stats.Supporting_Information_Table_S2_Trait_Model_EvolutionTable of trait model AICc and weighted AICc values.Supporting_Information_Table_S3 Model Adequacy TestsTable of model adequacy tests using Arbutus (R package).
DOI: 10.5061/dryad.m06n200
title: Data from: The genomes of polyextremophilic Cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

description: The role and extent of horizontal gene transfer (HGT) in eukaryotes are
 hotly disputed topics that impact our understanding of the origin of
 metabolic processes and the role of organelles in cellular evolution. We
 addressed this issue by analyzing 10 novel Cyanidiales genomes and
 determined that 1% of their gene inventory is HGT-derived. Numerous HGT
 candidates share a close phylogenetic relationship with prokaryotes that
 live in similar habitats as the Cyanidiales and encode functions related
 to polyextremophily. HGT candidates differ from native genes in
 GC-content, number of splice sites, and gene expression. HGT candidates
 are more prone to loss, which may explain the absence of a eukaryotic
 pan-genome. Therefore, the lack of a pan-genome and cumulative effects
 fail to provide substantive arguments against our hypothesis of recurring
 HGT followed by differential loss in eukaryotes. The maintenance of 1%
 HGTs, even under selection for genome reduction, underlines the importance
 of non-endosymbiosis related foreign gene acquisition.
description: Cyanidiales single gene
 trees parsed for evidence of HGTCyanidiales single gene
 trees parsed for evidence of HGTRossoni-et-al-SingleGeneTrees.zip.fasta files corresponding to each orthogroup in the analysis.fasta files corresponding to each orthogroup in the analysisRossoni-et-al-orthogroups_fasta.tar.gzPhylogenetic trees and alignments for orthogroupsPhylogenetic trees and alignments for orthogroupsRossoni-et-al-orthogroup_trees.tar.gzAssemblies, protein predictions and annotationsGenome assemblies, protein predictions and annotations for each of the ten Galdieria and Cyanidioschyzon strains studiedRossoni_et_al_2019.zip
DOI: 10.5061/dryad.88dd3vk
title: Data from: Disassembly of an epibenthic assemblage in a sustained severely hypoxic event in a northeast Pacific basin

description: As global ocean deoxygenation proceeds and the frequency of extreme
 low-oxygen (hypoxic) events increases, seafloor ecosystems will inevitably
 be affected. Our study examines how benthic community responses scale with
 the severity and spatial extent of hypoxia. Saanich Inlet is a natural
 model system for testing the effects of hypoxic conditions that determine
 the benthic megafaunal community structure during annual deoxygenation and
 reoxygenation. In 2016, an anomalously severe and widespread hypoxic event
 occurred in the fjord after a decade of oxygen decline at a rate of
 0.07 mL L−1 y−1 as measured by a cabled seafloor observatory. We use a
 living ecological time-series generated from remotely operated vehicle
 surveys to assess how the benthic megafaunal community disassembled in
 response to this extreme hypoxic event. Three benthic surveys at similar
 times in 2013 and 2016 reveal large increases in the area of seafloor
 bathed in anoxic and hypoxic waters in the latter year. Both bottom oxygen
 and species depth distributions shoaled from 2013 to 2016, accompanied by
 a 56% overall decline in megafauna. The abundant habitat-forming
 pennatulacean octocoral, Halipteris willemoesi, decreased in abundance by
 92.3% from fall 2013 to fall 2016, and pandalid shrimp disappeared from
 the community. Hypoxia-tolerant species experienced milder losses, and two
 new species occurred in 2016 – one a predator on the coral. Co-occurrence
 analyses revealed loss of significant community segregation from 2013 to
 2016, and a re-mix of pairwise species co-occurrences in the latter year.
 The loss of oxygenated habitat compressed species into narrower depth
 ranges and led to disassembly probably through niche space constriction,
 while decimation of some populations eliminated key community
 associations. Community fragmentation and disruption of interactions is a
 possible outcome for many marine benthic ecosystems as marine hypoxia
 intensifies.
description: Gasbarro_etal(2019_JMS)_DataData are animal counts and environment data collected during three remotely operated vehicle imagery surveys in Saanich Inlet, Vancouver Island, British Columbia, Canada in 2016. Each row entry equals a second of annotated ROV video with associated metadata (e.g. video file properties), water column data (e.g. depth, temperature, oxygen), or species data (presence/absence or counts). Extended details can be found with the associated README file.
DOI: 10.5061/dryad.434gv5p
title: Data from: Geographic scale and disturbance influence intraspecific trait variability in leaves and roots of North American understory plants

description: 1. Considering intraspecific trait variability (ITV) in ecological studies
 has improved our understanding of species persistence and coexistence.
 These advances are based on the growing number of leaf ITV studies over
 local gradients, but logistical constraints have prevented a solid
 examination of ITV in root traits or at scales reflecting species’
 geographic ranges. 2. We compared the magnitude of ITV in above- and
 below-ground plant organs across three spatial scales (biophysical region,
 locality, plot). We focused on six understory species (four herbs, two
 shrubs) that occur both in disturbed and undisturbed habitats across
 boreal and temperate Canadian forests. We aimed to document ITV structure
 over wide ecological and geographical scales by asking: 1) What is the
 breadth of ITV across species range-scale?; 2) What proportion of ITV is
 captured at different spatial scales, particularly when local scale
 disturbances are considered? and 3) Is the variance structure consistent
 between leaf and analogous root traits, and between morphological and
 chemical traits? 3. Following standardized methods, we sampled 818
 populations across 79 forest plots simultaneously, including disturbed and
 undisturbed stands, spanning four biophysical regions (~5200 km). Traits
 measured included specific leaf area (SLA), specific root length (SRL),
 and leaf and root nutrient concentrations (N, P, K, Mg, Ca). We used
 variance decomposition techniques to characterize ITV structure across
 scales. 4. Our results show that an important proportion of ITV occurred
 at the local scale when sampling includes contrasting environmental
 conditions resulting from local disturbance. A certain proportion of the
 variability in both leaf and root traits remained unaccounted for by the
 three sampling scales included in the design (36% on average) and a
 largest amount for SRL (54%). Substantial differences in magnitude of ITV
 were found among the six species, and between analogous traits, suggesting
 that trait distribution was influenced by species strategy and reflects
 the extent of understory environment heterogeneity. 5. Even for species
 with broad geographical distributions, a large proportion of
 within-species trait variability can be captured by sampling locally
 across ecological gradients. This has practical implications for sampling
 design and trait selection for both local studies and continental scale
 modeling.
description: AubinEtAl_CoVitas_ITVTrait data collected for the CoVitas project that was used in the publication. Please see Metadata file for more details (in xlsx format)
DOI: 10.5061/dryad.hr62h5f
title: Data from: Recurrent gene co-amplification on Drosophila X and Y chromosomes

description: Y chromosomes often contain amplified genes which can increase dosage of
 male fertility genes and counteract degeneration via gene conversion. Here
 we identify genes with increased copy number on both X and Y chromosomes
 in various species of Drosophila, a pattern that has previously been
 associated with sex chromosome drive involving the Slx and Sly gene
 families in mice. We show that recurrent X/Y co-amplification appears to
 be an important evolutionary force that has shaped gene content evolution
 of sex chromosomes in Drosophila. We also demonstrate that convergent
 acquisition and amplification of testis expressed gene families are common
 on Drosophila sex chromosomes, and especially on recently formed ones, and
 we carefully characterize one putative novel X/Y co-amplification system.
 We find that co-amplification of the S-Lap1/GAPsec gene pair on both the X
 and the Y chromosome occurred independently several times in members of
 the D. obscura group, where this normally autosomal gene pair is
 sex-linked due to a sex chromosome - autosome fusion. We explore several
 evolutionary scenarios that would explain this pattern of
 co-amplification. Investigation of gene expression and short RNA profiles
 at the S-Lap1/GAPsec system suggest that, like Slx/Sly in mice, these
 genes may be remnants of a cryptic sex chromosome drive system, however
 additional transgenic experiments will be necessary to validate this
 model. Regardless of whether sex chromosome drive is responsible for this
 co-amplification, our findings suggest that recurrent gene duplications
 between X and Y sex chromosomes could have a widespread effect on genomic
 and evolutionary patterns, including the epigenetic regulation of sex
 chromosomes, the distribution of sex-biased genes, and the evolution of
 hybrid sterility.
description: Drosophila Illumina
 genome assembliesIllumina TruSeq gDNA
 libraries were prepared from adult females and sequenced with 100bp PE
 reads. Reads were error-corrected with BFC and assembled with
 IDBA.drosophila_genome_assemblies.tar.gz