cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2hv53
title: Data from: Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos

description: Recent conceptual and methodological advances have increased the ability
 to apply multifaceted approaches to species delimitation, which is
 particularly useful in delimiting recently diversified species where
 single lines of evidence lead to incorrect species delimitation or
 assignment of individuals to species (e.g. cryptic, morphological species
 and paraphyletic, hybridizing species). Species of the Australian Gehyra
 gecko radiation have historically proven difficult to delimit due the
 group’s uniform, almost continent-wide geographic distribution and
 conservative morphology, contrasting high chromosomal and genetic
 diversity. Using an integrated approach to species delimitation taking
 advantage of morphological, geographic distributional and multi-locus
 genetic data, we investigate the diversity within three Gehyra species
 from the Australian arid zone. Our results show that these species
 represent eight distinct phylogenetic lineages, which display different
 patterns of morphological distinction and reproductive isolation. Using a
 recently developed Bayesian species delimitation method, we also find
 different levels of support for putative species dependent on priors for
 population size and timing of diversification assumed. Our results show
 that the current taxonomy does not adequately account for the diversity of
 the group. Discrepancies between lines of evidence indicate that
 diversification of the group is recent and ongoing, thus posing challenges
 for both species concepts and delimitation.
description: ND2
 alignmentND2
 dataND2
 montvar.nexH3
 alignmentH3 histone
 alignmentFINAL
 H3.nexPRL-R
 alignmentPRL-R
 alignmentFINAL
 PRLR.nex
DOI: 10.5061/dryad.5dj78
title: Data from: Phase-dependent climate-predator interactions explain three decades of variation in neonatal caribou survival

description: 1. Climate can have direct and indirect effects on population dynamics via
 changes in resource competition or predation risk, but this influence can
 be modulated by density- or phase-dependent processes. We hypothesized
 that for ungulates, climatic conditions close to parturition have a
 greater influence on the predation risk of neonates during population
 declines, when females are already under nutritional stress triggered by
 food limitation. 2. We examined the presence of phase-dependent
 climate-predator interactions on neonatal ungulate survival by comparing
 spatial and temporal fluctuations in climatic conditions, cause specific
 mortality, and per capita resource limitation. We determined
 cause-specific fates of 1384 caribou (Rangifer tarandus) from 10 herds in
 Newfoundland, spanning more than 30 years during periods of numerical
 increase and decline, while exposed to predation from black bears (Ursus
 americanus) and coyotes (Canis latrans). 3. We conducted Cox proportional
 hazards analysis for competing risks, fit as a function of weather
 metrics, to assess pre- and post-partum climatic influences on survival on
 herds in population increase and decline phases. We used cumulative
 incidence functions to compare temporal changes in risk from predators. 4.
 Our results support our main hypothesis; when caribou populations
 increased, weather conditions preceding calving were the main determinants
 of cause-specific mortality, but when populations declined, weather
 conditions during calving also influenced predator-driven mortality.
 Cause-specific analysis showed that weather conditions can differentially
 affect predation risk between black bears and coyotes with specific
 variables increasing the risk from one species and decreasing the risk
 from the other. 5. For caribou, nutritional stress appears to increase
 predation risk on neonates, an interaction which is exacerbated by
 susceptibility to climatic events. These findings support the
 phase-dependent climate-predator (PDCP) interactions framework, where
 maternal body condition influences susceptibility to climate-related
 events and, subsequently, risk from predation.
description: Survival
 dataRaw survival
 dataSurvival_Dryad.csv
DOI: 10.5061/dryad.v21bb
title: Data from: Ground squirrel tail-flag displays alter both predatory strike and ambush site selection behaviours of rattlesnakes

description: Many species approach, inspect, and signal toward their predators. These
 behaviours are often interpreted as predator-deterrent signals—honest
 signals that indicate to predators that continued hunting is likely to be
 futile. However, many of these putative predator-deterrent signals are
 given when no predator is present, and it remains unclear if and why such
 signals deter predators. We examined the effects of one such signal, the
 tail-flag display of California ground squirrels, which is frequently
 given both during and outside direct encounters with northern Pacific
 rattlesnakes. We video recorded and quantified the ambush foraging
 responses of rattlesnakes to tail-flagging displays from ground squirrels.
 We found that tail-flagging deterred snakes from striking squirrels, most
 likely by advertising squirrel vigilance (i.e., readiness to dodge a snake
 strike). We also found that tail-flagging by adult squirrels increased the
 likelihood that snakes would leave their ambush site, apparently by
 elevating the vigilance of nearby squirrels which reduces the
 profitability of the ambush site. Our results provide some of the first
 empirical evidence of the mechanisms by which a prey display, although
 frequently given in the absence of a predator, may still deter predators
 during encounters.
description: SqrlStrikeFactors.4withstrikeoutcome&dodgeField data of free-ranging rattlesnake strike behaviour in response to ground squirrel tail-flagging displays.SnakeHuntingDataCoxSurvUpdated3Field data of free-ranging rattlesnake ambush site selection behaviours in response to tail-flagging displays from ground squirrels.
DOI: 10.5061/dryad.hf887
title: Data from: Few genetic and environmental correlations between life history and stress resistance traits affect adaptation to fluctuating thermal regimes

description: Laboratory selection in thermal regimes that differed in the amplitude and
 the predictability of daily fluctuations had a marked effect on stress
 resistance and life history traits in Drosophila simulans. The observed
 evolutionary changes are expected to be the result of both direct and
 correlated responses to selection. Thus, a given trait might not evolve
 independently from other traits because of genetic correlations among
 these traits. Moreover, different test environments can induce novel
 genetic correlations because of the activation of environmentally
 dependent genes. To test whether and how genetic correlations among stress
 resistance and life history traits constrain evolutionary adaptation, we
 used three populations of D. simulans selected for 20 generations in
 constant, predictable and unpredictable daily fluctuating thermal regimes
 and tested each of these selected populations in the same three thermal
 regimes. We explored the relationship between genetic correlations between
 traits and the evolutionary potential of D. simulans by comparing genetic
 correlation matrices in flies selected and tested in different thermal
 test regimes. We observed genetic correlations mainly between
 productivity, body size, starvation and desiccation tolerance, suggesting
 that adaptation to the three thermal regimes was affected by correlations
 between these traits. We also found that the correlations between some
 traits such as body size and productivity or starvation tolerance and
 productivity were determined by test regime rather than selection regime
 that is expected to limit genetic adaptation to thermal regimes in these
 traits. The results of this study suggest that several traits and several
 environments are needed to explore adaptive responses, as genetic and
 environmentally induced correlations between traits as results obtained in
 one environment cannot be used to predict the response of the same
 population in another environment.
description: raw
 dataThis is a collection of
 phenotypic values of several life history and stress resistance traits in
 flies laboratory natural selected in a constant, predictable and
 unpredictable daily fluctuating thermal regimesall.txt
DOI: 10.5061/dryad.678
title: Data from: Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae)

description: The possibility of gene tree incongruence in a species-level phylogenetic
 analysis of the genus Ips (Coleoptera: Scolytidae) was investigated based
 on mitochondrial 16S rRNA and nuclear Elongation factor-1α sequences, and
 existing Cytochrome Oxidase I and non-molecular data sets. Separate
 cladistic analyses of the data partitions resulted in partially discordant
 most-parsimonious trees but revealed only low conflict of the phylogenetic
 signal. Interactions among data partitions, which differed in the level of
 sequence divergence (COI &gt; 16S &gt; EF-1α), base composition,
 and homoplasy, revealed that much of the branch support only emerges in
 the simultaneous analysis, in particular for deeper nodes in the tree
 which are almost entirely supported due to "hidden support"
 (sensu Gatesy et al., 1999). Apparent incongruence between data partitions
 is in part due to suboptimal alignments and bias of character
 transformations, but there is little evidence to invoke incongruent
 phylogenetic histories of genetic loci. There is also no justification for
 eliminating or downweighting gene partitions based on their level of
 homoplasy or apparent incongruence with other partitions, as the signal
 only emerges in the interaction of all data. In comparison to the
 traditional taxonomy, the pini, plastographus and perturbatus groups are
 polyphyletic, whereas the grandicollis group is monophyletic except for
 the inclusion of the (monophyletic) calligraphus group. The latidens group
 and some European species are distantly related and closer to other genera
 within Ipini. Our robust cladogram was used to revise the classification
 of Ips. We provide new diagnoses for Ips and four subgeneric taxa.
description: Ips Phenetic
 AlignmentIps.phenetic.alignment.nexusIps Poy g1 Data SetIps.poy.g1.nexusIps Poy g2 Data SetIps.poy.g2.nexusIps Poy g3 Data SetIps.poy.g3.nexus
DOI: 10.5061/dryad.5428h
title: Data from: Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests

description: Is active restoration the best approach to achieve ecological restoration
 success (the return to a reference condition, that is, old-growth forest)
 when compared to natural regeneration in tropical forests? Our
 meta-analysis of 133 studies demonstrated that natural regeneration
 surpasses active restoration in achieving tropical forest restoration
 success for all three biodiversity groups (plants, birds, and
 invertebrates) and five measures of vegetation structure (cover, density,
 litter, biomass, and height) tested. Restoration success for biodiversity
 and vegetation structure were 34 to 56% and 19 to 56% higher in natural
 regeneration than in active restoration systems, respectively, after
 controlling for key biotic and abiotic factors (forest amount,
 precipitation, time elapsed since restoration started, and past
 disturbance). Biodiversity responses were based primarily on ecological
 metrics of abundance and species richness (74%), both of which take far
 less time to achieve restoration success than similarity and composition.
 This finding challenges the widely held notion that natural forest
 regeneration has limited conservation value and that active restoration
 should be the default ecological restoration strategy. The proposition
 that active restoration achieves greater restoration success than natural
 regeneration may have arisen because of comparisons lacking controlled
 biotic and abiotic factors. We did not find any difference between active
 restoration and natural regeneration outcomes for vegetation structure
 when we did not control for these factors. Future policy priorities should
 align the identified patterns of biophysical and ecological conditions
 where each or both restoration approaches are more successful,
 cost-effective, and compatible with socioeconomic incentives for tropical
 forest restoration.
description: DataMeta_analysis_controlledMeta_analysis_uncontrolled
DOI: 10.5061/dryad.tp030
title: Data from: Identification and distribution of the NBS-LRR gene family in the Cassava genome

description: Background: Plant resistance genes (R genes) exist in large families and
 usually contain both a nucleotide-binding site domain and a leucine-rich
 repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot
 esculenta) is a valuable resource for analysing the genomic organization
 of resistance genes in this crop. Results: With searches for Pfam domains
 and manual curation of the cassava gene annotations, we identified 228
 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of
 the total predicted genes and show high sequence similarity to proteins
 from other plant species. Furthermore, 34 contained an N-terminal
 toll/interleukin (TIR)-like domain, and 128 contained an N-terminal
 coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on
 the chromosomes. These clusters are mostly homogeneous, containing
 NBS-LRRs derived from a recent common ancestor. Conclusions: This study
 provides insight into the evolution of NBS-LRR genes in the cassava
 genome; the phylogenetic and mapping information may aid efforts to
 further characterize the function of these predicted R genes.
description: NBS_peptide_sequencesAminoacid sequences for the NBS domain of all genes used in the phylogenetic analysis are included in this file.Figure_1_alignmentRaw clustalW alignment for the tree in Figure 1Figure_2_and_additional_file_6_alignmentRaw clustalW alignment for the trees in Figure 3 and Additional File 6Figure_3_and_additional_file_6_alignment.alnFigure_1Alignment in MEGA format used to generate the phylogenetic tree in Figure 1Figure_3Alignment in MEGA format used to generate the phylogenetic tree in Figure 3Additional_file_6Alignment in MEGA format used to generate the phylogenetic tree in Additional File 6
DOI: 10.5061/dryad.gp5g0j0
title: Data from: Environmental pleiotropy and population demography direct adaptation under antibiotic selection

description: Evolutionary rescue following environmental change requires mutations
 permitting population growth in the new environment. If change is severe
 enough to prevent most of the population reproducing, rescue becomes
 reliant on mutations already present. If change is sustained, the fitness
 effects in both environments, and how they are associated---termed
 `environmental pleiotropy'---may determine which alleles are
 ultimately favoured. A population's demographic history---its size
 over time---influences the variation present. Although demographic history
 is known to affect the probability of evolutionary rescue, how it
 interacts with environmental pleiotropy during severe and sustained
 environmental change remains unexplored. Here, we demonstrate how these
 factors interact during antibiotic resistance evolution, a key example of
 evolutionary rescue fuelled by pre-existing mutations with pleiotropic
 fitness effects. We combine published data with novel simulations to
 characterise environmental pleiotropy and its effects on resistance
 evolution under different demographic histories. Comparisons among
 resistance alleles typically revealed no correlation for fitness---i.e.
 neutral pleiotropy---above and below the sensitive strain's minimum
 inhibitory concentration. Resistance allele frequency following
 experimental evolution showed opposing correlations with their fitness
 effects in the presence and absence of antibiotic. Simulations
 demonstrated that effects of environmental pleiotropy on allele
 frequencies depended on demographic history. At the population level, the
 major influence of environmental pleiotropy was on mean fitness, rather
 than the probability of evolutionary rescue or diversity. Our work
 suggests that determining both environmental pleiotropy and demographic
 history is critical for predicting resistance evolution, and we discuss
 the practicalities of this during in vivo evolution.
description: R scripts and data to
 reproduce figuresData were collected from
 published literature (see associated publication). Scripts were written by
 the authors.data.zipR scripts for simulations and simulation analysesScripts were written by the authors.simulation.zip
DOI: 10.5061/dryad.1241
title: Data from: A quantitative study of worker reproduction in queenright colonies of the Cape honey bee Apis mellifera capensis

description: Reproduction by workers is rare in honey bee colonies that have an active
 queen. By not producing their own offspring and preventing other workers
 from producing theirs, workers are thought to increase their inclusive
 fitness due to their higher average relatedness towards queen-produced
 male offspring compared with worker-produced male offspring. But there is
 one exception. Workers of the Cape honey bee Apis mellifera capensis are
 able to produce diploid female offspring via thelytokous parthenogenesis
 and thus produce clones of themselves. As a result, worker reproduction
 and tolerance towards worker-produced offspring is expected to be more
 permissive than in arrhenotokous (sub)species where worker offspring are
 male. Here we quantify the extent to which A. m. capensis workers
 contribute to reproduction in queenright colonies using microsatellite
 analyses of pre-emergent brood. We show that workers produced 10.2% of
 workers and 0.48% of drones. Most of the workers' contribution
 towards the production of new workers coincided with the colonies
 producing new queens during reproductive swarming.
description: Table
 S1.pdfGenotypes of
 pre-emergent workers (PEW) at four microsatellite lociTable
 S2.pdfGenotypes of
 pre-emergent drones (PED) of all 8 colonies
DOI: 10.5061/dryad.1m8tg17
title: Data from: Impact of ecological redundancy on the performance of machine learning classifiers in vegetation mapping

description: Vegetation maps are models of the real vegetation patterns and are
 considered important tools in conservation and management planning. Maps
 created through traditional methods can be expensive and time‐consuming,
 thus, new more efficient approaches are needed. The prediction of
 vegetation patterns using machine learning shows promise, but many factors
 may impact on its performance. One important factor is the nature of the
 vegetation–environment relationship assessed and ecological redundancy. We
 used two datasets with known ecological redundancy levels (strength of the
 vegetation–environment relationship) to evaluate the performance of four
 machine learning (ML) classifiers (classification trees, random forests,
 support vector machines, and nearest neighbor). These models used climatic
 and soil variables as environmental predictors with pretreatment of the
 datasets (principal component analysis and feature selection) and involved
 three spatial scales. We show that the ML classifiers produced more
 reliable results in regions where the vegetation–environment relationship
 is stronger as opposed to regions characterized by redundant vegetation
 patterns. The pretreatment of datasets and reduction in prediction scale
 had a substantial influence on the predictive performance of the
 classifiers. The use of ML classifiers to create potential vegetation maps
 shows promise as a more efficient way of vegetation modeling. The
 difference in performance between areas with poorly versus well‐structured
 vegetation–environment relationships shows that some level of
 understanding of the ecology of the target region is required prior to
 their application. Even in areas with poorly structured
 vegetation–environment relationships, it is possible to improve classifier
 performance by either pretreating the dataset or reducing the spatial
 scale of the predictions.
description: Underlying environmental
 matrix and training sites used for the machine learning
 predictionsEnvironmental
 matrices.zip
DOI: 10.5061/dryad.2m7b0
title: Data from: Pacman profiling: a simple procedure to identify stratigraphic outliers in high-density deep-sea microfossil data

description: The deep-sea microfossil record is characterized by an extraordinarily
 high density and abundance of fossil specimens, and by a very high degree
 of spatial and temporal continuity of sedimentation. This record provides
 a unique opportunity to study evolution at the species level for entire
 clades of organisms. Compilations of deep-sea microfossil species
 occurrences are, however, affected by reworking of material, age model
 errors, and taxonomic uncertainties, all of which combine to displace a
 small fraction of the recorded occurrence data both forward and backwards
 in time, extending total stratigraphic ranges for taxa. These data
 outliers introduce substantial errors into both biostratigraphic and
 evolutionary analyses of species occurrences over time. We propose a
 simple method—Pacman—to identify and remove outliers from such data, and
 to identify problematic samples or sections from which the outlier data
 have derived. The method consists of, for a large group of species,
 compiling species occurrences by time and marking as outliers calibrated
 fractions of the youngest and oldest occurrence data for each species. A
 subset of biostratigraphic marker species whose ranges have been
 previously documented is used to calibrate the fraction of occurrences to
 mark as outliers. These outlier occurrences are compiled for samples, and
 profiles of outlier frequency are made from the sections used to compile
 the data; the profiles can then identify samples and sections with
 problematic data caused, for example, by taxonomic errors, incorrect age
 models, or reworking of sediment. These samples/sections can then be
 targeted for re-study.
description: Lazarus_2012_Paleobiology_AppendicesAppendices 1 and 2. 1-tabular data extracted from or calculated from the Neptune database for Cenozoic radiolarian occurrences. 2-histograms (pdf plates) of occurences in time and effects of pacman data trimming for selected species of radiolarians. Details of table formats in readme.txt file included. File is zip archive, created with OS X 10.6 system 'compress'.