cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h8n6m
title: Data from: Consequences of seed origin and biological invasion for early establishment of a North American grass species

description: Local, wild-collected seeds of native plants are recommended for use in
 ecological restoration to maintain patterns of adaptive variation.
 However, some environments are so drastically altered by exotic, invasive
 weeds that original environmental conditions may no longer exist. Under
 these circumstances, cultivated varieties selected for improved
 germination and vigor may have a competitive advantage at highly disturbed
 sites. This study investigated differences in early establishment and
 seedling performance between wild and cultivated seed sources of the
 native grass, Poa secunda, both with and without competition from the
 invasive exotic grass, Bromus tectorum. We measured seedling survival and
 above-ground biomass at two experimental sites in western Montana, and
 found that the source of seeds selected for restoration can influence
 establishment at the restoration site. Cultivars had an overall advantage
 when compared with local genotypes, supporting evidence of greater vigor
 among cultivated varieties of native species. This advantage, however,
 declined rapidly in the presence of B. tectorum and most accessions were
 not significantly different for growth and survival in competition plots.
 Only one cultivar had a consistent advantage despite a strong decline in
 its performance when competing with invasive plants. As a result,
 cultivated varieties did not meet expectations for greater establishment
 and persistence relative to local genotypes in the presence of invasive,
 exotic species. We recommend the use of representative local or regional
 wild seed sources in restoration to minimize commercial selection, and a
 mix of individual accessions (wild, or cultivated when necessary) in
 highly invaded settings to capture vigorous genotypes and increase the
 odds native plants will establish at restoration sites.
description: FieldSurveyDataThis file contains data collected from Poa secunda grown at a field site in western Montana during the 2013 growing season. The first four columns refer to the plant's location within the field study area (Cell, Plot, Block, and Site). The fifth and sixth columns identify the grass origin (Accession and Source). For the seventh column, Treatment, grasses were either grown with (Challenged) or without (Unchallenged) Bromus tectorum. Plants were monitored over four consecutive surveys (Survey1-Survey4). The remaining columns represent data recorded for Poa secunda variables at each survey. These variables include Germinants (number of germinants out of four seeds planted), Survival (presence/absence), Herbivory (presence/absence), Cover (average Bromus tectorum canopy cover per plot), and Biomass. Microsoft Office Excel software was used to create the data file.
DOI: 10.5061/dryad.j8kp5
title: Data from: Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera: Pentatomidae)

description: The sequences of 18S and 28S rDNAs have been used as molecular markers to
 resolve phylogenetic relationships of Heteroptera for two decades. The
 complete sequences of 18S rDNAs have been used in many studies, while in
 most studies only partial sequences of 28S rDNAs have been used due to
 technical difficulties of amplifying the complete lengths. In this study,
 we amplified the complete 18S and 28S rDNA sequences of Eurydema
 maracandica Oshanin, 1871, and reconstructed the secondary structure
 models of the corresponding rRNAs. In addition, and more importantly, all
 of the length variable regions of 18S rRNA were compared among 37 families
 of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was
 compared among 51 families based on 84 sequences. It was found that 8
 length variable regions could potentially serve as molecular
 synapomorphies for some monophyletic groups. Therefore discoveries of more
 molecular synapomorphies for specific clades can be anticipated from
 amplification of complete 18S and 28S rDNAs of more representatives of
 Heteroptera.
description: Supplementary file
 1Supplementary file
 2Supplementary file
 3Supplementary file
 4Supplementary file
 5
DOI: 10.5061/dryad.bb206
title: Data from: How parallel is parallel evolution? A comparative analysis in fishes

description: Evidence of phenotypic parallelism is often used to infer the
 deterministic role played by natural selection. However, variation in the
 extent or direction of divergence is often evident among independent
 evolutionary replicates, raising the following question: just how
 parallel, overall, is parallel evolution? We answer this question through
 a comparative analysis of studies of fishes, a taxon where parallel
 evolution has been much discussed. We first ask how much of the
 among-population variance in phenotypic traits can be explained by
 different “environment” types, such as high predation versus low predation
 or benthic versus limnetic. We then use phenotypic change vector analysis
 to quantify variation in the direction (vector angles) and magnitude
 (vector lengths) of environment-associated divergence. All analyses show
 high variation in the extent of parallelism—from very high to very low,
 along with everything in between—highlighting the importance of
 quantifying parallelism rather than just asserting its presence.
 Interestingly, instances of low extents of parallelism represent important
 components of divergence in many cases, promising considerable
 opportunities for inferences about the factors shaping phenotypic
 divergence.
description: Oke et al 2017 AmNat
 study metadataInformation for original
 studies included in our analyses. All traits from all studies were not
 necessarily included, see article main text for inclusion
 criteria.Oke et al 2017 AmNat
 trait dataTrait level data, linked
 to individual studies using study identifier. Includes only those traits
 that met inclusion criteria.Oke et al 2017 AmNat
 population dataPopulation level data
 for each trait. Linked to trait level data using trait identifier.
 Includes only those traits that met inclusion criteria.
DOI: 10.5061/dryad.11vf0
title: Data from: Genetic basis of between-individual and within-individual variance of docility

description: Between-individual variation in phenotypes within a population is the
 basis of evolution. However, evolutionary and behavioural ecologists have
 mainly focused on estimating between-individual variance in mean trait and
 neglected variation in within-individual variance, or predictability of a
 trait. In fact, an important assumption of mixed-effects models used to
 estimate between-individual variance in mean traits is that
 within-individual residual variance (predictability) is identical across
 individuals. Individual heterogeneity in the predictability of behaviours
 is a potentially important effect but rarely estimated and accounted for.
 We used 11,389 measures of docility behaviour from 1,576 yellow-bellied
 marmots (Marmota flaviventris) to estimate between-individual variation in
 both mean docility and its predictability. We then implemented a double
 hierarchical animal model to decompose the variances of both mean trait
 and predictability into their environmental and genetic components. We
 found that individuals differed both in their docility and in their
 predictability of docility with a negative phenotypic covariance. We also
 found significant genetic variance for both mean docility and its
 predictability but no genetic covariance between the two. This analysis is
 one of the first to estimate the genetic basis of both mean trait and
 within-individual variance in a wild population. Our results indicate that
 equal within-individual variance should not be assumed. We demonstrate the
 evolutionary importance of the variation in the predictability of
 docility, and illustrate potential bias in models ignoring variation in
 predictability. We conclude that the variability in the predictability of
 a trait should not be ignored, and present a coherent approach for its
 quantification.
description: Docility
 dataData including docility
 scores, trial number (scaled), day of the year (scaled), time of the day
 (0: AM; 1:PM), age (0:juveniles, 1: yearlings; 2:adults), year and
 individual identitydatafinal.csvPedigreePruned pedigree including only individuals with docility data and their ancestors.pedigreefinal.csv
DOI: 10.5061/dryad.627rt
title: Data from: Functional traits explain ecosystem function through opposing mechanisms

description: The ability to explain why multispecies assemblages produce greater
 biomass compared to monocultures, has been a central goal in the quest to
 understand biodiversity effects on ecosystem function. Species
 contributions to ecosystem function can be driven by two processes: niche
 complementarity and a selection effect that is influenced by fitness
 (competitive) differences, and both can be approximated with measures of
 species’ traits. It has been hypothesised that fitness differences are
 associated with few, singular traits while complementarity requires
 multidimensional trait measures. Here, using experimental data from plant
 assemblages, I show that the selection effect was strongest when trait
 dissimilarity was low, while complementarity was greatest with high trait
 dissimilarity. Selection effects were best explained by a single trait,
 plant height. Complementarity was correlated with dissimilarity across
 multiple traits, representing above and below ground processes. By
 identifying the relevant traits linked to ecosystem function, we obtain
 the ability to predict combinations of species that will maximise
 ecosystem function.
description: Species
 traitsspecies_traits_final2016.csvplanted plotsThis gives initial plot treatmentsplanted.csvBiomassraw_biomass.csvComplementarity and selection effectscomp_select.csvabundances
DOI: 10.5061/dryad.258h4
title: Data from: Gene flow and the maintenance of species boundaries

description: Hybrid zones are regions where individuals from genetically differentiated
 populations meet and mate, resulting in at least some offspring of mixed
 ancestry. Patterns of gene flow (introgression) in hybrid zones vary
 across the genome, allowing assessment of the role of individual genes or
 genome regions in reproductive isolation. Here, we document patterns of
 introgression between two recently diverged species of field crickets. We
 sample at a very fine spatial scale and genotype crickets for 110 highly
 differentiated SNPs identified through transcriptome scans. Using both
 genomic and geographic cline analysis, we document remarkably abrupt
 transitions (less than 100 m) in allele frequencies for 50 loci, despite
 high levels of gene flow at other loci. These are among the steepest
 clines documented for any hybridizing taxa. Furthermore, the cricket
 hybrid zone provides one of the clearest examples of the semi-permeability
 of species boundaries. Comparisons between data from the fine scale
 transect and data (for the same set of markers) from sampling a much
 larger area in a different region of the cricket hybrid zone reveal
 consistent patterns of introgression for individual loci. The consistency
 in patterns of introgression between these two distant and distinct
 regions of the hybrid zone suggests that strong selection is acting to
 maintain abrupt discontinuities within the hybrid zone, and that genomic
 regions with restricted introgression likely include genes that contribute
 to non-ecological prezygotic barriers.
description: Data analyses
 RScripts of data analyses
 using RMolEcol_scripts.txtDIST1UTDATR input file for concordance and geographic cline analysesalldataR input file for genomic cline analyses and figuresIndividual_dataSummary file of individual dataCline_dataSummary file of cline data
DOI: 10.5061/dryad.9hn0m
title: Data from: Ocean currents, individual movements and genetic structuring of populations

description: Ocean currents profoundly impact all life in the oceans and over a broad
 size spectra species may show both horizontal and vertical movements to
 stay on preferred locations. As a corollary it might be expected that
 individuals in preferred oceanic habitats may simply drift with flows. We
 explored these scenarios by both satellite tracking young pelagic
 loggerhead turtles and examining the genetic structuring of individuals on
 coastal foraging areas across the Mediterranean in relation to ocean flows
 measured both with Lagrangian drifters and a numerical ocean circulation
 model for the area. Both patterns of movement (n = 18 turtles ranging in
 size from 41.2 to 68.5 cm CCL tracked for up to 460 days) and genetic
 structuring (n = 165 individuals from six sites across the ocean basin)
 suggested that ocean flows profoundly impact the movements of immature
 turtles and suggest a pattern of largely passive drift within an ocean
 basin that, throughout, is broadly favourable for developing loggerhead
 turtles. The situation contrasts with more heterogeneous habitats in the
 Atlantic and Pacific, where larger amounts of directional swimming may be
 required to avoid sub-optimum areas.
description: Satellite tracking data
 Caretta carettaDate, latitude,
 longitude and acuracy of location.CarettaOriginal.xls
DOI: 10.5061/dryad.jc181bs
title: Data from: The role of history and ecology as drivers of song divergence in Bell’s and Sagebrush sparrows (Artemisiospiza, Aves: Passerellidae)

description: Bell’s and Sagebrush sparrows (Artemisiospiza belli and A. nevadensis) are
 phenotypically and genetically distinct, but data have yielded
 contradictory findings for A. belli subspecies. Disjunct populations of A.
 b. canescens from the San Joaquin Valley and Mojave Desert are
 phenotypically indistinguishable but diagnosable from Coast Range A. b.
 belli. However, San Joaquin Valley A. b. canescens shares allozymes and
 mtDNA with A. b. belli whereas Mojave Desert A. b. canescens is
 genetically distinct. Furthermore, Great Basin A. nevadensis is closer in
 mtDNA to non-desert A. belli subspecies than to Mojave Desert A. b.
 canescens, with whom it contacts across an aridland transition. We
 assessed concordance of song with genetics and phenotype for these taxa,
 and also analyzed songs and mtDNA for A. b. clementeae which is endemic to
 arid San Clemente Island off the coast of southern California. Songs of
 open, arid habitat populations (A. nevadensis, A. b. canescens, A. b.
 clementeae) are consistently more similar to each other than they are to
 songs of coastal A. b. belli. We examined bioclimatic and land cover
 conditions to understand the basis for these patterns across ecoregions,
 and discuss the effect of the acoustic environment on song.
description: R CodeAll R Code for
 analysesArtemesiospiza.RSong DataData collected on quantitative song characteristics and note type and ordering.SongLibrary.txtsongData_filledSong data input file for analysis in RWorldclim DataGPS data points and data extracted from Worldclim v1.4Amphispiza_loc_worldclim_forPCA.csvND2 alignmentND2 Gene - DNA sequence alignmentND2.phyCytB alignmentND2 Gene - DNA sequence alignmentCytB.phy
DOI: 10.5061/dryad.k16gv
title: Data from: Landscape context explains changes in the functional diversity of regenerating forests better than climate or species richness

description: Aim A rich literature on forest succession provides general expectations
 for the steps forests go through while reassembling after disturbance, yet
 we still have a surprisingly poor understanding of why the outcomes of
 forest recovery after logging (or other disturbances) vary so extensively.
 In this paper, we test the hypothesis that regional species pool, system
 productivity, climate and landscape structure are important drivers of
 forest reassembly outcomes. Location Transect 1,500 km in length along the
 east coast of Australia. Time period Survey of 50- to 60-year-old rain
 forest regrowth and primary forest conducted in 2012 and 2013. Major taxa
 studied Rain forest plants. Methods In this study, we compare species and
 functional diversity patterns in pairs of remnant and regrowth
 (‘secondary’) rain forests spread across a 1,500 km climate and
 productivity gradient along the east coast of Australia. Our controlled
 natural experiment was designed to test the importance of regional species
 pool, system productivity, climate and landscape structure as drivers of
 species and functional diversity in regenerating forests. Notably, our
 study design allowed us to hold soil type, general forest type and
 disturbance history relatively constant in order to test our hypotheses
 effectively. Results Counter to expectations, few tested factors were
 strongly related to the recovery of species or functional diversity in
 regenerating Australian rain forests. The extent of local forest
 fragmentation was the only factor strongly related to differences between
 regrowth forests and primary forest remnants, and then only for functional
 diversity. We found no evidence that species diversity is a reasonable
 proxy for, or potential driver of, functional diversity patterns. Main
 conclusions Our findings suggest that forest functional recovery over
 decades is influenced more by regional landscape context than distinct
 assembly processes operating across climate and productivity gradients.
description: Sams_Mayfield_Rf1_AllThis file contains all of the data used in this paper. The file contains nine Excel sheets. The first is a summary of what is contained in each sheet and the remaining eight are pairs of metadata and raw data files. Each metadata sheet matches the name of the relevant datasheet. Data in this file include trait, climate, abundance and landscape data.
DOI: 10.5061/dryad.4fj54
title: Data from: Climate impacts on trans-ocean dispersal and habitat in gray whales from the Pleistocene to 2100

description: Arctic animals face dramatic habitat alteration due to ongoing climate
 change. Understanding how such species have responded to past glacial
 cycles can help us forecast their response to today's changing
 climate. Gray whales are among those marine species likely to be strongly
 affected by Arctic climate change, but a thorough analysis of past climate
 impacts on this species has been complicated by lack of information about
 an extinct population in the Atlantic. While little is known about the
 history of Atlantic gray whales or their relationship to the extant
 Pacific population, the extirpation of the Atlantic population during
 historical times has been attributed to whaling. We used a combination of
 ancient and modern DNA, radiocarbon dating and predictive habitat
 modelling to better understand the distribution of gray whales during the
 Pleistocene and Holocene. Our results reveal that dispersal between the
 Pacific and Atlantic was climate dependent and occurred both during the
 Pleistocene prior to the last glacial period and the early Holocene
 immediately following the opening of the Bering Strait. Genetic diversity
 in the Atlantic declined over an extended interval that predates the
 period of intensive commercial whaling, indicating this decline may have
 been precipitated by Holocene climate or other ecological causes. These
 first genetic data for Atlantic gray whales, particularly when combined
 with predictive habitat models for the year 2100, suggest that two recent
 sightings of gray whales in the Atlantic may represent the beginning of
 the expansion of this species' habitat beyond its currently realized
 range.
description: Final DNA sequence
 assemblyDNA alignment of all
 sequences used in the study.DNA_alignment_for_Dryad.fastawhales_finalAnalysis_mccTree file used to build Figure 1Summary of habitat envelope parametersData on all habitat envelope parameters used, including computer-generated and expert-modified, and text explaining rationale for modifications.
DOI: 10.5061/dryad.6vs80
title: Data from: Economic costs and health-related quality of life for hand, foot and mouth disease (HFMD) patients in China

description: Background: Hand, foot and mouth disease (HFMD) is a common illness in
 China that mainly affects infants and children. The objective of this
 study is to assess the economic cost and health-related quality of life
 associated with HFMD in China. Method: A telephone survey of caregivers
 were conducted in 31 provinces across China. Caregivers of
 laboratory-confirmed HFMD patients who were registered in the national
 HFMD enhanced surveillance database during 2012-2013 were invited to
 participate in the survey. Total costs included direct medical costs
 (outpatient care, inpatient care and self-medication), direct non-medical
 costs (transportation, nutrition, accommodation and nursery), and indirect
 costs for lost income associated with caregiving. Health utility weights
 elicited using EuroQol EQ-5D-3L and EQ-Visual Analogue Scale (VAS) were
 used to calculate associated loss in quality adjusted life years (QALYs).
 Results: The subjects comprised 1136 mild outpatients, 1124 mild
 inpatients, 1170 severe cases and 61 fatal cases. The mean total costs for
 mild outpatients, mild inpatients, severe cases and fatal cases were $201
 (95%CI $187, $215), $1072 (95%CI $999, $1144), $3051 (95%CI $2905, $3197)
 and $2819 (95%CI $2068, $3571) respectively. The mean QALY losses per HFMD
 episode for mild outpatients, mild inpatients and severe cases were 3.6
 (95%CI 3.4, 3,9), 6.9 (95%CI 6.4, 7.4) and 13.7 (95%CI 12.9, 14.5) per
 1000 persons. Cases who were diagnosed with EV-A71 infection and had
 longer duration of illness were associated with higher total cost and QALY
 loss. Conclusion: HFMD poses a high economic and health burden in China.
 Our results provide economic and health utility data for
 cost-effectiveness analysis for HFMD vaccination in China.
description: Dataset for Economic
 Burden and HRQoL of HFMDHFMD-orignal.xlsx
DOI: 10.5061/dryad.1fg41
title: Data from: Foraging activity pattern is shaped by water loss rates in a diurnal desert rodent

description: Although animals fine-tune their activity to avoid excess heat, we still
 lack a mechanistic understanding of such behaviors. As the global climate
 changes, such understanding is particularly important for projecting
 shifts in the activity patterns of populations and communities. We studied
 how foraging decisions vary with biotic and abiotic pressures. By tracking
 the foraging behavior of diurnal desert spiny mice in their natural
 habitat and estimating the energy and water costs and benefits of
 foraging, we asked how risk management and thermoregulatory requirements
 affect foraging decisions. We found that water requirements had the
 strongest effect on the observed foraging decisions. In their arid
 environment, mice often lose water while foraging for seeds and cease
 foraging even at high energetic returns when water loss is high. Mice also
 foraged more often when energy expenditure was high and for longer times
 under high seed densities and low predation risks. Gaining insight into
 both energy and water balance will be crucial to understanding the forces
 exerted by changing climatic conditions on animal energetics, behavior,
 and ecology.
description: Foraging
 dataNotes: "chip"
 is the id identifier of each golden spiny mouse. "Ta" is the
 average ambient temperature measured at the foraging position (1 to 4) and
 habitat (bb or ub). "Tb" is the average body temperature
 measured from the golden spiny mouse. "energy expenditure" and
 "evaporative water" loss are the metabolic costs of foraging
 calculated using the endotherm model. "Mass" is the body mass of
 the golden spiny mouse. "Start.gud" is the estimated amounts of
 seeds at the position and habitat at the beginning of the hour, estimated
 by fitting a harvest rate curve to the foraging activity.
 "Duration" is the amount of time spent at the foraging
 patch.Levy_et_al_2016.xlsx