cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.364mb
title: Data from: Differences in spatial synchrony and interspecific concordance inform guild-level population trends for aerial insectivorous birds

description: Many animal species exhibit spatiotemporal synchrony in population
 fluctuations, which may provide crucial information about ecological
 processes driving population change. We examined spatial synchrony and
 concordance among population trajectories of five aerial insectivorous
 bird species: chimney swift Chaetura pelagica, purple martin Progne subis,
 barn swallow Hirundo rustica, tree swallow Tachycineta bicolor, and
 northern rough-winged swallow Stelgidopteryx serripennis. Aerial
 insectivores have undergone severe guild-wide declines that were
 considered more prevalent in northeastern North America. Here, we
 addressed four general questions including spatial synchrony within
 species, spatial concordance among species, frequency of declining trends
 among species, and geographic location of declining trends. We used
 dynamic factor analysis to identify large-scale common trends underlying
 stratum-specific annual indices for each species, representing population
 trajectories shared by spatially synchronous populations, from 46 yr of
 North American Breeding Bird Survey data. Indices were derived from
 Bayesian hierarchical models with continuous autoregressive spatial
 structures. Stratum-level spatial concordance among species was assessed
 using cross-correlation analysis. Probability of long-term declining
 trends was compared among species using Bayesian generalized linear
 models. Chimney swifts exhibited declining trends throughout North
 America, with less severe declines through the industrialized Mid-Atlantic
 and Great Lakes regions. Northern rough-winged swallows exhibited
 declining trends throughout the west. Spatial concordance among species
 was limited, the proportion of declining trends varied among species, and
 contrary to previous reports, declining trends were not more prevalent in
 the northeast. Purple martins, barn swallows, and tree swallows exhibited
 synchrony across smaller spatial scales. The extensive within-species
 synchrony and limited concordance suggest that population trajectories of
 these aerial insectivores are responding to large-scale but complex and
 species- and region-specific environmental conditions (e.g. climate, land
 use). A single driver of trends for aerial insectivores as a guild appears
 unlikely.
description: Appendix 4: Dynamic
 factor analysis codeR script containing code
 to run dynamic factor analysis. See the ReadMe file for full
 description.Micheletal_DynamicFactorAnalysisCode.RAppendix 5: Bayesian linear model codeR script containing code to run Bayesian linear model. See the ReadMe file for full description.Micheletal_BayesianLM.RAppendix 6: Cross-correlation analysis codeR script containing code to run cross-correlation analysis (concordance). See the ReadMe file for full description.Micheletal_CrossCorrelations.R
DOI: 10.5061/dryad.1dh4c
title: Data from: Molecular study of the Amazonian Macabea cattle history

description: Macabea cattle are the only Bos taurus breed that have adapted to the wet
 tropical conditions of the Amazon. This breed has integrated into the
 culture of the indigenous Shuar-Asuar nations probably since its origins,
 being one of the few European zoogenetic resources assimilated by the
 deep-jungle Amazon communities. Despite its potential for local endogenous
 sustainable development, this breed is currently endangered. The present
 study used molecular genetics tools to investigate the within- and
 between-breeds diversity, in order to characterize the breed population,
 define its associations with other breeds, and infer its origin and
 evolution. The within-breed genetic diversity showed high values, as
 indicated by all genetic parameters, such as the mean number of alleles
 (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the
 expected heterozygosity (He = 0.72±0.02). The between-breeds diversity
 analysis, which included factorial correspondence analysis, Reynolds
 genetic distance, neighbor-joining analysis, and genetic structure
 analysis, showed that the Macabea breed belongs to the group of the
 American Creoles, with a Southern-Spain origin. Our outcomes demonstrated
 that the Macabea breed has a high level of purity and null influences of
 exotic cosmopolitan breeds with European or Asiatic origin. This breed is
 an important zoogenetic resource of Ecuador, with relevant and unique
 attributes; therefore, there is an urgent need to develop conservation
 strategies for the Macabea breed.
description: AllelefrequenciesAllele frequencies of the breed incluted in the paper. EC: Ecuadorian Creole; HV: Hartón del Valle; FRI: Holstein Friesian; BON: Blanco Orejinegro; MA: Marismeña; BC: Berrenda en Colorado; BWS: Brown Swiss; SIM: Simmental; HER: Herford; CHAR: Charolais; JER: Jersey; RGA: Rubia Gallega; MAC: Macabea; ZE: Zebu; NEL: Nellore; BRH: Brahman; GYR: Gyr
DOI: 10.5061/dryad.b1301
title: Data from: The emergence of performance trade-offs during local adaptation: insights from experimental evolution

description: Environmental heterogeneity is considered a general explanation for
 phenotypic diversification, particularly when heterogeneity causes
 populations to diverge via local adaptation. Performance trade-offs, such
 as those stemming from antagonistic pleiotropy, are thought to contribute
 to the maintenance of diversity in this scenario. Specifically, alleles
 that promote adaptation in one environment are expected to promote
 maladaptation in alternative environments. Contrary to this expectation,
 however, alleles that underlie locally adaptive traits often fail to
 exhibit fitness costs in alternative environments. Here, we attempt to
 explain this paradox by reviewing the results of experimental evolution
 studies, including a new one of our own, that examined the evolution of
 trade-offs during adaptation to homogeneous versus heterogeneous
 environments. We propose that when pleiotropic effects vary, whether or
 not trade-offs emerge among diverging populations will depend critically
 on ecology. For example, adaptation to a locally homogeneous environment
 is more likely to occur by alleles that are antagonistically pleiotropic
 than adaptation to a locally heterogeneous environment, simply because
 selection is blind to costs associated with environments that are not
 experienced locally. Our literature review confirmed the resulting
 prediction that performance trade-offs were more likely to evolve during
 selection in homogeneous than heterogeneous environments. The nature of
 the environmental heterogeneity (spatial versus temporal) and the length
 of the experiment also contributed in predictable ways to the likelihood
 that performance trade-offs evolved.
description: Adsorption
 ratesThese are the adsorption
 rate data of the generalists evolved in a heterogeneous and homogeneous
 environments.adsorption rate
 data.csv
DOI: 10.5061/dryad.253q2
title: Data from: Assessment of the quality of reporting in randomized controlled trials of acupuncture in the Korean literature using the CONSORT statement and the STRICTA guidelines

description: Objectives: This study aimed to assess the completeness of reporting of
 RCTs of acupuncture in the Korean literature. Design: Systematic review.
 Methods: We searched 12 Korean databases and 7 Korean journals to identify
 eligible RCTs of acupuncture published from 1996 to July 2011. We used the
 Consolidated Standards of Reporting Trials (CONSORT) checklist for
 parallel RCTs and the revised STandards for Reporting Interventions in
 Clinical Trials of Acupuncture (STRICTA) to assess the quality of
 reporting in Korean RCTs. We compared the completeness of reporting of
 CONSORT and STRICTA items in RCTs published in two time periods (1996-2004
 referred to as the early period and 2005-2011 referred to as the late
 period). Results: We analysed 146 eligible RCTs using the CONSORT
 statement concerning RCTs of both needling and non-needling acupuncture
 and the STRICTA guidelines for 90 trials of needling acupuncture. Among
 the 103 RCTs in the late period, the proportion of RCTs that completely
 reported the CONSORT items of outcome definition (15.5%), sample size
 calculation (2.9%), randomisation (56%), allocation concealment (5.8%),
 implementation of allocation (11.7%), outcome assessor blinding (20.3%),
 flow of participants (25.2%), number of participants analysed (19.4%),
 ancillary analyses (0.0%), adverse events (24.3%), generalisability of
 findings (1.9%) and overall evidence (32.0%) remained small. Among the 61
 RCTs of needling acupuncture in the late period, the STRICTA items of
 setting/context (24.6%) and practitioner background (27.9%) showed
 incomplete reporting. The completeness of reporting improved over time in
 several CONSORT and STRICTA items. Conclusion: The completeness of
 reporting of Korean RCTs of acupuncture was suboptimal according to the
 CONSORT and revised STRICTA statements. Trial authors and journal editors
 should use the CONSORT statement and the STRICTA guidelines for
 transparent reporting in Korean RCTs of acupuncture. The endorsement of
 the CONSORT and revised STRICTA statements in author instructions is also
 required.
description: Stata raw dataset for
 CONSORT STRICTA analysesSource of information:
 randomised controlled trials published in the Korean literature. Software:
 Stata version 13 SE. Description of variables: labels provided in the
 file. Codes of item assessments: (1: yes or reported) (0: no or not
 reported) (9: not applicable).CONSORT STRICTA for
 dryad.dta
DOI: 10.5061/dryad.nk513
title: Data from: Proxies in practice: calibration and validation of multiple indices of animal abundance

description: The abundance of individuals in a population is a fundamental metric in
 basic and applied ecology, but sampling protocols yielding precise and
 unbiased estimates of abundance are often cost prohibitive. Proxies of
 abundance are therefore common, but require calibration and validation.
 There are many ways to calibrate a proxy, and it is not obvious which will
 perform best. We use data from eight populations of Chinook salmon
 (Oncorhynchus tshawytscha) on the Oregon coast where multiple proxies of
 abundance were obtained contemporaneously with independent mark-recapture
 estimates. We combined multiple proxy values associated with a single
 level of abundance into a univariate index and then calibrated that index
 to mark-recapture estimates using several different techniques. We tested
 our calibration methods using leave-one-out cross validation and
 simulation. Our cross-validation analysis did not definitively identify a
 single best calibration technique for all populations, but we could
 identify consistently inferior approaches. The simulations suggested that
 incorporating the known mark-recapture uncertainty into the calibration
 technique added bias and imprecision. Cross validation techniques should
 be used to test multiple methods of calibrating multiple proxies to an
 estimate of abundance. Critical uncertainties with the application of
 calibrated proxies still exist, and cost-benefit analysis should be
 performed to help identify optimal monitoring designs.
description: Data
 A1.Microsoft Excel workbook
 with data used in the evaluation of methods to combine proxy data across
 multiple survey sites within a single population of Chinook salmon
 (Oncorhynchus tshawytscha) and then calibrate to mark-recapture estimates
 of total population size. Each sheet contains a given population’s
 mark-recapture point estimate and standard error through time. The peak
 count recorded during at various sites (s1, s2, …) within the population
 are also given. Fractional peak counts were imputed from a longer time
 series of counts that extends beyond the years mark-recapture studies were
 performed.Data.xlsx
DOI: 10.15468/dl.zqanyz
title: Occurrence Download

description: A dataset containing 430 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eubotryoides grayana",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 430 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001302-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j5148
title: Data from: Increased nitrogen input enhances Kandelia obovata seedling growth in the presence of invasive Spartina alterniflora in subtropical regions of China

description: Mangroves in China are severely affected by the rapid invasion of the
 non-native species Spartina alterniflora. Although many studies have
 addressed the possible impacts of S. alterniflora on the performance of
 mangrove seedlings, how excessive nitrogen (N) input due to eutrophication
 affects the interactions between mangrove species and S. alterniflora
 remains unknown. Here, we report the results from a mesocosm experiment
 using seedlings of the native mangrove species Kandelia obovata and the
 exotic S. alterniflora grown in monoculture and mixed culture under no
 nitrogen addition and nitrogen (N) addition treatments for 18 months.
 Without N addition, the presence of S. alterniflora inhibited the growth
 of K. obovata seedlings. Excessive N addition significantly increased the
 growth rate of K. obovata in both cultures. However, the positive and
 significantly increasing relative interaction intensity index under
 excessive N input suggested that the invasion of S. alterniflora could
 favour the growth of K. obovata under eutrophication conditions. Our
 results imply that excessive N input in southeastern China can increase
 the competitive ability of mangrove seedlings against invasive S.
 alterniflora.
description: Biomass and height
 dataBiomass
 data.xlsx
DOI: 10.5061/dryad.100
title: Data from: Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

description: We examined three parallel data sets with respect to qualities relevant to
 phylogenetic analysis of 20 exemplar monocotyledons and related
 dicotyledons. The three data sets represent restriction site variation in
 the inverted repeat region of the chloroplast genome, and nucleotide
 sequence variation in the chloroplast-encoded gene rbcL and in the
 mitochondrion-encoded gene atpA, the latter of which encodes the *-subunit
 of mitochondrial ATP synthase. The plant mitochondrial genome has been
 little-used in plant systematics, in part because nucleotide sequence
 evolution in enzyme-encoding genes of this genome evolve relatively
 slowly. The three data sets were examined in separate and combined
 analyses, with a focus on patterns of congruence, homoplasy, and data
 decisiveness. Data decisiveness (described by P. Goloboff) is a measure of
 robustness of support for most-parsimonious trees by a data set in terms
 of the degree to which those trees are shorter than the average length of
 all possible trees. Because indecisive data sets require relatively fewer
 additional steps than decisive ones to be optimized on nonparsimonious
 trees, they will have a lesser tendency to be incongruent with other data
 sets. One consequence of this relationship between decisiveness and
 character incongruence is that if incongruence is used as a criterion of
 noncombinability, decisive data sets, which provide robust support for
 relationships, are more likely to be assessed as noncombinable with other
 data sets than are indecisive data sets, which provide weak support for
 relationships. For the sampling of taxa in this study, the atpA data set
 has about half as many cladistically informative nucleotides as the rbcL
 data set per site examined, and is less homoplastic and more decisive. The
 rbcL data set, which is the least decisive of the three, exhibits the
 lowest levels of character incongruence. Whatever the molecular
 evolutionary cause of this phenomenon, it seems likely that the poorer
 performance of rbcL than atpA, in terms of data decisiveness, is due to
 both its higher overall level of homoplasy and the fact that it is
 performing especially poorly at nonsynonymous sites.
description: Davis et al Data
 Matrixdavisarc.ss
DOI: 10.5061/dryad.39td9
title: Data from: Disentangling population strategies of two cladocerans adapted to different ultraviolet regimes

description: Zooplankton have evolved several mechanisms to deal with environmental
 threats, such as ultraviolet radiation (UVR), and in order to identify
 strategies inherent to organisms exposed to different UVR environments, we
 here examine life-history traits of two lineages of Daphnia pulex. The
 lineages differed in the UVR dose they had received at their place of
 origin from extremely high UVR stress at high-altitude Bolivian lakes to
 low UVR stress near the sea level in temperate Sweden. Nine life-history
 variables of each lineage were analyzed in laboratory experiments in the
 presence and the absence of sub-lethal doses of UVR (UV-A band), and we
 identified trade-offs among variables through structural equation modeling
 (SEM). The UVR treatment was detrimental to almost all life-history
 variables of both lineages; however, the Daphnia historically exposed to
 higher doses of UVR (HighUV) showed a higher overall fecundity than those
 historically exposed to lower doses of UVR (LowUV). The total offspring
 and ephippia production, as well as the number of clutches and number of
 offspring at first reproduction, was directly affected by UVR in both
 lineages. Main differences between lineages involved indirect effects that
 affected offspring production as the age at first reproduction. We here
 show that organisms within the same species have developed different
 strategies as responses to UVR, although no increased physiological
 tolerance or plasticity was shown by the HighUV lineage. In addition to
 known tolerance strategies to UVR, including avoidance, prevention, or
 repairing of damages, we here propose a population strategy that includes
 early reproduction and high fertility, which we show compensated for the
 fitness loss imposed by UVR stress.
description: Life history data of
 Daphnia pulex from an UVR experimentMean values of life
 history variables of two Daphnia pulex lineages, from high and low lands,
 that where exposed to UV radiation in a 2x2 designee.Life_table_D_pulex.xlsx
DOI: 10.5061/dryad.823f0
title: Data from: Are prenatal maternal resources more important in competitive than in benign postnatal environments?

description: According to theoretical models, the optimal solution of the life-history
 trade-off between the number and size of offspring depends on the quality
 of the environment. Offspring size should be more important for their
 fitness in more competitive environments. This idea was rarely
 experimentally tested in taxa with prolonged periods of parental postnatal
 care, such as in birds. Here we manipulated the offspring rearing
 environment by enlarging or reducing brood size. Enlarged broods suffered
 greater mortality rates and raised smaller fledglings. Egg size had a
 significant positive effect on fledging mass and length of tarsus and a
 nonsignificant effect on wing length. These effects were similar in
 enlarged-sized as well as reduced-sized broods. We only found a tendency
 for the predicted interaction between treatment and egg size in the case
 of nestling mass where egg size had a positive effect in enlarged broods
 but none in reduced broods. In contrast, in one year we found an opposite
 interaction where egg size positively affected offspring survival only in
 reduced broods. More studies that manipulate the offspring rearing
 environment and follow offspring over the long term are needed to draw
 general conclusions about context-dependence of early maternal effects.
description: dataset
DOI: 10.5061/dryad.vc60q
title: Data from: Camouflage, detection and identification of moving targets

description: Nearly all research on camouflage has investigated its effectiveness for
 concealing stationary objects. However, animals have to move, and patterns
 that only work when the subject is static will heavily constrain
 behaviour. We investigated the effects of different camouflages on the
 three stages of predation—detection, identification and capture—in a
 computer-based task with humans. An initial experiment tested seven
 camouflage strategies on static stimuli. In line with previous literature,
 background-matching and disruptive patterns were found to be most
 successful. Experiment 2 showed that if stimuli move, an isolated moving
 object on a stationary background cannot avoid detection or capture
 regardless of the type of camouflage. Experiment 3 used an identification
 task and showed that while camouflage is unable to slow detection or
 capture, camouflaged targets are harder to identify than uncamouflaged
 targets when similar background objects are present. The specific details
 of the camouflage patterns have little impact on this effect. If one has
 to move, camouflage cannot impede detection; but if one is surrounded by
 similar targets (e.g. other animals in a herd, or moving background
 distractors), then camouflage can slow identification. Despite previous
 assumptions, motion does not entirely ‘break’ camouflage.
description: Participant median
 response timesData are median response
 times for each participant in 3 visual psychophysics experiments testing 7
 different camouflage strategies and a plain grey control. Exp 1 involved a
 single stationary target in three sizes and Exp 2 involved a single moving
 target in three sizes. The same participants were used in Exp 1 & 2
 and each completed all conditions. Exp 3 involved an elliptical target and
 circular distractors which could be plain or match the target. Each
 participant completed all conditions.Data summary for
 paper.xlsx