cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vr315
title: Data from: Religion does matter for climate change attitudes and behavior

description: Little research has focused on the relationship between religion and
 climate change attitudes and behavior. Further, while there have been some
 studies examining the relationship between environmental attitudes and
 religion, most are focused on Christian denominations and secularism, and
 few have examined other religions such as Buddhism. Using an online survey
 of 1,927 Australians we examined links between membership of four
 religious groupings (Buddhists, Christian literalists and non-literalists,
 and Secularists) and climate change attitudes and behaviors. Differences
 were found across religious groups in terms of their belief in: (a) human
 induced climate change, (b) the level of consensus among scientists, (c)
 their own efficacy, and (d) the need for policy responses. We show, using
 ordinal regression, that religion explains these differences even after
 taking into account socio-demographic factors, knowledge and environmental
 attitude, including belief in man’s dominion over nature. Differences in
 attitude and behavior between these religious groups suggest the
 importance of engaging denominations to encourage change in attitudes and
 behavior among their members.
description: Australia's
 attitudes towards climate change _PLOSONE data 100715Data collected during
 December 2011 by the Online Research Unit. Data analysed using
 SPSS.Australia's attitudes
 towards climate change _PLOSONE data
 160915(2).sav
DOI: 10.5061/dryad.d8f84
title: Data from: Genome-wide differential expression of synaptic long non-coding RNAs in autism spectrum disorder

description: A genome-wide differential expression of long noncoding RNAs (lncRNAs) was
 identified in blood specimens of autism spectrum disorder (ASD). A total
 of 3929 lncRNAs were found to be differentially expressed in ASD
 peripheral leukocytes, including 2407 that were upregulated and 1522 that
 were downregulated. Simultaneously, 2591 messenger RNAs (mRNAs), including
 1789 upregulated and 821 downregulated, were also identified in ASD
 leukocytes. Functional pathway analysis of these lncRNAs revealed
 neurological pathways of the synaptic vesicle cycling, long-term
 depression and long-term potentiation to be primarily involved. Thirteen
 synaptic lncRNAs, including nine upregulated and four downregulated, and
 19 synaptic mRNAs, including 12 upregulated and seven downregulated, were
 identified as being differentially expressed in ASD. Our identification of
 differential expression of synaptic lncRNAs and mRNAs suggested that
 synaptic vesicle transportation and cycling are important for the delivery
 of synaptosomal protein(s) between presynaptic and postsynaptic membranes
 in ASD. Finding of 19 lncRNAs, which are the antisense, bi-directional and
 intergenic, of HOX genes may lead us to investigate the role of HOX genes
 involved in the development of ASD. Discovery of the lncRNAs of SHANK2-AS
 and BDNF-AS, the natural antisense of genes SHANK2 and BDNF, respectively,
 indicates that in addition to gene mutations, deregulation of lncRNAs on
 ASD-causing gene loci presents a new approach for exploring possible
 epigenetic mechanisms underlying ASD. Our study also opened a new avenue
 for exploring the use of lncRNA(s) as biomarker(s) for the early detection
 of ASD.
description: ASD-lncRNAExpression profile of lncRNAs in ASD peripheral bloods
DOI: 10.5061/dryad.241m4
title: Data from: Sperm whales reduce foraging effort during exposure to 1-2 kHz sonar and killer whale sounds

description: The time and energetic costs of behavioral responses to incidental and
 experimental sonar exposures, as well as control stimuli, were quantified
 using hidden state analysis of time series of acoustic and movement data
 recorded by tags (DTAG) attached to 12 sperm whales (Physeter
 macrocephalus) using suction cups. Behavioral state transition modeling
 showed that tagged whales switched to a non-foraging, non-resting state
 during both experimental transmissions of low-frequency active sonar from
 an approaching vessel (LFAS; 1–2 kHz, source level 214 dB re 1 μPa m, four
 tag records) and playbacks of potential predator (killer whale, Orcinus
 orca) sounds broadcast at naturally occurring sound levels as a positive
 control from a drifting boat (five tag records). Time spent in foraging
 states and the probability of prey capture attempts were reduced during
 these two types of exposures with little change in overall locomotion
 activity, suggesting an effect on energy intake with no immediate
 compensation. Whales switched to the active non-foraging state over
 received sound pressure levels of 131–165 dB re 1 μPa during LFAS
 exposure. In contrast, no changes in foraging behavior were detected in
 response to experimental negative controls (no-sonar ship approach or
 noise control playback) or to experimental medium-frequency active sonar
 exposures (MFAS; 6–7 kHz, source level 199 re 1 μPa m, received sound
 pressure level [SPL] = 73–158 dB re 1 μPa). Similarly, there was no
 reduction in foraging effort for three whales exposed to incidental,
 unidentified 4.7–5.1 kHz sonar signals received at lower levels (SPL =
 89–133 dB re 1 μPa). These results demonstrate that similar to predation
 risk, exposure to sonar can affect functional behaviors, and indicate that
 increased perception of risk with higher source level or lower frequency
 may modulate how sperm whales respond to anthropogenic sound.
description: Time series of behavior
 states during baseline and controlled exposure experiments from 12 DTAG
 recordsData set used to model
 effects of sonar and killer whale sound playbacks on sperm whale
 state-switching, probability of buzzing and locomotion effort in 1-min
 time steps. Each row represents 1-min time steps. Columns give the
 identifier for each tagged whale (tagid), seconds since tag-on (sfromtot),
 depth at the start of the 1-min bin (depth), estimated behavior state
 (state; 1-surface, 2-descent, 3-layer restricted search, 4-ascent,
 5-drifting, 6-active non-foraging), probability of the state (state_prob),
 presence/absence of terminal echolocation buzz (buzz), locomotion effort
 measured by overall dynamic body acceleration (ODBA), and experimental
 phase (experiment). The remaining columns show candidate exposure
 covariates, as described in Table 2 of the manuscript.spermwhale_sonar_state_series.csv
DOI: 10.5061/dryad.qj177
title: Data from: Biodiversity assessment among two Nebraska prairies: a comparison between traditional and phylogenetic diversity indices

description: Background: Conservation of the evolutionary diversity among organisms
 should be included in the selection of priority regions for preservation
 of Earth’s biodiversity. Traditionally, biodiversity has been determined
 from an assessment of species richness (S), abundance, evenness, rarity,
 etc. of organisms but not from variation in species’ evolutionary
 histories. Phylogenetic diversity (PD) measures evolutionary differences
 between taxa in a community and is gaining acceptance as a biodiversity
 assessment tool. However, with the increase in the number of ways to
 calculate PD, end-users and decision-makers are left wondering how metrics
 compare and what data are needed to calculate various metrics. New
 information: In this study, we used massively parallel sequencing to
 generate over 65,000 DNA characters from three cellular compartments for
 over 60 species in the asterid clade of flowering plants. We estimated
 asterid phylogenies from character datasets of varying nucleotide
 quantities, and then assessed the effect of varying character datasets on
 resulting PD metric values. We also compared multiple PD metrics with
 traditional diversity indices (including S) among two endangered grassland
 prairies in Nebraska (U.S.A.). Our results revealed that PD metrics varied
 based on the quantity of genes used to infer the phylogenies; therefore,
 when comparing PD metrics between sites, it is vital to use comparable
 datasets. Additionally, various PD metrics and traditional diversity
 indices characterize biodiversity differently and should be chosen
 depending on the research question. Our study provides empirical results
 that reveal the value of measuring PD when considering sites for
 conservation, and it highlights the usefulness of using PD metrics in
 combination with other diversity indices when studying community assembly
 and ecosystem functioning. Ours is just one example of the types of
 investigations that need to be conducted across the tree of life and
 across varying ecosystems in order to build a database of phylogenetic
 diversity assessments that lead to a pool of results upon which a guide
 through the plethora of PD metrics may be prepared for use by ecologists
 and conservation planners.
description: asterids-cpmtnucSequence alignment of 76 plastid genes, six mitochondrial genes, and three nuclear repeat regions for 62 asterid taxa plus 3 outgroupsasterids-matKSequence alignment of the plastid matK gene for 62 asterid taxa plus 3 outgroupsasterids-rbcLSequence alignment of the plastid rbcL gene for 62 asterid taxa plus 3 outgroupsasterids-rbcLmatKSequence alignment of concatenated plastid rbcL and matK genes for 62 asterid taxa plus 3 outgroups
DOI: 10.5061/dryad.9j7j0
title: Data from: The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putative new ring species complex

description: The Indo-Malayan bioregion has provided some of the most spectacular
 discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced
 bulbul) over the last 25 years. Yet, very little is known about the
 processes that led to the current biodiversity in this region. We
 reconstructed the phylogeographic history of a group of closely related
 passerines, the Alophoixus bulbuls. These birds are continuously
 distributed in Indo-Malaya around the Thailand lowlands such that their
 distribution resembles a ring. Our analyses revealed a single colonization
 event of the mainland from Sundaland with sequential divergence of taxa
 from southwest to northeast characterized by significant gene flow between
 parapatric taxa, and reduced or ancient gene flow involving the two taxa
 at the extremities of the ring. We detected evidence of population
 expansion in two subspecies, including one that was involved in the
 closing of the ring. Hence, our analyses indicate that the diversification
 pattern of Alophoixus bulbuls fits a ring species model driven by
 geographic isolation. To our knowledge, the Alophoixus bulbuls represent
 the first case of a putative broken ring species complex in Indo-Malaya.
 We also discuss the implications of our results on our understanding of
 the biogeography in Indo-Malaya.
description: Input files for the
 different analysesThe compressed folder
 includes the input files used for the following analyses: a) gene trees,
 b) species tree, c) Structure, d) Isolation with migration model analyses,
 e) the phased sequence data for all loci and f) a spreadsheet to make the
 link between the acronyms used in the analyses input files and the Tissue
 number/localities/subspeciesDryad
 submission.zip
DOI: 10.5061/dryad.rq122
title: Data from: Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish

description: How population size influences quantitative genetic variation and
 differentiation among natural, fragmented populations remains unresolved.
 Small, isolated populations might occupy poor quality habitats and lose
 genetic variation more rapidly due to genetic drift than large
 populations. Genetic drift might furthermore overcome selection as
 population size decreases. Collectively, this might result in directional
 changes in additive genetic variation (VA) and trait differentiation (QST)
 from small to large population size. Alternatively, small populations
 might exhibit larger variation in VA and QST if habitat fragmentation
 increases variability in habitat types. We explored these alternatives by
 investigating VA and QST using nine fragmented populations of brook trout
 varying 50-fold in census size N (179-8416) and 10-fold in effective
 number of breeders, Nb (18-135). Across 15 traits, no evidence was found
 for consistent differences in VA and QST with population size and almost
 no evidence for increased variability of VA or QST estimates at small
 population size. This suggests that (i) small populations of some species
 may retain adaptive potential according to commonly adopted quantitative
 genetic measures and (ii) populations of varying sizes experience a
 variety of environmental conditions in nature, however extremely large
 studies are likely required before any firm conclusions can be made.
description: Trait measurements and
 pedigrees for Cape Race brook trout populationsIndividual trait
 measurements and pedigrees used in animal models to estimate quantitative
 genetic parameters for fifteen traits for nine brook trout populations
 from Cape Race, Newfoundland, Canada.CR_traits_pedigrees.xlsxCape Race breeding design summaryA table summarizing, per population, the number of females and males used to generate families as well as the range and mean number of crosses per male for the common garden experiment used to estimate quantitative genetic parameters for Cape Race brook trout populations.CR.breeding.design.summary.xlsxQuantitative genetic parameter values and QST values for Cape Race brook trout populationsQuantitative genetic parameter values (QGV) and QST values for fifteen traits for nine brook trout populations estimated from animal models and used to generate figures and in statistical analyses.CR.QGV.QST.xlsxR code for animal models and statistical analysesExamples of R code specifying animal models to estimate quantitative genetic parameters and QST using the software package "MCMCglmm", as well as code for generating the posterior distribution of Pearson's correlation coefficient and for simple and partial Mantel tests (software package "vegan").CR_R_code.txt
DOI: 10.5061/dryad.v32h4
title: Data from: Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals

description: The evolutionary success of reef-building corals is often attributed to
 their symbiotic relationship with photosynthetic dinoflagellates of the
 genus Symbiodinium, but metabolic interactions between the partners and
 the molecular bases of light-enhanced calcification (LEC) are not well
 understood. Here, the metabolic bases of the interaction between the coral
 Acropora millepora and its dinoflagellate symbiont were investigated by
 comparing gene expression levels under light and dark conditions at the
 whole transcriptome level. Among the 497 differentially expressed genes
 identified, a suite of genes involved in cholesterol transport was found
 to be upregulated under light conditions, confirming the significance of
 this compound in the coral symbiosis. Although ion transporters likely to
 have roles in calcification were not differentially expressed in this
 study, expression levels of many genes associated with skeletal organic
 matrix composition and organization were higher in light conditions. This
 implies that the rate of organic matrix synthesis is one factor limiting
 calcification at night. Thus, LEC during the day is likely to be a
 consequence of increases in both matrix synthesis and the supply of
 precursor molecules as a result of photosynthetic activity.
description: GSE70488Branch tips from three adult colonies of Acropora millepora were sampled at midday and midnight. cDNA libraries were sequences with the Illumina Hiseq 2000 technic. Reads were mapped onto A. millepora's transcriptome (Bioproject PRJNA74409) with the BWA alignment tool. The count table obtained was used to assess differential expression of transcripts with EdgeR and sSeq packages. GSE70488 contains RNAseq raw files (DAY1-3 and NIGHT1-3), the count table and the differential expression results from EdgeR and sSeq.Day and Night Combined CountsCombined count data from the mapped reads for each sample. BWA parameters were -n 0.05 and -k 5Combined_Counts.txtDay_Vs_Night_EdgeRDifferential expression results obtained with EdgeRDay_vs_Night_sSeqDifferential expression results obtained with sSeq.Millepora annotation fileAcropora millepora GO annotation filesupp_file_S9.xlsx
DOI: 10.5061/dryad.ng8p1
title: Data from: Are there age-related differences in the ability to learn configural responses?

description: Age is often associated with a decline in cognitive abilities that are
 important for maintaining functional independence, such as learning new
 skills. Many forms of motor learning appear to be relatively well
 preserved with age, while learning tasks that involve associative binding
 tend to be negatively affected. The current study aimed to determine
 whether age differences exist on a configural response learning task,
 which includes aspects of motor learning and associative binding. Young (M
 = 24 years) and older adults (M = 66.5 years) completed a modified version
 of a configural learning task. Given the requirement of associative
 binding in the configural relationships between responses, we predicted
 older adults would show significantly less learning than young adults.
 Older adults demonstrated lower performance (slower reaction time and
 lower accuracy). However, contrary to our prediction, older adults showed
 similar rates of learning as indexed by a configural learning score
 compared to young adults. These results suggest that the ability to
 acquire knowledge incidentally about configural response relationships is
 largely unaffected by cognitive aging. The configural response learning
 task provides insight into the task demands that constrain learning
 abilities in older adults.
description: Worksheet with
 demographics and performance dataWorksheets contain (1)
 demographics, (2) summary of demographics, (3) musical experience
 questionnaire data, (4) mapping phase data from eprime, (5) configural
 learning task data from eprime. All formulas are retained in the merged
 files with eprime output, to see how we derived basic performance data
 such as RT and accuracy.ConfiguralLearningData.xlsx
DOI: 10.7284/164372
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AR84-01 using a SeaBird SBE-911+ instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/163391
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AR84-05 using a SeaBird SBE-911+ instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.bf771
title: Data from: A spatial theory for characterizing predator–multiprey interactions in heterogeneous landscapes

description: Trophic interactions in multiprey systems can be largely determined by
 prey distributions. Yet, classic predator–prey models assume spatially
 homogeneous interactions between predators and prey. We developed a
 spatially informed theory that predicts how habitat heterogeneity alters
 the landscape-scale distribution of mortality risk of prey from predation,
 and hence the nature of predator interactions in multiprey systems. The
 theoretical model is a spatially explicit, multiprey functional response
 in which species-specific advection–diffusion models account for the
 response of individual prey to habitat edges. The model demonstrates that
 distinct responses of alternative prey species can alter the consequences
 of conspecific aggregation, from increasing safety to increasing predation
 risk. Observations of threatened boreal caribou, moose and grey wolf
 interacting over 378 181 km2 of human-managed boreal forest support this
 principle. This empirically supported theory demonstrates how distinct
 responses of apparent competitors to landscape heterogeneity, including to
 human disturbances, can reverse density dependence in fitness correlates.
description: Wolf
 dataData used to carry out
 habitat selection analysis of molvesWolf.xlsxMoose dataData used to carry out habitat selection analysis of mooseMoose.xlsxmortality_CaribouData used to analyse the probability of mortality of 145 radio-collar caribou as a function of their distance from the nearest road of cut.
DOI: 10.7284/164177
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AR86-02 using a SeaBird SBE-911+ instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/164170
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AR86-03 using a SeaBird SBE-911+ instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.20r6d
title: Data from: Context matters: sexual signaling loss in digital organisms

description: Sexual signals are important in attracting and choosing mates; however,
 these signals and their associated preferences are often costly and
 frequently lost. Despite the prevalence of signaling system loss in many
 taxa, the factors leading to signal loss remain poorly understood. Here,
 we test the hypothesis that complexity in signal loss scenarios is due to
 the context-dependent nature of the many factors affecting signal loss
 itself. Using the Avida digital life platform, we evolved 50 replicates of
 ~250 lineages, each with a unique combination of parameters, including
 whether signaling is obligate or facultative; genetic linkage between
 signaling and receiving genes; population size; and strength of preference
 for signals. Each of these factors ostensibly plays a crucial role in
 signal loss, but was found to do so only under specific conditions. Under
 obligate signaling, genetic linkage, but not population size, influenced
 signal loss; under facultative signaling, genetic linkage does not have
 significant influence. Somewhat surprisingly, only a total loss of
 preference in the obligate signaling populations led to total signal loss,
 indicating that even a modest amount of preference is enough to maintain
 signaling systems. Strength of preference proved to be the strongest
 single force preventing signal loss, as it consistently overcame the
 potential effects of drift within our study. Our findings suggest that
 signaling loss is often dependent on not just preference for signals,
 population size, and genetic linkage, but also whether signals are
 required to initiate mating. These data provide an understanding of the
 factors (and their interactions) that may facilitate the maintenance of
 sexual signals.
description: sigloss_dataThis file contains all of the raw data from the avida experiments.
DOI: 10.7284/164203
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AR86-04 using a SeaBird SBE-911+ instrument system onboard the platform RV Neil Armstrong

description: Original (unprocessed) data collected during a Field_expedition