cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cv86385c
title: Data from: Advanced technologies and data management practices in environmental science: lessons from academia

description: Environmental scientists stand uniquely poised to capitalize on recent
 advancements in technology, computation, and data management, however, it
 is unknown the degree to which this is occurring. We analyzed survey
 responses of 445 graduate students in California to evaluate understanding
 and use of such advances in the environmental sciences. Of students who
 had completed their degree, 64.3% had completed the data life cycle, 30.5%
 had archived research data so that it is available online, and 61.4% had
 no plans to create metadata for research data sets. Roughly one-third of
 students used an environmental sensor and collaborated with someone
 outside their expertise. Results varied by students’ research status and
 by university type. Doing excellent science in this data-intensive age may
 necessitate greater emphasis by university programs on data management
 best practices borrowed from information technology, and skills
 supplemented by unique training opportunities, courses, counsel from
 technological specialists, and unconventional collaborations.
description: eEcology_Survey_questionsThis file contains the survey questions used in our study. This is a documentation file associated with our data files, it is not a data file itself.UC_survey_data_raw_finalPrivateInst_survey_data_raw_finalCSU_survey_data_raw_finaleEcology_data_readme
DOI: 10.5061/dryad.rj74424
title: Data from: Cognitive function after spinal cord injury: a systematic review

description: Objective: To systematically examine the incidence of cognitive impairment
 in individuals with spinal cord injury (SCI), as well as identify
 potential contributing and confounding factors. Methods: Studies
 quantitatively reporting cognitive ability after spinal cord injury were
 searched electronically via Medline, CINAHL, Embase, and PsycINFO. Manual
 screening for references within articles was also performed. A total of
 2,481 studies were screened and a total of 70 were included in this
 review, 21 reporting cognitive function after SCI compared to an
 able-bodied control group and 49 with no able-bodied controls. Studies
 were analyzed for the incidence of impairment and the interactions with
 concomitant traumatic brain injury, psychological or somatic complaints,
 decentralized cardiovascular control, sleep apnea, neurologic level of
 injury, and age. Results: There is a high volume of evidence reporting
 substantial cognitive impairment in individuals with SCI. Potential
 co-contributors include concomitant brain injury, psychological or somatic
 comorbidities, decentralized cardiovascular control, and sleep apnea.
 Cognitive functioning was negatively correlated with age. No clear
 agreement was found for the incidence of cognitive impairment or its
 association with level of injury. Conclusion: Current evidence suggests
 that individuals with SCI should be examined and addressed for cognitive
 impairment. Future studies aimed at identifying potential secondary
 causative factors should employ stringent controls for co-occurring brain
 trauma since it appears to be a major contributor and confounder to
 impaired cognition.
description: Supplementary figure e-1
 pptLiterature search
 flowchart and study selection criteriaTable e-1- Example of a
 search strategyExample of a keyword
 literature search conducted in MEDLINETable e-2- Studies
 comparing SCI subjects to able-bodied controlsList of studies
 comparing cognitive function between individuals with spinal cord injury
 and able-bodied controls.Table e-3- studies
 reporting cognitive ability after SCI with no able-bodied
 controlsList of studies
 reporting cognitive function after spinal cord injury without able-bodied
 controls.Supplementary references
 61-123_Sachdeva et al
DOI: 10.5061/dryad.5hn8n
title: Data from: Arthropod distribution in a tropical rainforest: tackling a four dimensional puzzle

description: Quantifying the spatio-temporal distribution of arthropods in tropical
 rainforests represents a first step towards scrutinizing the global
 distribution of biodiversity on Earth. To date most studies have focused
 on narrow taxonomic groups or lack a design that allows partitioning of
 the components of diversity. Here, we consider an exceptionally large
 dataset (113,952 individuals representing 5,858 species), obtained from
 the San Lorenzo forest in Panama, where the phylogenetic breadth of
 arthropod taxa was surveyed using 14 protocols targeting the soil, litter,
 understory, lower and upper canopy habitats, replicated across seasons in
 2003 and 2004. This dataset is used to explore the relative influence of
 horizontal, vertical and seasonal drivers of arthropod distribution in
 this forest. We considered arthropod abundance, observed and estimated
 species richness, additive decomposition of species richness,
 multiplicative partitioning of species diversity, variation in species
 composition, species turnover and guild structure as components of
 diversity. At the scale of our study (2km of distance, 40m in height and
 400 days), the effects related to the vertical and seasonal dimensions
 were most important. Most adult arthropods were collected from the
 soil/litter or the upper canopy and species richness was highest in the
 canopy. We compared the distribution of arthropods and trees within our
 study system. Effects related to the seasonal dimension were stronger for
 arthropods than for trees. We conclude that: (1) models of beta diversity
 developed for tropical trees are unlikely to be applicable to tropical
 arthropods; (2) it is imperative that estimates of global biodiversity
 derived from mass collecting of arthropods in tropical rainforests embrace
 the strong vertical and seasonal partitioning observed here; and (3) given
 the high species turnover observed between seasons, global climate change
 may have severe consequences for rainforest arthropods.
description: Abundance data of San
 Lorenzo arthropods in PanamaDryad2015.txt
DOI: 10.5061/dryad.tj693
title: Data from: Mating opportunities and energetic constraints drive variation in age-dependent sexual signalling

description: When males repeatedly produce energetically expensive sexual signals,
 trade-offs between current and future investment can cause plasticity in
 age-dependent signalling. Such variation is often interpreted as alternate
 adaptive strategies: live fast and die young vs. slow and steady. An
 alternative (yet rarely tested) explanation is that condition-dependent
 constraints on allocation cause variation in signalling with age (‘late
 bloomers’ do not have early investment options). Testing this hypothesis
 is challenging because resource acquisition and allocation are difficult
 to measure, and energetic reserves both affect and are affected by
 reproductive effort. We simultaneously manipulated acquisition (through
 dietary nutrition) and access to potential mates (as a proxy for
 manipulating sexual trait allocation) in male decorated crickets
 (Gryllodes sigillatus), while measuring age- and signalling
 effort-mediated changes in energy storage components. Increased diet
 quality caused increased signalling effort and energy storage, while
 access to females increased both the likelihood of and time spent
 signalling. Males with lower resource budgets signalled less, but still
 suffered energetic storage loss and viability costs. Our results suggest
 that energetic constraints, rather than strategic resource accumulation,
 reduced signalling levels in males with lower resource acquisition
 ability. Our findings imply a non-adaptive explanation for age-dependent
 variation in sexual signalling, and an important role for energetic
 constraints in maintaining the honesty of costly behavioural displays.
description: Individual calling
 dataCalling effort data:
 each row represents an observation for one night's calling (in
 seconds) for an individual male. Variables include individual ID, Group
 (males were sacrificed at different timepoints), Diet_cen (diet treatment,
 centred with single-unit deviations), Mating_num (female-access treatment,
 not centred, single-unit deviations), callDay (days post-eclosion for the
 recording), sumSecs (number of seconds the male spent calling), Lifespan,
 F_presence (whether a female was present or not), F_history (how many
 previous night's a male had had access to
 females).df_call.csvIndividual life history dataData on individual morphology, energy storage, lifespan, treatment groups, etc. Also includes flags for energy storage where the measurements were outside the normal range. Scaled mass index (SMI) is given for eclosion (0), and end of weeks 1 and 2 post-eclosion.df_morph.csv
DOI: 10.5061/dryad.88m82
title: Data from: Incorporating an ontogenetic perspective into evolutionary theory of sexual size dimorphism

description: Sexual size dimorphism (SSD) describes divergent body sizes of adult males
 and females. While SSD has traditionally been explained by sexual and
 fecundity selection, recent advances in physiology and developmental
 biology emphasize that SSD would occur proximately because of sexual
 differences in ontogenetic growth trajectories (i.e., growth rate and
 duration). Notably, these ontogenetic traits are subject to energetic or
 time constraints and thus traded off with fitness components (e.g.,
 survival and reproduction). To elucidate the importance of such
 ontogenetic trade-offs in the evolution of SSD, we developed a new
 theoretical framework by extending quantitative genetic models for the
 evolution of sexual dimorphism in which we reinterpret the trait as body
 size and reformulate sex-specific fitness in size-dependent manners. More
 specifically, we assume that higher growth rate or longer growth duration
 leads to larger body size and higher reproductive success but incurs the
 cost of lower survivorship or shorter reproduction period. We illustrate
 how two sexes would optimize ontogenetic growth trajectories in
 sex-specific ways and exhibit divergent body sizes. The present framework
 provides new insights into the evolutionary theory of SSD and predictions
 for empirical testing.
description: Supplementary
 information F3Parameter effects on
 male and female body sizes and SSD level (male-to-female body sizes) at
 the equilibrium in the case that growth rate evolves (Scenario
 1).figure
 3.nbSupplementary
 information F4Parameter effects on
 male and female body sizes and SSD level (male-to-female body sizes) at
 the equilibrium in the case that growth duration evolves (Scenario
 2).figure
 4.nbSupplementary
 information F5Literature data on the
 SSD level in relation to the sexual differences in life history
 parameters.figure
 5.nbcode_figure
 5.txt
DOI: 10.5061/dryad.96c20
title: Data from: A survey of palaeontological sampling biases in fishes based on the phanerozoic record of Great Britain

description: Fishes represent more than half of all living vertebrate species, but
 patterns of fish diversity remain little explored in the fossil record. A
 compendium of fossil occurrences from Great Britain was assembled in order
 to address a series of questions concerning the palaeontological record of
 fishes. There are broad similarities between British richness trajectories
 and those compiled from global data, including an initial peak in the
 mid-Palaeozoic (Devonian or Carboniferous, depending on the compilation),
 with a late Palaeozoic trough followed by a sharp rise in diversity in the
 Late Cretaceous and Paleogene. The British dataset is too small to reveal
 any significant differences in richness between time bins using
 subsampling, but a modeling approach based on sampling and geological
 proxies consistently shows lower-than-predicted richness in the
 Silurian-Devonian and higher-than-predicted richness in the Late
 Cretaceous and Eocene. This positive excursion is robust to the exclusion
 of data from the early Eocene London Clay Lagerstätte. Chondrichthyans
 (sharks, rays, and ratfishes) and osteichthyans (ray-finned and
 lobe-finned fishes) show contrasting relationships with geological and
 sampling proxies, possibly reflecting different taphonomic profiles or
 idiosyncratic variation in the relative proportion of freshwater and
 marine deposits over the British Phanerozoic.
description: R code and
 dataAll R code and data
 required to replicate the analyses presented in the
 paperDryad_data.xlsx
DOI: 10.5061/dryad.6nd4k
title: Data from: Quercus suber dieback alters soil respiration and nutrient availability in Mediterranean forests

description: An increase in tree mortality rates has been recently detected in forests
 world-wide. However, few works have focused on the potential consequences
 of forest dieback for ecosystem functioning. Here we assessed the effect
 of Quercus suber dieback on carbon, nitrogen and phosphorus cycles in two
 types of Mediterranean forests (woodlands and closed forests) affected by
 the aggressive pathogen Phytophthora cinnamomi. We used a spatially
 explicit neighbourhood approach to analyse the direct effects of Q. suber
 dieback on soil variables, comparing the impact of Q. suber trees with
 different health status, as well as its potential long-term indirect
 effects, comparing the impact of non-declining coexistent species. Quercus
 suber dieback translated into lower soil respiration rates and phosphorus
 availability, whereas its effects on nitrogen varied depending on forest
 type. Coexistent species differed strongly from Q. suber in their effects
 on nutrient availability, but not on soil respiration rates. Our models
 showed low interannual but high intra-annual variation in the ecosystem
 impacts of tree dieback. Synthesis. Our results support that tree dieback
 might have important short- and long-term impacts on ecosystem processes
 in Mediterranean forests. With this work, we provide valuable insights to
 fill the existent gap in knowledge on the ecosystem-level impacts of
 forest dieback in general and P. cinnamomi-driven mortality in particular.
 Because the activity and range of this pathogen is predicted to increase
 due to climate warming, these impacts could also increase in the near
 future altering ecosystem functioning world-wide.
description: Raw data for neighbor
 trees and soil variablesThere are two
 spreadsheets with data. The spreadsheet "soil dataset" contains
 the raw soil data. The spreadsheet "tree dataset" contains the
 information about neighbour trees (species, position, size and defoliation
 index). After each data spreadsheet there is a spreadshet with the
 associated metadata, where a description of all the variables and units
 can be found.dataset_cicles.xls
DOI: 10.5061/dryad.g3b5272
title: Data from: Metformin reverses early cortical network dysfunction and behavior changes in Huntington’s disease

description: Catching primal functional changes in early, “very far from disease onset”
 (VFDO) stages of Huntington’s disease is likely to be the key to a
 successful therapy. Focusing on VFDO stages, we assessed neuronal
 microcircuits in premanifest Hdh150 knock-in mice. Employing in vivo
 two-photon Ca2+ imaging, we revealed an early pattern of circuit
 dysregulation in the visual cortex- one of the first regions affected in
 premanifest Huntington’s disease - characterized by an increase in
 activity, an enhanced synchronicity and hyperactive neurons. These
 findings are accompanied by aberrations in animal behavior. We furthermore
 show that the anti-diabetic drug metformin diminishes aberrant Huntingtin
 protein load and fully restores both, early network activity patterns and
 behavioral aberrations. This network-centered approach reveals a critical
 window of vulnerability far before clinical manifestation and establishes
 metformin as a promising candidate for a chronic therapy starting early in
 premanifest Huntington’s disease pathogenesis long before the onset of
 clinical symptoms.
description: Figure
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 5Figure 1-fig suppl
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 -fig supplement 1
DOI: 10.5061/dryad.95tv3
title: Data from: Mimetic divergence and the speciation continuum in the mimic poison frog Ranitomeya imitator

description: While divergent ecological adaptation can drive speciation, understanding
 the factors that facilitate or constrain this process remains a major goal
 in speciation research. Here, we study two mimetic transition zones in the
 poison frog Ranitomeya imitator, a species that has undergone a Müllerian
 mimetic radiation to establish four morphs in Peru. We find that mimetic
 morphs are strongly phenotypically differentiated, producing geographic
 clines with varying widths. However, distinct morphs show little neutral
 genetic divergence, and landscape genetic analyses implicate
 isolation-by-distance as the primary determinant of among-population
 genetic differentiation. Mate choice experiments suggest random mating at
 the transition zones, although certain allopatric populations show a
 preference for their own morph. We present evidence that this preference
 may be mediated by color-pattern specifically. These results contrast with
 an earlier study of a third transition zone, in which a mimetic shift was
 associated with reproductive isolation. Overall, our results suggest that
 the three known mimetic transition zones in R. imitator reflect a
 speciation continuum, which we have characterized at the geographic,
 phenotypic, behavioral, and genetic level. We discuss possible
 explanations for variable progress toward speciation, suggesting that
 multifarious selection on both mimetic color-pattern and body size may be
 responsible for generating reproductive isolation.
description: DIYABC_infileABC_infile.mssDIYABC - All scenariosall scenarios.txtDIYABC - Six best scenariosfinal 6 scenarios.txtColor-pattern data: Banded-striped transectbanded-striped color-pattern data.xlsxColor-pattern data: Spotted-striped transectstriped-spotted combined dataset FINAL 2014.xlsxclineSolverMale mass (g) datamale mass.xlsxMate choice data: Banded/striped, free-release trialsbanded-striped mate choice data.xlsxMate choice data: Spotted/striped, free-release trialsspotted-striped mate choice data.xlsxMate choice data: Banded/striped, plastic model experimentplastic model mate choice data.xlsxMicrosatellite data: Banded-striped transectbanded-striped microsatellite dataset.xlsxMicrosatellite data: Spotted-striped transectspotted-striped microsatellite dataset.xlsx
DOI: 10.5061/dryad.kb27f3t1
title: Data from: There is more than one way to skin a G matrix

description: Because of its importance in directing evolutionary trajectories there has
 been considerable interest in comparing variation among genetic
 variance-covariance ( G) matrices. Numerous statistical approaches have
 been suggested but no general analysis of the relationship among these
 methods has previously been published. In this paper we used data from a
 half-sib experiment and simulations to explore the results of applying
 eight tests (T method, modified Mantel test, Bartlett’s test, Flury
 hierarchy, Jackknife-MANOVA, Jackknife-eigenvalue test, random skewers,
 selection skewers). Whereas a randomization approach produced acceptable
 estimates those from a bootstrap were typically unacceptable and we
 recommend randomization as the preferred method. All methods except the
 Jackknife-eigenvalue test gave similar results although a fine scale
 analysis suggested that the former group can be subdivided into two or
 possibly three groups, hierarchical tests, skewers, and the rest
 (Jackknife-MANOVA, Modified Mantel, T method, probably Bartlett’s). An
 advantage of the jackknife methods is that they permit tests of
 association with other factors, such as in this case, temperature and sex.
 We recommend applying all the tests described in this paper, with the
 exception of the T method, and provide R functions for this purpose.
description: MATRIX_ANALYSESContains the R codes, a readme file and sample data
DOI: 10.5061/dryad.fb006
title: Data from: Nutrient presses and pulses differentially impact plants, herbivores, detritivores and their natural enemies

description: Anthropogenic nutrient inputs into native ecosystems cause fluctuations in
 resources that normally limit plant growth, which has important
 consequences for associated food webs. Such inputs from agricultural and
 urban habitats into nearby natural systems are increasing globally and can
 be highly variable, spanning the range from sporadic to continuous.
 Despite the global increase in anthropogenically-derived nutrient inputs
 into native ecosystems, the consequences of variation in subsidy duration
 on native plants and their associated food webs are poorly known.
 Specifically, while some studies have examined the effects of nutrient
 subsidies on native ecosystems for a single year (a nutrient pulse),
 repeated introductions of nutrients across multiple years (a nutrient
 press) better reflect the persistent nature of anthropogenic nutrient
 enrichment. We therefore contrasted the effects of a one-year nutrient
 pulse with a four-year nutrient press on arthropod consumers in two salt
 marshes. Salt marshes represent an ideal system to address the
 differential impacts of nutrient pulses and presses on ecosystem and
 community dynamics because human development and other anthropogenic
 activities lead to recurrent introductions of nutrients into these natural
 systems. We found that plant biomass and %N as well as arthropod density
 fell after the nutrient pulse ended but remained elevated throughout the
 nutrient press. Notably, higher trophic levels responded more strongly
 than lower trophic levels to fertilization, and the predator/prey ratio
 increased each year of the nutrient press, demonstrating that food web
 responses to anthropogenic nutrient enrichment can take years to fully
 manifest themselves. Vegetation at the two marshes also exhibited an
 apparent tradeoff between increasing %N and biomass in response to
 fertilization. Our research emphasizes the need for long-term, spatially
 diverse studies of nutrient enrichment in order to understand how
 variation in the duration of anthropogenic nutrient subsidies affects
 native ecosystems.
description: Murphy et al
 data