cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.38d4j60
title: Data from: Quantifying floristic and structural forest maturity: an attribute-based method for wet eucalypt forests

description: 1. Maintaining developmental heterogeneity of ecological communities
 within landscapes is crucial for sustainable native forest management.
 Consequently, methods to assess forest maturity (i.e. the degree to which
 the forest contains attributes and supports processes characteristic of
 late-successional forests) are valuable for making management decisions.
 However, no consistent, pragmatic method to quantify maturity that
 incorporates multiple ecosystem elements is available for many forest
 systems, including Australian wet eucalypt forests. 2. We draw upon forest
 community dynamics theory to develop a method to quantify maturity based
 on forest attributes, and use this method to create two metrics of wet
 eucalypt forest floristic and structural maturity. We then test the
 ability of remotely-sensed and field-collected variables to predict these
 metrics. 3. Both the floristic and structural maturity metrics performed
 well at capturing underlying trends of forest maturation. Remotely-sensed
 LiDAR (Light Detection and Ranging) and photo-interpretation data provided
 estimates of moderate accuracy for both floristic and structural maturity
 (R2 = 0.57-0.77). Field variables that are relatively efficient and
 accurate to measure provided greater model accuracy (R2 = 0.73-0.85).
 Including more complex field variables increased model accuracy to high
 levels (R2 = 0.93). Therefore, while maturity predicted from
 remote-sensing data enables a useful and accessible large-scale maturity
 measure, field indices would provide a more accurate means of assessing
 maturity at the local stand level. 4. Synthesis and applications: The
 metrics developed in this study provide a powerful tool for undertaking
 consistent assessments of wet eucalypt forest maturity. This assessment
 tool could improve forest management by providing information to optimise
 practices such as prioritising stands for retention or harvesting,
 determining the effectiveness of restoration or management practices, and
 monitoring changes in maturity over time. The method could be adapted to
 any forest system that undergoes well-defined directional development.
description: Field data - Quantifying
 floristic and structural forest maturityThis file contains all
 field data. The first tab describes what is included.Original Data FINAL for
 uploading.xlsx
DOI: 10.5061/dryad.1536g
title: Data from: Do space-for-time assessments underestimate the impacts of logging on tropical biodiversity? An Amazonian case study using dung beetles

description: Human alteration of the global environment is leading to a pervasive loss
 of biodiversity. Most studies evaluating human impacts on biodiversity
 occur after the disturbance has taken place using spatially distinct sites
 to determine the undisturbed reference condition. This approach is known
 as a space-for-time (SFT) substitution. However, SFT substitution could be
 underestimating biodiversity loss if spatial controls fail to provide
 adequate inferences about pre-disturbance conditions. We compare the SFT
 substitution with a before–after control–impact (BACI) approach by
 assessing dung beetles before and after a logging exploration in the
 Brazilian Amazon. We sampled 34 logging management units, of which 29 were
 selectively logged with different intensities after our first collection.
 We used dung beetle species richness, species composition and biomass as
 our biodiversity response metrics and the gradient of selective logging
 intensity as our explanatory metric. Only the BACI approach consistently
 demonstrated the negative impacts of logging intensification on all dung
 beetle community metrics. Moreover, the BACI approach explained
 significantly more of the variance in all the relationships and it doubled
 the estimates of species loss along the gradient of logging intensity when
 compared to SFT. Synthesis and applications. Our results suggest that
 space-for-time (SFT) substitution may greatly underestimate the
 consequences on local species diversity and community turnover. These
 results have important implications for researchers investigating human
 impacts on biodiversity. Incentivizing before–after control–impact (BACI)
 approaches will require longer-term funding to gather the data and
 stronger links between researchers and landowners. However, BACI
 approaches are accompanied by many logistical constraints, making the
 continued use of SFT studies inevitable in many cases. We highlight that
 non-significant results and weak effects should be viewed with caution.
description: França_et_al_SelectiveLogging_BrazilianAmazon_DungBeetle_13032016This dataset results from the PhD research “Ecological Impacts of selective logging in the Amazon: lessons from dung beetles” developed by Filipe França to understand the impacts of selective logging in the Brazilian Amazon on the dung beetle diversity, physiology and associated ecological functions. For dataset descriptions see the file 'README.docx'.
DOI: 10.5061/dryad.c670tq2
title: Data from: On-demand sildenafil as a treatment for Raynaud phenomenon: a series of n-of-1 trials

description: Background: Treatment of Raynaud phenomenon (RP) with phosphodiesterase-5
 inhibitors has shown moderate efficacy. Adverse effects decrease the
 risk–benefit profile of these drugs, and patients may not be willing to
 receive long-term treatment. On-demand single doses before or during
 exposure to cold may be a good alternative. Objective: To assess the
 efficacy and safety of on-demand sildenafil in RP. Design: Series of
 randomized, double-blind, n-of-1 trials. (ClinicalTrials.gov:
 NCT02050360). Setting: Outpatients at a French university hospital.
 Participants: Patients with primary or secondary RP. Intervention: Each
 trial consisted of a multiple crossover study in a single patient. Repeat
 blocks of 3 periods of on-demand treatment were evaluated: 1 week of
 placebo, 1 week of sildenafil at 40 mg per dose, and 1 week of sildenafil
 at 80 mg per dose, with a maximum of 2 doses daily. Measurements: Raynaud
 Condition Score (RCS) and frequency and daily duration of attacks. Skin
 blood flow in response to cooling also was assessed with laser speckle
 contrast imaging. Mixed-effects models were used and parameters were
 estimated in a Bayesian framework to determine individual and aggregated
 efficacy. Results: 38 patients completed 2 to 5 treatment blocks. On the
 basis of aggregated data, the probability that sildenafil at 40 mg or 80
 mg was more effective than placebo was greater than 90% for all outcomes
 (except for RCS with sildenafil, 80 mg). However, the aggregated effect
 size was not clinically relevant. Yet, substantial heterogeneity in
 sildenafil's efficacy was observed among participants, with
 clinically relevant efficacy in some patients. Limitation: The response to
 sildenafil was substantially heterogeneous among patients. Conclusion:
 Despite a high probability that sildenafil is superior to placebo,
 substantial heterogeneity was observed in patient response and aggregated
 results did not show that on-demand sildenafil has clinically relevant
 efficacy. In this context, the use of n-of-1 trials may be an original and
 relevant approach in RP.
description: PROFIL_DATAThe data in plain text format with variables names as header 2306 observations on 50 variablesmodel_1Final modelmodel_3Final model with informative priors for the effect of sildenafilmodel_4Final model with interaction between treatment and primary or secondary RP
DOI: 10.5061/dryad.k6j12
title: Data from: Confirmation of independent introductions of an exotic plant pathogen of Cornus species, Discula destructiva, on the east and west coasts of North America

description: Cornus florida (flowering dogwood) and C. nuttallii (Pacific dogwood) are
 North American native tree species that belong to the big-bracted group of
 dogwoods. Cornus species are highly valued for their ornamental
 characteristics, and have fruits that contain high fat content for
 animals. Also, they are an important understory tree in natural forests.
 Dogwood anthracnose, caused by Discula destructiva, was observed in the
 late 1970s on the east and west coasts of the United States and by 1991
 had quickly spread throughout most of the native ranges of C. florida and
 C. nuttalli. We investigated the genetic diversity and population
 structure of 93 D. destructiva isolates using 47 microsatellite loci
 developed from the sequenced genome of the type strain of D. destructiva.
 Clone-corrected data indicated low genetic diversity and the presence of
 four genetic clusters that corresponded to two major geographic areas, the
 eastern United States and the Pacific Northwest, and to the two collection
 time periods when the isolates were collected (pre- and post-1993).
 Linkage disequilibrium was present in five out of six subpopulations,
 suggesting that the fungus only reproduced asexually. Evidence of
 population bottlenecks was indicated across four identified genetic
 clusters, and was probably the result of the limited number of founding
 individuals on both coasts. These results support the hypothesis that D.
 destructiva is an exotic pathogen with independent introductions on the
 east and west coasts of North America. We also tested the
 cross-amplification of these microsatellite primers to other Discula
 species. Genomic DNA from 17 isolates of four other Discula species and
 two isolates of Juglanconis species (formerly Melanconis species) were
 amplified by 17 of 47 primer pairs. These primers may be useful for
 investigating the genetic diversity and population structure of these
 Discula species.
description: ALL microsatellite data
 for the manuscriptMicrosatellite data in
 base pairs in an Excel fileDATA PONE D 17 13946
 TRIGIANO.xlsxSupplemental Tables 1
 and 2S1 Table Pairwise
 Population Differences for D. DestructivaSupplemental Fig.
 1Linkage Disequilibrium
 Tests for D. destructivaSupplemental Fig
 2Delta K analysis for D.
 destructiva populationSupplemental Fig
 3Dendrogram of Discula
 destructiva isolates
DOI: 10.5061/dryad.6v79q
title: Data from: Direct and indirect genetic effects of sex-specific mitonuclear epistasis on reproductive ageing

description: Mitochondria are involved in ageing and their function requires
 coordinated action of both mitochondrial and nuclear genes. Epistasis
 between the two genomes can influence lifespan but whether this also holds
 for reproductive senescence is unclear. Maternal inheritance of
 mitochondria predicts sex differences in the efficacy of selection on
 mitonuclear genotypes that should result in differences between females
 and males in mitochondrial genetic effects. Mitonuclear genotype of a
 focal individual may also indirectly affect trait expression in the mating
 partner. We tested these predictions in the seed beetle Callosobruchus
 maculatus, using introgression lines harbouring distinct mitonuclear
 genotypes. Our results reveal both direct and indirect sex-specific
 effects of mitonuclear epistasis on reproductive ageing. Females
 harbouring coadapted mitonuclear genotypes showed higher lifetime
 fecundity due to slower senescence relative to novel mitonuclear
 combinations. We found no evidence for mitonuclear coadaptation in males.
 Mitonuclear epistasis not only affected age-specific ejaculate weight, but
 also influenced male age-dependent indirect effects on traits expressed by
 their female partners (fecundity, egg size, longevity). These results
 demonstrate important consequences of sex-specific mitonuclear epistasis
 for both mating partners, consistent with a role for mitonuclear genetic
 constraints upon sex-specific adaptive evolution.
description: Mitonuclear line female
 reproductive traitsThis file contains data
 on mitonuclear line female fecundity, fertility and
 weight.MitoReprodSenesc_FemaleData_Dryad.txtMitonuclear line female lifespanThis file contains data on mitonuclear line female lifespan and lifetime fecundity.MitoReprodSenesc_FemaleLifespanData_Dryad.txtMitonuclear line male dataThis file has data on male ejaculate weight and lifespan, and reference female lifespan, fecundity, fertility and offspring hatching successMitoReprodSenesc_MaleData_Dryad.txtMitonuclear line ref female egg sizeThis file has data on mitonuclear line male mates' egg size.MitoReprodSenesc_MaleEggSize_Dryad.txt
DOI: 10.5061/dryad.50r80407
title: Data from: Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K–T boundary in Madagascar

description: The geographic and temporal origins of Madagascar's biota have long
 been in the center of debate. We reconstructed a time-tree including
 nearly all native nonflying and nonmarine vertebrate clades present on the
 island, from DNA sequences of two single-copy protein-coding nuclear genes
 (BDNF and RAG1) and a set of congruent time constraints. Reconstructions
 calculated with autocorrelated or independent substitution rates over
 clades agreed in placing the origins of the 31 included clades in
 Cretaceous to Cenozoic times. The two clades with sister groups in South
 America were the oldest, followed by those of a putative Asian ancestry
 that were significantly older than the prevalent clades of African
 ancestry. No colonizations from Asia occurred after the Eocene, suggesting
 that dispersal and vicariance of Asian/Indian groups were favored over a
 comparatively short period during, and shortly after, the separation of
 India and Madagascar. Species richness of clades correlates with their age
 but those clades that have a large proportion of species diversity in
 rainforests are significantly more species-rich. This finding suggests an
 underlying pattern of continuous speciation through time in
 Madagascar's vertebrates, with accelerated episodes of adaptive
 diversification in those clades that succeeded radiating into the
 rainforests.
description: RAG1
 AlignmentAlignment of DNA
 sequences of a fragment of the Regulation-activating gene I
 (RAG1).Rag11.fasBDNF AlignmentAlignment of a fragment of the Brain-drerived neurotrophic factor gene (BDNF)BDNF1.fas
DOI: 10.5061/dryad.98j4qv2
title: Data from: Environmental stress increases the magnitude of nonadditive genetic variation in offspring fitness in the frog Crinia georgiana

description: When organisms encounter heterogeneous environments, selection may favor
 the ability of individuals to tailor their phenotypes to suit the
 prevailing conditions. Understanding the genetic basis of plastic
 responses is therefore vital for predicting whether susceptible
 populations can adapt and persist under new selection pressures. Here, we
 investigated whether there is potential for adaptive plasticity in
 development time in the quacking frog Crinia georgiana, a species
 experiencing a drying climate. Using a North Carolina II breeding design,
 we exposed 90 family groups to two water depth treatments (baseline and
 low-water) late in larval development. We estimated the contribution of
 additive and non-additive sources of genetic variation to early offspring
 fitness under both environments. Our results revealed a marked decline in
 larval fitness under the stressful (low-water) rearing environment, but
 also that additive genetic variation was negligible for all traits.
 However, in most cases we found significant sire-by-dam interactions,
 indicating the importance of non-additive genetic variation for offspring
 fitness. Moreover, sire-by-dam interactions were modified by the
 treatment, indicating that patterns of non-additive genetic variance
 depend on environmental context. For all traits, we found higher levels of
 non-additive genetic variation (relative to total phenotypic variation)
 when larvae were reared under stressful conditions, suggesting that the
 fitness costs associated with incompatible parental crosses (e.g.
 homozygous deleterious recessive alleles) will only be expressed when
 water availability is low. Taken together, our results highlight the need
 to consider patterns of non-additive genetic variation under contrasting
 selective regimes when considering the resilience of species to
 environmental change.
description: Six data files
 containing Crinia georgiana embryonic, tadpole and metamorph traits from
 sire-by-dam 90 familiesData files contain
 Crinia georgiana traits (survival, development rate, tadpole and metamorph
 morphology and metamorph jumping performance) for 90 sire-by-dam families.
 Fixed effects were water depth treatment, ovum size and corticosterone
 concentrations in the yolk. Random effects were sire, dam, block (and all
 interactions). Please see Materials and Methods for detailed
 description.6 data
 files.zip
DOI: 10.5061/dryad.d1k17
title: Data from: Human cytomegalovirus epidemiology and relationship to tuberculosis and cardiovascular disease risk factors in a rural Ugandan cohort

description: Human cytomegalovirus (HCMV) infection has been associated with increased
 mortality, specifically cardiovascular disease (CVD), in high-income
 countries (HICs). There is a paucity of data in low- and middle-income
 countries (LMICs) where HCMV seropositivity is higher. Serum samples from
 2,174 Ugandan individuals were investigated for HCMV antibodies and data
 linked to demographic information, co-infections and a variety of CVD
 measurements. HCMV seropositivity was 83% by one year of age, increasing
 to 95% by five years. Female sex, HIV positivity and active pulmonary
 tuberculosis (TB) were associated with an increase in HCMV IgG levels in
 adjusted analyses. There was no evidence of any associations with risk
 factors for CVD after adjusting for age and sex. HCMV infection is
 ubiquitous in this rural Ugandan cohort from a young age. The association
 between TB disease and high HCMV IgG levels merits further research. Known
 CVD risk factors do not appear to be associated with higher HCMV antibody
 levels in this Ugandan cohort.
description: RAW_DATAData from: Human cytomegalovirus epidemiology and relationship to tuberculosis and cardiovascular disease risk factors in a rural Ugandan cohort
DOI: 10.5061/dryad.25kd9
title: Data from: Effects of climatic and geological processes during the Pleistocene on the evolutionary history of the northern cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae)

description: Climatic and geological processes associated with glaciation cycles during
 the Pleistocene have been implicated in influencing patterns of genetic
 variation and promoting speciation of temperate flora and fauna. However,
 determining the factors promoting divergence and speciation is often
 difficult in many groups because of our limited understanding of potential
 vicariant barriers and connectivity between populations. Pleistocene
 glacial cycles are thought to have significantly influenced the
 distribution and diversity of subterranean invertebrates; however, impacts
 on subterranean aquatic vertebrates are less clear. We employed several
 hypothesis-driven approaches to assess the impacts of Pleistocene climatic
 and geological changes on the Northern Cavefish, Amblyopsis spelaea, whose
 current distribution occurs near the southern extent of glacial advances
 in North America. Our results show that the modern Ohio River has been a
 significant barrier to dispersal and is correlated with patterns of
 genetic divergence. We infer that populations were isolated in two refugia
 located north and south of the Ohio River during the most recent two
 glacial cycles with evidence of demographic expansion in the northern
 isolate. Finally, we conclude that climatic and geological processes have
 resulted in the formation of cryptic forms and advocate recognition of two
 distinct phylogenetic lineages currently recognized as Amblyopsis spelaea.
description: Amblyopsis-Final-ND2mitochondrial ND2, Nexus formatAmblyopsis-Final-S7nuclear S7 intron, Nexus formatAmblyopsis-Final-RAG1nuclear RAG1 gene, coding region, Nexus formatAmblyopsis-Final-RHOnuclear RHO (rhodopsin), coding region, Nexus formatAmblyopsis-Final-TBRnuclear TBR gene, coding region, Nexus format
DOI: 10.5061/dryad.rg832
title: Data from: Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago

description: Loss of coral reef resilience can lead to dramatic changes in benthic
 structure, often called regime shifts, which significantly alter ecosystem
 processes and functioning. In the face of global change and increasing
 direct human impacts, there is an urgent need to anticipate and prevent
 undesirable regime shifts and, conversely, to reverse shifts in already
 degraded reef systems. Such challenges require a better understanding of
 the human and natural drivers that support or undermine different reef
 regimes. The Hawaiian archipelago extends across a wide gradient of
 natural and anthropogenic conditions and provides us a unique opportunity
 to investigate the relationships between multiple reef regimes, their
 dynamics and potential drivers. We applied a combination of exploratory
 ordination methods and inferential statistics to one of the most
 comprehensive coral reef datasets available in order to detect, visualize
 and define potential multiple ecosystem regimes. This study demonstrates
 the existence of three distinct reef regimes dominated by hard corals,
 turf algae or macroalgae. Results from boosted regression trees show
 nonlinear patterns among predictors that help to explain the occurrence of
 these regimes, and highlight herbivore biomass as the key driver in
 addition to effluent, latitude and depth.
description: Benthic, fish,
 geospatial and environmental dataJouffray et
 al.-DATA.xlsx