cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d5k7p
title: Data from: Is environmental legislation conserving tropical stream faunas? a large-scale assessment of local, riparian and catchment-scale influences on Amazonian stream fish

description: 1.Agricultural expansion and intensification are major threats to tropical
 biodiversity. In addition to the direct removal of native vegetation,
 agricultural expansion often elicits other human-induced disturbances,
 many of which are poorly addressed by existing environmental legislation
 and conservation programmes. This is particularly true for tropical
 freshwater systems, where there is considerable uncertainty about whether
 a legislative focus on protecting riparian vegetation is sufficient to
 conserve stream fauna. 2.To assess the extent to which stream fish are
 being effectively conserved in agricultural landscapes, we examined the
 spatial distribution of assemblages in river basins to identify the
 relative importance of human impacts at instream, riparian, and catchment
 scales, in shaping observed patterns. We used an extensive dataset on the
 ecological condition of 83 low-order streams distributed in three river
 basins in the eastern Brazilian Amazon. 3.We collected and identified
 24,420 individual fish from 134 species. Multiplicative diversity
 partitioning revealed high levels of compositional dissimilarity (DS)
 among stream sites (DS = 0.74 to 0.83) and river basins (DS = 0.82), due
 mainly to turnover (77.8 to 81.8%) rather than nestedness. The highly
 heterogeneous fish faunas in small Amazonian streams underscore the vital
 importance of enacting measures to protect forests on private lands
 outside of public protected areas. 4.Instream habitat features explained
 more variability in fish assemblages (15-19%) than riparian (2-12%),
 catchment (4-13%) or natural covariates (4-11%). Although grouping species
 into functional guilds allowed us to explain up to 31% of their abundance
 (i.e. for nektonic herbivores), individual riparian- and catchment-scale
 predictor variables that are commonly a focus of environmental legislation
 explained very little of the observed variation (partial R2 values mostly
 &lt; 5%). 5.Policy implications. Current rates of agricultural
 intensification and mechanisation in tropical landscapes are
 unprecedented, yet the existing legislative frameworks focusing on
 protecting riparian vegetation seem insufficient to conserve stream
 environments and their fish assemblages. To safeguard the species-rich
 freshwater biota of small Amazonian streams, conservation actions must
 shift towards managing whole basins and drainage networks, as well as
 agricultural practices in already-cleared land.
description: Fish species and
 functional guild composition, and environmental predictor variables from
 Amazonian streamsThis is the complete
 dataset used in the manuscript. It includes fish species composition per
 stream site, functional guild composition per stream site and
 environmental predictor variables per stream site. For dataset
 descriptions see the file 'README.docx'.Leal_et_al_Conservation_Amazon_streamFish.xlsx
DOI: 10.5061/dryad.pg8gf
title: Data from: Chromosome inversions and ecological plasticity in the main African malaria mosquitoes

description: Chromosome inversions have fascinated the scientific community, mainly
 because of their role in the rapid adaption of different taxa to changing
 environments. However, the ecological traits linked to chromosome
 inversions have been poorly studied. Here, we investigated the roles
 played by 23 chromosome inversions in the adaptation of the four major
 African malaria mosquitoes to local environments in Africa. We studied
 their distribution patterns by using spatially explicit modeling and
 characterized the ecogeographical determinants of each inversion range. We
 then performed hierarchical clustering and constrained ordination analyses
 to assess the spatial and ecological similarities among inversions. Our
 results show that most inversions are environmentally structured,
 suggesting that they are actively involved in processes of local
 adaptation. Some inversions exhibited similar geographical patterns and
 ecological requirements among the four mosquito species, providing
 evidence for parallel evolution. Conversely, common inversion
 polymorphisms between sibling species displayed divergent ecological
 patterns, suggesting that they might have a different adaptive role in
 each species. These results are in agreement with the finding that
 chromosomal inversions play a role in Anopheles ecotypic adaptation. This
 study establishes a strong ecological basis for future genome-based
 analyses to elucidate the genetic mechanisms of local adaptation in these
 four mosquitoes.
description: TableS1Chromosomal inversion data from An. gambiaeTableS2Chromosomal inversion data from An. coluzziiTableS3Chromosomal inversion data from An. arabiensisTableS4Chromosomal inversion data from An. funestus
DOI: 10.5061/dryad.dj342
title: Data from: An adaptive radiation of frogs in a Southeast Asian island archipelago

description: Living amphibians exhibit a diversity of ecologies, life histories, and
 species-rich lineages that offers opportunities for studies of adaptive
 radiation. We characterize a diverse clade of frogs (Kaloula,
 Microhylidae) in the Philippine island archipelago as an example of an
 adaptive radiation into three primary habitat specialists or ecotypes. We
 use a novel phylogenetic estimate for this clade to evaluate the tempo of
 lineage accumulation and morphological diversification. Because
 species-level phylogenetic estimates for Philippine Kaloula are lacking,
 we employ dense population sampling to determine the appropriate
 evolutionary lineages for diversification analyses. We explicitly take
 phylogenetic uncertainty into account when calculating diversification and
 disparification statistics and fitting models of diversification.
 Following dispersal to the Philippines from Southeast Asia, Kaloula
 radiated rapidly into several well-supported clades. Morphological
 variation within Kaloula is partly explained by ecotype and accumulated at
 high levels during this radiation, including within ecotypes. We pinpoint
 an axis of morphospace related directly to climbing and digging behaviors
 and find patterns of phenotypic evolution suggestive of ecological
 opportunity with partitioning into distinct habitat specialists. We
 conclude by discussing the components of phenotypic diversity that are
 likely important in amphibian adaptive radiations.
description: Multiple
 AlignmentNexus file containing
 multiple alignment of mitochondrial DNA sequences used in phylogenetic
 analyses.Blackburn_et_al_Kaloula_mtDNA.nexMeasurement dataMeasurements (in millimeters) of specimens used in morphometric analyses.Kaloula_measurements.xls
DOI: 10.5061/dryad.1584
title: Data from: The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population

description: Loci with higher levels of population differentiation than the neutral
 expectation are traditionally interpreted as evidence of ongoing selection
 that varies in space. This article emphasizes an alternative explanation
 which has been largely overlooked to date: in species subdivided into
 large subpopulations, enhanced differentiation can also be the signature
 left by the fixation of an unconditionally favourable mutation on its
 chromosomal neighbourhood. To discriminate among the two alternative
 scenarios one needs to investigate how genetic structure varies along the
 chromosomal region of the locus. Local hitchhiking is shown to generate a
 single sharp peak of differentiation centred on the adaptive polymorphism
 and the standard signature of a selective sweep only in those
 subpopulations where the allele is favoured. Global hitchhiking produces
 two domes of differentiation on either side of the fixed advantageous
 mutation and signatures of a selective sweep in every subpopulation,
 albeit of different magnitude. Investigating population differentiation
 around a locus that strongly differentiates two otherwise genetically
 similar populations of the marine mussel Mytilus edulis, plausible
 evidence for the global hitchhiking hypothesis has been obtained. Global
 hitchhiking is a neglected phenomenon that might prove to be important in
 species with large population sizes such as many marine invertebrates.
description: 10-0237-Sequences.fas10-0237-Simulators.zip
DOI: 10.15468/dl.w4ew4p
title: Occurrence Download

description: A dataset containing 7020 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (December, November, October, September, August, July, June, May, April, March, February, January)",
 "OccurrenceStatus is Present",
 "TaxonKey is Lasiurus borealis"
 ]
}

 The dataset includes 7020 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000564-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qv4kq75
title: Data from: Longitudinal analysis of impulse control disorders in Parkinson’s disease

description: Objective: To investigate the longitudinal dose-effect relationship
 between dopamine replacement therapy and impulse control disorders (ICDs)
 in Parkinson’s disease (PD). Methods: We used data from a multicentre
 longitudinal cohort of consecutive PD patients with ≤5y disease duration
 at baseline followed annually up to 5y. ICDs were evaluated during
 face-to-face semi-structured interviews with movement disorder
 specialists. Generalized estimating equations Poisson models with robust
 variance were used to study the association between several time-dependent
 definitions of dopamine agonist (DA) use, taking dose and duration of
 treatment into account, and ICDs at each visit; other antiparkinsonian
 drugs were also examined. Results: Among 411 patients (40.6% women; mean
 age=62.3y, average follow-up=3.3y, SD=1.7y), 356 (86.6%) took DA at least
 once since disease onset. In 306 patients without ICDs at baseline, the 5y
 cumulative incidence of ICDs was 46.1% (95% CI=37.4-55.7; DA
 ever-users=51.5% [41.8-62.1]; DA never-users=12.4% [4.8-30.0]). ICDs
 prevalence increased from 19.7% at baseline to 32.8% after 5y. ICDs were
 associated with ever DA use (prevalence ratio, PR=4.23 [1.78, 10.09]).
 Lifetime average daily dose and duration of treatment were independently
 associated with ICDs, with significant dose-effect relations. Similar
 analyses for levodopa were not in favour of a strong association. ICDs
 progressively resolved after DA discontinuation. Conclusions: In this
 longitudinal study of PD patients characterized by a high prevalence of DA
 treatment, the 5y cumulative incidence of ICDs was ~46%. ICDs were
 strongly associated with DA use, with a dose-effect relationship; both
 increasing duration and dose were associated with ICDs. ICDs progressively
 resolved after DA discontinuation.
description: Supplementary
 material• e-Methods • Table e-1.
 Association of levodopa use with ICDs. • Table e-2. Association of other
 types of antiparkinsonian drugs with ICDs. • Table e-3. Association
 between alternative definitions of dopamine agonist use (described in
 Figure e1) and ICDs. • Table e-4. Association of dopamine agonist use with
 ICDs; ICDs also include hobbyism and hypercreativity • Figure e-1.
 Alternative definitions of dopamine agonist useCorvol_Supp_material_revision_final.pdf
DOI: 10.5061/dryad.t7n48
title: Data from: Clinical and laboratory predictors of influenza infection among individuals with influenza-like illness presenting to an urban Thai hospital over a five-year period

description: Early diagnosis of influenza infection maximizes the effectiveness of
 antiviral medicines. Here, we assess the ability for clinical
 characteristics and rapid influenza tests to predict PCR-confirmed
 influenza infection in a sentinel, cross-sectional study for
 influenza-like illness (ILI) in Thailand. Participants meeting criteria
 for acute ILI (fever &gt; 38°C and cough or sore throat) were
 recruited from inpatient and outpatient departments in Bangkok, Thailand,
 from 2009-2014. The primary endpoint for the study was the occurrence of
 virologically-confirmed influenza infection (based upon detection of viral
 RNA by RT-PCR) among individuals presenting for care with ILI. Nasal and
 throat swabs were tested by rapid influenza test (QuickVue) and by RT-PCR.
 Vaccine effectiveness (VE) was calculated using the case test-negative
 method. Classification and Regression Tree (CART) analysis was used to
 predict influenza RT-PCR positivity based upon symptoms reported. We
 enrolled 4572 individuals with ILI; 32.7% had detectable influenza RNA by
 RT-PCR. Influenza cases were attributable to influenza B (38.6%),
 A(H1N1)pdm09 (35.1%), and A(H3N2) (26.3%) viruses. VE was highest against
 influenza A(H1N1)pdm09 virus and among adults. The most important symptoms
 for predicting influenza PCR-positivity among patients with ILI were
 cough, runny nose, chills, and body aches. The accuracy of the CART
 predictive model was 72.8%, with an NPV of 78.1% and a PPV of 59.7%.
 During epidemic periods, PPV improved to 68.5%. The PPV of the QuickVue
 assay relative to RT-PCR was 93.0% overall, with peak performance during
 epidemic periods and in the absence of oseltamivir treatment. Clinical
 criteria demonstrated poor predictive capability outside of epidemic
 periods while rapid tests were reasonably accurate and may provide an
 acceptable alternative to RT-PCR testing in resource-limited areas.
description: PMK_Influenza_2009_2014Deidentified data for individuals presenting with influenza-like illness to PMK hospital (inpatient and outpatient) from 2009-2014Deidentified_data_for_PLOS_2009_2014.csv
DOI: 10.5061/dryad.9r6b3
title: Data from: Mechanisms and fitness consequences of laying decisions in a migratory raptor

description: Seasonal decline in breeding performance is a commonly observed pattern in
 birds, but disentangling the contributions of environmental conditions
 (“timing” hypothesis) and individual quality (“quality” hypothesis) to
 such a pattern is challenging. Moreover, despite the strong selection for
 early breeding, the individual optimization model predicts that each
 individual has an optimal breeding window. We investigated the causes and
 consequences of laying decisions in the lesser kestrel (Falco naumanni) by
 combining a long-term dataset on reproductive traits with information on
 food availability. A marked seasonal decline was found in breeding
 success, mostly mediated by a decline in clutch size. The “timing”
 hypothesis, supported by the decline in consumption of mole crickets, key
 prey for prelaying females, seems to explain the seasonal trend in clutch
 size, as this pattern was recorded in both higher (adults) and lower
 (yearlings) quality individuals. Contrarily, the higher proportion of
 yearlings breeding late in the season, rather than a decay in food
 availability during chick rearing, seems to drive the decline in fledging
 success, giving support to the “quality” hypothesis. Advanced breeding and
 increased clutch size, as proxies of reproductive effort, were not offset
 by lower survival. Low repeatability in both these traits suggests that
 individual quality is a dynamic attribute and reproduction costs are
 minimized by individual optimization. Understanding the mechanisms driving
 individual breeding decisions is critical to anticipate species’ ability
 to cope with environmental changes. Here, we show that lesser kestrels
 failing the prelaying food window opportunity compromise reproductive
 performance, mostly regardless of their individual quality.
description: LesserKestrel_breeding_parameters_whole_datasetBreeding parameters of Lesser Kestrel (Falco naumanni) in Castro Verde, Portugal, between 2003-2014.LessserKestrel_breeding_parameters_ringed_birds_datasetBreeding parameters, age and recapture data of Lesser Kestrels (Falco naumanni) ringed between 2003 and 2014 at Castro Verde, PortugalLesserKestrel_chick_dataBiometries (mass and wing lenght) and posterior recruitment in the population of Lesser Kestrel (Falco naumanni) chicks ringed as fledglings between 2003 and 2014 in Castro Verde Portugal. Information on brood (clutch size, laying date) of each chick is also provided.LesserKestrel_female_mass_wingWeight and wing length of female Lesser Kestrels (Falco naumanni) captured during the incubation period between 2003 and 2014 in Castro Verde, Portugal.grasshoppers_transects_abundanceMean number of grasshoppers counted in walked transects in fallow grassland patches around Lesser Kestrel (Falco naumanni) colonies between 2012 and 2015.grasshopper_molecricket_pelletsMean number of grasshoppers (Acrididae and Tetigonidae) and mole crickets (Gryllotalpidae) found in Lesser Kestrel (Falco naumanni) pellets collected in several colonies between 2007-2008 and 2012-2014.
DOI: 10.5061/dryad.b973n
title: Data from: A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna

description: Aim: The phylogeographical history of wide-ranging Palaearctic species is
 not well understood. Here, we present a range-wide phylogeographical study
 of the wasp spider, Argiope bruennichi (Scopoli, 1772), a highly
 dispersive and widely distributed Palaearctic species. We aim to identify
 glacial refugia and patterns of interglacial gene flow across the
 Palaearctic. Location: Palaearctic region, including the Azores, Madeira,
 Europe, North Africa and Asia. Methods: We conduct a range-wide
 phylogeographical survey. Our study is based on nuclear and mitochondrial
 DNA markers, as well as morphological characters. We use species
 distribution models to predict the species’ current range as well as its
 historical distribution during and shortly after the Last Glacial Maximum
 (LGM). Results: All analysed genetic markers and morphological characters
 support the divergence of a lineage in eastern Asia from the remainder of
 the Palaearctic. Within the Western Palaearctic, a less pronounced
 divergence into an Azorean and a European clade is found. Species
 distribution models predict a pronounced loss of suitable habitat for
 Western Palaearctic lineages during the LGM, whereas the range of East
 Asian populations remained largely unaffected. Main conclusions: Our
 results highlight the existence of non-European glacial refugia for
 Palaearctic species, particularly in East Asia. The current genetic
 structure is best explained by the recent recolonization of the Western
 Palaearctic from eastern Asia, or repeated interglacial contact of
 populations.
description: Sample list for all
 included populationsSample
 list.xlsMicrosatellite
 dataMicrosatellite_Data.txtAnonymous nuclear sequence alignment SA11SA11_nuclear.fasAnonymous nuclear sequence alignment SA24SA24_nuclear.fasAlignment of Macaronesian COI sequencesCOI_Aignment_Azores_Madeira.fasPrimer sequencesPrimer_Sequences.xlsx
DOI: 10.5061/dryad.bg43c
title: Data from: The effect of immigration on the adaptation of microbial communities to warming

description: Theory predicts that immigration can either enhance or impair the rate at
 which species and whole communities adapt to environmental change,
 depending on the traits of genotypes and species in the source pool
 relative to local conditions. These responses in turn will determine how
 well whole communities function in changing environments. We tested the
 effects of immigration and experimental warming on microbial communities
 during an 81 day field experiment. The effects of immigration depended on
 the warming treatment. In warmed communities immigration was detrimental
 to community growth whereas in ambient communities it was beneficial. This
 result is explained if colonists came from a local species pool
 pre-adapted to ambient conditions. Loss of metabolic diversity, however,
 was buffered by immigration in both environments. Communities showed
 increasing local adaptation to temperature conditions during the
 experiment and this was independent of whether or not they received
 immigration. Genotypes that comprised the communities were not locally
 adapted, however, indicating that community local adaptation can be
 independent of adaptation of component genotypes. Our results are
 consistent with a greater role for species interactions rather than
 adaptation of constituent species in determining local adaptation of whole
 communities, and confirm that immigration can either enhance or impair
 community responses to environmental change depending on the environmental
 context.
description: community growth and
 diversity during evolution experimentMicrobial community
 growth rates (total change in OD600 over 24 to 96 hours) measured in
 triplicate at two assay temperatures every 9 days for 81 days. Shannon
 diversity and community evenness are both calculated for experimental
 blocks 1, 3 and 5 from samples taken on days 27, 54 and 81. Time is
 reported in hours. Temperature reported in degrees
 Celsius.biolog metabolism data
 during evolution experimentCommunity carbohydrate
 use during experimental evolution. Carbohydrate use (with threshold of
 OD600 &gt; 0.2) for starting community and across sampling days 27, 54 and
 81 and change in carbohydrate use. Column, biologcarb, refers to the
 carbohydrate at that well position on biolog GN2
 microplate.Isolate and community
 local adaptationIsolate and community
 local adaptation at day 81 of experimental evolution.isolate and community local
 adaptation.csv