cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3j7f6
title: Data from: Species co-occurrence networks show reptile community reorganization under agricultural transformation

description: Agricultural transformation represents one of the greatest threats to
 biodiversity, causing degradation and loss of habitat, leading to changes
 in the richness and composition of communities. These changes in richness
 and composition may, in turn, lead to altered species co-occurrence, but
 our knowledge of this remains limited. We used a novel co-occurrence
 network approach to examine the impact of agricultural transformation on
 reptile community structure within two large (&gt; 172 000 km2; 224
 sites) agricultural regions in southeastern Australia. We contrasted
 assemblages from sites surrounded by intact and modified landscapes and
 tested four key hypotheses that agricultural transformation leads to (H1)
 declines in species richness, (H2) altered assemblages, (H3) declines in
 overall co-occurrence, and (H4) complex restructuring of pairwise
 associations. We found that modified landscapes differed in composition
 but not richness compared with intact sites. Modified landscapes were also
 characterized by differences in co-occurrence network structure; with
 species sharing fewer sites with each other (reduced co-occurrence
 connectance), fewer highly-connected species (truncation of the frequency
 distribution of co-occurrence degree) and increased modularity of
 co-occurrence networks. Critically, overall loss of co-occurrence was
 underpinned by complex changes to the number and distribution of pair-wise
 co-occurrence links, with 41–44% of species also gaining associations with
 other species. Change in co-occurrence was not correlated with changes in
 occupancy, nor by functional trait membership, allowing a novel
 classification of species susceptibility to agricultural transformation.
 Our study reveals the value of using co-occurrence analysis to uncover
 impacts of agricultural transformation that may be masked in conventional
 studies of species richness and community composition.
description: Species table used in
 the calculation of co-occurrence networksThis is a site by
 species occurence table used for all analyses within the manuscript. The
 data contains information regarding species detections (presence/absence)
 by sites (with each row identifying each of the 5 distinct survey events
 for each site [data was aggregated by site for richness and compositional
 analyses]). Data on the level of agricultulral transformation
 (%_surrouding_naiveness) and the region (Western and Tablelands) are
 provided both as continuous and factor values.Dryad_data.csv
DOI: 10.5061/dryad.9rh6v
title: Data from: Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia.

description: Southeastern Asia is a recognised hotspot for emerging infectious
 diseases, many of which have an animal origin. Mammarenavirus infections
 contribute significantly to the human disease burden in both Africa and
 the Americas, but little data exists for Asia. To date only two
 mammarenaviruses, the widely spread lymphocytic choriomeningitis virus and
 the recently described Wēnzhōu virus have been identified in this region,
 but the zoonotic impact in Asia remains unknown. Here we report the
 presence of a novel mammarenavirus and of a genetic variant of the Wēnzhōu
 virus and provide evidence of mammarenavirus-associated human infection in
 Asia. The association of these viruses with widely distributed mammals of
 diverse species, commonly found in human dwellings and in peridomestic
 habitats, illustrates the potential for widespread zoonotic transmission
 and adds to the known aetiologies of infectious diseases for this region.
description: IgG
 Dengue-Influenza-like_Group 1IgG_Dengue-Influenza-like_group
 1_eLife_edit.xlsxIgG Healthy
 Individual_Group 2IgG_Healthy individual_group
 2_eLife_edit.xlsxPCR Meningo-encephalitis
 patients_Group 3PCR_Meningo-encephalitis
 patients_group 3_eLife_edit.xlsPCR_Group
 4-8PCR_group
 4-8_eLife_edit.xlsx
DOI: 10.5061/dryad.6v728j1
title: Data from: Early modulation of intra-cortical inhibition during the observation of action mistakes

description: Errors while performing an action are fundamental for learning. During
 interaction others’ errors must be monitored and taken into account to
 allow joint action coordination and imitation learning. This monitoring
 relies on an action observation network (AON) mainly based on
 parietofrontal recurrent circuits. Although different studies suggest that
 inappropriate actions may rapidly be inhibited during execution, little is
 known about the modulation of the AON when an action misstep is shown.
 Here we used single and paired pulse transcranial magnetic stimulation to
 assess corticospinal excitability, intracortical facilitation and
 intracortical inhibition at different time intervals (120, 180, 240 ms)
 after the visual presentation of a motor execution error. Results show a
 specific and early (120 ms) decrease of intracortical inhibition likely
 because of a significant mismatch between the observed erroneous action
 and observer’s expectations. Indeed, as proposed by the top-down
 predictive framework, the motor system may be involved in the generation
 of these error signals and our data show that this mechanism could rely on
 the early decrease of intracortical inhibition within the corticomotor
 system.
description: Behavioral
 dataIncorrect answers or RTs
 lower than 100 ms or higher than 1000 ms were discarded from the analysis
 (less than 7% of trials). RTs were analyzed by paired-samples two-tailed
 t-tests (significance threshold, P &lt; 0.05). The same analysis was
 applied to responses accuracy.Neurophysiological data:
 Baseline modulationBaseline spTMS MEPs
 recorded at the beginning, and at the end of the experiment.The 2 × 2
 ANOVA between the TMS protocols (SICI, ICF) recorded in the two baseline
 (pre, post) .Baseline
 modulation.xlsxNeurophysiological data:
 Generic action observation modulation1)comparison between
 baseline spTMS MEPs and pooled action observation conditions. 2)The ANOVA
 on MEPs amplitude during action observation and baseline in the two
 different protocols: ppTMS 3ms , ppTMS 12ms.3)The ANOVA on intracortical
 excitability modulations (ratio between ppTMS and spTMS): CFC and sICI
 during generic action observation and baselineGeneric action observation
 modulation.xlsxNeurophysiological data:
 Error-related modulation1)The 3 × 3 ANOVA on
 spTMS between the condition(Correct, Control, Execution Error) and TMS
 timing (120 ms, 180 ms, 240 ms). In the spTMS protocol, the dependent
 variable was MEPs amplitude normalized by the average baseline. 2)The
 2 × 3 × 3 repeated-measures ANOVA on the intracortical modulation index.
 index of intracortical modulation (iMEP) is the mean ratio
 (ppTMScondition/spTMScondition) over the same mean ratio at baseline
 (ppTMSbaseline/spTMSbaseline), separately for each ppTMS protocols (sICI,
 ICF). The relationship between the effect found in each condition was then
 expressed into percentages:
 [(PPcondition/SPcondition)(PPbaseline/SPbaseline)]∗100Error-related
 modulation.xlsx
DOI: 10.5061/dryad.km53t
title: Data from: When anthropogenic-related disturbances overwhelm demographic persistence mechanisms

description: 1. Population decline is associated with increased vulnerability to
 extinction, but also with possible density-, frequency-, or
 distance-related ‘rarity advantages’ that increase recruitment success as
 individuals become isolated from their congeners. Distinguishing between
 these alternatives (risk versus recovery of rare populations via
 demographic processes) has become critical, given how anthropogenic
 disturbances are causing population declines globally. 2. Here, we
 demonstrate how distance-related rarity advantages are evident in
 spatially isolated recruits of a canopy-dominant but regionally rare
 species of oak that appears to be suffering recruitment collapse. As
 distance from parent trees increased, seedlings had significantly more
 leaves and experienced reduced insect browsing and intraspecific
 competition. Long-term field-based experimental treatments revealed these
 advantages to be associated with rapid rates of juvenile maturation and
 survival that are unobserved in natural settings. 3. The discrepancy
 between the experimental and natural settings was explained by trophic
 collapse and habitat loss - two changes ubiquitous to many terrestrial
 ecosystems – that combine to concentrate vertebrate herbivores in habitat
 remnants and cause 100% juvenile mortality via the browsing of taller
 juveniles. Exotic grass cover, long associated with oak recruitment
 failure, significantly suppressed seedling height and leaf production, but
 appeared to delay mortality by hiding shorter seedlings from vertebrate
 herbivores. 4. Synthesis. Our work demonstrates how rarity advantages have
 the potential to positively influence the population performance of a
 declining species, but are short-circuited by intense herbivory associated
 with human-based environmental change. Regionally, there appear to be few
 existing conditions on the contemporary landscape that favor juvenile
 survival, suggesting ongoing recruitment difficulties without
 intervention. Our work clarifies how extinction risk can in some cases be
 best defined by how anthropogenic disturbances affect, and are offset by,
 demographic-based persistence mechanisms, than simply by present-day
 abundance or distribution.
description: Duwyn-MacDougall JECOL
 data
DOI: 10.5061/dryad.ph416
title: Data from: Thermal constraints on microhabitat selection and mating opportunities

description: Hot tropical environments constrain ectotherm mating opportunities when
 mate selection occurs on the surface. Thus, microhabitats and refugia can
 become a qualitative trait in mate selection. In fiddler crabs, the
 enlarged claw of males can act as a heat sink, which becomes advantageous
 when surface temperatures reach 50 °C during the day and crabs are
 actively seeking to mate. Uca mjoebergi females prefer male burrows found
 in the shade; therefore, we investigated the thermal constraints imposed
 on males and females in shaded and unshaded habitats. Crab surface
 activity decreased and body temperature increased as the day progressed,
 with more crabs active in shaded than sunny microhabitats. Body
 temperature was lower in male crabs found in burrows relative to crabs on
 the surface. Male claw size explained 10% of body temperature. Our results
 add further support to the hypothesis that thermal constraints imposed on
 males can be overcome by the large claw acting as a heat sink and the
 burrow acting as a refuge from heat. Classic sexually selected traits,
 including ornaments and behaviours, can have a secondary purpose in
 thermoregulation.
description: data
 fileDRYAD
 data.xls
DOI: 10.5061/dryad.cj36j
title: Data from: Separating intrinsic and environmental contributions to growth and their population consequences

description: Among-individual heterogeneity in growth is a commonly observed phenomenon
 that has clear consequences for population and community dynamics yet has
 proved difficult to quantify in practice. In particular, observed
 among-individual variation in growth can be difficult to link to any given
 mechanism. Here, we develop a Bayesian state-space framework for modeling
 growth that bridges the complexity of bioenergetic models and the
 statistical simplicity of phenomenological growth models. The model allows
 for intrinsic individual variation in traits, a shared environment,
 process stochasticity, and measurement error. We apply the model to two
 populations of steelhead trout (Oncorhynchus mykiss) grown under common
 but temporally varying food conditions. Models allowing for individual
 variation match available data better than models that assume a single
 shared trait for all individuals. Estimated individual variation
 translated into a roughly twofold range in realized growth rates within
 populations. Comparisons between populations showed strong differences in
 trait means, trait variability, and responses to a shared environment.
 Together, individual- and population-level variation have substantial
 implications for variation in size and growth rates among and within
 populations. State-dependent life-history models predict that this
 variation can lead to differences in individual life-history expression,
 lifetime reproductive output, and population life-history diversity.
description: Steelhead Size
 DataThis file contains
 length and weight time series for individual steelhead trout raised in
 tanks in Santa Cruz California during 2006. Individual fish were measured
 on a series of days starting in spring 2006 to spring 2007. The fish were
 derived from two hatcheries (Scott Creek Hatchery and Coleman National
 Fish Hatchery, denoted as "Scott" and "Coleman"
 respectively) and raised in set of tanks. The tank number in which each
 fish grew is noted in the file. The fish were fed two rations levels (high
 or low) and the ration associated with each time is noted in the column
 labeled "Ration." The sequence of feeding treatments determine
 the "Treatment" column which has four levels (1,2,3, or 4). See
 the publication for more detailed information.Steelhead Ration
 ScheduleThis file shows the
 sequence of high and low ration treatments for each tank and the date at
 which changes in ration occurred.
DOI: 10.5061/dryad.c8234
title: Data from: A preliminary range-wide distribution model for the Sacramento Valley red fox

description: The Sacramento Valley red fox Vulpes vulpes patwin of California is a
 newly named subspecies recently found to be distinct both from other
 native red foxes and nearby introduced populations. The Sacramento Valley
 red fox experienced a historical demographic bottleneck resulting in a
 critically small genetic effective population size, causing concern over
 its current status and management requirements, yet little is known about
 its contemporary abundance, demographic trajectory, or habitat use. The
 hot, arid Sacramento Valley contrasts starkly in climate and physiography
 with the boreal habitats of other indigenous red foxes in western North
 America, indicating the need to obtain information specifically on the
 habitat requirements of this subspecies. A 3-y effort to locate
 reproductive den sites throughout the Sacramento Valley resulted in 42
 independent dens, which we used to obtain preliminary information on
 habitat use and to develop a distribution model for this subspecies, and
 28 Sacramento Valley red foxes killed by vehicles, which we used as
 independent data to test the models. Foxes were present significantly more
 than expected in grasslands and less than expected in wetlands and flooded
 agriculture and also tended to occur in proximity to human development,
 potentially as refuges from coyotes Canis latrans. We used Maxent to build
 predictive models. The best model, which incorporated vegetation/land-use
 classes and proximity to human development, identified 24% of the study
 area as predicted-presence habitat, which contained 76% of the den sites
 used to construct the model and 89% of independent locations used to test
 the model. Our model greatly narrowed the area over which foxes are
 predicted to occur and will facilitate future surveys to assess occupancy
 and ultimately abundance and population trends.
description: FigureA1Locations of 42 Sacramento Valley red fox (Vulpes vulpes patwin) den sites (black circles) and 28 road kills (red circles) in reference to 4 land-cover types used in Maxent modeling, Sacramento Valley, California, 2007–2009.SacksTableA1Locations and land-cover type coding of 42 Sacramento Valley red fox den sites used in Maxent modelingSacksTableA2Locations of 28 native Sacramento Valley red fox road killsFigureA2Locations of 70 Sacramento Valley red fox (Vulpes vulpes patwin) den sites and road kills (black circles) in reference to geographic landmarks and two Maxent model predicting distribution in the Sacramento Valley, California: (A) the full model, based on vegetation type, distance to grasslands, distance to development, and (B) a 2-variable model, based on vegetation type and distance to grasslands (i.e., excluding distance to development). All data shown were collected during 2007–2009.
DOI: 10.5061/dryad.jm8s7
title: Data from: Physiological and ecological drivers of early spring blooms of a coastal phytoplankter

description: Climate affects the timing and magnitude of phytoplankton blooms that fuel
 marine food webs and influence global biogeochemical cycles. Changes in
 bloom timing have been detected in some cases, but the underlying
 mechanisms remain elusive, contributing to uncertainty in long-term
 predictions of climate change impacts. Here we describe a 13-year hourly
 time series from the New England shelf of data on the coastal
 phytoplankter Synechococcus, during which the timing of its spring bloom
 varied by 4 weeks. We show that multiyear trends are due to
 temperature-induced changes in cell division rate, with earlier blooms
 driven by warmer spring water temperatures. Synechococcus loss rates shift
 in tandem with division rates, suggesting a balance between growth and
 loss that has persisted despite phenological shifts and environmental
 change.
description: Temperature,
 Synechococcus concentration, division rates, and loss
 ratesFile contains
 tab-delimited columns of date, temperature (degree Celsius), Synechococcus
 concentration (cells per mL), division rate (1/d), and loss rate (1/d) at
 the Martha's Vineyard Coastal Observatory for 2003-2016. Unavailable
 data are indicated with a NaN.Science_pubdata_for_Dryad2.txtNutrient dataFile contains tab-delimited columns of date, nitrate+nitrite, ammonium, phosphate and silicate concentrations (micromolar) at the Martha's Vineyard Coastal Observatory from 2003-2015. Values are means of 2-3 technical replicates. Missing entries are denoted by NaNs.Science_pubdata_for_Dryad_nuts.txt
DOI: 10.5061/dryad.vj64m
title: Data from: Range-wide population structure of European sea bass Dicentrarchus labrax

description: The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the
 coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many
 opportunities for differentiation throughout its large natural range.
 However, evidence for this has been incompletely documented geographically
 and with an insufficient number of markers. Therefore, its full range was
 sampled at 22 sites and individuals were genotyped with a suite of mapped
 markers, including 14 microsatellite loci (N = 536) and 46 neutral or
 gene-linked single nucleotide polymorphisms (SNPs; N = 644). We confirm
 that the Atlantic and Mediterranean basins harbour two distinct lineages.
 Within the Atlantic Ocean no pattern was obvious based on the
 microsatellite and SNP genotypes, except for a subtle difference between
 South-eastern and North-eastern Atlantic sea bass attributed to limited
 introgression of alleles of Mediterranean origin. SNP genotypes of the
 Mediterranean lineage differentiated into three groups, probably under the
 influence of geographical isolation. The Western Mediterranean group
 showed genetic homogeneity without evidence for outlier loci. The Adriatic
 group appeared as a distinct unit. The Eastern Mediterranean group showed
 a longitudinal gradient of genotypes and most interestingly an outlier
 locus linked to the somatolactin gene. Overall, the spatial pattern fits
 those observed with other taxa of between-basin segregation and
 within-basin connectivity, which concurs well with the swimming
 capabilities of European sea bass. Evidence from a few outlier loci in
 this and other studies encourages further exploration of its regional
 connectivity and adaptive evolution.
description: Microsatellite
 genotypesSNP
 genotypes
DOI: 10.5061/dryad.mr00v92
title: Data from: Macroecological drivers of zooplankton communities across the mountains of western North America

description: Disentangling the environmental and spatial drivers of biological
 communities across large scales increasingly challenges modern ecology in
 a rapidly changing world. Here, we investigate the hierarchical and
 trait-based organization of regional and local factors of zooplankton
 communities at a macroscale of 1,240 mountain lakes and ponds spanning
 western North America (California, USA, to Yukon Territory, Canada).
 Variation partitioning was used to test the hypothesized importance of
 climate, connectivity, catchment features, and exotic sportfish to
 zooplankton beta-diversity in the context of key functional traits (body
 size and reproductive dispersal potential) given the pronounced
 environmental heterogeneity (e.g. thermal gradients), topographic
 barriers, and legacy of stocked fish in mountainous regions. Dispersal
 limitation was inferred from multispecies patch connectivity estimates
 based on nearest and average distances to occupied patches. Environmental
 heterogeneity best explained community composition as catchment/lake
 features (morphometry, land cover, and lithology) collectively captured
 greater variation than did climate (temperature, precipitation, and solar
 radiation), local stocking, or connectivity; however, single climatic
 variables captured the most variation individually. Macrospatial variation
 by larger obligate sexual species was better explained than that by
 smaller cyclically parthenogenetic asexual species. Our results provide
 several novel insights into the macroecology of zooplankton of the North
 American Cordillera, demonstrating their stronger associations to
 climatically driven aquatic-terrestrial habitat coupling than dynamics
 arising from introduced salmonids, human land-use, or species dispersal.
 These findings highlight the clear and important role of these communities
 as bioindicators of the limnological impacts of accelerating rates of
 climate change, as their responses appear relatively not confounded by
 local human perturbations or dispersal limitation.
description: Cumulative zooplankton
 occurrence and fish introduction recordsCompilation of
 historical zooplankton occurrence records for lakes and ponds across
 western North America (see Appendix 1 in Supplementary Material for
 details of zooplankton data handling and detailed references).
 FISH_STOCKING refers to introduced fish status (present/absent) at time of
 sampling (see Appendix 3 for details/data sources). RECENT_DATE,
 RECENT_REF, RESEARCH_GROUP, and #_YEARS_SAMPLED refer to the most recent
 confirmed zooplankton sampling date, abbreviated zooplankton sampling
 reference, research group or taxonomist, and number of sampling years
 integrated for species occurrence estimates, respectively (see Appendix 5
 for further details).Loewen et al. 2018.
 Ecography_Data_Dryad.csv