cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9g182
title: Data from: Exceptional convergence on the macroevolutionary landscape in island lizard radiations

description: G. G. Simpson, one of the chief architects of evolutionary biology’s
 modern synthesis, proposed that diversification occurs on a
 macroevolutionary adaptive landscape, but landscape models are seldom used
 to study adaptive divergence in large radiations. We show that for
 Caribbean Anolis lizards, diversification on similar Simpsonian landscapes
 leads to striking convergence of entire faunas on four islands. Parallel
 radiations unfolding at large temporal scales shed light on the process of
 adaptive diversification, indicating that the adaptive landscape may give
 rise to predictable evolutionary patterns in nature, that adaptive peaks
 may be stable over macroevolutionary time, and that available geographic
 area influences the ability of lineages to discover new adaptive peaks.
description: Phylogenetic trees and
 trait data for Greater Antillean Anolis lizardsSee ReadMe
 fileMahler_et_al_2013_Data.zip
DOI: 10.15468/dl.ddf3p5
title: Occurrence Download

description: A dataset containing 349 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Lacewings (Neuroptera) 02"
 ]
}

 The dataset includes 349 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000650-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.83pm53m
title: Data from: Environmental constraints on size-dependent signaling affects mating and rival interactions

description: Advertisement signals can convey information about a sender’s
 characteristics, such as body size. The reliability of signals, however,
 can be reduced when signal production is partially dependent on the
 environment. Here we show that display site properties can affect signal
 production and consequently signal attractiveness in a size-dependent
 manner. We recorded male túngara frogs (Physalaemus pustulosus) while
 manipulating water levels in order to constrain calling. We found that
 water level affected male call properties in a size-dependent manner, with
 call amplitude being less affected in smaller males when forced to call in
 shallow water. Next, we tested how size-dependent and display
 site-dependent signaling affected female choice and rival competition.
 Both males and females showed the strongest response to the call of a
 large male when he was calling at the deepest water levels. However,
 females showed no preference for large over small males when both were
 recorded in shallow water levels, or, depending on the call rate and
 timing of calls, even preferred small males. Likewise, males responded
 equally to large and small rivals recorded calling during shallow water
 level trials. Our experiments show that display site properties can
 influence signal production and attractiveness in a size-dependent manner.
 These results can have important consequences for the evolution of
 signaling, as small males may be able to use their size to their advantage
 when selecting appropriate display sites and thereby outcompete large
 males.
description: Data and R scripts water
 level body sizeThe data sheets of the
 male signaling experiment, female phonotaxis experiment and male field
 playback experiment, including metadata on the columns. Followed by R
 scripts that show our analyses.Dryad_waterlevelsize.xlsx
DOI: 10.5061/dryad.5s68j
title: Data from: Population demography and heterozygosity-fitness correlations in natural guppy populations: an examination using sexually selected fitness traits

description: Heterozygosity-fitness correlations (HFCs) have been examined in a wide
 diversity of contexts, and the results are often used to infer the role of
 inbreeding in natural populations. Although population demography,
 reflected in population-level genetic parameters such as allelic diversity
 or identity disequilibrium, is expected to play a role in the emergence
 and detectability of HFCs, direct comparisons of variation in HFCs across
 many populations of the same species, with different genetic histories,
 are rare. Here, we examined the relationship between individual
 microsatellite heterozygosity and a range of sexually selected traits in
 660 male guppies from 22 natural populations in Trinidad. Similar to
 previous studies, observed HFCs were weak overall. However, variation in
 HFCs among populations was high for some traits (although these variances
 were not statistically different from zero). Population-level genetic
 parameters, specifically genetic diversity levels (number of alleles,
 observed/expected heterozygosity) and measures of identity disequilibrium
 (g2 and heterozygosity-heterozygosity correlations) were not associated
 with variation in population-level HFCs. This latter result indicates that
 these metrics do not necessarily provide a reliable predictor of HFC
 effect sizes across populations. Importantly, diversity and identity
 disequilibrium statistics were not correlated, providing empirical
 evidence that these metrics capture different essential characteristics of
 populations. A complex genetic architecture likely underpins multiple
 fitness traits, including those associated with male fitness, which may
 have reduced our ability to detect HFCs in guppy populations. Further
 advances in this field would benefit from additional research to determine
 the demographic contexts in which HFCs are most likely to occur.
description: Fitness and
 microsatellite dataExcel workbook of all
 fitness and microsatellite data used in the analysis. The first worksheet
 contains the data, the second worksheet contains an explanation of column
 headings.data.xlsx
DOI: 10.5061/dryad.8682
title: Data from: Aging in the natural world: comparative data reveal similar mortality patterns across primates

description: Human senescence patterns – late onset of mortality increase, slow
 mortality acceleration, and exceptional longevity – are often described as
 unique in the animal world. Using an individual-based dataset from
 longitudinal studies of wild populations of seven primate species, we show
 that contrary to assumptions of human uniqueness, human senescence falls
 within the primate continuum of aging, the tendency for males to have
 shorter lifespans and higher age-specific mortality than females
 throughout much of adulthood is a common feature in many, but not all,
 primates, and the aging profiles of primate species do not reflect
 phylogenetic position. These findings suggest that mortality patterns in
 primates are shaped by local selective forces rather than phylogenetic
 history.
description: DryadDataThese data appear in the supplemental online material for this article. Details of field studies and column descriptions may be found in the publication.BaboonComputationWorksheetExcel workbook showing the computational details for estimating the hazard rates for female and male baboons in this study. Male deaths were estimated based on age-structure beginning at their dispersal age. These ratios were further adjusted to reflect the rate at which the female population was growing.
DOI: 10.5061/dryad.qj195
title: Data from: Does functional soil microbial diversity contribute to explain within-site plant β-diversity in an alpine grassland and a dehesa meadow in Spain?

description: Questions Once effects of hydrological and chemical soil properties have
 been accounted for, does soil microbial diversity contribute to explain
 change in plant community structure (i.e. within-site β-diversity)? If so,
 at what spatial scale does microbial diversity operate? Location La Mina
 in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna
 Larga in the Urbión Peaks, Soria, central-northern Spain (alpine
 grassland). Methods The abundance of vascular plant species, soil
 Gram-negative microbial functional types and soil chemical properties (pH,
 available P, extractable cations) were sampled at both sites, for which
 hydrological models were available. RDA was used to partition variation in
 plant community structure into hydrological, chemical and microbial
 components. Spatial filters, arranged in scalograms, were used to test for
 the spatial scales at which plant community structure changes. Results In
 the case of the dehesa the diversity of soil Gram-negative microbes,
 weakly driven by soil pH, contributed to a small extent (adj-R2 = 2%) and
 at a relative medium spatial scale to explain change in plant community
 structure. The abundance of a few dehesa species, both annual (Trifolium
 dubium, Vulpia bromoides) and perennial (Poa bulbosa, Festuca ampla), was
 associated with either increasing or decreasing soil microbial diversity.
 In the alpine meadow the contribution was negligible. Conclusions
 Microbial diversity can drive community structure, although in the
 hierarchy of environmental factors structuring communities it appears to
 rank lower than other soil factors. Still, microbial diversity appears to
 promote or restrain individual plant species. This paper aims to encourage
 future studies to use more comprehensive and insightful techniques to
 assess microbial diversity and to combine this with statistical approaches
 such as that used here.
description: Laguna
 LargaLagunaLarga
 dataset.xlsLaMina
 dataset
DOI: 10.5061/dryad.1j741
title: Data from: Dynamics of marsh-mangrove ecotone since the mid-Holocene: a palynological study of mangrove encroachment and sea level rise in the Shark River Estuary, Florida

description: Sea level rise and the associated inland shift of the marsh-mangrove
 ecotone in south Florida have raised many scientific and management
 concerns in recent years. Holocene paleoecological records can provide an
 important baseline to shed light on the long-term dynamics of vegetation
 changes across this ecotone in the past, which is needed to predict the
 future. In this study, we present palynological, X-ray fluorescence, and
 loss-on ignition data from four sedimentary cores recovered from a 20-km
 marine-to-freshwater transect along the Shark River Estuary, southwest
 Everglades, to document the patterns and processes of coastal vegetation
 changes in response to sea level rise since the mid-Holocene. Our record
 indicates that freshwater marsh progressively replaced marl prairies at
 the Shark River Estuary between 5700 and 4400 cal yr BP. As marine
 transgression continued, marine influence reached the threshold necessary
 for mangroves to establish at the current mouth of the Shark River Slough
 at 3800 cal yr BP. During the next 3000 years, although sea level rise in
 the Western North Atlantic slowed down to 0.4 mm/yr, a spatial and
 temporal gradient was evident as the marsh-mangrove ecotone shifted inland
 by 20 km from 3800 to 800 cal yr BP, accompanied by a gradual landward
 replacement of freshwater marsh by mangrove forest. If sea level continues
 to rise at 2.33 mm/yr in the 21st century in south Florida, it is possible
 that marine influence will reach the threshold for mangroves to establish
 in the central Everglades, and we could expect a much more aggressive
 mangrove encroachment toward the northern and interior parts of south
 Florida in the next few centuries.
description: LOI
 dataLoss-on-ignition data
 for core SRS-4, SRS-5, SRS-6, and SRMPollen
 dataPollen data for core
 SRS-4, SRS-5, SRS-6, and SRMXRF
 dataX-ray fluorescence data
 for core SRS-4, SRS-5, SRS-6, and SRMSRM BACON settings and
 agesBACON data for core
 SRM
DOI: 10.5061/dryad.dj050
title: Data from: The role of marine reserves in the replenishment of a locally-impacted population of anemonefish on the Great Barrier Reef

description: The development of parentage analysis to track the dispersal of juvenile
 offspring has given us unprecedented insight into the population dynamics
 of coral reef fishes. These tools now have the potential to inform
 fisheries management and species conservation, particularly for small
 fragmented populations under threat from exploitation and disturbance. In
 this study we resolve patterns of larval dispersal for a population of the
 anemonefish Amphiprion melanopus in the Keppel Islands (southern Great
 Barrier Reef). Habitat loss and fishing appear to have impacted this
 population and a network of no-take marine reserves currently protects 75%
 of the potential breeders. Using parentage analysis, we estimate that 21%
 of recruitment in the island group was generated locally, and that
 breeding adults living in reserves were responsible for 79% (31 out of 39)
 of these of locally-produced juveniles. Overall, the network of reserves
 was fully connected via larval dispersal; however one reserve was
 identified as a critical source of larvae for the island group. The
 population in the Keppel Islands also appears to be well-connected to
 other source populations at least 60 km away, given that 79% (145 out of
 184) of the juveniles sampled remained unassigned in the parentage
 analysis. We estimated the effective size of the A. melanopus
 metapopulation to be 745 (582-993 95% CI) and recommend continued
 monitoring of its genetic status. Maintaining connectivity with
 populations beyond the Keppel Islands and recovery of local recruitment
 habitat, potentially through active restoration of host anemone
 populations, will be important for its long-term persistence.
description: microsatellite
 genotypes_Amelanopusgenotypes across 22
 microsatellite markers for A.melanopus collected in the Keppel
 IslandsFig2_assignment
 dataparentage assignment
 data used to create Figure 2 dispersal mapFig3_connection
 frequency datafrequency data used to
 create Figure 3Fig4_colony level
 dispersal dataassignment data used to
 create Figure 4Fig5_dispersal distance
 datadispersal distance and
 frequency data used to create Figure 5
DOI: 10.5061/dryad.rg638
title: Data from: Experimental evolution reveals high insecticide tolerance in Daphnia inhabiting farmland ponds

description: Exposure of non-target populations to agricultural chemicals is an
 important aspect of global change. We quantified the capacity of natural
 Daphnia magna populations to locally adapt to insecticide exposure through
 a selection experiment involving carbaryl exposure and a control. Carbaryl
 tolerance after selection under carbaryl exposure did not increase
 significantly compared to the tolerance of the original field populations.
 However, there was evolution of a decreased tolerance in the control
 experimental populations compared to the original field populations. The
 magnitude of this decrease was positively correlated with land use
 intensity in the neighbourhood of the ponds from which the original
 populations were sampled. The genetic change in carbaryl tolerance in the
 control rather than in the carbaryl treatment suggests widespread
 selection for insecticide tolerance in the field associated with land use
 intensity, and suggests that this evolution comes at a cost. Our data
 suggest a strong impact of current agricultural land use on non-target
 natural Daphnia populations.
description: worksheet
 data-analysisData are saved in excel
 to be able to upload in statistical software. Different data-files were
 the final data ACO is the most important sheet.Mieke_ecotox_rworksheet_2nd
 analysis.xlsx
DOI: 10.5061/dryad.fn4m3
title: Data from: Hydrology controls recruitment of two invasive cyprinids: bigheaded carp reproduction in a navigable large river

description: In the Mississippi River Basin of North America, invasive bigheaded carp
 (silver carp Hypophthalmichthys molitrix and bighead carp H. nobilis, also
 referred to as Asian carp) have spread rapidly over the past several
 decades. In the Illinois River, an important tributary of the Upper
 Mississippi River, reproduction appears to be sporadic and frequently
 unsuccessful, yet bigheaded carp densities in this river are among the
 highest recorded on the continent. Understanding the causative factors
 behind erratic recruitment in this commercially-harvested invasive species
 is important for both limiting their spread and managing their harvest. We
 analyzed weekly catch records from 15 years of a standardized monitoring
 program to document the emergence of age-0 bigheaded carp in relation to
 environmental conditions. The appearance of age-0 fish was generally
 linked to hydrographic attributes, which probably serve as a cue for
 spawning. However, we found profound differences in the number of age-0
 fish among years, which varied by as much as five orders of magnitude in
 successive years. The strong link between summer flooding and age-0 fish
 production we observed emphasizes the importance of understanding the
 hydrologic context in which sustained invasions occur. Despite evidence of
 sporadic recruitment, bigheaded carp populations in the Illinois River
 appear to be consistent or increasing because of particularly strong,
 episodic year classes.
description: Bigheaded Carp Catch
 DataData on bigheaded carp
 sampled between 2000 and 2014 in the Illinois River, Illinois, USA, as
 part of the Long-Term Resource Monitoring Element of the Army Corps of
 Engineers Upper Mississippi River Restoration Program.Carp_Catch_Data.csvHatch dates usedEstimated hatch dates for bigheaded carp used in the analysis.Hatch_dates_used.csvStage Height DataStage height of the Illinois River, Illinois, USA, used to estimate changing hydrologic conditions related to bigheaded carp spawning.USGS_Stage_Height_Data.csv
DOI: 10.5061/dryad.32v7b
title: Data from: Evaluating in vitro-in vivo extrapolation of toxicokinetics

description: Prioritizing the risk posed by thousands of chemicals potentially present
 in the environment requires exposure, toxicity, and toxicokinetic (TK)
 data, which are often unavailable. Relatively high throughput, in vitro TK
 (HTTK) assays and in vitro-to-in vivo extrapolation (IVIVE) methods have
 been developed to predict TK, but most of the in vivo TK data available to
 benchmark these methods are from pharmaceuticals. Here we report on new,
 in vivo rat TK experiments for 26 non-pharmaceutical chemicals with
 environmental-relevance. Both intravenous and oral dosing were used to
 calculate bioavailability. These chemicals, and an additional 19 chemicals
 (including some pharmaceuticals) from previously published in vivo rat
 studies, were systematically analyzed to estimate in vivo TK parameters
 (e.g., volume of distribution (Vd), elimination rate). For each of the
 chemicals, rat-specific HTTK data were available and key TK predictions
 were examined: oral bioavailability, clearance, Vd, and uncertainty. For
 the non-pharmaceutical chemicals, predictions for bioavailability were not
 effective. While no pharmaceutical was absorbed at less than 10%, the
 fraction bioavailable for non-pharmaceutical chemicals was as low as 0.3%.
 Total clearance was generally more under-estimated for non-pharmaceuticals
 and Vd methods calibrated to pharmaceuticals may not be appropriate for
 other chemicals. However, the steady-state, peak, and time-integrated
 plasma concentrations of non-pharmaceuticals were predicted with
 reasonable accuracy. The plasma concentration predictions improved when
 experimental measurements of bioavailability were incorporated. In
 summary, HTTK and IVIVE methods are adequately robust to be applied to
 high throughput in vitro toxicity screening data of
 environmentally-relevant chemicals for prioritizing based on human health
 risks.
description: TableS9-InVivoData-2017-12-11Plasma concentration vs. time toxicokinetic data collected for a variety of chemicals in Sprague-Dawley rat.TableS11-TKSummaryStats-2017-12-11Model TK statistics (Cmax, AUC) for in vivo rat studies.TableS10-PropertiesandEstimates-2017-12-11Estimated TK properties (e.g., Volume of Distribution, Fraction bioavailable) for in vivo rat studies.
DOI: 10.5061/dryad.3vk01
title: Data from: Ocean acidification affects fish spawning but not paternity at CO2 seeps

description: Fish exhibit impaired sensory function and altered behaviour at levels of
 ocean acidification expected to occur owing to anthropogenic carbon
 dioxide emissions during this century. We provide the first evidence of
 the effects of ocean acidification on reproductive behaviour of fish in
 the wild. Satellite and sneaker male ocellated wrasse (Symphodus
 ocellatus) compete to fertilize eggs guarded by dominant nesting males.
 Key mating behaviours such as dominant male courtship and nest defence did
 not differ between sites with ambient versus elevated CO2 concentrations.
 Dominant males did, however, experience significantly lower rates of pair
 spawning at elevated CO2 levels. Despite the higher risk of sperm
 competition found at elevated CO2, we also found a trend of lower
 satellite and sneaker male paternity at elevated CO2. Given the importance
 of fish for food security and ecosystem stability, this study highlights
 the need for targeted research into the effects of rising CO2 levels on
 patterns of reproduction in wild fish.
description: Supplementary material
 and dataMilazzo et al SUPPL MATERIAL
 AND DATA.doc
DOI: 10.15468/dl.uwd55b
title: Occurrence Download

description: A dataset containing 9337261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-101.26 41.05,-68.37 41.05,-68.37 57.29,-101.26 57.29,-101.26 41.05))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 9337261 records from 618 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000605-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/ck9gd5vbkr
title: PNG highland tephras

description: Descriptions and maps of Late Pleistocene tephras in the highlands of Papua New Guinea
DOI: 10.17632/tvf9nwtdhn
title: Raw data for manuscript "Heterotypic droplet formation by pro-inflammatory S100A9 and neurodegenerative disease-related alpha-synuclein"

description: Raw data for manuscript "Heterotypic droplet formation by pro-inflammatory S100A9 and neurodegenerative disease-related alpha-synuclein". Fluorescence microscopy images, brightfield microscopy images, LLPS and aggregation kinetics, Cryo-EM data.
DOI: 10.6084/m9.figshare.13303457.v1
title: mnist.pkl.gz

description: MNIST dataset originally hosted on https://deeplearning.net, re-hosted here because deeplearning.net is currently inaccessible.
DOI: 10.6084/m9.figshare.26089359.v1
title: HiGTS_2021s2

description: HiGTS is a high temporal resolution global gridded dataset of human thermal stress metrics. Derived using climate variables from ERA5-Land and ERA5, the HiGTS consists of hourly gridded maps of Universal Thermal Climate Index (UTCI), Universal Thermal Stress (UTS), and daily Thermal Stress Duration (TSD) at 0.1° × 0.1° spatial resolution over the global land surface.HiGTS_2021s2 contains the data from April 1, 2021 to June 30, 2021.
DOI: 10.6084/m9.figshare.3513617.v1
title: Appendix B. Rationale and discussion for model parameters (with references).

description: Rationale and discussion for model parameters (with references).