cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xe36tw
title: Occurrence Download

description: A dataset containing 242221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Central Oregon Community College, Laboratory of Tree-Ring Research Natural History Collection, Washington State University Marion Ownbey Herbarium, Oregon State University Bryophyte Collection, Washington State University Herbarium, A global database for the distributions of crop wild relatives, BLM - National Invasive Species Information Management System - Plants, Oregon State University Vascular Plant Collection, Pl@ntNet automatically identified occurrences)",
 "GadmGid is one of (USA.38.22_1, USA.38.20_1, USA.38.9_1, USA.38.18_1, USA.38.16_1, USA.38.10_1)",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 242221 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021379-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16909580
title: Dataset associated with PickET - An unsupervised method for localizing macromolecules in cryo-electron tomograms

description: This repository contains the input tomograms and the segmentations generated for them using PickET. These correspond to the ones shown in the figures in the PickET manuscript
DOI: 10.5281/zenodo.16909581
title: Dataset associated with PickET - An unsupervised method for localizing macromolecules in cryo-electron tomograms

description: This repository contains the input tomograms and the segmentations generated for them using PickET. These correspond to the ones shown in the figures in the PickET manuscript
DOI: 10.5061/dryad.bb2p8
title: Data from: Competition both drives and impedes diversification in a model adaptive radiation

description: Competitors are known to be important in governing the outcome of
 evolutionary diversification during an adaptive radiation, but the precise
 mechanisms by which they exert their effects remain elusive. Using the
 model adaptive radiation of Pseudomonas fluorescens, we show
 experimentally that the effect of competition on diversification of a
 focal lineage depends on both the strength of competition and the ability
 of the competitors to diversify. We provide evidence that the extent of
 diversification in the absence of interspecific competitors depends on the
 strength of resource competition. We also show that the presence of
 competitors can actually increase diversity by increasing interspecific
 resource competition. Competitors that themselves are able to diversify
 prevent diversification of the focal lineage by removing otherwise
 available ecological opportunities. These results suggest that the
 progress of an adaptive radiation depends ultimately on the strength of
 resource competition, an effect that can be exaggerated or impeded by the
 presence of competitors.
description: fitness,density&diversityThis file contains 24-hour competitive fitness estimates, and diversity and density measure over time.
DOI: 10.15468/dl.sj83sa
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Gyalopion canum",
 "Year 1960-2026"
 ]
}

 The dataset includes 26 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000770-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nf2h5
title: Data from: Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales

description: The relative roles of historical processes, environmental filtering, and
 ecological interactions in the organization of species assemblages vary
 depending on the spatial scale. We evaluated the phylogenetic and
 morphological relationships between species and individuals (i.e., inter-
 and intraspecific variability) of Neotropical nonvolant small mammals
 coexisting in grassland-forest ecotones, in landscapes and in regions,
 that is, three different scales. We used a phylogenetic tree to infer
 evolutionary relationships, and morphological traits as indicators of
 performance and niche similarities between species and individuals.
 Subsequently, we applied phylogenetic and morphologic indexes of diversity
 and distance between species to evaluate small mammal assemblage
 structures on the three scales. The results indicated a repulsion pattern
 near forest edges, showing that phylogenetically similar species coexisted
 less often than expected by chance. The strategies for niche
 differentiation might explain the phylogenetic repulsion observed at the
 edge. Phylogenetic and morphological clustering in the grassland and at
 the forest interior indicated the coexistence of closely related and
 ecologically similar species and individuals. Coexistence patterns were
 similar whether species-trait values or individual values were used. At
 the landscape and regional scales, assemblages showed a predominant
 pattern of phylogenetic and morphological clustering. Environmental
 filters influenced the coexistence patterns at three scales, showing the
 importance of phylogenetically conserved ecological tolerances in enabling
 taxa co-occurrence. Evidence of phylogenetic repulsion in one region
 indicated that other processes beyond environmental filtering are
 important for community assembly at broad scales. Finally, ecological
 interactions and environmental filtering seemed important at the local
 scale, while environmental filtering and historical colonization seemed
 important for community assembly at broader scales.
description: DRYAD_Luza_et_al.Data is organized in dynamic spreadsheets. Basic trapping unity was a sampling point composed by two traps (See Sampling of non-volant small mammals on Material and methods). Sampling unities used in data analysis were transects composed by eight trapping points. The file “Data_bank_Luza_et_al.” is composed by two spreadsheets: Occurrence_data and Individual_traits. Species traits and information about phylogenetic reconstruction will be available with the manuscript and appendices.Databank_Luza_et_al..xlsx
DOI: 10.5061/dryad.45595
title: Data from: Effects of pesticide mixtures on host-pathogen dynamics of the amphibian chytrid fungus

description: Anthropogenic and natural stressors often interact to affect organisms.
 Amphibian populations are undergoing unprecedented declines and
 extinctions with pesticides and emerging infectious diseases implicated as
 causal factors. Although these factors often co-occur, their effects on
 amphibians are usually examined in isolation. We hypothesized that
 exposure of larval and metamorphic amphibians to ecologically relevant
 concentrations of pesticide mixtures would increase their post-metamorphic
 susceptibility to the fungus Batrachochytrium dendrobatidis (Bd), a
 pathogen that has contributed to amphibian population declines worldwide.
 We exposed five anuran species (Pacific treefrog, Pseudacris regilla;
 spring peeper, Pseudacris crucifer; Cascades frog, Rana cascadae; northern
 leopard frog, Lithobates pipiens; and western toad, Anaxyrus boreas) from
 three families to mixtures of four common insecticides (chlorpyrifos,
 carbaryl, permethrin, and endosulfan) or herbicides (glyphosate,
 acetochlor, atrazine, and 2,4-D) or a control treatment, either as
 tadpoles or as newly metamorphic individuals (metamorphs). Subsequently,
 we exposed animals to Bd or a control inoculate after metamorphosis and
 compared survival and Bd load. Bd exposure significantly increased
 mortality in Pacific treefrogs, spring peepers, and western toads, but not
 in Cascades frogs or northern leopard frogs. However, the effects of
 pesticide exposure on mortality were negligible, regardless of the timing
 of exposure. Bd load varied considerably across species; Pacific
 treefrogs, spring peepers, and western toads had the highest loads,
 whereas Cascades frogs and northern leopard frogs had the lowest loads.
 The influence of pesticide exposure on Bd load depended on the amphibian
 species, timing of pesticide exposure, and the particular pesticide
 treatment. Our results suggest that exposure to realistic pesticide
 concentrations has minimal effects on Bd-induced mortality, but can alter
 Bd load. This result could have broad implications for risk assessment of
 amphibians; the outcome of exposure to multiple stressors may be
 unpredictable and can differ between species and life stages.
description: MoralityDataMortalityData.xlsx is associated with Figure 1 and Table 1.BdLoadDataBdLoadData.xlsx is associated with Figure 2 and Table 2.
DOI: 10.5061/dryad.3tm02
title: Data from: The spatial scaling of saprotrophic fungal beta diversity in decomposing leaves

description: Assembly of fungal communities remains poorly understood in part because
 of the daunting range of spatial scales that may be involved in this
 process. Here, we use individual leaves as a natural sampling unit,
 comprising spatially distinct habitat and/or resource patches with unique
 histories and suites of resources. Spatial patterns in fungal beta
 diversity were tested for consistency with the metacommunity paradigms of
 species sorting and neutral dynamics. Thirty senesced leaves were
 collected from the forest floor (O horizon) in replicate upland forest,
 riparian forest and vernal pool habitats. We quantified spatial distance
 between leaves, and fungal community composition was assayed by terminal
 restriction fragment length polymorphism. Significant distance-decay
 relationships were detected at all but one upland site. This is the first
 study where changes in fungal community composition were quantified across
 discrete adjacent habitat patches, providing evidence that fungal distance
 decay is operational at a scale of centimetres. Although leaves of
 differing lignin contents were sampled from each site, leaf type was not
 consistently important in explaining variation in fungal community
 composition. However, depth of a leaf within the forest floor
 significantly influenced community composition at five of six sites.
 Environmental heterogeneity associated with depth could include moisture
 gradients, relative influence of soil or spore colonization, and impact of
 forest floor biotic community (i.e. collembola and earthworms). Because
 the influence of spatial distance and depth on fungal community
 composition could not be disentangled, both species-sorting and neutral
 processes may be embedded within the distance-decay relationships that we
 found.
description: LeafVarDepthJun2008TRFLPTRFLP profiles and sample informationL6_ProximityMatrixLeaf proximities at site L6.J1_ProximityMatrixLeaf proximities at site J1.H6_ProximityMatrixLeaf proximities at site H6.Q1_ProximityMatrixLeaf proximities at site Q1.14_ProximityMatrixLeaf proximities at site 14.J3_ProximityMatrixLeaf proximities at site J3.r_codeExamples of R code used to analyze data.
DOI: 10.5061/dryad.61m2s
title: Data from: Habitat segregation and ecological character displacement in cryptic African malaria mosquitoes

description: Understanding how divergent selection generates adaptive phenotypic and
 population diversification provides a mechanistic explanation of
 speciation in recently separated species pairs. Toward this goal, we
 sought ecological gradients of divergence between the cryptic malaria
 vectors Anopheles coluzzii and An. gambiae, and then looked for a
 physiological trait that may underlie such divergence. Using a large set
 of occurrence records and eco-geographical information, we built a
 distribution model to predict the predominance of the two species across
 their range of sympatry. Our model predicts two novel gradients along
 which the species segregate: distance from the coastline and altitude.
 Anopheles coluzzii showed a ‘bimodal’ distribution, predominating in xeric
 West African savannas and along the western coastal fringe of Africa. To
 test whether differences in salinity tolerance underlie this habitat
 segregation, we assessed the acute dose-mortality response to salinity of
 thirty-two larval populations from Central Africa. In agreement with its
 coastal predominance, Anophels coluzzii was overall more tolerant than An.
 gambiae. Salinity tolerance of both species, however, converged in urban
 localities, presumably reflecting an adaptive response to osmotic stress
 from anthropogenic pollutants. When comparing degree of tolerance in
 conjunction with levels of syntopy, we found evidence of character
 displacement in this trait.
description: Anopheles coluzzii &
 gambiae georeferenced frequenciesLarval Salinity
 Tolerance Bioassays Global DatasetLarval Salinity
 Tolerance Bioassays Rural Coastal Dataset
DOI: 10.5061/dryad.104t1
title: Data from: Don't put all eggs in one nest - spread them and cut time at risk

description: In many egg-laying animals, some females spread their clutch among several
 nests. The fitness effects of this reproductive tactic are debated. Using
 mathematical modelling and field observations we analyse an unexplored
 benefit of egg spreading in brood parasitic and other breeding systems:
 reduced time at risk for offspring. If a clutch takes many days to lay
 until incubation and embryo development starts after the last egg, a
 parasitic female by spreading her eggs can reduce offspring time in the
 vulnerable nest, at risk of predation or other destruction. The model
 suggests that she can achieve much of this benefit already by spreading
 her eggs among a few nests, even if her total clutch is large. Field data
 from goldeneye ducks Bucephala clangula show that egg spreading enables a
 fecund female to lay a much larger than average clutch, without increasing
 offspring time at risk in a nest. This advantage increases with female
 condition (fecundity) and can markedly raise female reproductive success.
 These results help explain the puzzle of nesting parasites in some
 precocial birds, which lay eggs in the nests of other females before
 laying in their own nest. Risk reduction by egg spreading may also play a
 role in the evolution of other breeding systems, for instance some forms
 of polyandry with male parental care.
description: Nesting parasites,
 laying sequencesEgg-laying sequence of
 14 females that laid eggs in one or more other nests before laying and
 starting incubation in her own nest. Eggs that she laid in other nests are
 represented by numbers; ® represents eggs that she laid in her own nest.
 For instance, female 2 started on 28 April by laying an egg in another
 nest (1), 3 days later laying another egg in the same nest (1). Two days
 later she laid an egg in a second nest (2) etc., until she on 18 May laid
 an egg in her own nest, then continuing with 7 more eggs in her own nest,
 the last of which she laid 30 May. Figure 4 is a simplified summary of
 these results, omitting non-laying days.Goldeneye egg time in
 nestAverage time spent in
 the same nest by the eggs of host and parasites, before incubation start
 in the nest. Based on Åhlund (2005, Fig. 1). Parasite eggs laid after the
 last host egg (incubation start) are not included.Timing data, laying
 parasitesAverage time (days)
 spent in the nest before incubation start, for the eggs of 13 females that
 laid eggs parasitically before laying in their own nest (laying parasites,
 see Fig. 5). For each female, “Observed time” is the average time her eggs
 spent in a nest before incubation start. “One-nest time” is the
 corresponding average time per egg, if the female had instead laid all her
 eggs in one nest, with the same timing between her successive eggs. These
 data were used for the regression analysis described in the paper (Fig.
 5).
DOI: 10.5061/dryad.kd3qm
title: Data from: Does aquatic foraging impact head shape evolution in snakes?

description: Evolutionary trajectories are often biased by developmental and historical
 factors. However, environmental factors can also impose constraints on the
 evolutionary trajectories of organisms leading to convergence of
 morphology in similar ecological contexts. The physical properties of
 water impose strong constraints on aquatic feeding animals by generating
 pressure waves that can alert prey and potentially push them away from the
 mouth. These hydrodynamic constraints have resulted in the independent
 evolution of suction feeding in most groups of secondarily aquatic
 tetrapods. Despite the fact that snakes cannot use suction they have
 invaded the aquatic milieu many times independently. Here we test whether
 the aquatic environment has constrained head shape evolution in snakes and
 whether shape converges on that predicted by biomechanical models. To do
 so, we used 3D geometric morphometrics and comparative, phylogenetically
 informed analyses on a large sample of aquatic snake species. Our results
 show that aquatic snakes partially conform to our predictions and have a
 narrower anterior part of the head and dorsally positioned eyes and
 nostrils. This morphology is observed irrespective of the phylogenetic
 relationships among species suggesting that the aquatic environment does
 indeed drive the evolution of head shape in snakes, thus biasing the
 evolutionary trajectory of this group of animals.
description: Data_Segall_et_al_2016PC scores of all the species included in the analysis. These scores were used for all statistical analyses performed.
DOI: 10.5061/dryad.k6n5k
title: Data from: The effects of experimental sleep apnea on cardiac and respiratory functions in 6 and 18 Month Old dystrophic mdx mice

description: Duchenne muscular dystrophy (DMD) is a fatal disease where over 90% of
 patients succumb to respiratory or cardiac failure. Sleep apnea and sleep
 disordered breathing (SDB) are noted in a plurality of DMD patients, and
 the resulting nocturnal episodic hypoxia (EH) cannot be ruled out as a
 contributing factor to cardiac and respiratory dysfunction. In this study,
 we investigated the impact of long-term episodic hypoxia, which mimics the
 cyclic hypoxia seen in sleep apnea, on cardiac and respiratory function in
 a murine model of DMD (mdx mice). Since the severity and prevalence of
 sleep apnea in DMD increases with age, we studied the impact of EH on
 young (6-month) and on older (18-month) mdx mice. Mice were either exposed
 for 12 weeks to EH (8 hours/day, 5 days/week) or to room air. We noted a
 significant increase in left ventricular (LV) dilatation (transthoracic
 echocardiography) on EH exposure in both age groups, but reduced LV
 contractility was seen only in 6-month old mice. With EH exposure, an
 increased fibrosis (hydroxyproline) was noted in both cardiac and
 diaphragm muscle in 18-month but not 6-month old mice. No significant
 change in relative diaphragm strength (in-vitro) was noted on EH exposure
 in 18-month old mice. In contrast, EH exposed 6-month old mice showed a
 significant increase in relative diaphragm strength. EH exposure did not
 result in any significant change in ventilatory parameters (barometric
 plethysmography) in awake 6-month old mdx mice. In contrast, 18-month old
 mdx mice showed considerable ventilatory dysfunction, consistent with
 reduced ventilatory reserve. Our findings highlight that sleep apnea
 impacts respiratory and cardiac function in muscular dystrophy, and that
 EH can have divergent effects on both systems. To our knowledge, this is
 the first comprehensive study to investigate the impact of EH on cardiac
 and respiratory function in mdx mice.
description: Chaudhari_Figure 1
 DataChaudhari_Figure 2
 DataChaudhari_Figure 3
 DataChaudhari_Figure 4
 DataTable
 data_Chaudhari
DOI: 10.5061/dryad.3571q4t
title: Data from: Genetic basis to hybrid inviability is more complex than hybrid male sterility in Caenorhabditis nematodes

description: Hybrid male sterility often evolves before female sterility or inviability
 of hybrids, implying that the accumulation of divergence between separated
 lineages should lead hybrid male sterility to have a more polygenic basis.
 However, experimental evidence is mixed. Here, we use the nematodes
 Caenorhabditis remanei and C. latens to characterize the underlying
 genetic basis of asymmetric hybrid male sterility and hybrid inviability.
 We demonstrate that hybrid male sterility is consistent with a simple
 genetic basis, involving a single X-autosome incompatibility. We also show
 that hybrid inviability involves more genomic compartments, involving
 diverse nuclear-nuclear incompatibilities, a mito-nuclear incompatibility,
 and maternal effects. These findings demonstrate that male sensitivity to
 genetic perturbation may be genetically simple compared to hybrid
 inviability in Caenorhabditis and motivates tests of generality for the
 genetic architecture of hybrid incompatibility across the breadth of
 phylogeny.
description: proportion of males
 sterileThe proportion of males
 sterile for each direction of the F1 hybrid backcrosshybrid male
 sterility.txtbackcross
 viabilityViability of hybrids
 from egg to L1 and L1 to adult for each direction of the F1 hybrid
 backcrossexample maximum
 likelihoodExample R script used to
 run the maximum likelihood analysis in this manuscript.example max likelihood
 .R
DOI: 10.5061/dryad.97mg240
title: Data from: Directional selection reduces developmental canalization against genetic and environmental perturbations in Drosophila wings

description: Natural selection may enhance or weaken the robustness of phenotypes
 against genetic or environmental perturbations. However, important aspects
 of the relationship between adaptive evolution and canalization remain
 unclear. Recent work showed that the evolution of larger wing size in a
 high altitude natural population of Drosophila melanogaster was
 accompanied by decanalized wing development – specifically a loss of
 robustness to genetic perturbation. But this study did not address
 environmental robustness, and it compared populations that may have
 numerous biological differences. Here, we perform artificial selection on
 this same trait in D. melanogaster (larger wing length) and directly test
 whether this directional selection resulted in decanalization. We find
 that in general, size-selected replicates show greater frequencies of wing
 defects than control replicates both after mutagenesis (genetic
 perturbation) and when subjected to high temperature stress (environmental
 perturbation), although the increase in defect frequency varies
 importantly among replicates. These results support the hypothesis that
 directional selection may result in the loss of both genetic and
 environmental robustness – offering a rare window into the relationship
 between adaptation and canalization.
description: Wing
 sizewing sizes for selection
 and control populations at generation three and tenWing_size_data.csvmutagenesis dataAll the measurements were based on the F2 (male) and F3 (female) offspring after the mutagenesis treatment.mutagenesis_data.csvtemperature treatment dataData for defects with and without heat stress for selection and control populationstemperature_treatment_data.csv