cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.46635
title: Data from: Adaptive morphological shifts to novel habitats in marine sculpin fishes

description: Sculpin fishes of the North American Pacific Coast provide an ideal
 opportunity to examine whether adaptive morphological character shifts
 have facilitated occupation of novel habitat types because of their
 well-described phylogeny and ecology. In this group, the basal-rooted
 species primarily occupy the subtidal habitat, whereas the species in the
 most distal clades are found in the intertidal. We tested multiple
 evolutionary models to determine whether changes in body size and changes
 in number of scales are adaptive for habitat use in sculpins. Based on a
 statistically robust, highly resolved molecular phylogeny of 26 species of
 sculpins, in combination with morphometric and habitat affinity data, our
 analyses show that an adaptive model based on habitat use best explains
 changes in body size and number of scales. The habitat model was
 statistically supported over models of neutral evolution, stabilizing
 selection across all habitats, and three clade-based models. We suggest
 that loss of scales and reduction of body size in the intertidal may
 facilitate cutaneous breathing in air when tidepools become hypoxic during
 low tides. This study demonstrates how the combined use of phylogenetic,
 ecological and statistical approaches helps to identify traits that are
 likely adaptive to novel habitats.
description: Knope_Scales_sculpin_adaptThis file is the R code that runs OUCH (Butler and King, Am Nat 2004) on the sculpin body size and scale data. Each line of code is annotated to describe its specific function.SculpsAdapChar14This is the .csv file that contains the data.
DOI: 10.5061/dryad.061qt
title: Data from: Coevolutionary dynamics of polyandry and sex-linked meiotic drive

description: Segregation distorters located on sex chromosomes are predicted to sweep
 to fixation and cause extinction via a shortage of one sex, but in nature
 they are often found at low, stable frequencies. One potential resolution
 to this long-standing puzzle involves female multiple mating (polyandry).
 Because many meiotic drivers severely reduce the sperm competitive ability
 of their male carriers, females are predicted to evolve more frequent
 polyandry and thereby promote sperm competition when a meiotic driver
 invades. Consequently, the driving chromosome's relative fitness
 should decline, halting or reversing its spread. We used formal modeling
 to show that this initially appealing hypothesis cannot resolve the puzzle
 alone: other selective pressures (e.g. low fitness of drive homozygotes)
 are required to establish a stable meiotic drive polymorphism. However,
 polyandry and meiotic drive can strongly affect one another's
 frequency, and polyandrous populations may be resistant to the invasion of
 rare drive mutants.
description: R script for Model
 1Contains the script to
 run the deterministic simulation used to investigate Model 1. The code is
 annotated.Model 2 Matlab
 scriptMatlab script for the
 simulation termed Model 2. The code is annotated.
DOI: 10.5061/dryad.r3n52bf0
title: Data from: Resource and competitive dynamics shape the benefits of public goods cooperation in a plant pathogen

description: Cooperative benefits depend on a variety of ecological factors. Many
 cooperative bacteria increase the population size of their groups by
 making a public good available. Increased local population size can
 alleviate the constraints of kin competition on the evolution of
 cooperation by enhancing the between-group fitness of cooperators. The
 cooperative pathogenesis of Agrobacterium tumefaciens causes infected
 plants to exude opines—resources that provide a nearly exclusive source of
 nutrient for the pathogen. We experimentally demonstrate that opines
 provide cooperative A. tumefaciens cells a within-group fitness advantage
 over saprophytic agrobacteria. Our results are congruent with a
 resource-consumer competition model, which predicts that cooperative,
 virulent agrobacteria are at a competitive disadvantage when opines are
 unavailable, but have an advantage when opines are available at sufficient
 levels. This model also predicts that freeloading agrobacteria that
 catabolize opines but cannot infect plants competitively displace the
 cooperative pathogen from all environments. However, we show that these
 cooperative public goods also promote increased local population size. A
 model built from the Price Equation shows that this effect on group size
 can contribute to the persistence of cooperative pathogenesis despite
 inherent kin competition for the benefits of pathogenesis.
description: Octopine as sole carbon,
 nitrogen sourceOctopine
 competitions_15955 and TGP101Octopine
 competitions_R10 and KYC55Octopine clonal
 populationsOctopine mediated 15955
 population elasticity_nitrogen limitingOctopine mediated 15955
 population elasticity_carbon limiting
DOI: 10.5061/dryad.qf45rf2
title: Data from: Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles

description: Behavioral isolation is thought to arise early in speciation due to
 differential sexual and/or natural selection favoring different
 preferences and traits in different lineages. Alternatively, behavioral
 isolation can arise due to reinforcement favoring traits and preferences
 that prevent maladaptive hybridization. In darters, female preference for
 male coloration has been hypothesized to drive speciation, because
 behavioral isolation evolves before F1 inviability. However, as with many
 long-lived organisms, the fitness of second generation hybrids has not
 been assessed because raising animals to adulthood in the lab is
 challenging. Recently, reinforcement of male preferences has been
 implicated in darters because male preference for conspecific females is
 high in sympatry but absent in allopatry in multiple species pairs. The
 hypothesis that reinforcement accounts for behavioral isolation in
 sympatry assumes that hybridization and postzygotic isolation are present.
 Here, we used genomic and morphological data to demonstrate that
 hybridization is ongoing between orangethroat and rainbow darters and used
 hybrids collected from nature to measure postzygotic barriers across two
 hybrid generations. We observed sex ratio distortion in adult F1s and a
 dramatic reduction in backcross survival. Our findings indicate that
 selection to avoid hybridization promotes the evolution of male-driven
 behavioral isolation via reinforcement in this system.
description: color_behavior_dataThe first sheet in this file includes color pattern data for male orangethroat (OT) and rainbow (RB) darters and for male wild-caught hybrids (WH) and lab-raised hybrids (LH). Df = dorsal fin, Af = anal fin, Lat = lateral side, R = red, B = blue, PR = proportion red, PB = proportion blue. The second sheet in this file includes data from the wild-caught hybrid male aggression trials. The third sheet in this file includes data from the wild-caught hybrid male dichotomous mate choice trials.
DOI: 10.5061/dryad.867ts
title: Data from: Parting ways: Parasite release in nature leads to sex-specific evolution of defense

description: We evaluate the extent to which males and females evolve along similar or
 different trajectories in response to the same environmental shift.
 Specifically, we use replicate experimental introductions in nature to
 consider how release from a key parasite (Gyrodactylus) generates similar
 or different defense evolution in male versus female guppies (Poecilia
 reticulata). After 8-12 generations of evolution, guppies were collected
 from the ancestral (parasite still present) and derived (parasite now
 absent) populations and bred for two generations in the laboratory to
 control for non-genetic effects. These F2 guppies were then individually
 infected with Gyrodactylus and infection dynamics were monitored on each
 fish. We found that parasite release in nature led to sex-specific
 evolutionary responses: males did not show much evolution of resistance,
 whereas females showed the evolution of increased resistance. Given that
 male guppies in the ancestral population had greater resistance to
 Gyrodactylus than did females, evolution in the derived populations led to
 reduction of sexual dimorphism in resistance. We argue that previous
 selection for high resistance in males constrained (relative to females)
 further evolution of the trait. We advocate more experiments considering
 sex-specific evolutionary responses to environmental change.
description: Dargentetal.evolsexesJEBFile includes: individual identifier ("identifier"), names of populations used ("pop"), sex of individuals ("sex"), years of field sample ("year"), individuals standard length in mm ("startsl"), type of treatment ("type", i.e. sham or infected=2 G. turnbulli), peak parasite load ("peakpara"), parasite rate of increase r0 ("ro0to10"), outlier status of the individual ("outlier"), relative condition index ("startkn"), death during infection ("died"), and last day in which the individual was counted for parasites ("last count", i.e. day of death).
DOI: 10.15468/dl.jbje2c
title: Occurrence Download

description: A dataset containing 468 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lissorhoptrus oryzophilus"
 ]
}

 The dataset includes 468 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001284-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dr491
title: Data from: Corrections for rooting volume and plant size reveal negative effects of neighbour presence on root allocation in pea

description: Plants are able to detect the presence of their neighbours belowground.
 The associated root responses may affect plant performance, plant-plant
 interactions and community dynamics, but the extent and direction of these
 responses is heavily debated. Some studies suggest that plants will
 over-proliferate roots in response to neighbours at the expense of
 reproduction, which was framed as a “tragedy of the commons”. Others
 proposed an “ideal free distribution” hypothesis, stating that plants
 produce roots simply as a function of the amount of available nutrients.
 However, experimental evidence for either hypothesis that is unbiased by
 confounding effects of rooting volume and plant size in their experimental
 setups is still lacking. We grew split-root pea plants in the presence or
 absence of a belowground neighbour at a range of rooting volumes, while
 providing equal amounts of nutrients per plant. Path analyses were used to
 disentangle the direct effects of neighbour presence on allocation
 patterns from the confounding effects of rooting volume and plant size.
 Within the chosen range of rooting volumes, the presence of a belowground
 neighbour generally reduced plant root mass by 21% and total mass by 9%. A
 doubling of rooting volume generally increased plant root mass by 18% and
 total mass by 11%. Pod mass was only directly and positively correlated
 with vegetative mass. The presence of a belowground neighbour induced less
 root allocation but more pod allocation, whereas increased rooting volume
 caused a reduction in reproductive allocation. A large part of these
 effects, however, was indirectly mediated through the influence on plant
 total mass. Synthesis: Not considering the effects of rooting volume and
 plant size may lead to misinterpretations of plant growth strategies in
 response to neighbours. Accounting for these factors, we found pea
 allocating less mass to roots in the presence of a belowground neighbour.
 The obtained results can help to reconcile the various responses to
 belowground neighbours as they are published in the literature.
description: data_Chen_et_al_Funct_EcolBiomass components of pea plants collected from a greenhouse experiment
DOI: 10.5061/dryad.89nj3
title: Data from: Chronic household air pollution exposure is associated with impaired alveolar macrophage function in Malawian non-smokers

description: Background: Household air pollution in low income countries is an
 important cause of mortality from respiratory infection. We hypothesised
 that chronic smoke exposure is detrimental to alveolar macrophage
 function, causing failure of innate immunity. We report the relationship
 between macrophage function and prior smoke exposure in healthy Malawians.
 Methods: Healthy subjects exposed daily to cooking smoke at home
 volunteered for bronchoalveolar lavage. Alveolar macrophage particulate
 content was measured as a known correlate of smoke exposure. Phagocytosis
 and intraphagosomal function (oxidative burst and proteolysis) were
 measured by a flow cytometric assay. Cytokine responses in macrophages
 were compared following re-exposure in vitro to wood smoke, before and
 after glutathione depletion. Results: Volunteers had a range of alveolar
 macrophage particulate loading. The macrophage capacity for phagosomal
 oxidative burst was negatively associated with alveolar macrophage
 particulate content (n = 29, r2 = 0.16, p = 0.033), but phagocytosis per
 se and proteolytic function were unaffected. High particulate content was
 associated with lower baseline CXCL8 release (ratio 0.51, CI 0.29–0.89)
 and lower final concentrations on re-exposure to smoke in vitro (ratio
 0.58, CI 0.34–0.97). Glutathione depletion augmented CXCL8 responses by
 1.49x (CI 1.02–2.17) compared with wood smoke alone. This response was
 specific to smoke as macrophages response to LPS were not modulated by
 glutathione. Conclusion: Chronic smoke exposure is associated with reduced
 human macrophage oxidative burst, and dampened inflammatory cytokine
 responses. These are critical processes in lung defence against infection
 and likely to underpin the relationship between air pollution and
 pneumonia.
description: Baseline data for all
 volunteers in studyAs reported in Table
 1Volunteer_baseline_Table_1.csvExperiment_Figure_2As reported in Figure 2 - relationship between the carbon score of alveolar macrophages from volunteers and the macrophage function: oxidative burst; proteolysis; phagocytosis. Activity indices are calculated as described in the manuscript.Experiment_Figure_3As reported in Figure 3 - the effect of pre-existing (in vivo) alveolar carbon exposure with subsequent (in vitro) wood smoke particulate exposureExperiment_Figure_4As reported in Figure 4 - the effect of in vitro exposure of alveolar macrophages to BSO 0.2mM as measured by total and oxidised glutathione concentrations in the cell lysateExperiment_Figure_5As reported in Figure 5 - The effect of woodsmoke particulates and LPS on ex vivo alveolar macrophages as measured by cytokine release into the cell culture supernatant by multiplex ELISA
DOI: 10.5061/dryad.mv60m
title: Data from: Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests

description: Arthropods represent most of global biodiversity, with the highest
 diversity found in tropical rainforests. Nevertheless, we have a very
 incomplete understanding of how tropical arthropod communities are
 assembled. We conducted a comprehensive mass-sampling of arthropod
 communities within three major habitat types of lowland Amazonian
 rainforest, including terra firme clay, white-sand, and seasonally-flooded
 forests in Peru and French Guiana. We examined how taxonomic and
 functional composition (at the family level) differed across these habitat
 types in the two regions. The overall arthropod community composition
 exhibited strong turnover among habitats and between regions. In
 particular, seasonally-flooded forest habitats of both regions comprised
 unique assemblages. Overall, 17.7% (26 of 147) of arthropod families
 showed significant preferences for a particular habitat type. We present a
 first reproducible arthropod functional classification among the 147 taxa
 based on similarity among 21 functional traits describing feeding source,
 major mouthparts and microhabitats inhabited by each taxon. We identified
 seven distinct functional groups whose relative abundance contrasted
 strongly across the three habitats, with sap and leaf feeders showing
 higher abundances in terra firme clay forest. Our novel arthropod
 functional classification provides an important complement to link these
 contrasting patterns of composition to differences in forest functioning
 across geographic and environmental gradients. This study underlines that
 both environment and biogeographical processes are responsible for driving
 arthropod taxonomic composition while environmental filtering is the main
 driver of the variance in functional composition.
description: Abundance of 147 taxa of
 tropical arthropodsArthropod communities
 were sampled weekly in the twelve permanent plots from August to November
 2010 in French Guiana and between May and September 2011 in Peru,
 corresponding to drier periods in each region. We employed a multiple
 trapping method composed of two types of flight interception trap (FIT),
 the Malaise trap (MT) and the Windowpane trap (WT); and two types of
 attractive traps: the Fruit trap (FT) and the Automatic Light trap
 (ALT)data
 JAE-DRYAD-Lamarre.xlsx
DOI: 10.5281/zenodo.15062022
title: Phylogenomic species delimitation of Australian Psyllaephagus (Hymenoptera: Encyrtidae), parasitoids of lerp-forming psyllids (Hemiptera: Psylloidea)

description: Mitogene and UCE alignments as the input for the phylogenies and species delimitation analyses, produced for McClelland 2025, thesis chapter 3: 

Phylogenomic species delimitation of Australian Psyllaephagus (Hymenoptera: Encyrtidae), parasitoids of lerp-forming psyllids (Hemiptera: Psylloidea)
DOI: 10.5281/zenodo.15062021
title: Phylogenomic species delimitation of Australian Psyllaephagus (Hymenoptera: Encyrtidae), parasitoids of lerp-forming psyllids (Hemiptera: Psylloidea)

description: Mitogene and UCE alignments as the input for the phylogenies and species delimitation analyses, produced for McClelland 2025, thesis chapter 3: 

Phylogenomic species delimitation of Australian Psyllaephagus (Hymenoptera: Encyrtidae), parasitoids of lerp-forming psyllids (Hemiptera: Psylloidea)
DOI: 10.5061/dryad.417qd58
title: Data from: Improved access to early diagnosis and complete treatment of malaria in Odisha, India

description: Background In 2013, the Comprehensive Case Management Programme (CCMP) was
 initiated to assess the impact of universal access to diagnosis and
 treatment and improved surveillance on malaria transmission in different
 settings in Odisha state, India. Methods Pairs of intervention and control
 sub-districts (blocks), matched on malaria incidence were selected in four
 districts with different transmission intensities. CCMP activities
 included training and supervision, ensuring no stock-outs of malaria tests
 and drugs, analysing verified surveillance data, stratifying areas based
 on risk factors, and appointing alternative providers to underserved
 areas. Composite risk scores were calculated for each sub-centre using
 principal component analysis. Post−pre changes (2013–2015 versus
 2011–2012) for annual blood examination rates (ABER) and annual parasite
 incidence (API) across intervention and control groups were assessed using
 difference-in-difference (DID) estimates, adjusted for malaria
 transmission risk. Results In the intervention sub-centres, the mean
 increase in ABER was 6.41 tests/sub-centre (95%CI 4.69, 8.14;
 p&lt;0.01) and in API was 9.2 cases diagnosed/sub-centre (95%CI 5.18,
 13.21; p&lt;0.01). The control sub-centres reported lower increases in
 ABER (2.84 [95%CI 0.35, 5.34]; p&lt;0.05) and API (3.68 [95%CI 0.45,
 6.90]; p&lt;0.05). The control-adjusted post–pre changes in API showed
 that 5.52 more cases (95%CI 0.34, 10.70; p&lt;0.05) were diagnosed,
 and a 3.6 more cases (95%CI 0.58, 6.56; p&lt;0.05) were tested per
 sub-centre in the intervention versus control areas. Larger differences in
 post–pre changes in API between intervention and control sub-centres were
 registered in the higher transmission-risk areas compared with the lower
 risk areas. All the changes were statistically significant. Conclusions
 Intensive intervention activities targeted at improved access to malaria
 diagnosis and treatment produced a substantial increase in blood
 examination and case notification, especially in inaccessible,
 hard-to-reach pockets. CCMP provides insights into how to achieve
 universal coverage of malaria services through a routine, state-run
 programme.
description: PONE-D-18-26811_dataDataset
DOI: 10.5061/dryad.d0753
title: Data from: Hold your breath beetle – mites!

description: Respiratory gas exchange in insects occurs via a branching tracheal
 system. The entrances to the air-filled tracheae are the spiracles, which
 are gate-like structures in the exoskeleton. The open or closed state of
 spiracles defines the three possible gas exchange patterns of insects. In
 resting insects, spiracles may open and close over time in a repeatable
 fashion that results in a discontinuous gas exchange (DGE) pattern
 characterized by periods of zero organism-to-environment gas exchange.
 Several adaptive hypotheses have been proposed to explain why insects
 engage in DGE, but none have attracted overwhelming support. We provide
 support for a previously untested hypothesis that posits that DGE
 minimizes the risk of infestation of the tracheal system by mites and
 other agents. Here, we analyze the respiratory patterns of 15 species of
 ground beetle (Carabidae), of which more than 40% of individuals harbored
 external mites. Compared with mite-free individuals, infested one's
 engaged significantly more often in DGE. Mite-free individuals
 predominantly employed a cyclic or continuous gas exchange pattern, which
 did not include complete spiracle closure. Complete spiracle closure may
 prevent parasites from invading, clogging, or transferring pathogens to
 the tracheal system or from foraging on tissue not protected by thick
 chitinous layers.
description: Hold_your_breat_beetle_mites_dataData
DOI: 10.5061/dryad.fr89c0c
title: Data from: Optogenetic dissection of descending behavioral control in Drosophila

description: In most animals, the brain makes behavioral decisions that are transmitted
 by descending neurons to the nerve cord circuitry that produces behaviors.
 In insects, only a few descending neurons have been associated with
 specific behaviors. To explore how descending neurons control an
 insect's movements, we developed a novel method to systematically
 assay the behavioral effects of activating individual neurons on freely
 behaving terrestrial D. melanogaster. We calculated a two-dimensional
 representation of the entire behavior space explored by these flies and we
 associated descending neurons with specific behaviors by identifying
 regions of this space that were visited with increased frequency during
 optogenetic activation. Applying this approach across a large collection
 of descending neurons, we found that (1) activation of most of the
 descending neurons drove stereotyped behaviors, (2) in many cases multiple
 descending neurons activated similar behaviors, and (3)
 optogenetically-activated behaviors were often dependent on the behavioral
 state prior to activation.
description: Movies of
 optogenetically activated split-Gal4 linesEach movie contains 1
 second before and after optogenetic stimulation for all experimental
 (retinal +) and control (retinal -) flies for all stimulation
 trials.opto_movies.zip