cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0pv6570
title: Data from: Rapid change in host specificity in a field population of the biological control organism Pasteuria penetrans

description: In biological control, populations of both the biological control agent
 and the pest have the potential to evolve, and even to coevolve. This
 feature marks the most powerful and unpredictable aspect of biological
 control strategies. In particular, evolutionary change in host specificity
 of the biological control agent could increase or decrease its efficacy.
 Here, we tested for change in host specificity in a field population of
 the biological control organism Pasteuria penetrans. Pasteuria penetrans
 is an obligate parasite of the plant parasitic nematodes Meloidogyne spp.,
 which are major agricultural pests. From 2013 through 2016, we collected
 yearly samples of P. penetrans from eight plots in a field infested with
 M. arenaria. Plots were planted either with peanut (Arachis hypogaea) or
 with a rotation of peanut and soybean (Glycine max). To detect temporal
 change in host specificity, we tested P. penetrans samples annually for
 their ability to attach to (and thereby infect) four clonal lines of M.
 arenaria. After controlling for temporal variation in parasite abundance,
 we found that P. penetrans from each of the eight plots showed temporal
 variation in their attachment specificity to the clonal host lines. The
 trajectories of change in host specificity were largely unique to each
 plot. This result suggests that local forces, at the level of individual
 plots, drive change in specificity. We hypothesize that coevolution with
 local M. arenaria hosts may be one such force. Lastly, we observed an
 overall reduction in attachment using samples from rotation relative to
 peanut plots. This result may reflect lower abundance of P. penetrans
 under crop rotation, potentially due to suppressed density of host
 nematodes. As a whole, the results show local change in specificity on a
 yearly basis, consistent with evolution of a biological control organism
 in its ability to infect and suppress its target pest.
description: Data_for_ChangGibson2018_EvolAppData file for Chang, Gibson et al. Evolutionary Applications. Each row presents the results of the bioassay of 25 nematodes in each clonal line x plot x treatment x year combination. Column "Year" indicates the year the soil sample was collected. Column "SEM" (single-egg mass line) indicates the clonal host line used for testing the soil (or the heterogeneous Greenhouse line). Column "Plot" indicates which plot the soil sample was drawn from. Column "Treatment" indicates whether or not the plot was part of the Peanut or Rotation treatments. Column "Replicate" is a repeat of the "Plot" column, but with unique identifiers. Columns "A" through "AD" show the number of endospores attached to individual nematodes within each of the combinations indicated by the beginning columns.ChangGibsonetal2018_RScriptsR Markdown file containing scripts for analyses and figures in the paper.
DOI: 10.5061/dryad.8k28p34
title: Data from: Temperature-dependent oxygen limitation and the rise of Bergmann’s Rule in species with aquatic respiration

description: Bergmann’s Rule is the propensity for species-mean body size to decrease
 with increasing temperature. Temperature-dependent oxygen limitation has
 been hypothesized to help drive temperature–size relationships among
 ectotherms, including Bergmann’s Rule, where organisms reduce body size
 under warm oxygen-limited conditions, thereby maintaining aerobic scope.
 Temperature-dependent oxygen limitation should be most pronounced among
 aquatic ectotherms that cannot breathe aerially, as oxygen solubility in
 water decreases with increasing temperature. We use
 phylogenetically-explicit analyses to show that species-mean adult size of
 aquatic salamanders with branchial or cutaneous oxygen uptake becomes
 small in warm environments and large in cool environments, whereas body
 size of aquatic species with lungs (i.e., that respire aerially), as well
 as size of semi aquatic and terrestrial species do not decrease with
 temperature. We argue that oxygen limitation drives the evolution of small
 size in warm aquatic environments for species with aquatic respiration.
 More broadly, the stronger decline in size with temperature observed in
 aquatic vs terrestrial salamander species mirrors the relatively strong
 plastic declines in size observed previously among aquatic vs terrestrial
 invertebrates, suggesting that temperature-dependent oxygen availability
 can help drive patterns of plasticity, micro- and macroevolution.
description: Dryad.SVLBody-size data coupled with corresponding range size data, temperature data, and habitat data used in all analysesDryad.Water.TemperatureWater temperature data collected from the literature, describing water temperature for various populations of aquatic salamanders. Descriptions of each temperature estimate and references are given.
DOI: 10.5061/dryad.42517
title: Data from: The genetics of extreme microgeographic adaptation: an integrated approach identifies a major locus underlying leaf trichome divergence in Yellowstone Mimulus guttatus

description: Microgeographic adaptation provides a particularly interesting context for
 understanding the genetic basis of phenotypic divergence, and may also
 present unique empirical challenges. In particular, plant adaptation to
 extreme soil mosaics may generate barriers to gene flow or shifts in
 mating system that confound simple genomic scans for adaptive loci. Here,
 we combine three approaches - QTL mapping of candidate intervals in
 controlled crosses, population resequencing (PoolSeq), and analyses of
 wild recombinant individuals - to investigate one trait associated with
 Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in
 Yellowstone National Park. We mapped a major QTL causing dense leaf
 trichomes in thermally-adapted plants to a &lt; 50kb region of Linkage
 Group 14 (Tr14) previously implicated in trichome divergence between
 independent M. guttatus populations. A PoolSeq scan of Tr14 region
 revealed a cluster of six genes, co-incident with the inferred QTL peak,
 with high allele frequency differences sufficient to explain observed
 phenotypic differentiation. One of these, the R2R3 MYB transcription
 factor Migut.N02661, is a plausible functional candidate, and was also
 strongly-associated (r2 = 0.27) with trichome phenotype in analyses of
 wild-collected admixed individuals. Although functional analyses will be
 necessary to definitively link molecular variants in Tr14 with trichome
 divergence, our analyses are a major step in that direction. They point to
 a simple, and parallel, genetic basis for one axis of Mimulus guttatus
 adaptation to an extreme habitat, suggest a broadly conserved genetic
 basis for trichome variation across flowering plants, and pave the way for
 further investigations of this challenging case of microgeographic
 incipient speciation.
description: Data for
 MEC-16-0039R1The excel file contains
 4 sheets with datasets from this paper.This file contains datasets
 analyzed in Hendrick et al. 2016 paper on trichome variation in
 Yellowstone Mimulus guttatus 1. SdtrichQTL - phenotypes and marker
 genotypes from an outbred F2 mapping population (AHQT x AHQNT), grown
 under short daylengths and cool temperature conditions 2. AHQF2_2015 -
 pehnotypes and genotypes from an inbred line F2 (AHQT x AHQNT) grown under
 long daylength conditions in greenhouse 3. AHQgradient_markerpopgen -
 STRUCTURE input file for AHQT (plots 1-6), AHQNT (plots 14-17), AND
 AHQ_Canyon (plots 7-13) populations, marker information is in Lekberg et
 al. 2012 4. AHQG15-trichadmixture - marker genotypes and phenotypes for
 wild Tr14-recombinant AHQNT AND AHQ_Canyon individuals grown under common
 garden conditionsAHQtrichomes_Dryad.xlsx
DOI: 10.5061/dryad.m21m300
title: Data from: Dressed to impress: breeding plumage as a reliable signal of innate immunity

description: Animal signals involved in sexual selection are often indicators of
 individual quality. The assumption that sexual characters such as breeding
 plumage may indicate immune state has rarely been tested in free-living
 migratory birds, particularly in relation to innate immunity. If sexual
 characters indeed reflect immune condition, then these could be used to
 evaluate individual quality. Melanin is a common pigment used in animal
 communication that mitigates the effects of oxidative stress and has
 positive effects on energy homeostasis, important functions during the
 strenuous activity of long-distance flights. However, melanin is also
 immunosuppressive, and the melanised patches of breeding plumage may to
 some extent compromise immune responsiveness. We studied melanin-based
 secondary sexual characters (SSC) in a long-distance migratory wader, the
 Black-tailed godwit (Limosa limosa), and found that breeding plumage
 features of male and female godwits are linked to components of innate
 immunity. Males with a larger colour extension had higher circulating
 levels of haptoglobin and hemolysis activity, while they also presented a
 lower body condition; whereas females presented a negative trend between
 colour and bar extension and hemolysis activity, and a positive trend for
 natural antibodies. The association between signal, immune state and
 physical condition in males suggests a cost for signal production and
 immune condition during prenuptial migration. Sex differences in how
 signals relate with immune capacity are a likely consequence of
 sex-specific signalling roles and energy demands. Our results indicate
 that male godwit breeding plumage reflects innate immunity state, and is
 therefore a likely signal for females to use during mate choice as an
 honest indicator of male’s capacity to allocate energy/resources to both
 expensive traits during periods of energetic constraint.
description: Female_and_Male_Full_DatabaseFull database regarding male and female morphometrics (tarsus length, weight and body condition), innate immunity results (haptoglobin, hemolysis-hemagglutination assay, leukocyte proportions, WBC and H/L index) as well as the melanin-based secondary sexual characters (bars, orange, color extent, bill color, percentage of bill orange color and number of wintering feathers). Columns Cell PC1 and PC2 as well as SSC1, SSC2 and SSC3, result from the PCA analysis done as described on the methods section of this paper.Feather_coloration_RawResults_Females_and_MalesRaw results of spectrophotometric data of breast feather coloration of male and female and feather coloration PCA results.
DOI: 10.5061/dryad.b2c80
title: Data from: The distribution of fruit and seed toxicity during development for eleven Neotropical trees and vines in Central Panama

description: Secondary compounds in fruit mediate interactions with natural enemies and
 seed dispersers, influencing plant survival and species distributions. The
 functions of secondary metabolites in plant defenses have been
 well-studied in green tissues, but not in reproductive structures of
 plants. In this study, the distribution of toxicity within plants was
 quantified and its influence on seed survival was determined in Central
 Panama. To investigate patterns of allocation to chemical defenses and
 shifts in allocation with fruit development, I quantified variation in
 toxicity between immature and mature fruit and between the seed and
 pericarp for eleven species. Toxicity of seed and pericarp was compared to
 leaf toxicity for five species. Toxicity was measured as reduced hyphal
 growth of two fungal pathogens, Phoma sp. and Fusarium sp., and reduced
 survivorship of brine shrimp, Artemia franciscana, across a range of
 concentrations of crude extract. I used these measures of potential
 toxicity against generalist natural enemies to examine the effect of fruit
 toxicity on reductions of fruit development and seed survival by
 vertebrates, invertebrates, and pathogens measured for seven species in a
 natural enemy removal experiment. The seed or pericarp of all vertebrate-
 and wind-dispersed species reduced Artemia survivorship and hyphal growth
 of Fusarium during the immature and mature stages. Only mature fruit of
 two vertebrate-dispersed species reduced hyphal growth of Phoma.
 Predispersal seed survival increased with toxicity of immature fruit to
 Artemia during germination and decreased with toxicity to fungi during
 fruit development. This study suggests that fruit toxicity against
 generalist natural enemies may be common in Central Panama. These results
 support the hypothesis that secondary metabolites in fruit have adaptive
 value and are important in the evolution of fruit-frugivore interactions.
description: Bioassay data describing
 activity of crude extracts from fruits in Central PanamaMeasurements of fungal
 hyphal growth and brine shrimp survivorship in crude extracts of fruit
 collected from Central Panamadata_PLOSONE.RR code for analysesScript_Analyses.RR functions used in analysesScript_Functions.R
DOI: 10.3886/e244681
title: FiCli: Fish and Climate Change Database (ver. 3.0, October 2024)

description: Inland fishes provide important ecosystem services to communities worldwide and are especially vulnerable to the impacts of climate change. Fish respond to climate change in diverse and nuanced ways which creates challenges for practitioners of fish conservation, climate change adaptation, and management. Although climate change is known to affect fish globally, a comprehensive online, public database of how climate change has impacted inland fishes worldwide and adaptation or management practices that may address these impacts does not exist. We conducted an extensive, systematic primary literature review to identify peer-reviewed journal publications describing projected and documented examples of climate change impacts on inland fishes. From this standardized Fish and Climate Change database, FiCli, researchers and managers can query fish families, species, response types, or geographic locations to obtain summary information on inland fish responses to climate change and recommended management actions. The FiCli provides access to comprehensive published information to inform inland fish Inland fishes provide important ecosystem services to communities worldwide and are especially vulnerable to the impacts of climate change. Related External Resources: https://rconnect.usgs.gov/ficli
description: (Downloaded 2026-01-26)
DOI: 10.3886/e244681v1
title: FiCli: Fish and Climate Change Database (ver. 3.0, October 2024)

description: Inland fishes provide important ecosystem services to communities worldwide and are especially vulnerable to the impacts of climate change. Fish respond to climate change in diverse and nuanced ways which creates challenges for practitioners of fish conservation, climate change adaptation, and management. Although climate change is known to affect fish globally, a comprehensive online, public database of how climate change has impacted inland fishes worldwide and adaptation or management practices that may address these impacts does not exist. We conducted an extensive, systematic primary literature review to identify peer-reviewed journal publications describing projected and documented examples of climate change impacts on inland fishes. From this standardized Fish and Climate Change database, FiCli, researchers and managers can query fish families, species, response types, or geographic locations to obtain summary information on inland fish responses to climate change and recommended management actions. The FiCli provides access to comprehensive published information to inform inland fish Inland fishes provide important ecosystem services to communities worldwide and are especially vulnerable to the impacts of climate change. Related External Resources: https://rconnect.usgs.gov/ficli
description: (Downloaded 2026-01-26)
DOI: 10.5061/dryad.67st708
title: Data from: Analysis of a meningococcal meningitis outbreak in Niger – potential effectiveness of reactive prophylaxis

description: Background: Seasonal epidemics of bacterial meningitis in the African
 Meningitis Belt carry a high burden of disease and mortality. Reactive
 mass vaccination is used as a control measure during epidemics, but the
 time taken to gain immunity from the vaccine reduces the flexibility and
 effectiveness of these campaigns. Targeted reactive antibiotic prophylaxis
 could be used to supplement reactive mass vaccination and further reduce
 the incidence of meningitis, and the potential effectiveness and
 efficiency of these strategies should be explored. Methods and Findings:
 Data from an outbreak of meningococcal meningitis in Niger, caused
 primarily by Neisseria meningitidis serogroup C, is used to estimate
 clustering of meningitis cases at the household and village level. In
 addition, reactive antibiotic prophylaxis and reactive vaccination
 strategies are simulated to estimate their potential effectiveness and
 efficiency, with a focus on the threshold and spatial unit used to declare
 an epidemic and initiate the intervention. There is village-level
 clustering of suspected meningitis cases after an epidemic has been
 declared in a health area. Risk of suspected meningitis among household
 contacts of a suspected meningitis case is no higher than among members of
 the same village. Village-wide antibiotic prophylaxis can target
 subsequent cases in villages: across of range of parameters pertaining to
 how the intervention is performed, up to 220/672 suspected cases during
 the season are potentially preventable. On the other hand, household
 prophylaxis targets very few cases. In general, the village-wide strategy
 is not very sensitive to the method used to declare an epidemic. Finally,
 village-wide antibiotic prophylaxis is potentially more efficient than
 mass vaccination of all individuals at the beginning of the season, and
 than the equivalent reactive vaccination strategy. Conclusions:
 Village-wide antibiotic prophylaxis should be considered and tested
 further as a response against outbreaks of meningococcal meningitis in the
 Meningitis Belt, as a supplement to reactive mass vaccination.
description: Data for ciprofloxacin
 prophylaxis as meningitis outbreak response modeling
 studyThere are three separate
 .csv files. The first contains information relative to the villages of the
 study area. The second contains information relative to the households of
 meningitis cases. The third contains information relative to the
 individual meningitis cases.Niger ciprofloxacin modeling
 study.zip
DOI: 10.5061/dryad.pq3j34p
title: Data from: Immediate impact of a hurricane on the structure of a tropical butterfly community

description: More intense and frequent hurricanes may lead to long-lasting effects to
 tropical ecosystems. Here we describe the immediate impact on the
 butterfly community of a lowland forest in Belize, following Hurricane
 Earl. Species richness and abundance increased post-hurricane, likely
 driven by convergence of the organisation between the canopy and
 understory communities.
description: OpenAccessData_ButterflyManuscriptExcel file with four sheets. Providing data on the species and number of individuals caught in each trap before and after the hurricane; traits measured of individual butterflies caught in each trap before and after the hurricane, and the range and number of host plants for each butterfly species gathered from online sources; habitat variables measured within 5m radius of each trap before and after the hurricane; and data from six 100m transects walked within the study site to estimate the level of damage caused to the forest stand following the hurricane.
DOI: 10.5061/dryad.610pf
title: Data from: Intrinsic factors drive spatial genetic variation in a highly vagile species, the wedge-tailed eagle (Aquila audax), in Tasmania

description: Knowledge of dispersal in a species, both its quantity and the factors
 influencing it, are crucial for our understanding of ecology and
 evolution, and for species conservation. Here we quantified and formally
 assessed the potential contribution of extrinsic factors on individual
 dispersal in the threatened Tasmanian population of wedge-tailed eagle,
 Aquila audax. As successful breeding by these individuals appears strongly
 related to habitat, we tested the effect of landscape around sampling
 sites on genetic diversity and spatial genetic variation, as these are
 influenced by patterns of dispersal. Similarly, we also tested whether
 habitat intervening sampling sites could explain spatial genetic
 variation. Twenty microsatellites were scored, but only a small proportion
 of spatial genetic variation (4.6%) could be explained by extrinsic
 factors, namely habitat suitability and elevation between sites. However,
 significant clinal genetic variation was evident across Tasmania, which we
 explain by intrinsic factors, likely high natal philopatry and occasional
 long-distance dispersal. This study demonstrates that spatial genetic
 variation can be detected in highly vagile species at spatial scales that
 are small relative to putative dispersal ability, although here there was
 no substantial relationship with landscape factors tested.
description: Aquila audax
 microsatellite dataData for 20
 microsatellite loci Tasmanian Aquila audax, in genepop
 format.A.audax-microsatellite-data.txtAquila audax sample locationsSample locations for 154 Aquila audax tissues in Tasmania.A.audax-sample-locations.xlsx