cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h6231
title: Data from: The role of hermaphrodites in the experimental evolution of increased outcrossing rates in Caenorhabditis elegans

description: Background: Why most organisms reproduce via outcrossing rather than
 selfing is a central question in evolutionary biology. It has long ago
 been suggested that outcrossing is favoured when it facilitates adaptation
 to novel environments. We have previously shown that the experimental
 evolution of increased outcrossing rates in populations of the
 male-hermaphrodite nematode Caenorhabditis elegans were correlated with
 the experimental evolution of increased male fitness. However, it is
 unknown whether outcrossing led to adaptation, and if so, which fitness
 components can explain the observed increase in outcrossing rates.
 Results: Using experimental evolution in six populations with initially
 low standing levels of genetic diversity, we show with head-to-head
 competition assays that population-wide fitness improved during 100
 generations. Since outcrossing rates increased during the same period,
 this result demonstrates that outcrossing is adaptive. We also show that
 there was little evolution of hermaphrodite fitness under conditions of
 selfing or under conditions of outcrossing with unrelated tester males. We
 nonetheless find a positive genetic correlation between hermaphrodite
 self-fitness and population-wide fitness, and a negative genetic
 correlation between hermaphrodite mating success and population-wide
 fitness. These results suggest that the several hermaphrodite traits
 measured are fitness components. Tradeoffs expressed in hermaphrodites,
 particularly noticed between self-fitness and mating success, may in turn
 explain their lack of change during experimental evolution. Conclusions:
 Our findings indicate that outcrossing facilitates adaptation to novel
 environments. They further indicate that the experimental evolution of
 increased outcrossing rates depended little on hermaphrodites because of
 fitness tradeoffs between selfing and outcrossing. Instead, the evolution
 of increased outcrossing rates appears to have resulted from unhindered
 selection on males.
description: READMEDescription of the
 contents of the data package: 1. One text file, named
 "Population_fitness.txt" 2. One text file, named
 "Male_fitness.txt" 3. One text file, named
 "Hermaphrodite_fitness.txt"population_fitnessmale_fitnesshermaphrodite_fitness
DOI: 10.15468/dl.9mhhc3
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Dendrobium aphyllum"
 ]
}

 The dataset includes 95 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001313-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7nr70
title: Data from: Two eggs, two different constraints: a potential explanation for the puzzling intra-clutch egg size dimorphism in Eudyptes penguins

description: Phenotypic plasticity and phenotypic stability are major components of the
 adaptive evolution of organisms to environmental variation. The invariant
 two-egg clutch size of Eudyptes penguins has recently been proposed to be
 a unique example of a maladaptive phenotypic stability, while their egg
 mass is a plastic trait. We tested whether this phenotypic plasticity
 during reproduction might result from constraints imposed by migration
 (migratory carry-over effect) and breeding (due to the depletion of female
 body reserves). For the first time, we examined whether these constraints
 differ between eggs within clutches and between egg components (yolk and
 albumen). The interval between colony return and clutch initiation
 positively influenced the yolk mass, the albumen mass, and the subsequent
 total egg mass of first-laid eggs. This time interval had only a slight
 negative influence on the yolk mass of second-laid eggs and no influence
 on their albumen and subsequent total masses. For both eggs, female body
 mass at laying positively influenced albumen and total egg masses. Female
 investment into the entire clutch was not related to the time in the
 colony before laying but increased with female body mass. These novel
 results suggest that the unique intraclutch egg size dimorphism exhibited
 in Eudyptes penguins, with first-laid eggs being consistently smaller than
 second-laid eggs, might be due to a combination of constraints: a
 migratory carry-over effect on the first-laid egg and a body reserve
 depletion effect on the second-laid egg. Both these constraints might
 explain why the timing of reproduction, especially egg formation, is
 narrow in migratory capital breeders.
description: Poisbleau et al. 2015
 E&E BDDOriginal data collected
 in the field on females and eggs.
DOI: 10.5061/dryad.h32j9
title: Data from: Signals of selection in outlier loci in a widely dispersing species across an environmental mosaic

description: Local adaptation reflects a balance between natural selection and gene
 flow and is classically thought to require the retention of locally
 adapted alleles. However, organisms with high dispersal potential across a
 spatially or temporally heterogeneous landscape pose an interesting
 challenge to this view requiring local selection every generation or when
 environmental conditions change to generate adaptation in adults. Here, we
 test for geographical and sequence-based signals of selection in five
 putatively adaptive and two putatively neutral genes identified in a
 previous genome scan of the highly dispersing purple sea urchin,
 Strongylocentrotus purpuratus. Comparing six populations spanning the
 species’ wide latitudinal range from Canada to Baja California, Mexico, we
 find positive tests for selection in the putative adaptive genes and not
 in the putative neutral genes. Specifically, we find an excess of
 low-frequency and nonsynonymous polymorphisms in two transcription factors
 and a transporter protein, and an excess of common amino acid
 polymorphisms in the two transcription factors, suggestive of spatially
 balancing selection. We test for a genetic correlation with temperature, a
 dominant environmental variable in this coastal ecosystem. We find mild
 clines and a stronger association of genetic variation with temperature
 than latitude in four of the five putative adaptive loci and a signal of
 local adaptation in the Southern California Bight. Overall, patterns of
 genetic variation match predictions based on spatially or temporally
 balancing selection in a heterogeneous landscape and illustrate the value
 of geographical and coalescent tests on candidate loci identified in a
 genome-wide scan for selection.
description: Genomic sequence data
 from eight nuclear exons in the purple sea urchin, Strongylocentrotus
 purpuratusThis data submission
 includes sequence data in fasta format for 8 nuclear exons from 165
 field-collected purple sea urchins from Bamfield, Canada to Baja
 California, Mexico. Genomic DNA was sequenced in both forward and reverse
 directions, and visualized and cleaned using Sequencher software. Each
 file is named by the gene identifier corresponding to the S. purpuratus
 genome (spbase.org). Each sequence is named with a five digit code
 identifying the individual urchin sequenced, followed by the gene number
 for that locus. The five digit individual identifier consists of three
 letters, "P" for "purpuratus," followed by two letters
 for the sample site, followed by two numbers identifying the individual.
 Location codes are as follows: BM – Bamfield, Canada; BB – Boiler Bay,
 Oregon; PP – Patrick’s Point, California; MY – Monterey, California; SD –
 San Diego, California; BJ – La Bufadora, Baja California, Mexico; PB –
 Punta Baja, Baja California, Mexico; SC – Punta San Carlos, Baja
 California, Mexico. See Table 2 of the paper for latitude /longitude
 details.Pespeni_MolEcol2013_SequenceData.zip
DOI: 10.5061/dryad.rb7g719t
title: Data from: Group-size diversity in public goods games

description: Public goods games are models of social dilemmas where cooperators pay a
 cost for the production of a public good while defectors free ride on the
 contributions of cooperators. In the traditional framework of evolutionary
 game theory, the payoffs of cooperators and defectors result from
 interactions in groups formed by binomial sampling from an infinite
 population. Despite empirical evidence showing that group-size
 distributions in nature are highly heterogeneous, most models of social
 evolution assume that the group size is constant. In this paper, I remove
 this assumption and explore the effects of having random group sizes on
 the evolutionary dynamics of public goods games. By a straightforward
 application of Jensen's inequality, I show that the outcome of
 general nonlinear public goods games depends not only on the average group
 size but also on the variance of the group-size distribution. This general
 result is illustrated with two nonlinear public goods games (the public
 goods game with discounted or synergistic benefits and the
 volunteer's dilemma) and three different group-size distributions
 (Poisson, geometric, and Waring). The results suggest that failing to
 acknowledge the natural variation of group sizes can lead to an
 underestimation of the actual level of cooperation exhibited in evolving
 populations.
description: READMEReadMe
 fileplot_fig2R script for generating Fig. 2plot_fig3R script for generating Fig. 3plot_fig5R script for generating Fig. 5common_functionsR script with several functions required by the other scriptsgen_data_fig2rightR script for generating the data required to plot the right panel of Fig. 2
DOI: 10.5061/dryad.5bn554h
title: Data from: Life-history and behavioral trait covariation across 3 years in Temnothorax ants

description: Consistent among- individual differences in behavior have been described
 in numerous taxa. More recently, the hypothesis that such behavioral
 variation may also correlate to life-history traits, such as investment in
 current or future reproduction, has been proposed as a potential
 explanation for why variation is maintained among and within populations.
 A continual challenge in measuring the integration of these traits, or the
 Pace – of – Life Syndrome, is to find a reliable and quantifiable proxy
 for energy allocation between reproduction and self-maintenance. Here, I
 address this challenge using the eusocial insects, Temnothorax ants, in a
 common garden experiment to directly quantify energy allocation by
 tracking the number of sterile workers (somatic effort) and winged
 reproductive ants (reproductive effort) produced across years. I use
 colonies collected from populations previously demonstrated to show
 significant differences in a risk-tolerance behavioral syndrome. I provide
 an empirical test of the Pace – Of – Life Syndrome hypothesis between two
 populations of Temnothorax ants over three years. I find strong evidence
 for a Pace – Of – Life Syndrome between populations and weaker, but
 present support for a within population POLS. More risk-tolerant
 populations also allocate more energy towards reproduction and grow faster
 across years. This study then emphasizes the value of a more holistic
 study of among-individual variation. Additionally, it suggests more
 research is needed on understanding how and why traits may correlate in
 some populations, but remain independent in others.
description: compiled_POLS_3yr
DOI: 10.15468/dl.9wvc63
title: Occurrence Download

description: A dataset containing 364 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tor putitora"
 ]
}

 The dataset includes 364 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001312-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63m81
title: Data from: Morphological support for a clade comprising two vermiform mite lineages: Eriophyoidea (Acariformes) and Nematalycidae (Acariformes)

description: A morphology-based parsimony analysis (50 taxa; 110 characters) focused on
 relationships among basal acariform mites places Eriophyoidea (formerly in
 Trombidiformes) within Nematalycidae (Sarcoptiformes). Although both taxa
 have worm-like bodies, this grouping is unexpected because it combines
 obligate plant inhabitants (Eriophyoidea) with obligate inhabitants of
 deep-soil or mineral regolith (Nematalycidae sensu stricto). The
 Eriophyoidea + Nematalycidae clade, which is strongly supported (Bremer
 =5; bootstrap =85%), retains moderately good support (Bremer=3;
 bootstrap=66%) when three ratio-based characters pertaining to body shape
 are excluded. A total of eleven unambiguous synapomorphies unite all or
 some of Nematalycidae with Eriophyoidea. These include an annulated
 opisthosoma, an unpaired vi seta on the prodorsum, fusion of the palp
 trochanter with the palp femur, and a large relative distance between the
 anus and the genitalia. Three of the four Triassic genera of
 eriophyoid-like mites were also included in our analysis. Although all
 four genera have been tentatively placed within a new superfamily, we
 found no support for the monophyly of this group. One other interesting
 result of the analysis is the placement of a “living fossil”,
 Proterorhagia oztotloica (Proterorhagiidae), as sister to the rest of
 Acariformes. However, support for this relationship is weak.
description: Morphological data on
 basal Acariformes formatted for phylogenetic analysis in
 PAUPIncludes representatives
 of all families of Endeostigmata. Data also includes many representatives
 of basal Trombidiformes. This dataset was generated to test hypotheses on
 the phylogenetic location of Eriophyoidea. It includes 6 species of
 Nematalycidae and 8 species of Eriophyoidea (including 3 Triassic
 species). Character coding is explained in detail in the text of the
 associated publication.Basal_Acariformes.txt
DOI: 10.5061/dryad.5fp4g
title: Data from: Digestive capacity and toxicity cause mixed diets in red knots that maximize energy intake rate

description: In energy-maximizing animals, preferences for different prey can be
 explained by ranking them by their energetic content. However, diet choice
 also depends on characteristics of the predator such as the need to ingest
 necessary nutrients, and constraints imposed by digestion and toxins in
 food. In combination, these factors can lead to mixed diets in which the
 energetically most profitable food is not eaten exclusively even when it
 is abundant. We studied diet choice in red knots (Calidris canutus
 canutus) feeding on mollusks at a West-African wintering site. At this
 site, the birds fed primarily on two species of bivalves, a thick-shelled
 one (Dosinia isocardia) that imposed a digestive constraint, and a
 thin-shelled one that imposed a toxin constraint (Loripes lucinalis). The
 latter species is toxic due to its symbiotic association with
 sulphide-oxidizing bacteria. We estimated experimentally the parameters of
 a linear programming model that includes both digestive and toxin
 constraints, leading to the prediction that red knots should eat a mixture
 of both mollusk species to maximize energy intake. The model correctly
 predicted the preferences of the captive birds, which depended on the
 digestive quality and toxicity of their previous diet. At our study site,
 energy maximizing red knots appear to select a mixed diet as a result of
 the simultaneous effects of digestive and toxin constraints.
description: data experiment
 1Intake rates of captive
 red knots (Calidris canutus canutus) were measured, feeding for 6 hours on
 monospecific diets of either Loripes lucinalis or Dosinia Isocardia. Shown
 are ash-free dry flesh intake rate in mg/s (AFDMIR), dry shell mass intake
 in mg/s (DMIR) and water intake in ml/hour (WaterIR). Further details can
 be found in Oudman et al. (2014, American Naturalist).data experiment
 2Diet
 choice of captive red knots (Calidris canutus canutus) were determined
 after being fed a diet of either Loripes lucinalis or Dosinia isocardia,
 by offering both species simultaneously in seperate piles on a tray.
 Trials ended after 20 prey choices, or after one hour (1 case, 13
 ingestions). Species of each prey ingestion was recorded. Further details
 can be found in Oudman et al. (2014, American
 Naturalist)
DOI: 10.5061/dryad.nd764
title: Data from: Long-term reproductive impairment in a seabird after the Prestige oil spill

description: Large oil spills are dramatic perturbations on marine ecosystems, and
 seabirds are one of the worst affected organisms in such events. It has
 been argued that oil spills may have important long-term consequences on
 marine organisms, but supporting evidence remains scarce. The European
 shag (Phalacrocorax aristotelis) was strongly impacted at population level
 by the Prestige oil spill, the biggest spillage in the eastern North
 Atlantic. In this paper, we report on the long-term consequences on
 reproduction of this coastal seabird, using temporal and spatial
 replicated data (before–after–control–impact design). Our study revealed
 long-term reproductive impairment during at least the first 10 years since
 the Prestige oil spill. Annual reproductive success did not differ before
 the impact, but after the impact it was reduced by 45% in oiled colonies
 compared with unoiled ones. This is a rare documentation of long-term
 effects after a major oil spill, highlighting the need for long-term
 monitoring in order to assess the real impact of this type of disturbance
 on marine organisms.
description: data-set used in study
 of long-term effects of the Prestige oil spill in the European
 shagThis file contains data
 on reproductive success, climatic variables values (NAO and SST), and
 presence/absence of American mink in the colonies of European shag needed
 for the analyses presented in our study. Information about periods
 (before/after Prestige) and areas (oiled/unoiled) is also
 presentedlong-term data
 set.xlsx
DOI: 10.5061/dryad.7rq20
title: Data from: Ants show a leftward turning bias when exploring unknown nest sites

description: Behavioural lateralization in invertebrates is an important field of study
 because it may provide insights into the early origins of lateralization
 seen in a diversity of organisms. Here, we present evidence for a leftward
 turning bias in Temnothorax albipennis ants exploring nest cavities and in
 branching mazes, where the bias is initially obscured by thigmotaxis
 (wall-following) behaviour. Forward travel with a consistent turning bias
 in either direction is an effective nest exploration method, and a simple
 decision-making heuristic to employ when faced with multiple directional
 choices. Replication of the same bias at the colony level would also
 reduce individual predation risk through aggregation effects, and may lead
 to a faster attainment of a quorum threshold for nest migration. We
 suggest the turning bias may be the result of an evolutionary interplay
 between vision, exploration and migration factors, promoted by the
 ants' eusociality.
description: Turning bias
 dataData for two experiments
 investigating turning bias in ants exploring unknown nest sites and
 branching mazes.Turning_bias_data.xlsx
DOI: 10.15468/dl.ktcxk4
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Dendrocalamus giganteus"
 ]
}

 The dataset includes 65 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001314-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kf168rc
title: Data from: Responses of growing‐season soil respiration to water and nitrogen addition as affected by grazing intensity

description: 1. Most grasslands in the world, including the semi-arid steppe in China,
 are threatened by nitrogen deposition, precipitation change, and livestock
 grazing, which greatly affect soil carbon processes (e. g., soil
 respiration). Although the individual effects of nitrogen deposition and
 precipitation change on soil respiration are well understood, how their
 effects on soil respiration are altered by different grazing intensities
 is unclear. 2. To determine how the effects of nitrogen deposition and
 precipitation change on soil respiration are affected by grazing
 intensity, we conducted an experiment in a semi-arid steppe involving
 areas that experienced 10 years of no, light, moderate, or heavy grazing.
 These areas were treated with water addition (110 mm, 30% of the mean
 annual precipitation) and nitrogen addition (10.5 g m-2 yr-1). 3. Our
 results showed that relative to no grazing, grazing decreased
 growing-season soil respiration by 10-19%. The decline in soil respiration
 was mainly via its negative effects on aboveground net primary
 productivity (ANPP) and the fungi:bacteria ratio with light grazing,
 mainly via its negative effects on ANPP and leaf nitrogen content with
 moderate grazing, and mainly via its negative effects on ANPP, root
 biomass, microbial biomass, and the fungi:bacteria ratio with heavy
 grazing. 4. Across all grazing intensities, both water and water+nitrogen
 addition increased growing-season soil respiration, whereas nitrogen
 addition decreased growing-season soil respiration. Water addition
 increased growing-season soil respiration mostly via its positive effect
 on ANPP with no grazing and with low grazing, and mostly via its positive
 effects on both plant and microbial variables with moderate and heavy
 grazing. The pathways determining the nitrogen addition-induced decline in
 growing-season soil respiration was the same within each of the four
 levels of grazing and mostly resulted from its negative effect on
 microbial variables. 5. Our results indicate that the effects of climate
 change on growing-season soil respiration and other soil carbon processes
 in grasslands depend on grazing intensity. The findings suggest that
 grazing intensity should be considered in future manipulation experiments
 and should be included in carbon models in order to accurately simulate
 soil carbon dynamics under scenarios of climate change in grassland
 ecosystems.
description: Data_Li_et
 al_FETreatments are described
 in the main text.