cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.654vb4g
title: Data from: Both trait-neutrality and filtering effects are validated by the vegetation patterns detected in the functional recovery of sand grasslands

description: Neutral theory of species assembly means that species assembly is governed
 by stochastic dispersal processes and fluctuations in established
 populations. An alternative theory suggests that assembly is strongly
 determined by functional trait filtering governed by abiotic and biotic
 filtering selecting species from the local species pool. To test these
 assumptions, in the current paper we analysed vegetation changes in the
 first 12 years of succession after heavy goose grazing on acidic sand.
 With trait-based analyses using permanent plots we addressed the following
 hypotheses: (i) High fluctuations in the trait values are typical in the
 first years; later a temporally divergent change in the trait patterns of
 sites with different vertical position became characteristic. (ii) In the
 functional diversity of regenerative and vegetative traits we expected
 different temporal patterns. We confirmed the first hypothesis, as in the
 first few years most traits displayed high fluctuations with no clear
 patterns. Our findings weakly supported the second hypothesis; while there
 were distinct patterns detected in the functional richness of traits,
 functional divergence and evenness displayed no clear distinctive
 patterns. We can conclude that both trait neutrality and filtering effects
 operate in the vegetation changes of the first period of secondary
 succession.
description: Torok-et-al-SREP-18-20675A-species-coverSpecies' percentage cover by site (U1, L1, U2, L2), plot (1-5) and year (1-12)Torok-et-al-SREP-18-20675A-species-traitsTraits of species used in the analyses. Abbreviations: ClonSpread - Clonal spreading ability; FlowStart - Starting month of flowering; FlowPeriod - Number of months of flowering; LDMC - Leaf dry matter content; LDW - Lead dry weight; SLA - Specific leaf area; SW - Thousand seed weight; TermVel - Terminal velocity; SBT - Seed bank type; WindPoll - Wind pollination; InsectPoll - Insect pollination; SelfPoll - Self-pollination. For further detailes and data sources see the original publication.
DOI: 10.5061/dryad.5k5k0
title: Data from: Linking innate immunogenetic variation with phenotypic traits in a wild population of tree swallows, Tachycineta bicolor

description: Unravelling the genetic basis of phenotypic variation among individuals is
 an important step in our understanding of evolution. Recent studies of
 innate immune genes, such as β -defensins, revealed that these genes had
 high levels of polymorphism. However, researchers have yet to quantify the
 effects of such variability on immune responses and fitness-related traits
 in wild populations. In this study, we assessed how the variability at six
 avian β -defensin (AvBD) genes was linked to an immune function and
 reproductive success in adult tree swallows (Tachycineta bicolor). We
 investigated the links between genetic variations using single nucleotide
 polymorphisms at AvBD genes, immune function as the bacterial killing
 ability (BKA) and fledging success. We assessed how female immunogenetics
 were linked to the presence of eggshell bacteria in their clutches and
 hatching success. We found weak associations between the presence of AvBD
 genes, BKA and eggshell bacteria. Our results suggested that homozygosity
 at some loci may be advantageous for defence against bacteria. Variability
 at β -defensin genes was not related to either hatching or fledging
 success. BKA of parents was positively linked with fledging success. More
 studies are needed to assess whether or not β -defensin genes are
 significantly affecting fitness-related traits in wild populations.
description: beta defensin BKA tree
 swallowsData collected in the
 field from tree swallows individuals in southern Quebec during the
 reproductive season 2013 and 2014. Contains alleles of beta-defensin,
 innate immune function BKA. Consult the ReadMe file for more
 info.BD_beta_bka_Schmitt.xlsx
DOI: 10.5061/dryad.3g23m
title: Data from: Positive selection underlies the species-specific binding of P. falciparum RH5 to human basigin

description: Plasmodium falciparum, the causative agent of the deadliest form of
 malaria, is a member of the Laverania subgenus, which includes
 ape-infecting parasites. P. falciparum is thought to have originated in
 gorillas, although infection is now restricted to humans. Laverania
 parasites display remarkable host-specificity, which is partially mediated
 by the interaction between parasite ligands and host receptors. We analyse
 the evolution of BSG (basigin) and GYPA (glycophorin A) in
 primates/hominins, as well as of their Plasmodium-encoded ligands, PfRH5
 and PfEBA175. We show that, in primates, positive selection targeted two
 sites in BSG (F27 and H102), both involved in PfRH5 binding. A population
 genetics–phylogenetics approach detected the strongest selection for the
 gorilla lineage: one of the positively selected sites (K191) is a major
 determinant of PfRH5 binding affinity. Analysis of RH5 genes indicated
 episodic selection on the P. falciparum branch; the positively selected
 W447 site is known to stabilize the interaction with human basigin.
 Conversely, we detect no selection in the receptor-binding region of
 EBA175 in the P. falciparum lineage. Its host receptor, GYPA, shows
 evidence of positive selection in all hominid lineages; selected codons
 include glycosylation sites that modulate PfEBA175 binding affinity. Data
 herein provide an evolutionary explanation for species-specific binding of
 the PfRH5-BSG ligand–receptor pair and support the hypothesis that
 positive selection at these genes drove the host shift leading to the
 emergence of P. falciparum as a human pathogen.
description: inter-species
 alignmentsAlignments used in
 inter-species analysesalignments.txtinter-species treesTrees used in inter-species analysestreesgammaMap_input_filesInput files used for the population genetics-phylogenetics analysis
DOI: 10.5061/dryad.q28b2
title: Data from: Are flies kind to kin? The role of intra- and inter-sexual relatedness in mediating reproductive conflict

description: As individual success often comes at the expense of others, interactions
 between the members of a species are frequently antagonistic, especially
 in the context of reproduction. In theory, this conflict may be reduced in
 magnitude when kin interact, as cooperative behaviour between relatives
 can result in increased inclusive fitness. Recent tests of the potential
 role of cooperative behaviour between brothers in Drosophila melanogaster
 have proved to be both exciting and controversial. We set out to replicate
 these experiments, which have profound implications for the study of kin
 selection and sexual conflict, and to expand upon them by also examining
 the potential role of kinship between males and females in reproductive
 interactions. While we did observe reduced fighting and courtship effort
 between competing brothers, contrary to previous studies we did not detect
 any fitness benefit to females as a result of the modification of male
 antagonistic behaviours. Furthermore, we did not observe any differential
 treatment of females by their brothers, as would be expected if the
 intensity of sexual conflict was mediated by kin selection. In the light
 of these results, we propose an alternative explanation for observed
 differences in male–male conflict and provide preliminary empirical
 support for this hypothesis.
description: happy_familiesBehavioural and fitness data collected from fruit flies placed in the following treatments 1) “related pair”, a single male from the same familial lineage as the target female; 2) “unrelated pair”, a single male from a different familial lineage than the target female; 3) “all related”, three males related to each other (same familial lineage) and to the target female; 4) “males related”, three males related to each other but from a different familial lineage than the target female; and 5) “all unrelated”, three males unrelated (different familial lineages) to either each other or to the target female.synthetic_datasetA synthetic dataset containing the fighting rate values for each of the familial lineages that were represented in the male combinations for every all unrelated vial; this was accomplished using our observations made for males from the appropriate corresponding males related vials. The three values (corresponding to the three males in an unrelated trio) in this synthetic dataset were ranked from most aggressive to least aggressive. The fighting rate in the corresponding "all unrelated" vial is also included.
DOI: 10.5061/dryad.8565n
title: Data from: Discrimination behavior mediates foraging quality versus quantity trade-offs: nut choice in wild rodents

description: Discrimination, the ability to distinguish sensory stimuli and respond
 accordingly, is a critical factor underscoring optimal foraging decisions.
 Nevertheless, little is known about how mammals discriminate between
 apparently similar foods of different quality. Here, we compared the
 foraging behavior of Chinese white-bellied rats, Niviventer confucianus,
 and Edwards’s long-tailed giant rats, Leopoldamys edwardsi, under natural
 conditions in the field and in a captive enclosure without
 predation/competition. We examined the behavioral processes involved in
 discriminating between sound (i.e., undamaged) and insect larvae-infested
 nuts of seguin chestnuts (Castanea seguinii) and demonstrated that both
 rats could discriminate nut quality, where nut examination improved the
 rats’ success rate at selecting sound nuts. Despite similar extents of
 discrimination-derived benefit in both settings for each species,
 differences between species-specific discrimination processes were
 identified. Chinese white-bellied rats engaged in a higher relative
 frequency and longer duration of nut examination in the enclosure than in
 the wild. This indicates that they alter their feeding strategy to
 trade-off selection for nut quality in captivity for a quantity-driven
 strategy in the field. In contrast, giant rats showed a consistent
 relative frequency of nut examination in both experimental settings. Their
 fixed strategy balanced food quality and quantity primarily to maximize
 caloric uptake without compromise when faced with predation or competition
 risk. We posit that this behavioral difference in optimal foraging between
 rat species is mediated by their differing, size-dependent energetic
 requirements as well as the higher competition pressure and predation risk
 faced by the approximately 8 times smaller white-bellied rats.
description: Field
 datadata for field
 experimentEnclosure
 datadata for enclosure
 experiment
DOI: 10.5061/dryad.7t3j55p
title: Data from: Exploring the causes of small effective population sizes in cyst nematodes using artificial Globodera pallida populations

description: The effective size of a population is the size of an ideal population
 which would undergo genetic drift at the same rate as the real population.
 The balance between selection and genetic drift depends on the effective
 population size (Ne), rather than the real numbers of individuals in the
 population (N). The objectives of the present study were to estimate Ne in
 the potato cyst nematode Globodera pallida and to explore the causes of a
 low Ne/N ratio in cyst nematodes using artificial populations. Using a
 temporal analysis of 24 independent populations, the median Ne was 58
 individuals (min Ne = 25 and max Ne = 228). Ne is commonly lower than N
 but in the case of cyst nematodes, the Ne/N ratio was extremely low. Using
 artificial populations showed that this low ratio did not result from
 migration, selection and overlapping generations, but could be explain by
 the fact that G. pallida populations deviate in structure from the
 assumptions of the ideal population by having unequal sex-ratios, high
 levels of inbreeding and a high variance in family sizes. The consequences
 of a low Ne, resulting in a strong intensity of genetic drift, could be
 important for their control because G. pallida populations will have a low
 capacity to adapt to changing environments.
description: Ne_G_pallidaGenotypic data (Genepop format) for each initial (Pi_A to Pi_G) and final Globodera pallida populations (Pf-01 to Pf-24).
DOI: 10.5061/dryad.1bt4q
title: Data from: Cytochrome P450 gene Cyp337 and heritability of fitness traits in the Glanville fritillary butterfly

description: Fitness-related life history traits often show substantial heritable
 genetic variation in natural populations, but knowledge of the genetic
 architecture of these traits is limited. In the Glanville fritillary
 butterfly, we measured the heritability of key life history traits in a
 large outdoor population cage during two years and generations, and
 combined this experiment with an association study of a set of candidate
 genes. The genes were selected on the basis of previous genomic and
 transcriptomic studies and have been linked to the physiology and life
 history of this or other arthropod species. Heritability was high and
 significant for two traits, post-diapause larval development time (h2 =
 0.37) and lifetime egg (and larval) production (h2 = 0.62); the latter is
 closely related to lifetime reproductive success and therefore fitness. We
 discovered a strong association between genetic polymorphism in the
 Cytochrome P450 gene Cyp337 and lifetime egg production, which accounted
 for 14% of the additive variance in egg production. This gene belongs to a
 group of Cytochrome P450 genes that have a well-documented role in host
 plant adaptations in Lepidoptera and other insects, and is likely to play
 an important role in the ecology and microevolution of the Glanville
 fritillary. This study provides a prime example of a gene associated with
 heritable fitness variation, measured under semi-natural ecological
 conditions.
description: Cyp337 and fitness
 traits in the Glanville fritillary butterfly: pedigree, phenotypic and SNP
 data.This file contains
 pedigree information, phenotypic data for 13 life history traits measured
 in an outdoor population cage, and genotypic data for 16 SNPs in 10 genes,
 for a parent (n = 82) and offspring (n = 204) generation of Glanville
 fritillary butterflies.Pedigree_phenotype_genotype_data.xlsx
DOI: 10.5061/dryad.3j07n
title: Data from: Population structure of the oldest known macroscopic communities from Mistaken Point, Newfoundland

description: The presumed affinities of the Terminal Neoproterozoic Ediacara biota have
 been much debated. However, even in the absence of concrete evidence for
 phylogenetic affinity, numerical paleoecological approaches can be
 effectively used to make inferences about organismal biology, the nature
 of biotic interactions, and life history. Here, we examine the population
 structure of three Ediacaran rangeomorph taxa (Fractofusus, Beothukis, and
 Pectinofrons), and one non-rangeomorph taxon (Thectardis) across five
 fossil surfaces around the Avalon Peninsula, Newfoundland, through
 analysis of size-frequency distributions using Bayesian Information
 Criterion (BIC). Best-supported models resolve communities of all studied
 Ediacaran taxa at Mistaken Point as single cohorts with wide variance.
 This result is best explained in terms of a “continuous reproduction”
 model, whereby Ediacaran organisms reproduce aseasonally, so that multiple
 size modes are absent from preserved communities. Modern benthic
 invertebrates (both as a whole and within specific taxonomic groups) in
 deeper-water settings reproduce both seasonally and aseasonally;
 distinguishing between biological (i.e., continuous reproductive
 strategies) and environmental (lack of a seasonal trigger) causes for this
 pattern is therefore difficult. However, we hypothesize that the observed
 population structure could reflect the lack of a trigger for reproduction
 in deepwater settings (i.e., seasonal flux of organic matter), until the
 explosive appearance of mesozooplankton near the base of the Cambrian.
description: Raw
 dataExcel file with raw data
 for all surfaces (univariate and multivariate). Measurements are
 retrodeformed, after mathematically removing tectonic bed-parallel
 shortening (see Clapham et al., 2003; Wood et al., 2003). Only complete
 measurements are used; measurements from incomplete/broken specimens are
 excluded.
DOI: 10.15468/dl.2xv6c2
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Sonora semiannulata",
 "Year 1960-2026"
 ]
}

 The dataset includes 58 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000859-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.93pr2
title: Data from: Habitat use, but not gene flow, is influenced by human activities in two ecotypes of Egyptian fruit bat (Rousettus aegyptiacus)

description: Understanding the ecological, behavioral and evolutionary response of
 organisms to changing environments is of primary importance in a
 human-altered world. It is crucial to elucidate how human activities alter
 gene flow and what are the consequences for the genetic structure of a
 species. We studied two lineages of the Egyptian fruit bat (Rousettus
 aegyptiacus) throughout the contact zone between mesic and arid ecozones
 in the Middle East to evaluate the species' response to the growing
 proportion of human-altered habitats in the desert. We integrated
 population genetics, morphometrics and movement ecology to analyze
 population structure, morphological variation and habitat use from GPS- or
 radio-tagged individuals from both desert and Mediterranean areas. We
 classified the spatial distribution and environmental stratification by
 describing physical-geographical conditions and land cover. We analyzed
 this information to estimate patch occupancy and used an isolation by
 resistance approach to model gene flow patterns. Our results suggest that
 lineages from desert and Mediterranean habitats, despite their admixture,
 are isolated by environment and by adaptation supporting their
 classification as ecotypes. We found a positive effect of human-altered
 habitats on patch occupancy and habitat use of fruit bats by increasing
 the availability of roosting and foraging areas. While this commensalism
 promotes the distribution of fruit bats throughout the Middle East, gene
 flow between colonies has not been altered by human activities. This
 discrepancy between habitat use and gene flow patterns may, therefore, be
 explained by the breeding system of the species and modifications of natal
 dispersal patterns.
description: Genotypes, colonies and
 geographic location of Rousettus aegyptiacusGenotypes (n=223) from
 26 sampling sites of Egyptian fruit bat (Rousettus aegyptiacus) in the
 Middle East using 18 microsatellites. Lat/Long coordinates (decimal
 degrees) of each sampling site are also provided.Dataset_Centeno-Cuadros_etalRousettus.xlsx
DOI: 10.5061/dryad.sc4s4
title: Data from: Field manipulations of resources mediate the transition from intraspecific competition to facilitation

description: 1. Population density affects individual performance, though its effects
 are often mixed. For sessile species, increases in population density
 typically reduce performance. Still, cases of positive density dependence
 do occur in these systems and demand explanation. The stress gradient
 hypothesis (SGH) predicts that under stressful conditions, positive
 effects of facilitation may outweigh the negative effects of competition.
 2. While some elements of the SGH are well studied, its potential to
 explain intraspecific facilitation has received little attention. Further,
 there have been questions regarding whether the SGH holds if the stressor
 is a resource. Most studies of interactions between the environment and
 intraspecific facilitation have relied on natural environmental gradients;
 manipulative studies are much rarer. 3. To test the effects of
 intraspecific density and resources, we manipulated resource availability
 over natural population densities for the marine bryozoan Watersipora
 subtorquata. 4. We found negative effects of density on colony performance
 in low resource environments, but mainly positive density-dependence in
 high resource environments. By adding resources, competition effects were
 reduced and the positive effects of facilitation were revealed. 5. Our
 results suggest that resource availability mediates the relative strength
 of competition and facilitation in our system. We also suggest that
 intraspecific facilitation is more common than may be appreciated and that
 environmental variation may act as mediators to the balance between
 negative and positive density-dependence.
description: J anim Ecol,
 Data190117,
 J anim Ecol, The data to dryad.xlsx
DOI: 10.5061/dryad.pc1b6
title: Data from: Generational shift in spring staging site use by a long-distance migratory bird

description: In response to environmental change, species have been observed altering
 their migratory behaviours. Few studies, however, have been able to
 determine whether these alterations resulted from inherited, plastic, or
 flexible changes. Here we present a unique observation of a rapid
 population-level shift in migratory routes — over 300 km from Spain to
 Portugal — by continental black-tailed godwits Limosa limosa limosa. This
 shift did not result from adult godwits changing staging sites, as adult
 site use was highly consistent. Rather, the shift resulted from young
 godwits predominantly using Portugal over Spain. We found no differences
 in reproductive success or survival among individuals using either staging
 site, indicating that the shift resulted from developmental plasticity
 rather than natural selection. Our results therefore suggest that new
 migratory routes can develop within a generation and that young
 individuals may be the agents of such rapid changes.
description: Verhoeven et
 al._Generational shift_All seen marked adultsData on adult staging
 site useVerhoeven et
 al._Generational shift_Juvenile DataData on staging site use
 youngVerhoeven et
 al._Generational shift_Parent and OffspringData on parent-offspring
 pairs (table S2)Verhoeven et
 al._Generational shift_Brood succes femalesData on brood success of
 females in the Haanmeer polderVerhoeven et
 al._Generational shift_Brood succes malesData on brood success of
 males in the Haanmeer polderVerhoeven et
 al._Generational shift_FigS1_ExtremaduraData on proportion
 resighted in Spain (Figure S1A)Verhoeven et
 al._Generational shift_FigS1_SadoTejoData on resighting
 proportion in Portugal (Figure S1B)Verhoeven et
 al._Generational shift_Juvenile SurvivalData for subsequent
 juvenile survival analysis