cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2v8c5g0
title: Data from: A meta-analysis of the agents of selection on floral traits

description: Floral traits are hypothesized to evolve primarily in response to
 selection by pollinators. However, selection can also be mediated by other
 environmental factors. To understand the relative importance of
 pollinator-mediated selection and its variation among trait and pollinator
 types, we analyzed directional selection gradients on floral traits from
 experiments that manipulated the environment to identify agents of
 selection. Pollinator-mediated selection was stronger than selection by
 other biotic factors (e.g. herbivores), but similar in strength to
 selection by abiotic factors (e.g. soil water), providing partial support
 for the hypothesis that floral traits evolve primarily in response to
 pollinators. Pollinator-mediated selection was stronger on pollination
 efficiency traits than on other trait types, as expected if efficiency
 traits affect fitness via interactions with pollinators, but other trait
 types also affect fitness via other environmental factors. In addition to
 varying among trait types, pollinator-mediated selection varied among
 pollinator taxa: selection was stronger when bees, long-tongued flies, or
 birds were the primary visitors than when the primary visitors were
 Lepidoptera or multiple animal taxa. Finally, reducing pollinator access
 to flowers had a relatively small effect on selection on floral traits,
 suggesting that anthropogenic declines in pollinator populations would
 initially have modest effects on floral evolution.
description: Database of estimates of
 selection on floral traits in experimentsDatabase of estimates of
 phenotypic selection on floral traits from experiments that manipulate the
 environment and measure selection. Only the N = 755 records that report
 both directional selection gradients and their associated standard errors
 are included. The are two worksheets: one containing the database, and one
 describing the information included in each column of the
 database.Exp_stud_NOTdup_Dryad.xlsEstimates of phenotypic selection on floral traits w/some records duplicatedDatabase of estimates of phenotypic selection on floral traits from experiments that manipulate the environment and measure selection. The are two worksheets: one containing the database, and one describing the information included in each column of the database. To facilitate the analyses reported in the associated manuscript, some records of selection have been duplicated. See manuscript for more information.Exp_stud_dup_Dryad.xlsx
DOI: 10.5061/dryad.20hd2
title: Data from: Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains

description: Modern molecular approaches have vastly improved diagnostic capabilities
 for differentiating among species of chicken infecting Eimeria.
 Consolidating information from multiple genetic markers, adding additional
 poultry Eimeria species and increasing the size of available data-sets is
 improving the resolving power of the DNA, and consequently our
 understanding of the genus. This study adds information from 25 complete
 mitochondrial DNA genomes from Australian chicken Eimeria isolates
 representing all 10 species known to occur in Australia, including OTU-X,
 −Y and −Z. The resulting phylogeny provides a comprehensive view of
 species relatedness highlighting where the OTUs align with respect to
 others members of the genus. All three OTUs fall within the Eimeria clade
 that contains only chicken-infecting species with close affinities to E.
 maxima, E. brunetti and E. mitis. Mitochondrial genetic diversity was low
 among Australian isolates likely reflecting their recent introduction to
 the country post-European settlement. The lack of observed genetic
 diversity is a promising outcome as it suggests that the currently used
 live vaccines should continue to offer widespread protection against
 Eimeria outbreaks in all states and territories. Flocks were frequently
 found to host multiple strains of the same species, a factor that should
 be considered when studying disease epidemiology in the field.
description: Eimeria_AA_ alignment_
 for_DRYAD28 species FASTA file of
 amino acid alignment (1,100 aa alignment) of mitochondrial DNA coding
 regions (Cytochrome b, COI, COIII) of poultry infecting Eimeria species
 and close relatives. Contains complete cytochrome b coding sequence (360
 amino acids); a partial COI coding sequence (486 amino acids); and partial
 COIII coding sequence (254 amino acids), and using Choleoeimeria sp. as
 outgroup.Nucleotide alignment for
 DRYADNucleotide_alignment_for_DRYAD.fsa 54 species FASTA file of complete mitochondrial DNA sequence alignment (6,628 bp alignment) of Eimeria species and their relatives.Nucleotide alignment E zuernii root DRYADNucleotide_alignment_E_zuernii_root_DRYAD.fsa 42 species FASTA file of complete mitochondrial DNA sequence alignment (6,488 bp alignment) focused on the chicken infecting Eimeria species and strains, and their nearest relatives using Eimeria zuernii as outgroup.
DOI: 10.5061/dryad.kb13m
title: Data from: European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

description: Extant populations of the European wildcat are fragmented across the
 continent, the likely consequence of recent extirpations due to habitat
 loss and over-hunting. However, their underlying phylogeographic history
 has never been reconstructed. For testing the hypothesis that the European
 wildcat survived the Ice Age fragmented in Mediterranean refuges, we
 assayed the genetic variation at 31 microsatellites in 668 presumptive
 European wildcats sampled in 15 European countries. Moreover, to evaluate
 the extent of subspecies/population divergence and identify eventual wild
 × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and
 North Africa and 294 random-bred domestic cats. Results of multivariate
 analyses and Bayesian clustering confirmed that the European wild and the
 domestic cats (plus the African wildcats) belong to two
 well-differentiated clusters (average ФST = 0.159, rst = 0.392, P &gt;
 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5%
 to 10% cryptic hybrids in southern and central European populations. In
 contrast, wild-living cats in Hungary and Scotland showed deep signatures
 of genetic admixture and introgression with domestic cats. The European
 wildcats are subdivided into five main genetic clusters (average ФST =
 0.103, rst = 0.143, P &gt; 0.001; AMOVA) corresponding to five
 biogeographic groups, respectively, distributed in the Iberian Peninsula,
 central Europe, central Germany, Italian Peninsula and the island of
 Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric
 Alps). Approximate Bayesian Computation simulations supported late
 Pleistocene–early Holocene population splittings (from c. 60 k to 10 k
 years ago), contemporary to the last Ice Age climatic changes. These
 results provide evidences for wildcat Mediterranean refuges in
 southwestern Europe, but the evolution history of eastern wildcat
 populations remains to be clarified. Historical genetic subdivisions
 suggest conservation strategies aimed at enhancing gene flow through the
 restoration of ecological corridors within each biogeographic units.
 Concomitantly, the risk of hybridization with free-ranging domestic cats
 along corridor edges should be carefully monitored.
description: European wildcat
 microsatellites datasetThe File contains the
 raw microsatellites database in GenAlEx format for 1124 cat samples used
 in the analyses, characterised by 31 loci. For each samples is provided
 the sampling location, as reported in Tables, Figures and main taxt of the
 manuscript.This file can be converted to other formats using
 GenAlEx.Sampling_DRYAD.xls
DOI: 10.5061/dryad.3k7v7
title: Data from: Evolution of body mass in the Pan-Alcidae (Aves, Charadriiformes): the effects of combining neontological and paleontological data

description: Hypotheses regarding the evolution of many clades are often generated in
 the absence of data from the fossil record and potential biases introduced
 by exclusion of paleontological data are frequently ignored. With regard
 to body size evolution, extinct taxa are frequently excluded because of
 the lack of body mass estimates—making identification of reliable clade
 specific body mass estimators crucial to evaluating trends on
 paleontological timescales. Herein, I identify optimal osteological
 dimensions for estimating body mass in extinct species of Pan-Alcidae
 (Aves, Charadriiformes) and utilize newly generated estimates of body mass
 to demonstrate that the combination of neontological and paleontological
 data produces results that conflict with hypotheses generated when extant
 species data are analyzed in isolation. The wing-propelled diving
 Pan-Alcidae are an ideal candidate for comparing estimates of body mass
 evolution based only on extant taxa with estimates generated including
 fossils because extinct species diversity (≥31 species) exceeds extant
 diversity, includes examples from every extant genera, and because
 phylogenetic hypotheses of pan-alcid relationships are not restricted to
 the 23 extant species. Phylogenetically contextualized estimation of body
 mass values for extinct pan-alcids facilitated evaluation of broad scale
 trends in the evolution of pan-alcid body mass and generated new data
 bearing on the maximum body mass threshold for aerial flight in
 wing-propelled divers. The range of body mass in Pan-Alcidae is found to
 exceed that of all other clades of Charadriiformes (shorebirds and allies)
 and intraclade body mass variability is recognized as a recurring theme in
 the evolution of the clade. Finally, comparisons of pan-alcid body mass
 range with penguins and the extinct †Plotopteridae elucidate potentially
 shared constraints among phylogenetically disparate yet ecologically
 similar clades of wing-propelled divers.
description: Appendix_1Microsoft Excel (.xlsx) file of measurement data for extant and extinct species of Pan-AlcidaeSmith_Supplementary DataMicrosoft Word (.docx) file with supplementary data pertaining to "Evolution of body mass in the Pan-Alcidae (Aves, Charadriiformes): the effects of combining neontological and paleontological data" by N. Adam Smith. Includes explanation of abbreviations used in the Excel file of measurement data (Appendix_1).SmithSupplement.docx
DOI: 10.5061/dryad.dh98c
title: Data from: Evolvability meets biogeography: evolutionary potential decreases at high and low environmental favourability

description: Understanding and forecasting the effects of environmental change on wild
 populations requires knowledge on a critical question: do populations have
 the ability to evolve in response to that change? However, our knowledge
 on how evolution works in wild conditions under different environmental
 circumstances is extremely limited. We investigated how environmental
 variation influences the evolutionary potential of phenotypic traits. We
 used published data to collect or calculate 135 estimates of evolvability
 of morphological traits of European wild bird populations. We
 characterized the environmental favourability of each population
 throughout the species' breeding distribution. Our results suggest
 that the evolutionary potential of morphological traits decreases as
 environmental favourability becomes high or low. Strong environmental
 selection pressures and high intra-specific competition may reduce
 species' evolutionary potential in low- and high- favourability
 areas, respectively. This suggests that species may be least able to adapt
 to new climate conditions at their range margins and at the centre. Our
 results underscore the need to consider the evolutionary potential of
 populations when studying the drivers of species distributions,
 particularly when predicting the effects of environmental change. We
 discuss the utility of integrating evolutionary dynamics into a
 biogeographical perspective to understand how environmental variation
 shapes evolutionary patterns. This approach would also produce more
 reliable predictions about the effect of environmental change on
 population persistence and therefore on biodiversity.
description: Data from: Evolvability
 meets biogeography: evolutionary potential decreases at high and low
 environmental favourabilityFav_CVa_wildbirds.xlsxData from: Evolvability meets biogeography: evolutionary potential decreases at high and low environmental favourabilityFav_Ia_wildbirds.xlsxSpecies distribution and environmental variablesHere we provide the environmental variables used to construct the SDM for each species. Description of the variables are given in the ESM of the paperSps_environmental_variables.csv
DOI: 10.5061/dryad.c80675fg
title: Data from: MHC diversity, malaria and lifetime reproductive success in collared flycatchers

description: Major Histocompatibility Complex (MHC) genes encode proteins involved in
 the recognition of parasite-derived antigens. Their extreme polymorphism
 is presumed to be driven by coevolution with parasites. Host-parasite
 coevolution was also hypothesised to optimize within-individual MHC
 diversity at the intermediate level. Here, we use unique data on lifetime
 reproductive success (LRS) of female collared flycatchers to test whether
 LRS is associated with within-individual MHC class II diversity. We also
 examined the association between MHC and infection with avian malaria.
 Using 454 sequencing, we found that individual flycatchers carry between 3
 and 23 functional MHC class II B alleles. Predictions of the optimality
 hypothesis were not confirmed by our data as the prevalence of blood
 parasites decreased with functional MHC diversity. Furthermore, we did not
 find evidence for an association between MHC diversity and LRS.
description: Alleles_detected_in_single_ampliconFASTA file. DNA sequences of MHC class II alleles which have been validated as true alleles according to criteria described in the paper, but have been detected only in a single amplicon, i.e. do not meet the two PCR criterion.Alleles_1PCR.fasAlleles_detected_in_at_least_two_ampliconsFASTA file. DNA sequences of MHC class II alleles which have been validated as true alleles according to criteria described in the paper. These alleles have been detected in at least two amplicon, thus meet the two PCR criterion.Alleles_2PCR.fasGenotypes_infection_LRSIndividual genotypes based on alleles as defined by amino acid sequences, malaria infection status and lifetime reproductive success.
DOI: 10.5061/dryad.dq70c
title: Data from: Variable molecular markers for the order Mantophasmatodea (Insecta)

description: The recently discovered insect order Mantophasmatodea currently comprises
 19 Southern African species. These mainly occur in allopatry, have high
 levels of colour polymorphism and communicate via species- and
 gender-specific vibratory signals. High levels of interspecific
 morphological conservatism mean that cryptic species are likely to be
 uncovered. These aspects of Mantophasmatodean biology make them an ideal
 group in which to investigate population divergence due to
 habitat-specific adaptation, sexual selection and potentially sensory
 speciation. Lack of appropriate genetic markers has thus far rendered such
 studies unfeasible. To address this need, the first microsatellite loci
 for this order were developed. Fifty polymorphic loci were designed
 specifically for Karoophasma biedouwense (Austrophasmatidae), out of which
 23 were labelled and tested for amplification across the order using 2-3
 individuals from 10 species, representing all four currently known
 families. A Bayesian COI topology was reconstructed and divergence dates
 within the order were estimated for the first time. Amplification success
 and levels of polymorphism were compared with genetic divergence and time
 since divergence. In agreement with studies on vertebrate taxa, both
 amplification and variability were negatively correlated with distance
 (temporal and genetic). The high number of informative loci will offer
 sufficient resolution for both broad level population genetic analysis and
 individual based pedigree or parentage analyses for most species in
 Austrophasmatidae, with at least some loci available for the other
 families. This resource will facilitate research into the evolutionary
 biology of this understudied but fascinating group.
description: READMEREADME file to describe
 all data files to accompany the publication Dool et al. Variable molecular
 markers for the order Mantophasmatodea (Insecta) published in Journal of
 Heredity.COI_treePrimerNote_FSTATPrimerNote_FSTAT-POPULATION NAMESMicrosatellite Sequences_KB1_KB50Dool_SupplTable 1_2_4_5_JHereditySupp_Table3_Genotypes
DOI: 10.5061/dryad.jm65k
title: Data from: Investigating the allelic evolution of an imperfect microsatellite locus in the Hawaiian mushroom Rhodocollybia laulaha

description: The evolutionary mechanisms that give rise to microsatellite alleles
 remain poorly understood in general and are especially understudied for
 fungal microsatellite loci. The unusual G28 microsatellite locus was
 developed from the Hawaiian mushroom Rhodocollybia laulaha. Here we employ
 a novel approach to test for allele size homoplasy and examine competing
 mechanistic models of microsatellite evolution in the context of
 biogeographic expectations for this locus based on Hawaiian geologic
 history. Seven G28 alleles have been identified from a sampling of 153
 individuals. The G28 locus is comprised of a tri-nucleotide, imperfect
 motif which permits examination of the relationships between alleles and
 allows for detection of potential size homoplasy within the repetitive
 element. Alignment of G28 allele sequence data across multiple unrelated
 individuals suggests that alleles of like size are homologous within
 Hawaii. A variety of gap coding methods are explored in the inference of
 allele evolution. Length differences between alleles appear to be the
 result of polymerase slippage at multiple positions in the repetitive
 element suggesting an intricate process of allelic evolution which is not
 necessarily stepwise. Complex migration scenarios must be invoked to
 explain the current geographic distribution of alleles if their evolution
 was in fact sequential (from longest to shortest or from shortest to
 longest) as predicted by the “progression rule”.
description: Keirle et al.,
 (SUPPLEMENTARY DOCUMENTS)
DOI: 10.5066/p1y9umut
title: Whole-Rock Geochemistry of Samples from the Bear Lodge Alkaline Complex, Wyoming: Data Supporting Petrogenetic and Mineral Resource Studies

description: Geochemical data include major, minor and trace element results for alkaline silicate igneous rock samples from the Bear Lodge alkaline complex. Samples were collected during field work from natural exposures/outcrops and drill core. Samples were analyzed by the GeoAnalytical Lab at Washington State University and U.S. Geological Survey contract laboratories, AGAT Labs and SGS Labs. Major, minor, and trace elements were determined via wavelength dispersive X-ray fluorescence (WDXRF), inductively coupled plasma-optical emission spectrometry (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS). Additional analytes determined were carbonate carbon by combustion and infrared detection (IR); fluoride and chloride by ion-selective electrode; ferrous iron by titration; non-essential and essential water by gravimetric methods, and total sulfur and total carbon by IR. Data are reported in comma-separated values (CSV) files. All column headers are described in the accompanying data dictionary.
DOI: 10.5061/dryad.127g7
title: Data from: Impact of a hurricane on the herpetofaunal assemblages of a successional chronosequence in a tropical dry forest

description: Land‐use change is the main cause of deforestation and degradation of
 tropical forest in Mexico. Frequently, these lands are abandoned leading
 to a mosaic of natural vegetation in secondary succession. Further
 degradation of the natural vegetation in these lands could be exacerbated
 by stochastic catastrophic events such as hurricanes. Information on the
 impact of human disturbance parallel to natural disturbance has not yet
 been evaluated for faunal assemblages in tropical dry forests. To evaluate
 the response of herpetofaunal assemblages to the interaction of human and
 natural disturbances, we used information of pre‐ and post‐hurricane
 herpetofaunal assemblages inhabiting different successional stages
 (pasture, early forest, young forest, intermediate forest, and old growth
 forest) of dry forest. Herpetofaunal assemblages were surveyed in all
 successional stages two years before and two years after the hurricane
 Jova that hit the Pacific Coast of Mexico on October 2011. We registered
 4093 individuals of 61 species. Overall, there were only slight effects of
 successional stage, hurricane Jova or the interaction between them on
 abundance, observed species richness and diversity of the herpetofauna.
 However, we found marked changes in estimated richness and composition of
 frogs, lizards, and snakes among successional stages in response to
 hurricane Jova. Modifications in vegetation structure as result of
 hurricane pass promoted particular changes in each successional stage and
 taxonomic group (anurans, lizards, and snakes). Secondary forests at
 different stages of succession may attenuate the negative effects of an
 intense, short‐duration, and low‐frequency natural disturbance such as
 hurricane Jova on successional herpetofaunal trajectories and species
 turnover.
description: BITR-17-051 Data
 Suazo-Ortuño et al.The data base contains
 all original field data of each sampling site. The data base includes the
 name of the sampling site, the name of all species registered as well an
 number of individuals at each of the surveys.