cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v84jr
title: Data from: A question of time: the land snail Murella muralis (Gastropoda: Pulmonata) reveals constrains to past ecological speciation

description: The lively debate about speciation currently focuses on the relative
 importance of factors driving population differentiation. While many
 studies are increasingly producing results on the importance of selection,
 little is known about the interaction between drift and selection.
 Moreover there is still little knowledge on the spatial-temporal scales at
 which speciation occurs, i.e. arrangement of habitat patches, abruptness
 of habitat transitions, climate and habitat changes interacting with
 selective forces. To investigate these questions, we quantified variation
 on a fine geographical scale analysing morphological (shell) and genetic
 datasets coupled with environmental data in the land snail Murella
 muralis, endemic to the Mediterranean island of Sicily. Analysis of a
 fragment of the mitochondrial DNA Cytochrome Oxidase I gene (COI) and
 eight nuclear microsatellite loci showed that genetic variation is highly
 structured at a very fine spatial scale by local palaeogeographical events
 and historical population dynamics. Molecular clock estimates, calibrated
 here specifically for Tyrrhenian land snails, provided a framework of
 palaeogeographical events responsible for the observed geographical
 variations and migration routes. Finally, we showed for the first time
 well documented lines of evidences of selection in the past, which
 explains divergence of land snail shell shapes. We suggest that time and
 palaeogeographical history acted as constraints in the progress along the
 ecological speciation continuum. Our study shows that testing for
 correlation among palaeogeography, morphology and genetic data on a fine
 geographical scale provides information fundamental for a detailed
 understanding of ecological speciation processes.
description: Murella_dryadHAPLOHaplotypes for all the individuals are given.Morphological dataMorphological data are given for all the individuals. Please, refer to the paper for codes.
DOI: 10.5061/dryad.m9c8tn8
title: Data from: Blood-brain barrier impairment and hypoperfusion are linked in cerebral small vessel disease

description: Objective: To investigate the link between BBB permeability and CBF and
 the relation with white matter hyperintensities (WMHs) in cerebral small
 vessel disease (cSVD). Methods: Twenty-seven patients with cSVD received
 dynamic susceptibility contrast and dynamic contrast-enhanced MRI to
 determine CBF and BBB permeability (expressed as leakage rate and volume),
 respectively. Structural MR images were segmented into normal appearing
 white matter (NAWM) and WMHs, for which a perilesional zone was defined.
 In these regions, we investigated the BBB permeability, CBF, and their
 relation using Pearson correlation r. Results: We found a decrease in CBF
 of 2.2 mL/min/100g(p&lt;0.01) and an increase in leakage volume of
 0.7%(p&lt;0.01) per mm closer to the WMHs in the perilesional zones.
 Lower CBF values correlated with higher leakage measures in the NAWM and
 WMHs (-0.53
description: e-Supplemental_ID_NEUROLOGY_2018_893248e-Supplemental of manuscript titled: Blood-Brain Barrier Impairment and Hypoperfusion are linked in Cerebral Small Vessel Disease by Wong et al.
DOI: 10.15468/dl.ukuefm
title: Occurrence Download

description: A dataset containing 723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Senticolis triaspis",
 "Year 1960-2026"
 ]
}

 The dataset includes 723 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000856-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rc1k8
title: Data from: Intrasexual selection favours an immune-correlated colour ornament in a dragonfly

description: Sexual signalling is predicted to shape the evolution of sex-specific
 ornamentation, and establishing the costs and benefits of ornamentation
 and the information that ornamentation provides to receivers is necessary
 to evaluating this adaptive function. Here, we assessed the adaptive
 function of a common colour ornament in insects, melanin wing
 ornamentation, using the dragonfly Pachydiplax longipennis. We
 hypothesized that greater ornamentation would improve territory-holding
 success by decreasing aggression that males receive from territorial
 rivals, but that more ornamented males may have shorter lifespans. Using
 mark–recapture field observations, we found that more ornamented males had
 greater territory-holding success and that viability selection did not act
 on wing melanization. We then compared the aggression of territorial
 rivals to decoy males before and after experimentally augmenting wing
 melanization, finding that males significantly reduced aggression
 following the manipulation. We next hypothesized that wing melanization
 would signal fighting ability to territorial rivals by reflecting
 condition via investment in the costly melanin synthesis pathway. We
 observed a positive relationship between ornamentation and the likelihood
 of winning territorial disputes, suggesting that wing melanization
 provides information about fighting ability to rivals. We also found a
 positive relationship between melanin-based immune defence and
 ornamentation, supporting a link between the signal and condition. We
 conclude that wing melanization is a condition-related signal of fighting
 ability and suggest that this may be a common mechanism promoting the
 evolution of melanin ornamentation.
description: Moore & Martin 2016
 JEB territorial tenuresTerritorial tenures and
 phenotypic values for all individuals in study.Moore_Martin_2016_JEB_terr_ten.csvMoore & Martin 2016 JEB territorial disputesOutcomes of all territorial disputesMoore_Martin_2016_JEB_terr_disp.csvMoore & Martin 2016 JEB longevity dataLongevity values for all dragonflies included in this studyMoore_Martin_2016_JEB_longevity.csvMoore & Martin 2016 JEB decoy experimentResponses of all territorial males to decoys pre- vs post-experimental augmentationMoore_Martin_2016_JEB_decoy_exp.csvMoore & Martin 2016 JEB immune assaysImmune assay scores and phenotypic values of dragonflies included in studyMoore_Martin_2016_JEB_immune_assay.csv
DOI: 10.5061/dryad.j22j1
title: Data from: Polymorphism at the Clock gene predicts phenology of long-distance migration in birds

description: Dissecting phenotypic variance in life history traits into its genetic and
 environmental components is at the focus of evolutionary studies and of
 pivotal importance to identify the mechanisms and predict the consequences
 of human-driven environmental change. The timing of recurrent life history
 events (phenology) is under strong selection, but the study of the genes
 that control potential environmental canalization in phenological traits
 is at its infancy. Candidate genes for circadian behaviour entrained by
 photoperiod have been screened as potential controllers of phenological
 variation of breeding and moult in birds, with inconsistent results.
 Despite photoperiodic control of migration is well established, no study
 has reported on migration phenology in relation to polymorphism at
 candidate genes in birds. We analysed variation in spring migration dates
 within four trans-Saharan migratory species (Luscinia megarhynchos;
 Ficedula hypoleuca; Anthus trivialis; Saxicola rubetra) at a Mediterranean
 island in relation to Clock and Adcyap1 polymorphism. Individuals with
 larger number of glutamine residues in the poly-Q region of Clock gene
 migrated significantly later in one or, respectively, two species
 depending on sex and whether the within-individual mean length or the
 length of the longer Clock allele was considered. The results hinted at
 dominance of the longer Clock allele. No significant evidence for
 migration date to covary with Adcyap1 polymorphism emerged. This is the
 first evidence that migration phenology is associated with Clock in birds.
 This finding is important for evolutionary studies of migration and sheds
 light on the mechanisms that drive bird phenological changes and
 population trends in response to climate change.
description: File including all data
 used in the articlePROG = line ID SPECIES =
 common species name ID = sample ID DATE = day of capture (day 1 = January
 1) AGE = age of individual (0 = second year; 1 = older) SEX = sex of the
 individual (1 = male; 2 = female) FAT = fat score (0-8 scale) MUSCLE =
 muscle score (0-3 scale) WING = wing lenght (mm x 10) MASS = body mass (g
 x 10) CLK_SHORT = Clock short allele lenght (Q-units) CLK_LONG = Clock
 long allele length (Q-units) CLK_MEAN = Clock mean allele length (Q-units)
 ADC_SHORT = Adcyap1 short allele length (bp units) ADC_LONG = Adcyap1 long
 allele length (bp units) ADC_MEAN = Adcyap1 mean allele length (bp
 units)Saino_et_al.txtClock and Adcyap1 genomic sequencesPartial genomic sequences of Clock and Adcyap1 genes of Anthus trivialis, Luscinia megarhynchos, Saxicola rubetra and Ficedula hypoleuca and Clustal multiple sequence alignement highlighting sequence differences among species.Clock and Adcyap 1 sequences.rtf
DOI: 10.5061/dryad.6g75n
title: Data from: Reciprocal translocation of small numbers of inbred individuals rescues immunogenetic diversity

description: Genetic rescue can reduce inbreeding depression and increase fitness of
 small populations, even when the donor populations are highly inbred. In a
 recent experiment involving two inbred island populations of the South
 Island robin, Petroica australis, reciprocal translocations improved
 microsatellite diversity and individual fitness. While microsatellite loci
 may reflect patterns of genome-wide diversity, they generally do not
 indicate the specific genetic regions responsible for increased fitness.
 We tested the effectiveness of this reciprocal translocation for rescuing
 diversity of two immunogenetic regions: toll-like receptor (TLR) and major
 histocompatibility complex (MHC) genes. We found that the relatively small
 number of migrants (seven and ten per island, respectively) effectively
 brought the characteristic TLR gene diversity of each source population
 into the recipient population. However, when migrants transmitted TLR
 alleles that were already present at high frequency in the recipient
 population, it was possible for offspring of mixed heritage to have
 decreased gene diversity compared to recipient population diversity prior
 to translocation. In contrast to TLRs, we did not observe substantial
 changes in MHC allelic diversity following translocation, with limited
 evidence of a decrease in differentiation, perhaps because most MHC
 alleles were observed at both sites prior to the translocation. Overall,
 we conclude that small numbers of migrants may successfully restore the
 diversity of immunogenetic loci with few alleles, but that translocating
 larger numbers of animals would provide additional opportunity for the
 genetic rescue of highly polymorphic immunity regions, such as the MHC,
 even when the source population is inbred.
description: TLR inferred haplotype
 sequencesZip archive containing
 sequence data in fasta format for each TLR gene. Sequences are the
 inferred haplotypes as determined using the software
 PHASE.Individual
 DataSample IDs, population
 of origin, hybrid/inbred status and sex for the individuals included in
 the analysis.TLR
 GenotypesTLR genotypes for each
 animal included in the analysis. Haplotype codes correspond to sequences
 provided in the archive "TLR inferred haplotype sequences.zip",
 also associated with this paper.MHC
 genotypesPresence/absence data
 for MHC sequences observed in each animal in the analysis. To relate
 sequence codes back to their original sequences, refer to Figure 3 and
 Supplementary Table S3 of the associated paper.
DOI: 10.5061/dryad.8515
title: Data from: A new malaria agent in African hominids.

description: Plasmodium falciparum is the major human malaria agent responsible for 200
 to 300 million infections and one to three million deaths annually, mainly
 among African infants. The origin and evolution of this pathogen within
 the human lineage is still unresolved. A single species, P. reichenowi,
 which infects chimpanzees, is known to be a close sister lineage of P.
 falciparum. Here we report the discovery of a new Plasmodium species
 infecting Hominids. This new species has been isolated in two chimpanzees
 (Pan troglodytes) kept as pets by villagers in Gabon (Africa). Analysis of
 its complete mitochondrial genome (5529 nucleotides including Cyt b, Cox I
 and Cox III genes) reveals an older divergence of this lineage from the
 clade that includes P. falciparum and P. reichenowi (approximately 21+/-9
 Myrs ago using Bayesian methods and considering that the divergence
 between P. falciparum and P. reichenowi occurred 4 to 7 million years ago
 as generally considered in the literature). This time frame would be
 congruent with the radiation of hominoids, suggesting that this Plasmodium
 lineage might have been present in early hominoids and that they may both
 have experienced a simultaneous diversification. Investigation of the
 nuclear genome of this new species will further the understanding of the
 genetic adaptations of P. falciparum to humans. The risk of transfer and
 emergence of this new species in humans must be now seriously considered
 given that it was found in two chimpanzees living in contact with humans
 and its close relatedness to the most virulent agent of malaria.
description: Ollomo_PLoSPathog_2009Nucleotide alignment concatenation of 4 mitochondrial genes for 17 Plasmodium species and one outgroup.Ollomo_PLoSPathog_2009_PHYMLMaximum likelihood tree inferred from the 4-gene concatenation using PHYML.
DOI: 10.5061/dryad.g8j01
title: Data from: Describing a developing hybrid zone between red wolves and coyotes in eastern North Carolina, USA

description: When hybridizing species come into contact, understanding the processes
 that regulate their interactions can help predict the future outcome of
 the system. This is especially relevant in conservation situations where
 human activities can influence hybridization dynamics. We investigated a
 developing hybrid zone between red wolves and coyotes in North Carolina,
 USA to elucidate patterns of hybridization in a system heavily managed for
 preservation of the red wolf genome. Using noninvasive genetic sampling of
 scat, we surveyed a 2880 km2 region adjacent to the Red Wolf Experimental
 Population Area (RWEPA). We combined microsatellite genotypes collected
 from this survey with those from companion studies conducted both within
 and outside the RWEPA to describe the gradient of red wolf ancestry. A
 total of 311 individuals were genotyped at 17 loci and red wolf ancestry
 decreased along an east–west gradient across the RWEPA. No red wolves were
 found outside the RWEPA, yet half of individuals found within this area
 were coyotes. Hybrids composed only 4% of individuals within this
 landscape despite co-occurrence of the two species throughout the RWEPA.
 The low proportion of hybrids suggests that a combination of active
 management and natural isolating mechanisms may be limiting intermixing
 within this hybrid system.
description: Unique_individual_genotypesA tab-delimited text file containing microsatellite genotypes for unique individual canids detected via non-invasive genetic sampling. The first line contains a header that includes locus names. The first column contains the identification number for each individual. The following columns contain alleles. Each locus is represented in two columns. Missing data are coded as zero.Individual_scat_locationsTab-delimited text file containing individual canids detected via non-invasive genetic sampling and their geographic coordinates. The first column contains the identification code for each individual. The second column contains the identification code for the individual fecal (scat) sample from which those individuals were genotyped. The third column contains the year the sample was collected. The remaining columns contain information for the geographic coordinates, which are in UTM. Note that for UTM coordinates are for the northern hemisphere.Red_wolf_coyote_original_genotypesGenePop file containing original genotypes used to simulate hybridization scenarios. The first population contains genotypes for coyotes captured in North Carolina and Virginia. The second population contains genotypes for the red wolves used to found the captive red wolf population.
DOI: 10.5061/dryad.56vf1
title: Data from: Key innovations and island colonization as engines of evolutionary diversification: a comparative test with the Australasian diplodactyloid geckos

description: The acquisition of key innovations and the invasion of new areas
 constitute two major processes that facilitate ecological opportunity and
 subsequent evolutionary diversification. Using a major lizard radiation as
 a model, the Australasian diplodactyloid geckos, we explored the effects
 of two key innovations (adhesive toepads and a snake-like phenotype) and
 the invasion of new environments (island colonization) in promoting the
 evolution of phenotypic and species diversity. We found no evidence that
 toepads had significantly increased evolutionary diversification, which
 challenges the common assumption that the evolution of toepads has been
 responsible for the extensive radiation of geckos. In contrast, a
 snakelike phenotype was associated with increased rates of body size
 evolution and, to a lesser extent, species diversification. However, the
 clearest impact on evolutionary diversification has been the colonization
 of New Zealand and New Caledonia, which were associated with increased
 rates of both body size evolution and species diversification. This
 highlights that colonizing new environments can drive adaptive
 diversification in conjunction or independently of the evolution of a key
 innovation. Studies wishing to confirm the putative link between a key
 innovation and subsequent evolutionary diversification must therefore show
 that it has been the acquisition of an innovation specifically, not the
 colonization of new areas more generally, that has prompted
 diversification.
description: datasetList of species (field: "species") with their body size ("max SVL (in mm)") and category (snake-like, padless, continental pad-bearer, NC pad-bearer or NZ pad-bearer) used for the analyses. In "source" appears the reference from which body size was obtained.Genbank_accession_numbersGenbank accession numbers of all the species used in the produce the time calibrated tree of the Australasian diplodactyloid geckos.
DOI: 10.5061/dryad.dd34q
title: Data from: Hypodermic self-insemination as a reproductive assurance strategy

description: Self-fertilization occurs in a broad range of hermaphroditic plants and
 animals, and is often thought to evolve as a reproductive assurance
 strategy under ecological conditions that disfavour or prevent
 outcrossing. Nevertheless, selfing ability is far from ubiquitous among
 hermaphrodites, and may be constrained in taxa where the male and female
 gametes of the same individual cannot easily meet. Here, we report an
 extraordinary selfing mechanism in one such species, the free-living
 flatworm Macrostomum hystrix. To test the hypothesis that adaptations to
 hypodermic insemination of the mating partner under outcrossing also
 facilitate selfing, we experimentally manipulated the social environment
 of these transparent flatworms and then observed the spatial distribution
 of received sperm in vivo. We find that this distribution differs
 radically between conditions allowing or preventing outcrossing, implying
 that isolated individuals use their needle-like stylet (male copulatory
 organ) to inject own sperm into their anterior body region, including into
 their own head, from where they then apparently migrate to the site of
 (self-)fertilization. Conferring the ability to self could thus be an
 additional consequence of hypodermic insemination, a widespread
 fertilization mode that is especially prevalent among simultaneously
 hermaphroditic animals and probably evolves due to sexual conflict over
 the transfer and subsequent fate of sperm.
description: Data_ScoringDay1Data_ScoringDay1_HatchlingsData_ScoringDay2
DOI: 10.15468/dl.m6mwxj
title: Occurrence Download

description: A dataset containing 408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phallus rugulosus"
 ]
}

 The dataset includes 408 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000857-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7t457
title: Data from: An Avida-ED digital evolution curriculum for undergraduate biology

description: We present an inquiry-based curriculum based on the digital evolution
 platform Avida-ED (http://​avida-ed.​msu.​edu). We designed an
 instructional sequence and lab book consisting of an introduction to
 Avida-ED and a set of three lessons focused on specific evolutionary
 concepts. These served to familiarize students with experimental evolution
 and Avida-ED. Students then developed independent Avida-ED research
 projects to test their own questions. Curriculum design and implementation
 occurred over the course or two semesters, with a pilot implementation in
 the first semester, followed by curriculum revision and full
 implementation in the second semester. The curriculum was implemented in
 an undergraduate Introductory Cell and Molecular Biology course at a major
 research university. Full implementation of the curriculum in semester two
 involved the use of Avida-ED mainly in the teaching lab in parallel with a
 bacterial antibiotic resistance experimental research stream, allowing
 students to draw connections between Avidian digital evolution and the
 evolution of antibiotic resistance in microbial populations. After
 carrying out the introductory exercises, students developed independent
 Avida-ED projects to test their own research questions, and presented
 their data to researchers in the NSF-funded BEACON Center for the Study of
 Evolution in Action. Preliminary results of our studies to assess the
 impacts of an Avida-ED curriculum indicate a positive effect on student
 learning of evolutionary concepts, particularly in increasing the level of
 complexity of student explanations about the random nature of mutation.
description: Analysis script for
 Dryad PackageThis is the analysis
 script that generates the figures for the publication. It is an R script
 that can be copied and pasted into R, or run from the command line if the
 file format is changed.Ex.1.posThis shows how many mutations occurred at each genome position for Example 1.Ex.1.mutsThis data file shows how many mutations each student found in Example 1.Ex.2.32This is the data file for Exercise 2.Ex.3This is the data for Exercise 3.Data.Fig.4This is the data needed for Figure 4.Affect.FallThis is the data file for student affect from the fall semesterAffect.SpringThis is the data file for the student affect from the spring term.Data.For.ProbitThis is the raw data needed for doing a Probit analysis.