cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kh049
title: Data from: Host-targeted RAD-Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast

description: Many organisms are expanding their ranges in response to changing
 environmental conditions. Understanding the patterns of genetic diversity
 and adaptation along an expansion front is crucial to assessing a species’
 long-term success. While next-generation sequencing techniques can reveal
 these changes in fine detail, ascribing them to a particular species can
 be difficult for organisms that live in close association with symbionts.
 Using a novel modified restriction-site associated DNA sequencing
 (RAD-Seq) protocol to target coral DNA, we collected 595 coral-specific
 single nucleotide polymorphisms (SNPs) from 189 colonies of the invasive
 coral Oculina patagonica from the Spanish Mediterranean coast, including
 established core populations and two expansion fronts. Surprisingly,
 populations from the recent northern expansion are genetically distinct
 from the westward expansion and core populations, and also harbor greater
 genetic diversity. We found that temperature may have driven adaptation
 along the northern expansion, as genome scans for selection found three
 candidate loci associated with temperature in the north but none in the
 west. We found no genomic signature of selection associated with
 artificial substrate, which has been proposed for explaining the rapid
 spread of O. patagonica. This suggests that this coral is simply an
 opportunistic colonizer of free space made available by coastal habitat
 modifications. Our results suggest that unique genetic variation, possibly
 due to limited dispersal across the Ibiza Channel, an influx of
 individuals from different depths, and/or adaptation to cooler
 temperatures along the northern expansion front may have facilitated the
 northward range expansion of O. patagonica in the western Mediterranean.
description: 2015_coralv3VCF file containing SNPsSNP036_oculina_bait_reads.fqfile containing the sequences generated from the symbiont-free coral colony used for sequence capture approachAllENVIRONMENTALVARIABLES_Dec2017file containing all environmental data (temperature max, mean, min, and range from 2 sources; depth; latitude; longitude)Genet+phasedNexus file containing sequences for all Oculina patagonica and several Cladocora colonies genotyped for a nuclear gene.2015_coralv3_vcfref595Fasta file containing the entire contig sequencesStructure/GenoDive input fileInput file generated for Structure and GenoDive11Feb2016_161
DOI: 10.5061/dryad.396v8n4
title: Data from: Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition

description: 1. Although interspecific competition plays a principle role in shaping
 species behaviour and demography, little is known about the
 population-level outcomes of competition between large carnivores, and the
 mechanisms that facilitate coexistence. 2. We conducted a multi-landscape
 analysis of two widely distributed, threatened large carnivore competitors
 to offer insight into coexistence strategies and assist with species-level
 conservation. 3. We evaluated how interference competition affects
 occupancy, temporal activity and population density of a dominant
 competitor, the lion (Panthera leo), and its subordinate competitor, the
 leopard (Panthera pardus). We collected camera-trap data over three years
 in ten study sites covering 5,070 km2. We used multispecies occupancy
 modelling to assess spatial responses in varying environmental and prey
 conditions and competitor presence, and examined temporal overlap and the
 relationship between lion and leopard densities across sites and years. 4.
 Results showed that both lion and leopard occupancy was independent of –
 rather than conditional on – their competitor’s presence across all
 environmental covariates. Marginal occupancy probability for leopard was
 higher in areas with more bushy, ‘hideable’ habitat, human (tourist)
 activity and topographic ruggedness, whereas lion occupancy decreased with
 increasing hideable habitat and increased with higher abundance of very
 large prey. Temporal overlap was high between carnivores and there was no
 detectable relationship between species densities. 4. Lions pose a threat
 to the survival of individual leopards, but they exerted no tractable
 influence on leopard spatial or temporal dynamics. Furthermore, lions did
 not appear to suppress leopard populations, suggesting that intraguild
 competitors can coexist in the same areas without population decline.
 Aligned conservation strategies that promote functioning ecosystems,
 rather than target individual species, are therefore advised to achieve
 cost- and space-effective conservation.
description: Camera trap
 dataCamera trap data of
 wildlife species from study sites in South Africa.Lion leopard
 densitiesDensities of lions and
 leopards from study sites in South Africa.
DOI: 10.5061/dryad.377mc
title: Data from: Influence of device accuracy and choice of algorithm for species distribution modelling of seabirds: a case study using black-browed albatrosses

description: Species distribution models (SDM) based on tracking data from different
 devices are used increasingly to explain and predict seabird
 distributions. However, different tracking methods provide different data
 resolutions, ranging from &lt; 10m to &gt;100km. To better
 understand the implications of this variation, we modeled the potential
 distribution of black-browed albatrosses Thalassarche melanophris from
 South Georgia that were simultaneously equipped with a Platform Terminal
 Transmitter (PTT) (high resolution) and a Global Location Sensor (GLS)
 logger (coarse resolution), and measured the overlap of the respective
 potential distribution for a total of nine different SDM algorithms. We
 found slightly better model fits for the PTT than for GLS data (AUC values
 0.958±0.048 vs. 0.95±0.05) across all algorithms. The overlaps of the
 predicted distributions were higher between device types for the same
 algorithm, than among algorithms for either device type. Uncertainty
 arising from coarse-resolution location data is therefore lower than that
 associated with the modeling technique. Consequently, the choice of an
 appropriate algorithm appears to be more important than device type when
 applying SDMs to seabird tracking data. Despite their low accuracy, GLS
 data appear to be effective for analyzing the habitat preferences and
 distribution patterns of pelagic species.
description: Dryad_JAV-01238 - raw
 SDM outputsRaw species distribution
 maps derived from nine different algorithms calculated based on occurrence
 infromations obtained from PTT and GLS tracking. The files are in ASCII
 format and can be read into any GIS application.Dryad_JAV-01238.zip
DOI: 10.5061/dryad.n35j4
title: Data from: Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

description: Convergent evolution represents one of the best lines of evidence for
 adaptation, but few cases of phenotypic convergence are understood at the
 genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad
 provide a classic example of phenotypic convergent evolution, where
 adaptation to low or high predation environments has been found for a
 variety of traits. A major advantage of this system is the possibility of
 long-term experimental studies in nature, including transplantation from
 high to low predation sites. We used genome scans of guppies from three
 natural high and low predation populations and from two experimentally
 established populations and their sources to examine whether phenotypic
 convergent evolution leaves footprints at the genome level. We used
 population genetic modeling approaches to reconstruct the demographic
 history and migration among sampled populations. Naturally colonized low
 predation populations had signatures of increased effective population
 size since colonization, while introduction populations had signatures of
 decreased effective population size. Only a small number of regions across
 the genome had signatures of selection in all natural populations.
 However, the two experimental populations shared many genomic regions
 under apparent selection, more than expected by chance. This overlap
 coupled with a population decrease since introduction provides evidence
 for convergent selection occurring in the two introduction populations.
 The lack of genetic convergence in the natural populations suggests that
 convergent evolution is lacking in these populations or that the effects
 of selection become difficult to detect after a long time period.
description: Full SNP
 datasetProvided is the SNP
 dataset file for guppies distributed across northen
 trinidad.submit_dryad_snps.tar.gz
DOI: 10.5061/dryad.4gh8b
title: Data from: The evolutionary history of polycotylid plesiosaurians

description: Polycotylidae is a clade of plesiosaurians that appeared during the Early
 Cretaceous and became speciose and abundant early in the Late Cretaceous.
 However, this radiation is poorly understood. Thililua longicollis from
 the Middle Turonian of Morocco is an enigmatic taxon possessing an
 atypically long-neck and, as originally reported, a series of unusual
 cranial features that cause unstable phylogenetic relationships for
 polycotylids. We reinterpret the holotype specimen of Thililua longicollis
 and clarify its cranial anatomy. Thililua longicollis possesses an
 extensive, foramina-bearing jugal, a premaxilla-parietal contact, and
 carinated teeth. Phylogenetic analyses of a new cladistic dataset based on
 first hand observation of most polycotylids, recovers Thililua and
 Mauriciosaurus as successive lineages at the base of the earliest Late
 Cretaceous polycotyline radiation. A new dataset summarizing the Bauplan
 of polycotylids reveal that their radiation produced an early burst of
 disparity during the Cenomanian-Turonian interval, with marked plasticity
 in relative neck length, but this did not arise as an ecological release
 following the extinction of ichthyosaurs and pliosaurids. This disparity
 vanished during and after the Turonian, which is consistent with a model
 of 'early experimentation/late constraint'. Two polycotylid
 clades, Occultonectia clade nov. and Polycotylinae, survived up to the
 Maastrichtian, but with low diversity.
description: ESM1 Supplementary
 informationBauplan data,
 supplementary methods, supplementary figures, supplementary
 tablesESM1
 Supp Info.docxESM2 Full Phylogenetic
 datasetNexus file with most
 parsimonious trees includedESM2
 Phylogenetic.nexESM3: Taxon ages for
 full phylogenetic datasetNumerical; per stage or
 substageESM3
 ages_full.txtESM4 Pruned Phylogenetic
 datasetNexus file with most
 parsimonious trees includedESM4 Pruned
 Phylogenetic.nexESM5 Taxon ages for
 pruned phylogenetic datasetNumerical; per stage or
 substageESM5
 ages_red.txtESM6 Numerical time
 binsNumerical ages, two
 binning methods (wide and per stage/substage)ESM6
 time_data.xlsxESM7 Ecomorphological
 dataReady-to-use text
 fileESM7
 ecodata.txtESM 8 R
 script–ESM8
 code.R
DOI: 10.5061/dryad.5k84d
title: Data from: Identifying signatures of sexual selection using genomewide selection components analysis

description: Sexual selection must affect the genome for it to have an evolutionary
 impact, yet signatures of selection remain elusive. Here we use an
 individual-based model to investigate the utility of genome-wide selection
 components analysis, which compares allele frequencies of individuals at
 different life history stages within a single population to detect
 selection without requiring a priori knowledge of traits under selection.
 We modeled a diploid, sexually reproducing population and introduced
 strong mate choice on a quantitative trait to simulate sexual selection.
 Genome-wide allele frequencies in adults and offspring were compared using
 weighted FST values. The average number of outlier peaks (i.e., those with
 significantly large FST values) with a quantitative trait locus in close
 proximity (“real” peaks) represented correct diagnoses of loci under
 selection, whereas peaks above the FST significance threshold without a
 quantitative trait locus reflected spurious peaks. We found that, even
 with moderate sample sizes, signatures of strong sexual selection were
 detectable, but larger sample sizes improved detection rates. The model
 was better able to detect selection with more neutral markers, and when
 quantitative trait loci and neutral markers were distributed across
 multiple chromosomes. Although environmental variation decreased detection
 rates, the identification of real peaks nevertheless remained feasible. We
 also found that detection rates can be improved by sampling multiple
 populations experiencing similar selection regimes. In short, genome-wide
 selection components analysis is a challenging but feasible approach for
 the identification of regions of the genome under selection.
description: summary data from
 simulation modelThese data are the
 average percent of real loci and the average number of spurious loci
 detected given the various parameter combinations tested by the
 model.Flanagan_and_Jones_molecol_data.docx.xlsxmultiple populations comparisonThis data contains Fst values for loci in replicate populations with the same QTLs, which were: chrom 0: 702, 978; chrom 1: 516, 341; chrom 2: 878, 76; chrom 3: 46, 153.12May_same-qtls_Fsts.txtpopulationsHeader file for C++ simulation programlife_cycleC++ program file for simulation modelchi_squareHeader file containing functions to calculate chi-square p-values for C++ simulation model.rand_numsC++ header file containing functions to calculate and use random numbers for simulation model program. File is available in GitHub at https://github.com/spflanagan/gwsca_simulation_model/blob/master/simulation_model/simulation_model/rand_nums.hSimulation_DataAll summary data from the simulation model (the average number of real and spurious peaks for all parameter combinations).
DOI: 10.5061/dryad.jn8hj0t
title: Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

description: Genetic surveys of the population structure of species can be used as
 resources for exploring their genomic architecture. By adjusting filtering
 assumptions, genome-wide single nucleotide polymorphism (SNP) datasets can
 be reused to give new insights into the genetic basis of divergence and
 speciation without targeted re-sampling of specimens. Filtering only for
 missing data and minor allele frequency, we used a combination of
 principle components analysis and linkage disequilibrium network analysis
 to distinguish three cohorts of variable SNPs in the mountain pine beetle
 in western Canada, including one that was sex-linked and one that was
 geographically associated. These marker cohorts indicate genomically
 localized differentiation, and their detection demonstrates an accessible
 and intuitive method for discovering potential islands of genomic
 divergence without a priori knowledge of a species’ genomic architecture.
 Thus, this method has utility for directly addressing the genomic
 architecture of species and generating new hypotheses for functional
 research.
description: 187_MPB_FemGenome175 Wild-caught and 13 lab-bred mountain pine beetle (Dendroctonus ponderosae) specimens from western Canada. Double-Digest RAD sequencing, aligned to the female D. ponderosae draft genome [Keeling et al. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biology. 2013;14(3):1. doi:10.1186/gb-2013-14-3-r27], and compiled in STACKSF1_in_F.vcf
DOI: 10.5061/dryad.218p2
title: Data from: Special features of RAD Sequencing data: implications for genotyping

description: RAD Sequencing (RAD-Seq) is an economical and efficient method for SNP
 discovery and genotyping. As with other sequencing-by-synthesis methods,
 RAD-Seq produces stochastic count data and requires sensitive analysis to
 develop or genotype markers accurately. We show that there are several
 sources of bias specific to RAD-Seq that are not explicitly addressed by
 current genotyping tools, namely restriction fragment bias, restriction
 site heterozygosity and PCR GC content bias. We explore the performance of
 existing analysis tools given these biases and discuss approaches to
 limiting or handling biases in RAD-Seq data. While these biases need to be
 taken seriously, we believe RAD loci affected by them can be excluded or
 processed with relative ease in most cases, and that most RAD loci will be
 accurately genotyped by existing tools.
description: Davey2012_MolEcol_Dryad_Submission.tarScripts and data files required to replicate figures and calculations for associated paper. Details in DESCRIPTION.md file, included in archive.
DOI: 10.5061/dryad.5124t
title: Data from: Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: a case study with ant cuticular bacteria

description: High-throughput sequencing of the 16S rRNA gene has considerably helped
 revealing the essential role of bacteria living on insect cuticles in the
 ecophysiology and behavior of their hosts. However, our understanding of
 host-cuticular microbiota feedbacks remains hampered by the difficulties
 to working with low bacterial DNA quantities as in individual insect
 cuticle samples, which are more prone to molecular biases and
 contaminations. Herein, we conducted a methodological benchmark on the
 cuticular bacterial loads retrieved from two Neotropical ant species of
 different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex
 penetrator (~5 mm). We evaluated the richness and composition of the
 cuticular microbiota, as well as the amount of biases and contamination
 produced by four DNA extraction protocols. We also addressed how bacterial
 communities’ characteristics would be affected by the number of
 individuals or individual body size used for DNA extraction. Most
 extraction methods yielded similar results in term of bacterial diversity
 and composition for A. cephalotes (~15 mm). In contrast, greater amounts
 of artifactual sequences and contaminations, as well as noticeable
 differences in bacterial communities’ characteristics were observed
 between the extraction methods for P. penetrator (~5 mm). We also found
 that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbor
 different bacterial communities. Our benchmark hence suggests that
 cuticular microbiota of single insect individuals can be reliably
 retrieved provided that blank controls, appropriate data cleaning, and
 standardization of individual body size are considered in the experiment.
description: Birer_et_al_cutants_samplesThis file contains geographic coordinates and other characteristics for each sampleBirer_et_al_cutants_fasta_uniq.tarThis tar.gz file contains 1 zipped fasta file of preprocessed sequencing data (i.e. assembled reads assigned to their original sample), corresponding each to cuticular bacteria amplicons.Birer_et_al_cutants_data_filteredThis txt file contains filtered sequencing data (i.e. after sequence clustering and spurious OTUs removal) corresponding to cuticular bacterial communities associated to Atta cephalotes and Pseudomyrmex penetrator (Formicidae).
DOI: 10.15468/dl.twf7a2
title: Occurrence Download

description: A dataset containing 2319 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Conopsis lineata",
 "Year 1000-2026"
 ]
}

 The dataset includes 2319 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000474-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6n332
title: Data from: Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans

description: Chlorarachniophyte algae possess complex plastids acquired by the
 secondary endosymbiosis of a green alga, and the plastids harbor a relict
 nucleus of the endosymbiont, the so-called nucleomorph. Due to massive
 gene transfer from the endosymbiont to the host, many proteins involved in
 plastid and nucleomorph are encoded by the nuclear genome. Genome
 sequences have provided a blueprint for the fate of endosymbiotically
 derived genes; however, transcriptional regulation of these genes remains
 poorly understood. To gain insight into the evolution of endosymbiotic
 genes, we performed genome-wide transcript profiling along the cell cycle
 of the chlorarachniophyte Bigelowiella natans, synchronized by light and
 dark cycles. Our comparative analyses demonstrated that transcript levels
 of 7,751 nuclear genes (35.7% of 21,706 genes) significantly oscillated
 along the diurnal/cell cycles, and those included 780 and 147 genes for
 putative plastid and nucleomorph-targeted proteins, respectively.
 Clustering analysis of those genes revealed the existence of
 transcriptional networks related to specific biological processes such as
 photosynthesis, carbon metabolism, translation, and DNA replication.
 Interestingly, transcripts of many plastid-targeted proteins in B. natans
 were induced before dawn, unlike other photosynthetic organisms. In
 contrast to nuclear genes, 99% nucleomorph genes were found to be
 constitutively expressed during the cycles. We also found that the
 nucleomorph DNA replication would be controlled by a nucleus-encoded
 viral-like DNA polymerase. The results of this study suggest that
 nucleomorph genes have lost transcriptional regulation along the diurnal
 cycles, and nuclear genes exert control over the complex plastid including
 the nucleomorph.
description: Bn_pasa.gene_structure_update_selected_modelsOriginal gene models generated by PASA.Bn_complete_genemodels_aaprotein sequences
DOI: 10.15468/dl.nbbyyd
title: Occurrence Download

description: A dataset containing 2641 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Royal Ontario Museum - Invertebrate Zoology",
 "TaxonKey is Glossiphoniidae"
 ]
}

 The dataset includes 2641 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000470-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxwyqx
title: Occurrence Download

description: A dataset containing 233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-80.59556 -8.82749,-49.51925 -9.98962,-47.7798 1.73527,-50.19019 2.23924,-80.59556 2.23924,-80.59556 -8.82749))",
 "TaxonKey is Pterygoplichthys pardalis"
 ]
}

 The dataset includes 233 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000472-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.