cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r25s5
title: Data from: Genomic evidence of gene flow during reinforcement in Texas Phlox

description: Gene flow can impede the evolution of reproductive isolating barriers
 between species. Reinforcement is the process by which pre-zygotic
 reproductive isolation evolves in sympatry due to selection to decrease
 costly hybridization. It is known that reinforcement can be prevented by
 too much gene flow, but we still do not know how often have pre-zygotic
 barriers evolved in the presence of gene flow or how much gene flow can
 occur during reinforcement. Flower color divergence in the native Texas
 wildflower, Phlox drummondii, is one of the best-studied cases of
 reinforcement. Here we use genomic analyses to infer gene flow between P.
 drummondii and a closely related sympatric species, P. cuspidata. We de
 novo assemble transcriptomes of four Phlox species to determine the
 phylogenetic relationships between these species, and find extensive
 discordance among gene tree topologies across genes. We find evidence of
 introgression between sympatric P. drummondii and P. cuspidata using the
 D-statistic, and use phylogenetic analyses to infer the predominant
 direction of introgression. We investigate geographic variation in gene
 flow by comparing the relative divergence of genes displaying discordant
 gene trees between an allopatric and sympatric sample. These analyses
 support the hypothesis that sympatric P. drummondii has experienced gene
 flow with P. cuspidata. We find that gene flow between these species is
 asymmetrical, which could explain why reinforcement caused divergence in
 only one of the sympatric species. Given the previous research in this
 system, we suggest strong selection can explain how reinforcement
 successfully evolved in this system despite gene flow in sympatry.
description: Genotypes at variable
 sitesWe provide the genotypes
 used to infer divergence between samples. At each polymorphic position we
 selected randomly one allele for each .sampleGenotypes_Dryad.txtDivergence_DryadGenetic divergence and phylogenies for ortholog clusters. For each cluster we show 4 and 5 species gene-tree topologies as well as categories used in Figure 4. We also sho values of genetic divergence (d) and RND for pairwise comparisons between the 5 samples (see paper for species codes).
DOI: 10.5061/dryad.1719f
title: Data from: Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

description: Defining subpopulations using genetics has traditionally used data from
 microsatellite markers to investigate population structure; however,
 single-nucleotide polymorphisms (SNPs) have emerged as a tool for
 detection of fine-scale structure. In Hudson Bay, Canada, three polar bear
 (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay
 (SH), and Western Hudson Bay (WH)) have been delineated based on
 mark–recapture studies, radiotelemetry and satellite telemetry, return of
 marked animals in the subsistence harvest, and population genetics using
 microsatellites. We used SNPs to detect fine-scale population structure in
 polar bears from the Hudson Bay region and compared our results to the
 current designations using 414 individuals genotyped at 2,603 SNPs.
 Analyses based on discriminant analysis of principal components (DAPC) and
 STRUCTURE support the presence of four genetic clusters: (i)
 Western—including individuals sampled in WH, SH (excluding Akimiski Island
 in James Bay), and southern FB (south of Southampton Island); (ii)
 Northern—individuals sampled in northern FB (Baffin Island) and Davis
 Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH
 (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS
 (Baffin Island). Population structure differed from microsatellite studies
 and current management designations demonstrating the value of using SNPs
 for fine-scale population delineation in polar bears.
description: ped SNP file for polar
 bears of the Hudson Bay regionThe following file
 (.ped) contains SNP data (3341) for 414 individual bears sampled in the
 Hudson Bay region. Each bear has a unique bear ID (see second column) and
 is also categorized by the subpopulation in which it is designated to (see
 column one). Columns three and four indicate the ancestry of the
 individual (parents) and are followed by the individual's sex (coded:
 1 = male, 2 =female). The remaining columns are the individual's
 genotype.ECE-2015-10-00703.ped.map file for polar bears of the Hudson Bay regionThe .map file contains information about the corresponding SNPs to the .ped file. Each line represents a single marker, see README file for the column descriptions.ECE-2015-10-00703.map
DOI: 10.13120/0wuxff
title: Sea turtles validated sightings reported by avvistAPP users

description: Validated sightings reported from 2019 onwards by avvistAPP users. avvistAPP is a free citizen science tool that allows everyone to actively contribute to the monitoring of marine animals. Available both in Google and Apple app stores. App description: https://doi.org/10.13120/h127-9v54
DOI: 10.5061/dryad.1tj60
title: Data from: Using multiple traits to assess the potential of introduced and native vines to proliferate in a tropical region

description: Predicting the invasive potential of introduced species remains an ongoing
 challenge due to the multiple interacting regional and global processes
 that facilitate the introduction and proliferation of alien species. This
 may be particularly true in regions where native species are increasingly
 reported as expanding and impacting ecosystems in ways indistinguishable
 from alien ones. Current approaches to assess the invasive potential of
 plants may be limited by the choice of traits used and the exclusion of
 native species. To overcome these limitations, we develop a novel approach
 that focuses on all species—native and alien—within a functional group of
 plants to predict their proliferation status. Our approach relied on the
 development of an extensive database of extrinsic and intrinsic traits for
 Puerto Rican vines with the goal of generating a predictive model of vine
 proliferation status. We test three hypotheses linking origin, extrinsic
 and intrinsic traits, and proliferation status. We found that the origin
 of proliferating vines was associated with only one out of seven traits,
 namely plant use. We also found that proliferation status was associated
 with all but two traits, namely life span and climbing mechanism. Finally,
 a classification tree analysis identified five variables as good
 predictors of proliferation status and used them to split the species into
 six groups characterized by a unique suite of traits, three of them
 included proliferating species. The development of tools to identify
 potential proliferating species is critical for management and
 conservation purposes. Tools that can minimize biases and make predictions
 based on trait data easily obtainable are particularly needed in regions
 with a high taxonomic and functional diversity, and with limited
 ecological knowledge of individual species. In addition, these tools
 should be capable of incorporating native species since an increasing
 number of native species are behaving like invasive aliens.
description: Vine species database
 (Appendix 2)Vine species reported in
 Puerto Rico, including information on their traits and the references
 supporting each record.Delagado_etal_2016_Appendix2.xlsx
DOI: 10.5061/dryad.dk563
title: Data from: Habitat continuity and stepping-stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea

description: Effective predictive and management approaches for species occurring in a
 metapopulation structure require good understanding of inter-population
 connectivity. In this study we ask whether population genetic structure of
 marine species with fragmented distributions can be predicted by
 stepping-stone oceanographic transport and habitat continuity, using as
 model an ecosystem-structuring brown alga, Cystoseira amentacea var.
 stricta. To answer this question, we analyzed the genetic structure and
 estimated the connectivity of populations along discontinuous rocky
 habitat patches in southern Italy, using microsatellite markers at
 multiple scales. In addition, we modelled the effect of rocky habitat
 continuity and ocean circulation on gene flow by simulating Lagrangian
 particle dispersal based on ocean surface currents allowing
 multigenerational stepping-stone dynamics. Populations were highly
 differentiated, at scales from few meters up to 1000s of kilometers. The
 best possible model fit to explain the genetic results combined current
 direction, rocky habitat extension and distance along the coast among
 rocky sites. We conclude that a combination of variables suitable habitat
 and oceanographic transport is a useful predictor of genetic structure.
 This relationship provides insight into the mechanisms of dispersal and
 the role of life history traits. Our results highlight the importance of
 spatially explicit modeling of stepping stone dynamics and oceanographic
 directional transport coupled with habitat suitability, to better describe
 and predict marine population structure and differentiation. This study
 also suggests the appropriate spatial scales for the conservation,
 restoration and management of species that are increasingly affected by
 habitat modifications.
description: microsatellite raw
 scoringColumn names: Pop=
 population code; ID= sample unique identifier; col 2 to 8 = marker names.
 Pop codes: CG= Capo Gallo, CR= Crotone, OT= Otranto, PA= Palermo
 (Altavilla), PP= Portopalo, SC= Sciacca (Mazara), TU=Torre Uluzzo,
 SE=Sant'Eliamsat_data.txtscripts used in R for linear modelsData were created in Rscripts.htmlData frame with distances among pairs of populationstab delimited table containing all the pairwise distances among populations, including geographical distance and obtained from particle dispersal model as well as calculated index of directionalityDF.txtparticle dispersal simulation videoexample of direct dispersal simulation from the sampling sites over one simulation period (jul-sept)Cystoseira Final 2.mp4autocorrelation kinship resutlsAutocorrelation file with distance and kinship coefficient among samples.autocorrelation_all.txtmarkers score input for genpopEdited microsatellite analysis result used as input in genpop, GenALEx and GENETIX.gen.gen
DOI: 10.5061/dryad.15512
title: Data from: Signatures of local adaptation in candidate genes of oaks (Quercus spp.) in respect to present and future climatic conditions

description: Testing how populations are locally adapted and predicting their response
 to their future environment is of key importance in view of climate
 change. Landscape genomics is a powerful approach to investigate genes and
 environmental factors involved in local adaptation. In a pooled amplicon
 sequencing approach of 94 genes in 71 populations, we tested if
 &gt;3,500 single nucleotide polymorphisms (SNPs) in the three most
 common oak species in Switzerland (Quercus petraea, Q. pubescens, Q.
 robur) show an association with abiotic factors related to local
 topography, historical climate, and soil characteristics. In the analysis
 including all species, the most frequently associated environmental
 factors were those best describing the habitats of the species. In the
 species-specific analyses, the most important environmental factors and
 associated SNPs greatly differed among species. However, we identified one
 SNP and seven genes that were associated with the same environmental
 factor across all species. We finally used regressions of allele
 frequencies of the most strongly associated SNPs along environmental
 gradients to predict the risk of non-adaptedness (RONA), which represents
 the average change in allele frequency at climate-associated loci
 theoretically required to match future climatic conditions. RONA is
 considerable for some populations and species (up to 48% in single
 populations) and strongly differs among species. Given the long generation
 time of oaks, some of the required allele frequency changes might not be
 realistic to achieve based on standing genetic variation. Hence, future
 adaptedness requires gene flow or planting of individuals carrying
 beneficial alleles from habitats currently matching future climatic
 conditions.
description: cpSNP allele
 frequenciesChloroplast SNP allele
 frequenciescpSNP_allele_frequencies.xlsxEnvironmental dataEnvironmental data from 1931-1960 and 2071-2100environmental_factors.xlsxnSSR genotypesMicrosatellite genotypesnSSR_genotypes.xlsxSNP allele frequencies in candidate genesSNP allele frequencies in candidate targetstargets_SNP_allele_frequencies.xlsxAmplified reference sequencesAmplified reference sequences of candidate genesamplified_reference_sequences.fasta
DOI: 10.5061/dryad.n5fr8
title: Data from: Domain-specific functions of Stardust in Drosophila embryonic development

description: In Drosophila, the adaptor protein Stardust is essential for the
 stabilization of the polarity determinant Crumbs in various epithelial
 tissues, including the embryonic epidermis, the follicular epithelium and
 photoreceptor cells of the compound eye. In turn, Stardust recruits
 another adaptor protein, PATJ, to the subapical region to support adherens
 junction formation and morphogenetic events. Moreover, Stardust binds to
 Lin-7, which is dispensable in epithelial cells but functions in
 postsynaptic vesicle fusion. Finally, Stardust has been reported to bind
 directly to PAR-6, thereby linking the Crumbs–Stardust–PATJ complex to the
 PAR-6/aPKC complex. PAR-6 and aPKC are also capable of directly binding
 Bazooka (the Drosophila homologue of PAR-3) to form the PAR/aPKC complex,
 which is essential for apical–basal polarity and cell–cell contact
 formation in most epithelia. However, little is known about the
 physiological relevance of these interactions in the embryonic epidermis
 of Drosophila in vivo. Thus, we performed a structure–function analysis of
 the annotated domains with GFP-tagged Stardust and evaluated the
 localization and function of the mutant proteins in epithelial cells of
 the embryonic epidermis. The data presented here confirm a crucial role of
 the PDZ domain in binding Crumbs and recruiting the protein to the
 subapical region. However, the isolated PDZ domain is not capable of being
 recruited to the cortex, and the SH3 domain is essential to support the
 binding to Crumbs. Notably, the conserved N-terminal regions (ECR1 and
 ECR2) are not crucial for epithelial polarity. Finally, the GUK domain
 plays an important role for the protein's function, which is not
 directly linked to Crumbs stabilization, and the L27N domain is essential
 for epithelial polarization independently of recruiting PATJ.
description: Figure S1 Expression of
 Sdt in embryogenesis.(A) Extracts of 0-16h
 old embryos of either sdtK85 germ lines clones (mated with males carrying
 an FM7-ChFP balancer and sorted against ChFP) or wild type flies were
 blotted against Sdt and Actin. Both bands seen above the 100kDa marker
 band appear to be specific. (B) Extracts of staged embryos were blotted
 against Sdt and Actin. (C-D) Heterozygous and zygotic mutant sdtK85
 embryos were stained with anti Sdt and DAPI. Note that the morphology of
 sdtK85 mutant embryos is already disturbed. Scale bars =
 50µm.Figure
 S1.tifFigure S2. Mislocalized
 Sdt variants do not displace endogenous PATJ or PAR-6(A-D) Sdt-GFP was
 ubiquitous expressed in wild type embryos and distribution of GFP, PATJ
 and PAR-6 was analyzed in stage 11-12 embryos. Scale bars =
 5µm.Figure
 S2.tif
DOI: 10.5061/dryad.3kq05
title: Data from: Living in the city: urban environments shape the evolution of a native annual plant

description: Urban environments are warmer, have higher levels of atmospheric CO2, and
 altered patterns of disturbance and precipitation than nearby rural areas.
 These differences can be important for plant growth and are likely to
 create distinct selective environments. We planted a common garden
 experiment with seeds collected from natural populations of the native
 annual plant Lepidium virginicum, growing in five urban and nearby rural
 areas in the northern United States to determine whether and how urban
 populations differ from those from surrounding rural areas. When grown in
 a common environment, plants grown from seeds collected from urban areas
 bolted sooner, grew larger, had fewer leaves, had an extended time between
 bolting and flowering, and produced more seeds than plants grown from
 seeds collected from rural areas. Interestingly, the rural populations
 exhibited larger phenotypic differences from one another than urban
 populations. Surprisingly, genomic data revealed that the majority of
 individuals in each of the urban populations were more closely related to
 individuals from other urban populations than they were to geographically
 proximate rural areas – the one exception being urban and rural
 populations from New York which were nearly identical. Taken together our
 results suggest that selection in urban environments favors different
 traits than selection in rural environments and that these differences can
 drive adaptation and shape population structure.
description: Yakub_Tiffin_GCB_full_data_3oct_2016phenotypic data on individual plantsYakub_Tiffin_GCB_GBS_forarlequinVariants identified by GBS and used for pop gen analyses (Dxy, Instruct)
DOI: 10.5061/dryad.t9j0j
title: Data from: DualPhos: a versatile, chemoselective reagent for two-carbon aldehyde to latent (E)-alkenal homologation and application in the total synthesis of phomolide G

description: Advances on the use of the 2-pinacolacetal-tripropylphosphonium salt
 DualPhos as a general reagent for the two-carbon aldehyde to alkenal
 homologation and a chemoselective iron (III) chloride mediated
 deprotection are described. The strategy allows isolation of the latent
 alkenal intermediates or direct hydrolysis to (E)-alkenals. The robust
 chemical stability of the latent alkenals is demonstrated in a total
 synthesis of the macrolactone phomolide G.
description: Experimental synthetic
 procedures and supporting data.All synthetic
 procedures, listing of data parameters and hard copies of spectroscopic
 data (NMR) are presented.R Soc Open Sci Supporting
 InformationCorrected.pdf
DOI: 10.5061/dryad.fs618
title: Data from: Non-reef environments impact the diversification of extant jacks, remoras and allies (Carangoidei, Percomorpha)

description: Various factors may impact the processes of diversification of a clade. In
 the marine realm, it has been shown that coral reef environments have
 promoted diversification in various fish groups. With the exception of
 requiem sharks, all the groups showing a higher level of diversity in
 reefs than in non-reef habitats have diets based predominantly on
 plankton, algae or benthic invertebrates. Here we explore the pattern of
 diversification of carangoid fishes, a clade that includes numerous
 piscivorous species (e.g. trevallies, jacks and dolphinfishes), using
 time-calibrated phylogenies as well as ecological and morphological data
 from both extant and fossil species. The study of carangoid morphospace
 suggests that reef environments played a role in their early radiation
 during the Eocene. However, contrary to the hypothesis of a
 reef-association-promoting effect, we show that habitat shifts to non-reef
 environments have increased the rates of morphological diversification
 (i.e. size and body shape) in extant carangoids. Piscivory did not have a
 major impact on the tempo of diversification of this group. Through the
 ecological radiation of carangoid fishes, we demonstrate that non-reef
 environments may sustain and promote processes of diversification of
 different marine fish groups, at least those including a large proportion
 of piscivorous species.
description: FREDERICH_figures_tables_ESMPdf file including figure S1, figure S2, table S1, table S2 and table S3.Carangoids_Specimen_listList of all studied specimens with accession numbers and related online databases.
DOI: 10.5061/dryad.3h2b7
title: Data from: Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs

description: The establishment of a region of suppressed recombination is a critical
 change during sex chromosome evolution, leading to such properties as Y
 (and W) chromosome genetic degeneration, accumulation of repetitive
 sequences and heteromorphism. Although chromosome inversions can cause
 large regions to have suppressed recombination, and inversions are
 sometimes involved in sex chromosome evolution, gradual expansion of the
 non-recombining region could potentially sometimes occur. We here test
 whether closer linkage has recently evolved between the sex-determining
 region and several genes that are partially sex-linked in Silene
 latifolia, using Silene dioica, a closely related dioecious plants whose
 XY sex chromosome system is inherited from a common ancestor. The S.
 latifolia pseudoautosomal region (PAR) includes several genes extremely
 closely linked to the fully Y-linked region. These genes were added to an
 ancestral PAR of the sex chromosome pair in two distinct events probably
 involving translocations of autosomal genome regions causing multiple
 genes to become partially sex-linked. Close linkage with the PAR boundary
 must have evolved since these additions, because some genes added in both
 events now show almost complete sex linkage in S. latifolia. We compared
 diversity patterns of five such S. latifolia PAR boundary genes with their
 orthologues in S. dioica, including all three regions of the PAR (one gene
 that was in the ancestral PAR and two from each of the added regions). The
 results suggest recent recombination suppression in S. latifolia, since
 its split from S. dioica.
description: Silene_samples_Heredity-Campos2016Table with the ids used in the alignments for all the samples and for each gene. We also include the species name, sex and location for each sample.cs3597_Lat-Dio_Campos2016Alignment of gene cs3597 in nexus format used in the DnaSP analyses.cs3597_Lat-Dio_Campos2016Alignment of gene cs3597 in fasta format.E559_Lat-Dio-Mar-Dic_Campos2016Alignment of gene E559 in nexus format used in the DnaSP analyses.E559_Lat-Dio-Mar-Dic_Campos2016Alignment of gene E559 in fasta format.cs935_Lat-Dio_Campos2016Alignment of gene cs935 in nexus format used in the DnaSP analyses.cs935_Lat-Dio_Campos2016Alignment of gene cs935 in fasta format.E523_Lat-Dio-Mar-Dic_Campos2016Alignment of gene E523 in nexus format used in the DnaSP analyses.E523_Lat-Dio-Mar-Dic_Campos2016Alignment of gene E523 in fasta format.E521_Lat-Dio_Campos2016Alignment of gene E521 in nexus format used in the DnaSP analyses.E521_Lat-Dio_Campos2016Alignment of gene E521 in fasta format.cs4991_Lat-Dio_Campos2016Alignment of gene cs4991 in nexus format used in the DnaSP analyses.cs4991_Lat-Dio_Campos2016Alignment of gene cs4991 in fasta format.