cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g8b96
title: Data from: Transcriptome sequencing reveals both neutral and adaptive genome dynamics in a marine invader

description: Species invasions cause significant ecological and economic damage, and
 genetic information is important to understanding and managing invasive
 species. In the ocean, many invasive species have high dispersal and gene
 flow, lowering the discriminatory power of traditional genetic approaches.
 High-throughput sequencing holds tremendous promise for increasing
 resolution and illuminating the relative contributions of selection and
 drift in marine invasion, but has not yet been used to compare the
 diversity and dynamics of a high-dispersal invader in its native and
 invaded ranges. We test a transcriptome-based approach in the European
 green crab (Carcinus maenas), a widespread invasive species with high gene
 flow and a well-known invasion history, in two native and five invasive
 populations. A panel of 10 809 transcriptome-derived nuclear SNPs
 identified significant population structure among highly bottlenecked
 invasive populations that were previously undifferentiated with
 traditional markers. Comparing the full data set and a subset of 9246
 putatively neutral SNPs strongly suggested that non-neutral processes are
 the primary driver of population structure within the species’ native
 range, while neutral processes appear to dominate in the invaded range.
 Non-neutral native range structure coincides with significant differences
 in intraspecific thermal tolerance, suggesting temperature as a potential
 selective agent. These results underline the importance of adaptation in
 shaping intraspecific differences even in high geneflow marine invasive
 species. They also demonstrate that high-throughput approaches have broad
 utility in determining neutral structure in recent invasions of such
 species. Together, neutral and non-neutral data derived from
 high-throughput approaches may increase the understanding of invasion
 dynamics in high-dispersal species.
description: Carcinus maenas cardiac
 transcriptome assemblyCardiac transcriptome of
 Carcinus maenas, derived from sequence for 84 individuals from seven sites
 in the native and invasive ranges. (Portugal, Norway, Newfoundland, Maine,
 New Jersey, California, and British Columbia) Assembled with CLC Genomics
 Workbench. Further details in associated publications.Carcinus_assembly.faNuclear SNP genotypes for Carcinus maenasIndividual genotypes for 84 Carcinus maenas individuals from seven sites in the native and invasive ranges. Genotypes given for 10,809 high-quality nuclear SNPs. Further detail in associated publications.CM_full_10809_genos.csvDryad_SNP_readmePutatively neutral SNPs for Carcinus maenasList of SNPs determined to be putatively neutral in Carcinus maenas. Codes as given in associated assembly and genotype data.Cmaenas_neutral_SNPs.txtPotentially non-neutral SNPs for Carcinus maenasList of SNPs determined to be potentially non-neutral in Carcinus maenas. Codes as given in associated assembly and genotype data.Cmaenas_non-neutral_SNPs.txt
DOI: 10.5061/dryad.1019
title: Data from: Mixture modeling of transcript abundance classes in natural populations

description: BACKGROUND: Populations diverge in genotype and phenotype under the
 influence of such evolutionary processes as genetic drift, mutation
 accumulation, and natural selection. Because genotype maps onto phenotype
 by way of transcription, it is of interest to evaluate how these
 evolutionary factors influence the structure of variation at the level of
 transcription. Here, we explore the distributions of cis-acting and
 trans-acting factors and their relative contributions to expression of
 transcripts that exhibit two or more classes of abundance among
 individuals within populations. RESULTS: Expression profiling using cDNA
 microarrays was conducted in Drosophila melanogaster adult female heads
 for 58 nearly isogenic lines from a North Carolina population and 50 from
 a California population. Using a mixture modeling approach, transcripts
 were identified that exhibit more than one mode of transcript abundance
 across the samples. Power studies indicate that sample sizes of 50
 individuals will generally be sufficient to detect divergent transcript
 abundance classes. The distribution of transcript abundance classes is
 skewed toward low frequency minor classes, which is reminiscent of the
 typical skew in genotype frequencies. Similar results are observed in
 reported data on gene expression in human lymphoblast cell lines, in which
 analysis of association with linked polymorphisms implies that cis-acting
 single nucleotide polymorphisms make only a modest contribution to bimodal
 distributions of transcript abundance. CONCLUSION: Population surveys of
 gene expression may complement genetical genomics as a general approach to
 quantifying sources of transcriptional variation. Differential expression
 of transcripts among individuals is due to a complex interplay of
 cis-acting and trans-acting factors.
description: MIAME Compliance
 ChecklistGurgel MIAME
 compliance.docArray
 AnnotationNic array
 annotation.xlsRaw Data for all
 ArraysNic
 raw arrays.xlsMeans Data
 SetGurgel
 LSmeans.xlsPopulation Effect Data
 SetPopulation
 effect.xlsTFC
 ParametersTFCparameters.xlsTFCsSAS CodeSAS scripts.doc
DOI: 10.5061/dryad.v8cp134
title: Data from: Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

description: The most important managed pollinator, the honeybee (Apis mellifera L.),
 has been subject to a growing number of threats. In Western Europe one
 such threat is large-scale introductions of commercial strains (C-lineage
 ancestry), which is leading to introgressive hybridization and even the
 local extinction of native honeybee populations (M-lineage ancestry).
 Here, we developed reduced assays of highly informative SNPs from 176
 whole genomes to estimate C-lineage introgression in the most diverse and
 evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis
 mellifera iberiensis). We started by evaluating the effects of sample size
 and sampling a geographically restricted area on the number of highly
 informative SNPs. We demonstrated that a bias in the number of fixed SNPs
 (FST=1) is introduced when the sample size is small (N≤10) and when
 sampling only captures a small fraction of a population’s genetic
 diversity. These results underscore the importance of having a
 representative sample when developing reliable reduced SNP assays for
 organisms with complex genetic patterns. We used a training dataset to
 design four independent SNP assays selected from pairwise FST between the
 Iberian and C-lineage honeybees. The designed assays, which were validated
 in holdout and simulated hybrid datasets, proved to be highly accurate and
 can be readily used for monitoring populations not only in the native
 range of A. m. iberiensis in Iberia but also in the introduced range in
 the Balearic islands, Macaronesia, and South America, in a time- and
 cost-effective manner. While our approach used the Iberian honeybee as
 model system, it has a high value in a wide range of scenarios for the
 monitoring and conservation of potentially hybridized domestic and
 wildlife populations.
description: SNP dataset retrieved
 from 176 whole-genome sequences (117 A. m. iberiensis, 28 A. m. carnica
 and 31 A. m. ligustica)The dataset contains a
 total of 2,366,382 SNPs detected between 117 A. m. iberiensis, 28 A. m.
 carnica and 31 A. m. ligustica. SNP calling was performed using three
 different variant calling tools: GATK's, SAMtools’ mpileup 1.1 and
 PLATYPUS 0.8.1 Details for SNP processing and quality control is provided
 in the paper and its supplementary information.iber_car_lig.vcf.gz
DOI: 10.5061/dryad.m0jk7
title: Data from: The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

description: Understanding the process of adaptation during rapid environmental change
 remains one of the central focal points of evolutionary biology. The
 recently formed White Sands system of southern New Mexico offers an
 outstanding example of rapid adaptation, with a variety of species having
 rapidly evolved blanched forms on the dunes that contrast with their close
 relatives in the surrounding dark soil habitat. In this study, we focus on
 two of the White Sands lizard species, Sceloporus cowlesi and Aspidoscelis
 inornata, for which previous research has linked mutations in the
 melanocortin-1 receptor gene (Mc1r) to blanched coloration. We sampled
 populations both on and off of the dunes and used a custom sequence
 capture assay based on probed fosmid libraries to obtain &gt;50kb of
 sequence around Mc1r and hundreds of other random genomic locations. We
 then used model-based statistical inference methods to describe the
 demographic and adaptive history characterizing the colonization of White
 Sands. We identified a number of similarities between the two focal
 species, including strong evidence of selection in the blanched
 populations in the Mc1r region. We also found important differences
 between the species, suggesting different colonization times, different
 genetic architecture underlying the blanched phenotype, and different ages
 of the beneficial alleles. Finally, the beneficial allele is dominant in
 S. cowlesi and recessive in A. inornata, allowing for a rare empirical
 test of theoretically expected patterns of selective sweeps under these
 differing models.
description: NimbleGen Capture Probe
 SequencesNimbleGen capture probe
 sequences designed against assemblies obtained from sequencing fosmids
 created from Aspidoscelis inornata and Sceloporus cowlesi
 DNA.probes.fasta
DOI: 10.5061/dryad.4hk28
title: Data from: Seascape genomics reveals fine-scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia

description: Understanding the drivers of dispersal among populations is a central
 topic in marine ecology and fundamental for spatially explicit management
 of marine resources. The extensive coast of Northwestern Australia
 provides an emerging frontier for implementing new genomic tools to
 comparatively identify patterns of dispersal across diverse and extreme
 environmental conditions. Here, we focused on the stripey snapper
 (Lutjanus carponotatus), which is important to recreational, charter-based
 and customary fishers throughout the Indo-West Pacific. We collected 1,016
 L. carponotatus samples at 51 locations in the coastal waters of
 Northwestern Australia ranging from the Northern Territory to Shark Bay
 and adopted a genotype-by-sequencing approach to test whether realized
 connectivity (via larval dispersal) was related to extreme gradients in
 coastal hydrodynamics. Hydrodynamic simulations using CONNIE and a more
 detailed treatment in the Kimberley Bioregion provided null models for
 comparison. Based on 4,402 polymorphic single nucleotide polymorphism loci
 shared across all individuals, we demonstrated significant genetic
 subdivision between the Shark Bay Bioregion in the south and all locations
 within the remaining, more northern bioregions. More importantly, we
 identified a zone of admixture spanning a distance of 180 km at the border
 of the Kimberley and Canning bioregions, including the Buccaneer
 Archipelago and adjacent waters, which collectively experiences the
 largest tropical tidal range and some of the fastest tidal currents in the
 world. Further testing of the generality of this admixture zone in other
 shallow water species across broader geographic ranges will be critical
 for our understanding of the population dynamics and genetic structure of
 marine taxa in our tropical oceans.
description: Report-DLu15-1902_ModUnfiltered DArTseq genotypes for 1016 L. carponotatus samples.
DOI: 10.5061/dryad.3s06b
title: Data from: Lesions to right posterior parietal cortex impair visual depth perception from disparity but not motion cues

description: The posterior parietal cortex (PPC) is understood to be active when
 observers perceive three-dimensional (3D) structure. However, it is not
 clear how central this activity is in the construction of 3D spatial
 representations. Here, we examine whether PPC is essential for two aspects
 of visual depth perception by testing patients with lesions affecting this
 region. First, we measured subjects' ability to discriminate depth
 structure in various 3D surfaces and objects using binocular disparity.
 Patients with lesions to right PPC (N = 3) exhibited marked perceptual
 deficits on these tasks, whereas those with left hemisphere lesions (N =
 2) were able to reliably discriminate depth as accurately as control
 subjects. Second, we presented an ambiguous 3D stimulus defined by
 structure from motion to determine whether PPC lesions influence the rate
 of bistable perceptual alternations. Patients' percept durations for
 the 3D stimulus were generally within a normal range, although the two
 patients with bilateral PPC lesions showed the fastest perceptual
 alternation rates in our sample. Intermittent stimulus presentation
 reduced the reversal rate similarly across subjects. Together, the results
 suggest that PPC plays a causal role in both inferring and maintaining the
 perception of 3D structure with stereopsis supported primarily by the
 right hemisphere, but do not lend support to the view that PPC is a
 critical contributor to bistable perceptual alternations.
description: MRI-derived lesion mask
 volumesThis folder contains
 lesion mask volumes (nifti format) for each patient that were created from
 T1 weighted MRI scans. Additionally, a standard MNI template volume and
 several parietal region of interest volumes are provided, along with a
 Matlab script that demonstrates how to load, plot and quantifying these
 volume data.MRI.zipStereoscopic task behavioural dataBehavioural data from all subjects on the stereoscopic tasks (dynamic, fine, and signal-in-noise) are provided in both .csv spreadsheet and .mat formats. The example Matlab code provided can be used to fit psychometric functions to these data, and produces the series of plots shown in Figure 3 of the paper.StereoscopicTask.zipBistable task behavioural dataPercept duration data (in seconds) for all subjects (patients and controls) on the bistable tasks is provided in .csv spreadsheet and .mat formats. The accompanying example Matlab script loads the duration data and calculates descriptive statistics for the rotating sphere task, which are plotted similarly to Figures 5 and 6 of the paper.BistableTasks.zip
DOI: 10.5061/dryad.gk2vc
title: Data from: Going where traditional markers have not gone before: utility of and promise for RAD-sequencing in marine invertebrate phylogeography and population genomics

description: Characterization of large numbers of single-nucleotide polymorphisms
 (SNPs) throughout a genome has the power to refine the understanding of
 population demographic history and to identify genomic regions under
 selection in natural populations. To this end, population genomic
 approaches that harness the power of next-generation sequencing to
 understand the ecology and evolution of marine invertebrates represent a
 boon to test long-standing questions in marine biology and conservation.
 We employed restriction-site-associated DNA sequencing (RAD-seq) to
 identify SNPs in natural populations of the sea anemone Nematostella
 vectensis, an emerging cnidarian model with a broad geographic range in
 estuarine habitats in North and South America, and portions of England. We
 identified hundreds of SNP-containing tags in thousands of RAD loci from
 30 barcoded individuals inhabiting four locations from Nova Scotia to
 South Carolina. Population genomic analyses using high-confidence SNPs
 resulted in a highly-resolved phylogeography, a result not achieved in
 previous studies using traditional markers. Plots of locus-specific FST
 against heterozygosity suggest that a majority of polymorphic sites are
 neutral, with a smaller proportion suggesting evidence for balancing
 selection. Loci inferred to be under balancing selection were mapped to
 the genome, where 90% were located in gene bodies, indicating potential
 targets of selection. The results from analyses with and without a
 reference genome supported similar conclusions, further highlighting
 RAD-seq as a method that can be efficiently applied to species lacking
 existing genomic resources. We discuss the utility of RAD-seq approaches
 in burgeoning Nematostella research as well as in other cnidarian species,
 particularly corals and jellyfishes, to determine phylogeographic
 relationships of populations and identify regions of the genome undergoing
 selection.
description: bowtie_alignments.tarAlignments of RAD sequence reads to the reference genome, as produced by BOWTIERAD_markers.tarRAD markers used in the population genomic analyses
DOI: 10.5061/dryad.4cf2p
title: Data from: Hybridization can promote adaptive radiation by means of transgressive segregation

description: Understanding the mechanisms of rapid adaptive radiation has been a
 central problem of evolutionary ecology. Recently, there is a growing
 recognition that hybridization between different evolutionary lineages can
 facilitate adaptive radiation by creating novel phenotypes. Yet,
 theoretical plausibility of this hypothesis remains unclear because, for
 example, hybridization can negate pre-existing species richness. Here, we
 theoretically investigate whether and under what conditions hybridization
 promotes ecological speciation and adaptive radiation by using an
 individual-based model to simulate genome evolution following
 hybridization between two allopatrically evolved lineages. The model
 demonstrated that transgressive segregation through hybridization can
 facilitate adaptive radiation, most powerfully when novel vacant
 ecological niches are highly dissimilar, phenotypic effect size of
 mutations is small, and there is moderate genetic differentiation between
 parental lineages. These results provide a theoretical basis for the
 effect of hybridization facilitating adaptive radiation.
description: ELE_Kagawa_TakimotoThe data file contains: (1) Java source code of the individual-based computer simulation in our paper, (2) R codes to produce figures from output files of the simulation, and (3) simulation results that we used to produce figures in our paper.
DOI: 10.5061/dryad.6k740
title: Data from: Local inter-species introgression is the main cause of extreme levels of intra-specific differentiation in mussels

description: Structured populations, and replicated zones of contact between species,
 are an ideal opportunity to study regions of the genome with unusual
 levels of differentiation; and these can illuminate the genomic
 architecture of species isolation, and the spread of adaptive alleles
 across species ranges. Here, we investigated the effects of gene flow on
 divergence and adaptation in the Mytilus complex of species, including
 replicated parental populations in quite distant geographical locations.
 We used target enrichment sequencing of 1269 contigs of a few Kb each,
 including some genes of known function, to infer gene genealogies at a
 small chromosomal scale. We show that geography is an important
 determinant of the genome-wide patterns of introgression in Mytilus, and
 that gene flow between different species, with contiguous ranges,
 explained up to half of the intra-specific outliers. This suggests that
 local introgression is both widespread and tends to affect larger
 chromosomal regions than purely intraspecific processes. We argue that
 this situation might be common, and this implies that genome scans should
 always consider the possibility of introgression from sister species,
 unsampled differentiated backgrounds, or even extinct relatives, e.g.
 Neanderthals in humans. The hypothesis that reticulate evolution over long
 periods of time contributes widely to adaptation, and to the spatial and
 genomic reorganisation of genetic backgrounds, needs to be more widely
 considered in order to make better sense of genome scans.
description: Probe set for the target
 enrichment experimentFour-column SureSelect
 probe template file: (1) TargetID represents the genomic target that is
 intended for capture; (2) ProbeID provides a means for you to identify
 your probes; (3) Sequence is the actual sequence of the synthesized
 probe;(4) Replication determines how many times a probe will be replicated
 in the library.probe_set_mytilus.zipFinal contig setFasta sequences of the final contig set (378 BAC contigs and 891 cDNA contigs) and a descriptive file containing the name of each contig, its length and type (BAC or cDNA).final_contig_set.zipVariants files (VCF)Three VCF files were used in this study: (1) SNP_GQ20_20%missing for FST analyses; (2) SNP_GQ30_20%missing for genealogies; (3) SNP_GQ20_0%missing for multivariate analyses. Only SNPs have been called.variant_files.zipFST resultsFSTmax and FST90 of each contig are given for the intraspecific comparisons: (1) M. trossulus Europe vs America; (2) M. edulis Europe vs America; (3) M. galloprovincialis Atlantic vs Mediterranee; (4) M. galloprovincialis Atlantic External vs Internal; (5) M. galloprovincialis Mediterranee West vs East; (6) M. edulis Europe External vs Internalfst_results.zip