cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5p5c0
title: Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

description: Understanding the evolutionary mechanisms generating parallel genomic
 divergence patterns among replicate ecotype pairs remains an important
 challenge in speciation research. We investigated the genomic divergence
 between the anadromous parasitic river lamprey (Lampetra fluviatilis) and
 the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in
 nine population pairs displaying variable levels of geographic
 connectivity. We genotyped 338 individuals with RAD sequencing and
 inferred the demographic divergence history of each population pair using
 a diffusion approximation method. Divergence patterns in geographically
 connected population pairs were better explained by introgression after
 secondary contact, whereas disconnected population pairs have retained a
 signal of ancient migration. In all ecotype pairs, models accounting for
 differential introgression among loci outperformed homogeneous migration
 models. Generating neutral predictions from the inferred divergence
 scenarios to detect highly differentiated markers identified greater
 proportions of outliers in disconnected population pairs than in connected
 pairs. However, increased similarity in the most divergent genomic regions
 was found among connected ecotype pairs, indicating that gene flow was
 instrumental in generating parallelism at the molecular level. These
 results suggest that heterogeneous genomic differentiation and parallelism
 among replicate ecotype pairs have partly emerged through restricted
 introgression in genomic islands.
description: DatasetRougemontRAD.tarContains the main file from Rougemont et al. study . 9 pairwise vcf used to compute diversity analysis, Fst, perform genome scan, etc..1 main genepop file containing data from the 9 populations pairs (8962 SNPs) 1 files containing the 40 more relevant SNPs used for hybrid identification Folded and Unfolded JSFS for diffusion approximation. Note: information on dadi are available at: https://github.com/QuentinRougemont/DemographicInferenceDatasetRougemontRAD2016.tar.gz
DOI: 10.5061/dryad.51db2
title: Data from: Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

description: Duration of dormancy regulates seasonal timing in many organisms and may
 be modulated by day length and temperature. Though photoperiodic
 modulation has been well studied, temperature modulation of dormancy has
 received less attention. Here, we leverage genetic variation in diapause
 in the apple maggot fly, Rhagoletis pomonella, to test whether gene
 expression during winter or following spring warming regulates diapause
 duration. We used RNAseq to compare transcript abundance during and after
 simulated winter between an apple-infesting population and a
 hawthorn-infesting population where the apple population ends pupal
 diapause earlier than the hawthorn-infesting population. Marked
 differences in transcription between the two populations during winter
 suggests that the ‘early’ apple population is developmentally advanced
 compared to the ‘late’ hawthorn population prior to spring warming, with
 transcripts participating in growth and developmental processes relatively
 up-regulated in apple pupae during the winter cold period. Thus,
 regulatory differences during winter ultimately drive phenological
 differences that manifest themselves in the following summer. Expression
 and polymorphism analysis identify candidate genes in the Wnt and insulin
 signaling pathways that contribute to population differences in
 seasonality. Both populations remained in diapause and displayed a pattern
 of up- and then down-regulation (or vice versa) of growth-related
 transcripts following warming, consistent with transcriptional repression.
 The ability to repress growth stimulated by permissive temperatures is
 likely critical to avoid mismatched phenology and excessive metabolic
 demand. Compared to diapause studies in other insects, our results suggest
 some overlap in candidate genes/pathways, though the timing and direction
 of changes in transcription are likely species-specific.
description: All Supplemental
 InfoAll supplementary tables
 as worksheets in Excel Workbook, and supplementary methods in MS Word
 file.SupplementAll.zipCheckDrosMetExpressionR script to compare R. pomonella expression data to gene expression during early pupal morphogenesis in Drosophila melanogaster.DEbtHostRacesAndDrosEarlyMetGenesAnnotation (flybase ids) for transcripts significantly differentially regulated between Rhagoletis host races also &gt;= 2-fold differentially regulated between 0 and 24 hours post pupariation in Drosophila melanogaster (see accompanying R script)
DOI: 10.5061/dryad.66vb3
title: Data from: Biogeographic and bathymetric determinants of brachiopod extinction and survival during the Late Ordovician Mass Extinction

description: The Late Ordovician Mass Extinction (LOME) coincided with dramatic climate
 changes, but there are numerous ways in which these changes could have
 driven marine extinctions. We use a palaeobiogeographic database of
 rhynchonelliform brachiopods to examine the selectivity of Late Ordovician
 – Early Silurian genus extinctions and evaluate which extinction drivers
 are best supported by the data. The first (latest Katian) pulse of the
 LOME preferentially affected genera restricted to deeper waters or to
 relatively narrow (&lt; 35°) palaeolatitudinal ranges. This pattern is
 only observed in the latest Katian, suggesting that it reflects drivers
 unique to this interval. Extinction of exclusively deeper-water genera
 implies that changes in water mass properties such as dissolved oxygen
 content played an important role. Extinction of genera with narrow
 latitudinal ranges suggests that interactions between shifting climate
 zones and palaeobiogeography may also have been important. We test the
 latter hypothesis by estimating whether each genus would have been able to
 track habitats within its thermal tolerance range during the
 greenhouse-icehouse climate transition. Models including these estimates
 are favoured over alternative models. We argue that the LOME, long
 regarded as nonselective, is highly selective along biogeographic and
 bathymetric axes that are not closely correlated with taxonomic identity.
description: Brachiopod genus local
 rangescsv file with the local
 stratigraphic ranges of brachiopod taxa (species where resolved, otherwise
 genera). Please contact authors with specific questions about the
 structure of the database and the meaning of column headings. R code for
 analysis of this dataset is included as Supplemental Material in the
 publication.Local.Ranges.csv
DOI: 10.5061/dryad.10qf3
title: Data from: Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

description: Different analytical methods can yield competing interpretations of
 evolutionary history and, currently, there is no definitive method for
 phylogenetic reconstruction using morphological data. Parsimony has been
 the primary method for analysing morphological data, but there has been a
 resurgence of interest in the likelihood-based Mk-model. Here, we test the
 performance of the Bayesian implementation of the Mk-model relative to
 both equal and implied-weight implementations of parsimony. Using
 simulated morphological data, we demonstrate that the Mk-model outperforms
 equal-weights parsimony in terms of topological accuracy, and
 implied-weights performs the most poorly. However, the Mk-model produces
 phylogenies that have less resolution than parsimony methods. This
 difference in the accuracy and precision of parsimony and Bayesian
 approaches to topology estimation needs to be considered when selecting a
 method for phylogeny reconstruction.
description: Data from: Bayesian
 methods outperform parsimony but at the expense of precision in the
 estimation of phylogeny from discrete morphological dataSimulated data matrices
 from 'Bayesian methods outperform parsimony but at the expense of
 precision in the estimation of phylogeny from discrete morphological
 data'oreilly2016matrices.zip
DOI: 10.5061/dryad.8gp06
title: Data from: Genomic and archaeological evidence suggest a dual origin of domestic dogs

description: The geographic and temporal origins of dogs remain controversial. We
 generated genetic sequences from 59 ancient dogs and a complete (28x)
 genome of a late Neolithic dog (dated to ~4800 calendar years before the
 present) from Ireland. Our analyses revealed a deep split separating
 modern East Asian and Western Eurasian dogs. Surprisingly, the date of
 this divergence (~14,000 to 6400 years ago) occurs commensurate with, or
 several millennia after, the first appearance of dogs in Europe and East
 Asia. Additional analyses of ancient and modern mitochondrial DNA revealed
 a sharp discontinuity in haplotype frequencies in Europe. Combined, these
 results suggest that dogs may have been domesticated independently in
 Eastern and Western Eurasia from distinct wolf populations. East Eurasian
 dogs were then possibly transported to Europe with people, where they
 partially replaced European Paleolithic dogs.
description: Mitochondrial DNA FASTA
 fileContains all the novel
 mtDNA sequence published in this studymtDNA.faMitochondrial DNA informationContains long. lat. and archeological site information for the mtDNA sequences in mtDNA.famtDNA_info.xlsxPlink file (bed)Contains genotype for 605 dogs605_dogs.bedPlink file (bim)Contains genotype for 605 dogs605_dogs.bimPlink file (fam)Contains genotype for 605 dogs605_dogs.famTree file (Nexus) based on Identity by StateTree in Figure 1a605_dogs_IBS.nex
DOI: 10.5061/dryad.h01gj
title: Data from: Oceanic distribution, behaviour, and a winter aggregation area of adult Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, in the Bay of Fundy, Canada

description: Seasonal distribution of adult Atlantic sturgeon was examined using pop-up
 satellite archival tags (PSATs) and ultrasonic transmitters deployed in
 the Saint John River, New Brunswick, Canada. Seven MK10 PSATs programmed
 for release in June 2012 and seven MiniPAT PSATs programmed for release in
 February and April 2013 were deployed in August 2011 and 2012,
 respectively. Eleven of 14 PSATs surfaced and transmitted depth and
 temperature data archived for the duration of their deployment (121–302
 days). Among these eleven PSATs, five were recovered and 15-sec archival
 data was downloaded. Following exit from the Saint John River in the fall,
 tagged fish occupied a mean monthly depth of 76.3–81.6 m at temperatures
 as low as 4.9˚C throughout the winter before returning to shallower areas
 in the spring. The majority of ultrasonic detections occurred in the Bay
 of Fundy, but fish were detected as far as Riviere Saint-Jean, Quebec,
 approximately 1500 km from the Bay of Fundy (representing long-distance
 migratory rates of up to 44 km/day). All PSATs were first detected in the
 Bay of Fundy. Tags that released in February and April were found 5–21 km
 offshore of the Saint John Harbour, while tags that released in June were
 first detected in near shore areas throughout the Bay of Fundy. The
 substrate at winter tag release locations (estimated from backward
 numerical particle-tracking experiments) consisted primarily of moraines
 and postglacial mud substrate with low backscatter strength, indicative of
 soft or smooth seabed. Based on the proximity of winter tag release
 locations, the consistent depths observed between fish, and previous
 research, it is suspected that a winter aggregation exists in the Bay of
 Fundy. This study expands the understanding of the marine distribution and
 range of Atlantic sturgeon on the east coast of Canada.
description: Taylor et al Atlantic
 sturgeon PLOS 2016 dataMetadata and raw data
 for Oceanic distribution, behaviour, and a winter aggregation area of
 adult Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, in the Bay of
 Fundy, Canada.Taylor et al Atlantic sturgeon
 PLOS 2016.zip
DOI: 10.5061/dryad.q72b7
title: Data from: Molecular Inversion Probes for targeted resequencing in non-model organisms

description: Applications that require resequencing of hundreds or thousands of
 predefined genomic regions in numerous samples are common in studies of
 non-model organisms. However few approaches at the scale intermediate
 between multiplex PCR and sequence capture methods are available. Here we
 explored the utility of Molecular Inversion Probes (MIPs) for the
 medium-scale targeted resequencing in a non-model system. Markers
 targeting 112 bp of exonic sequence were designed from transcriptome of
 Lissotriton newts. We assessed performance of 248 MIP markers in a sample
 of 85 individuals. Among the 234 (94.4%) successfully amplified markers
 80% had median coverage within one order of magnitude, indicating
 relatively uniform performance; coverage uniformity across individuals was
 also high. In the analysis of polymorphism and segregation within family,
 77% of 248 tested MIPs were confirmed as single copy Mendelian markers.
 Genotyping concordance assessed using replicate samples exceeded 99%. MIP
 markers for targeted resequencing have a number of advantages: high
 specificity, high multiplexing level, low sample requirement,
 straightforward laboratory protocol, no need for preparation of genomic
 libraries and no ascertainment bias. We conclude that MIP markers provide
 an effective solution for resequencing targets of tens or hundreds of kb
 in any organism and in a large number of samples.
description: Reference
 sequencesReference sequences in
 fasta formatref_for_248_mips.fastaDetails of MIP designThis Excel file contains the sequences of MIP probes as well as information about the position of MIPs on contigs from the Lissotriton reference transcriptome available at http://newtbase.eko.uj.edu.pl/mips_design.xlsxscripts_for_MIP_design.tarGzipped tar archive containing scripts used for MIP design. These scripts were developed by O'Roak et al. (2012) and slightly modified to fit our needs. Please note that there these scripts have been supplanted by the MIPGEN software available et https://github.com/shendurelab/MIPGENvcf_1st_experiment.tarGzipped tar archive containing vcf files for samples from the 1st experiment described in the paper.vcf_2nd_experiment.tarGzipped tar archive containing vcf files for samples from the 2nd experiment described in the paper.
DOI: 10.5061/dryad.10dk4
title: Data from: Fitness consequences of artificial selection on relative male genital size

description: Male genitalia often show remarkable differences among related species in
 size, shape and complexity. Across poeciliid fishes, the elongated fin
 (gonopodium) that males use to inseminate females ranges from 18 to 53% of
 body length. Relative genital size therefore varies greatly among species.
 In contrast, there is often tight within-species allometric scaling, which
 suggests strong selection against genital–body size combinations that
 deviate from a species’ natural line of allometry. We tested this
 constraint by artificially selecting on the allometric intercept, creating
 lines of males with relatively longer or shorter gonopodia than occur
 naturally for a given body size in mosquitofish, Gambusia holbrooki. We
 show that relative genital length is heritable and diverged 7.6–8.9%
 between our up-selected and down-selected lines, with correlated changes
 in body shape. However, deviation from the natural line of allometry does
 not affect male success in assays of attractiveness, swimming performance
 and, crucially, reproductive success (paternity).
description: Supplementary Data
 1_Gonopodium and SL for generations 1 to 9Excel file of standard
 length and gonopodium length measurements (cm) for all male Gambusia
 holbrooki from replicate selection lines over 9 generations of artificial
 selection on gonopodium length.Supplementary Data
 2_Gonopodium and SL for generation 10Supplementary Data
 3_Female choice trialsExcel file of
 association times of focal females with selection-line males in three-way
 choice trials.Supplementary Data
 4_Burst swimming performanceExcel file of
 burst-swimming performance measures for male and female selection-line
 fish: total distance, mean and maximum velocity and maximum acceleration
 in the first 38 millisec of a startle response trial.Supplementary Data
 5_Male reproductive successExcel file of number of
 offspring sired by selection line males in competitive paternity
 assays.Supps 6 to 13 for body
 shape.csv and .tps files and
 .R code for geometric morphometric analyses of male and female body shape
 differences among selection lines.Supp 14 to 17 for
 gono.csv and .tps files and
 .R code for geometric morphometric analyses of gonopodium shape
 differences among selection lines.Supplementary Data
 18_Within line fecundityExcel file of number of
 offspring produced over two clutches by within-line pairs of generation 9
 fish.RealisedHeritabilityDataExcel file used to calculate Response to selection & Selection differentials for relative gonopodium size in Up- and down-selected males. For calculation of realized heritabilities.
DOI: 10.5061/dryad.9mj14
title: Data from: Year-long monitoring of physico-chemical and biological variables provide a comparative baseline of coral reef functioning in the central Red Sea

description: Coral reefs in the central Red Sea are sparsely studied and in situ data
 on physico-chemical and key biotic variables are missing to provide an
 important comparative baseline. To fill this gap, we monitored three reefs
 along a cross-shelf gradient during a full year, simultaneously collecting
 data on currents, temperature, salinity, dissolved oxygen (DO),
 chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial
 communities of reef water, and bacterial and algal composition of
 epilithic biofilms. Some of these environmental parameters resemble
 projected ‘future ocean’ conditions. Summer temperatures (29 - 33 °C) and
 salinity levels (39 PSU) exceeded average maxima for coral reefs globally,
 while DO levels were comparably low (2 - 4 mg L-1). Reef environments were
 highly variable over time and between reefs. Temperature and salinity
 differences were most pronounced between seasons. Conversely, DO,
 chlorophyll-a, turbidity, and sedimentation varied strongest between
 reefs. Similarly, biotic communities were highly dynamic between reefs and
 seasons. Differences in bacterial biofilms were driven by differentially
 abundant bacterial taxa that belonged to the families Rhodobacteraceae,
 Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal
 biofilms, green crusts, brown crusts, and crustose coralline algae were
 most abundant and accounted for most of the variability of the
 communities. Higher bacterial diversity of biofilms coincided with
 increased algal cover during spring and summer. We identified temperature,
 salinity, DO, and chlorophyll-a as the physico-chemical drivers of biotic
 community structures by multivariate matching. These parameters are
 forecasted to change most with the progression of global warming and
 increased nutrient input, which also suggests an immediate bottom-up
 effect on Red Sea benthic communities as a result of climate change and
 anthropogenic influence. In conclusion, our study presents foundation data
 to provide a comparative baseline to support coral reef studies in the
 region and to gain insight into coral reef functioning in the Red Sea.
description: data_reefmonitoringCoral Reef Monitoring (1 year, central Red Sea); find details in the the README.txt
DOI: 10.57826/agimo/zrbsxy
title: MATSim Lausitz GitHub

description: See Metadata→Related Publication
DOI: 10.5061/dryad.bq135
title: Data from: Harvested populations are more variable only in more variable environments

description: The interaction between environmental variation and population dynamics is
 of major importance, particularly for managed and economically important
 species, and especially given contemporary changes in climate variability.
 Recent analyses of exploited animal populations contested whether
 exploitation or environmental variation has the greatest influence on the
 stability of population dynamics, with consequences for variation in yield
 and extinction risk. Theoretical studies however have shown that
 harvesting can increase or decrease population variability depending on
 environmental variation, and requested controlled empirical studies to
 test predictions. Here, we use an invertebrate model species in
 experimental microcosms to explore the interaction between selective
 harvesting and environmental variation in food availability in affecting
 the variability of stage-structured animal populations over 20
 generations. In a constant food environment, harvesting adults had
 negligible impact on population variability or population size, but in the
 variable food environments, harvesting adults increased population
 variability and reduced its size. The impact of harvesting on population
 variability differed between proportional and threshold harvesting,
 between randomly and periodically varying environments, and at different
 points of the time series. Our study suggests that predicting the
 responses to selective harvesting is sensitive to the demographic
 structures and processes that emerge in environments with different
 patterns of environmental variation.
description: Raw timeseries
 data_annotatedThis file contains the
 timeseries for eggs, juveniles, adult males and adult females mites from
 60 replicate populations exposed to three environmental variation
 treatments (constant, randomly variable and periodically variable) and
 four harvesting treatments (unharvested, juvenile harvested (40%/week),
 adult harvested (40% week) or threshold harvested ( all above 60% pop
 size). Each treatment combination has six replicate population tubes. The
 details are in comment boxes in the attached excel file. Body size data
 for constant and period environment populations are also supplied in sheet
 2 (i.e. data from Figure 4 in associated publication)Annotated
 masterTSraw_IDs_DRYAD_draft1.xls
DOI: 10.15468/dl.4eehr6
title: Occurrence Download

description: A dataset containing 303438 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The molluscs collection (IM) of the Muséum national d'Histoire naturelle (MNHN - Paris)"
 ]
}

 The dataset includes 303438 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001430-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.