cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gd809
title: Data from: Genes that affect Atlantic salmon growth in hatchery do not have the same effect in the wild

description: Dissecting the genetic mechanisms of phenotypic traits that influence
 fitness in diverse environments provides the important first step towards
 understanding the robustness of the observed genotype–phenotype
 associations, the role of genotype-by-environment interaction (GEI)
 shaping fitness trade-offs and maintaining genetic variation of
 quantitative traits. However, the molecular basis of complex traits in
 vertebrates has rarely, if ever, been studied simultaneously in natural
 and controlled laboratory environments. To evaluate whether the same
 genomic regions affect the growth of juvenile Atlantic salmon in wild and
 hatchery conditions, we mapped QTLs affecting the size-at-age of juvenile
 parr after the first summer utilizing the same mapping (family) material
 to avoid confounding effects of different genetic background. We
 identified three significant QTLs for fork length in the hatchery that
 were undetectable in the natural environment, while two QTLs detected in
 the wild were not observed when fish were reared in hatchery conditions.
 Altogether, four individual markers showed significant (P &lt; 0·05)
 genotype-by-environment interactions. The allelic effects for three QTLs
 observed in the hatchery were in the same direction in both environments,
 while for two QTLs the alleles associated with a larger body size in the
 wild showed the opposite (albeit non-significant) trend in the hatchery
 environment. Our results indicate that the growth of juvenile salmon in
 two contrasting environments is controlled by different genetic mechanisms
 that are most likely influenced by multiple processes, including food
 availability, inter- and intraspecific competition, and trade-offs between
 the costs and benefits of individual movement in the wild. Furthermore,
 the findings of the study imply that a substantial proportion of
 growth-related QTLs reported by earlier studies in a hatchery environment
 may represent QTLs specific to farmed conditions and hence have no effect
 on fish growth in the wild. For comprehensive understanding of the
 molecular, physiological and ecological mechanisms influencing complex
 traits, it is therefore crucial to evaluate the genotype–phenotype
 relationships under natural conditions, rather than relying solely on
 laboratory experiments.
description: Phenotype data and
 microsatellite genotypes of the parents and offspringsIndividual parent and
 offspring genotypes (51 segregating loci) and offspring phenotype data
 (body mass, fork length) in a wild and a hatchery
 environment.Vasemägi_et_al_2016_FE_Table_STRs&Mass&Length.xlsx
DOI: 10.5061/dryad.0t2c8
title: Data from: Ecoacoustic indices as proxies for biodiversity on temperate reefs

description: Diversity measurement techniques can present logistical and financial
 obstacles to conservation efforts. Ecoacoustics has recently emerged as a
 promising solution to these issues, providing a mechanism for measuring
 diversity using acoustic indices, which have proven to be beneficial in
 terrestrial habitats. This study investigates the application of acoustic
 measures as a tool for quick and effective marine diversity monitoring via
 direct, in situ comparison of ecoacoustics indices with species assemblage
 diversity measures from temperate rocky reefs. Acoustic recordings and
 visual surveys of reef fish abundance were collected at nine sites in
 north-eastern New Zealand. Three ecoacoustic indices originally developed
 for terrestrial use were then compared to three species assemblage
 diversity measures and compared using Pearson correlations. Additionally,
 four criteria for successful ecoacoustic indices were developed and tested
 as a means of standardizing future evaluation and use of acoustic indices:
 (i) positive correlations between species diversity and ecoacoustic
 indices in relevant frequency ranges, (ii) robustness to changes in
 spectral resolution, (iii) robustness to the presence of natural noise
 interference (i.e. wind) and (iv) robustness to the presence of
 anthropogenic noise. Acoustic Complexity Index (ACI) was significantly
 correlated with Pielou's Evenness (J′) and Shannon's index (H′).
 Neither Acoustic Richness (AR) nor ACI was impacted by changes in spectral
 resolution, but values of the Acoustic Entropy Index (H) increased
 significantly between fast Fourier transformation (FFT) sizes 512 and
 1024. H was consistently positively correlated with both H′ and estimated
 number of species (S) above a spectral resolution of c. 140·6 Hz (FFT size
 1024). Wind did not affect any of the acoustic indices. As anthropogenic
 noise was included in these investigations, both ACI and H were considered
 robust to its presence. While AR failed to meet all four criteria for a
 successful ecoacoustic indices, both ACI and H appeared to be appropriate
 for use on temperate reefs. In a time of accelerated global diversity
 loss, these two ecoacoustic indices show strong potential for use as
 efficient, non-invasive marine diversity measures.
description: Harris et al - Comet
 Rocks Fish SurveyHarris et al - Karamoroa
 Fish SurveyHarris et al - Mid Point
 Fish SurveyHarris et al - Nordic
 Fish SurveyHarris et al - OneSpot
 Fish SurveyHarris et al - Pinnacle
 Fish SurveyHarris et al - Rusty
 Ladder Fish SurveyHarris et al - Schiels
 Pool Fish SurveyHarris et al - Te Rere
 Fish SurveyComet
 RocksKaramuroaMid PointMidPoint.zipNordicReeftNordicReef.zipOneSpotPinnacleRustyLadderSchielsPoolTeRerelTeRere.zip
DOI: 10.15468/dl.7mghuc
title: Occurrence Download

description: A dataset containing 1525 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Amaranthus spinosus",
 "Year 2000-2026"
 ]
}

 The dataset includes 1525 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000817-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2pc6v
title: Data from: SNP discovery in European lobster (Homarus gammarus) using RAD sequencing

description: The European lobster (Homarus gammarus) is a decapod crustacean with a
 high market value and therefore their fisheries are of major importance to
 the economies they support. However, over-exploitation has led to profound
 stock declines in some regions such as Scandinavia and the Mediterranean.
 To manage this resource sustainably, knowledge of population structure and
 connectivity is crucial to inform management about dispersal, recruitment,
 stock identification and food traceability. We used restriction-site
 associated DNA sequencing to develop novel SNP markers from 55 individuals
 encompassing much of the species range; SNPs were quality filtered, ranked
 using F-statistics and the top 96 SNPs adequate for primer design were
 retained. SNP markers were developed with the aim of maximising the power
 to detect genetic differentiation between: (i) Atlantic and Mediterranean
 lobsters and (ii) Atlantic lobsters. This panel of SNPs provides a useful
 resource for future studies of population genetic structure and assignment
 in H. gammarus.
description: Homarus gammarus raw
 readsHomarus gammarus samples
 collected from the northeast Atlantic and Mediterranean. Contains 110
 paired-end fastq files generated by an Illumina HiSeq 100-150bp
 platform.Jenkins_et_al_2018_Con_Gen_Res_Raw_Reads.zip
DOI: 10.15468/dl.37pbxn
title: Occurrence Download

description: A dataset containing 1481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Atropa belladonna",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1481 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000816-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2mg27sh
title: Data from: A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context

description: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland
 preserves a rich array of vertebrate and other non-marine fossils
 providing an insight into the wider ecosystem and palaeoenvironment that
 existed during this pivotal stage of Earth history. It challenges
 hypotheses of a long-lasting post-extinction trough following the
 end-Devonian extinction event. The fauna recovered includes a wide size
 range of tetrapods, rhizodonts and dipnoans, from tiny juveniles or
 small-bodied taxa up to large adults, and more than one taxon of each
 group is likely. Some fauna, such as actinopterygians and chondrichthyans,
 are rare as macrofauna but are better represented in the microfossil
 assemblage. The fauna provides evidence of the largest Carboniferous
 lungfish ever found. The specimens are preserved in a localised,
 poorly-sorted conglomerate which was deposited in the deepest part of a
 river channel, the youngest of a group of channels. In addition to the
 fossils (micro- and macro-), the conglomerate includes locally-derived
 clasts of palaeosols and other distinctive elements of the surrounding
 floodplains. Charcoal fragments represent stem and possible trunk tissue
 from arborescent pteridosperms. Preservation of the fossils indicates some
 aerial exposure prior to transport, with abrasion from rolling. The
 findings presented here contrast with other published trends in vertebrate
 size that are used to interpret a reduction in maximum sizes during the
 Tournaisian. The richness of the fauna runs counter to the assumption of a
 depauperate non-marine fauna following the end-Devonian Hangenberg event,
 and charcoal content highlights the occurrence of fire, with the requisite
 levels of atmospheric oxygen during that stage.
description: Clack et al., CT
 scansA zip folder containing
 3 CT scans: tetrapod parasphenoid 2017.2.187; tetrapod ulna 2017.2.51;
 tetrapod neural arch 2017.2.189g.Dryad data
 Clack.zip
DOI: 10.5061/dryad.jf402
title: Data from: Pollutants and insecticides drive local adaptation in African malaria mosquitoes

description: The Anopheles gambiae complex contains a number of highly anthropophilic
 mosquito species that have acquired exceptional ability to thrive in
 complex human habitats. Thus, examining the evolutionary history of this
 Afrotropical mosquito may yield vital information on the selective
 processes that occurred during the adaptation to human-dominated
 environments. We performed reduced representation sequencing on 941
 mosquitoes of the Anopheles gambiae complex collected across four
 ecogeographic zones in Cameroon. We find evidence for genetic and
 geographic subdivision within An. coluzzii and An. gambiae sensu stricto –
 the two most significant malaria vectors in the region. Importantly, in
 both species, rural and urban populations are genetically differentiated.
 Genome scans reveal pervasive signatures of selection centered on genes
 involved in xenobiotic resistance. Notably, a selective sweep containing
 detoxification enzymes is prominent in urban mosquitoes that exploit
 polluted breeding sites. Overall, our study suggests that recent
 anthropogenic environmental modifications and widespread use of
 insecticides are driving population differentiation and local adaptation
 in vectors with potentially significant consequences for malaria
 epidemiology.
description: Anopheles gambiae sensu
 lato fastq files - part 1Individual fastq files
 for Anopheles gambiae sensu lato from Cameroon - part 1Anopheles_sl_fastq_part1.tar.gzAnopheles gambiae sensu lato fastq files - part 2Individual fastq files for Anopheles gambiae sensu lato from Cameroon - part 2Anopheles_sl_fastq_part2.tar.gz
DOI: 10.5061/dryad.6t8vq
title: Data from: A dataset of stereoscopic images and ground-truth disparity mimicking human fixations in peripersonal space

description: [No abstract entered]
description: GENUA PESTO - GENoa
 hUman Active fixation database: PEripersonal space STereoscopic images and
 grOund truth disparityGENUA PESTO is a large
 database of stereoscopic images (2700) obtained mimicking the human eye
 posture, i.e. including vergence and cyclotorsion. The database provides
 the stereoscopic pairs together with the ground-truth information of: 1.
 scene depth, 2. retinal disparity, 3. binocular occlusions, 4. depth
 edges, 5. camera position and orientation. The database is based on two
 virtual worlds (Kitchen and Office), each explored from 10 head positions,
 with 135 gaze directions (15 azimuths and 9 elevations). This is a link
 out to SourceForge
 to download
 GENUA_PESTO_USAGE_CODE:zip. This file contains the usage code for the
 GENUA PESTO database. For detailed information, please see the associated
 README file "GENUA_PESTO_USAGE_NOTES.pdf"GENUA_PESTO_USAGE_NOTES.pdfSTRAIGHTAHEAD DATASET (Azimuth = 0°, Elevation = 0°)This dataset contains, for each of the 10 considered head positions, and for each of the virtual environments, the stereoscopic pair and ground-truth disparity corresponding to the straight-ahead gaze direction (azimuth = 0°, elevation = 0°).STRAIGHTAHEAD.zipSTRAIGHT_AHEAD_METADATA.txtKITCHEN - Head Position: Azimuth -60°, Elevation 30°K_HP-02_001.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth -30°, Elevation 30°K_HP-01_001.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth 0°, Elevation 30°K_HP000_001.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth 30°, Elevation 30°K_HP001_001.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth 60°, Elevation 30°K_HP002_001.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth -60°, Elevation 45°K_HP-02_002.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth -30°, Elevation 45°K_HP-01_002.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth 0°, Elevation 45°K_HP000_002.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth 30°, Elevation 45°K_HP001_002.zipKITCHEN_METADATA.txtKITCHEN - Head Position: Azimuth 60°, Elevation 45°K_HP002_002.zipKITCHEN_METADATA.txtOFFICE - Head Position: Azimuth -60°, Elevation 30°O_HP-02_001.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth -30°, Elevation 30°O_HP-01_001.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth 0°, Elevation 30°O_HP000_001.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth 30°, Elevation 30°O_HP001_001.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth 60°, Elevation 30°O_HP002_001.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth -60°, Elevation 45°O_HP-02_002.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth -30°, Elevation 45°O_HP-01_002.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth 0°, Elevation 45°O_HP000_002.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth 30°, Elevation 45°O_HP001_002.zipOFFICE_METADATA.txtOFFICE - Head Position: Azimuth 60°, Elevation 45°O_HP002_002.zipOFFICE_METADATA.txt
DOI: 10.5061/dryad.b5hg8d6
title: Data from: Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron

description: Most neurogenesis in the mammalian brain is completed embryonically, but
 in certain areas the production of neurons continues throughout postnatal
 life. The functional properties of mature postnatally-generated neurons
 often match those of their embryonically-produced counterparts. However,
 we show here that in the olfactory bulb (OB), embryonic and postnatal
 neurogenesis produce functionally distinct subpopulations of dopaminergic
 (DA) neurons. We define two subclasses of OB DA neuron by the presence or
 absence of a key subcellular specialisation: the axon initial segment
 (AIS). Large AIS-positive axon-bearing DA neurons are exclusively produced
 during early embryonic stages, leaving small anaxonic AIS-negative cells
 as the only DA subtype generated via adult neurogenesis. These populations
 are functionally distinct: large DA cells are more excitable, yet display
 weaker and - for certain long-latency or inhibitory events - more
 broadly-tuned responses to odorant stimuli. Embryonic and postnatal
 neurogenesis can therefore generate distinct neuronal subclasses, placing
 important constraints on the functional roles of adult-born neurons in
 sensory processing.
description: Figure 1 - soma and
 positionFigure 2 -
 axonlessFigure 3 - single cell
 morphologyFigure 4 -
 developmentFigure 5 - long chase
 adult-bornFigure 6 -
 timelineFigure 7 - long chase
 E12 bornFigure 8 - slice
 physiologyFigure 9-10 - in vivo
 imaging - 1 of 2Figure 9-10 - in vivo
 imaging - 2 of 2
DOI: 10.15468/dl.k7hu65
title: Occurrence Download

description: A dataset containing 789 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudotsuga sinensis"
 ]
}

 The dataset includes 789 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000818-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dr06p8f
title: Data from: Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality

description: When ecologically divergent taxa encounter one another, hybrid zones can
 form when reproductive isolation is incomplete. The location of such
 hybrid zones can be influenced by environmental variables, and an
 ecological context can provide unique insights into the mechanisms by
 which species diverge and are maintained. Two ecologically differentiated
 species of small benthic fishes, the endemic and imperiled prairie chub,
 Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are
 locally sympatric within the upper Red River Basin of Texas. We integrated
 population genomic data and environmental data to investigate species
 divergence and the maintenance of species boundaries in these two species.
 We found evidence of advanced-generation asymmetric hybridization and
 introgression, with shoal chub alleles introgressing more frequently into
 prairie chubs than the reciprocal. Using a Bayesian Genomic Cline
 framework, patterns of genomic introgression were revealed to be quite
 heterogeneous, yet shoal chub alleles were found to have likely
 selectively introgressed across species boundaries significantly more
 often than prairie chub alleles, potentially explaining some of the
 observed asymmetry in hybridization. These patterns were remarkably
 consistent across two sampled geographic regions of hybridization. Several
 environmental variables were found to significantly predict individual
 admixture, suggesting ecological isolation might maintain species
 boundaries.
description: EnvironmentalData_IntrogressionChubsEnvironmental data from collection locales, including assignment probabilities (q).Sotola_IndChubFastq_AFastq files on individuals compressed into a .gz format. File 1.Sotola_IndChubFastq_BFastq files on individuals compressed into a .gz format. File 2.Sotola_IndChubFastq_CFastq files on individuals compressed into a .gz format. File 3.
DOI: 10.5061/dryad.75mt7
title: Data from: Using linkage maps as a tool to determine patterns of chromosome synteny in the genus Salvelinus

description: Next generation sequencing techniques have revolutionized the collection
 of genome and transcriptome data from non-model organisms. This manuscript
 details the application of restriction site associated DNA sequencing
 (RADseq) to generate a marker dense genetic map for Brook trout
 (Salvelinus fontinalis). The consensus map was constructed from three
 full-sib families totaling 176 F1 individuals. The map consisted of 42
 linkage groups with a total female map size of 2502.5 cM, and a total male
 map size of 1863.8 cM. Synteny was confirmed with Atlantic salmon for 38
 linkage groups, with Rainbow trout for 37 linkage groups, Arctic char for
 36 linkage groups, and with a previously published Brook trout linkage map
 for 39 linkage groups. Comparative mapping confirmed the presence of eight
 metacentric and 34 acrocentric chromosomes in Brook trout. Six metacentric
 chromosomes seem to be conserved with Arctic char suggesting there have
 been at least two species specific fusion and fission events within the
 genus Salvelinus. In addition, the sex marker (sdY; sexually dimorphic on
 the Y chromosome) was mapped to Brook trout BC35, which is homologous with
 Atlantic salmon Ssa09qa, Rainbow trout Omy25, and Arctic char AC04q.
 Ultimately, this linkage map will be a useful resource for studies on the
 genome organization of Salvelinus, and facilitates comparisons of the
 Salvelinus genome with Salmo and Oncorhynchus.
description: family3quality filtered single-end 100 base pair reads sequenced using RADseq (SbfI digest).family_3.zipfamily2Quality filtered Single end 100base pair reads sequenced using RADseq (SbfI digest).family 2.zipfamily1Quality filtered 100 base pair reads sequenced with RADseq (SbfI digest).family 1.zip
DOI: 10.5061/dryad.v5374
title: Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size

description: In vitro and in vivo evolution experiments on Escherichia coli revealed
 several principles of bacterial adaptation. However, few data are
 available in the literature describing the behavior of E. coli in its
 natural environment. We attempted here to study the evolution in the human
 gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup,
 through a longitudinal genomic study. We sequenced 24 isolates sampled at
 three different time points within a healthy individual over almost a
 year. We computed amutation rate of 6.90x10-7 per base per year of the
 chromosome for E. coli ED1a in healthy human gut. We observed a very
 limited genomic diversity, and could not detect any evidence of selection
 contrary to what is observed in experimental evolution over similar length
 of time. We therefore suggest that ED1a being well adapted to the healthy
 human gut evolves mostly neutrally with a low effective population size
 (Ne ≈ 500 – 1700).
description: ed1aSequence reference of
 Escherichia coli ed1a for breseq analysisNG-6445_1a311001_lib23155_1575_6Sequence corresponding to 1D0NG-6445_1b311001_lib23156_1575_4Sequence corresponding to 2D0NG-6445_1c311101_lib23157_1575_4Sequence corresponding to 3D0NG-6445_1d311001_lib23158_1575_6Sequence corresponding to 4D0NG-6445_1e311001_lib23159_1553_6Sequence corresponding to 5D0NG-6445_1f311001_lib23160_1553_6Sequence corresponding to 6M0NG-6445_1g311001_lib23161_1553_6Sequence corresponding to 7D0NG-6445_1h311001_lib23162_1553_6Sequence corresponding to 8D0NG-6445_ED1110902_lib23171_1587_5Sequence corresponding to 1D315NG-6445_Erick1300502_lib23163_1553_6Sequence corresponding to 1D211NG-6445_ED2110902_lib23172_1587_5Sequence corresponding to 2D315NG-6445_ED2300502_lib23164_1553_6Sequence corresponding to 2D211NG-6445_ED3110902_lib23173_1587_5Sequence corresponding to 3D315NG-6445_ED3300502_lib23165_1553_6Sequence corresponding to 3D211NG-6445_ED4110902_lib23174_1587_5Sequence corresponding to 4D315NG-6445_ED4300502_lib23166_1587_5Sequence corresponding to 4D211NG-6445_ED5110902_lib23175_1587_5Sequence corresponding to 5D315NG-6445_ED5300502_lib23167_1587_5Sequence corresponding to 5D211NG-6445_ED6110902_lib23176_1587_5Sequence corresponding to 6D315NG-6445_ED6300502_lib23168_1587_7Sequence corresponding to 6D211NG-6445_ED7110902_lib23177_1587_5Sequence corresponding to 7D315NG-6445_ED7300502_lib23169_1587_5Sequence corresponding to 7D211NG-6445_ED8110902_lib23178_1587_5Sequence corresponding to 8D315NG-6445_ED8300502_lib23170_1587_5Sequence corresponding to 8D211