cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k0v17
title: Data from: Between-sex genetic covariance constrains the evolution of sexual dimorphism in Drosophila melanogaster

description: Males and females share much of their genome, and as a result, intralocus
 sexual conflict is generated when selection on a shared trait differs
 between the sexes. This conflict can be partially or entirely resolved via
 the evolution of sex-specific genetic variation that allows each sex to
 approach, or possibly achieve, its optimum phenotype, thereby generating
 sexual dimorphism. However, shared genetic variation between the sexes can
 impose constraints on the independent expression of a shared trait in
 males and females, hindering the evolution of sexual dimorphism. Here, we
 examine genetic constraints on the evolution of sexual dimorphism in
 Drosophila melanogaster cuticular hydrocarbon (CHC) expression. We use the
 extended G matrix, which includes the between-sex genetic covariances that
 constitute the B matrix, to compare genetic constraints on two sets of CHC
 traits that differ in the extent of their sexual dimorphism. We find
 significant genetic constraints on the evolution of further dimorphism in
 the least dimorphic traits, but no such constraints for the most dimorphic
 traits. We also show that the genetic constraints on the least dimorphic
 CHCs are asymmetrical between the sexes. Our results suggest that there is
 evidence both for resolved and ongoing sexual conflict in D. melanogaster
 CHC profiles.
description: D mel CHC B matrix
 dataData used in analyses as
 described in the manuscript. Fitness data and CHC phenotype data used in
 selection analyses, and CHC phenotype and line data used to determine full
 G matrix (with B) and calculate genetic constraints. Notes within file
 describe the data in detail.dryad.xlsx
DOI: 10.5061/dryad.nf8gf
title: Data from: Spatiotemporal analysis of gene flow in Chesapeake Bay Diamondback Terrapins (Malaclemys terrapin)

description: There is widespread concern regarding the impacts of anthropogenic
 activities on connectivity among populations of plants and animals, and
 understanding how contemporary and historical processes shape
 metapopulation dynamics is crucial for setting appropriate conservation
 targets. We used genetic data to identify population clusters and quantify
 gene flow over historical and contemporary time frames in the Diamondback
 Terrapin (Malaclemys terrapin). This species has a long and complicated
 history with humans, including commercial over-harvesting and subsequent
 translocation events during the early twentieth century. Today, terrapins
 face threats from habitat loss and mortality in fisheries bycatch. To
 evaluate population structure and gene flow among Diamondback Terrapin
 populations in the Chesapeake Bay region, we sampled 617 individuals from
 15 localities, and screened individuals at 12 polymorphic microsatellite
 loci. Our goals were to demarcate metapopulation structure, quantify
 genetic diversity, estimate effective population sizes, and document
 temporal changes in gene flow. We found that terrapins in the Chesapeake
 Bay region harbor high levels of genetic diversity and form four
 populations. Effective population sizes were variable. Among most
 population comparisons, estimates of historical and contemporary terrapin
 gene flow were generally low (m ≈ 0.01). However, we detected a
 substantial increase in contemporary gene flow into Chesapeake Bay from
 populations outside the bay, as well as between two populations within
 Chesapeake Bay, possibly as a consequence of translocations during the
 early twentieth century. Our study shows that inferences across multiple
 time scales are needed to evaluate population connectivity, especially as
 recent changes may identify threats to population persistence.
description: Microsatellite
 Data.xlsx file containing
 genotypes for all surveyed individuals.TerpRawData.xlsxTerrapin GenepopGenepop input file containing all loci and individuals used for analysis.TerpGenePop.txtTerrapin Structure FileInput file for STRUCTURE analyses.TerpStructure.txtTerrapin Migrate-n FileInput file for MIGRATE analyses.TerpMigrate-n.txtTerrapin BayesassInput file for BAYESASS analysesTerpBayesass.txtTerrapin Len FileInput file (.len) for analysis in popABCTerpLen.lenTerrapin Summary StatisticsInput file (.sst) used for analysis in popABC.TerpSST.sstTerrapin ABC PriorsInput file (.prs) used for analysis in popABC.MuPriors.prsMode R ScriptAn R script (written by Joao Lopes) used to determine the mode, 2.5 and 97.5% for parameters estimated in popABC.get_modes.r∆m, m, and m(h) Matrices.xlsx file containing matrices for ∆m, m, and m(h).BA3-MigrateMatrix.xlsx
DOI: 10.5061/dryad.ff66h
title: Data from: Origin, evolution, and population genetics of the selfish Segregation distorter gene duplication in European and African populations of Drosophila melanogaster

description: Meiotic drive elements are a special class of evolutionarily “selfish
 genes” that subvert Mendelian segregation to gain preferential
 transmission at the expense of homologous loci. Many drive elements appear
 to be maintained in populations as stable polymorphisms, their equilibrium
 frequencies determined by the balance between drive (increasing frequency)
 and selection (decreasing frequency). Here we show that a classic,
 seemingly balanced, drive system is instead characterized by frequent
 evolutionary turnover giving rise to dynamic, rather than stable,
 equilibrium frequencies. The autosomal Segregation Distorter (SD) system
 of the fruitfly Drosophila melanogaster is a selfish coadapted meiotic
 drive gene complex in which the major driver corresponds to a partial
 duplication of the gene Ran-GTPase activating protein (RanGAP). SD
 chromosomes segregate at similar, low frequencies of 1–5% in natural
 populations worldwide, consistent with a balanced polymorphism.
 Surprisingly, our population genetic analyses reveal evidence for
 parallel, independent selective sweeps of different SD chromosomes in
 populations on different continents. These findings suggest that, rather
 than persisting at a single stable equilibrium, SD chromosomes turn over
 frequently within populations.
description: Fasta File of Sd-RanGAP
 duplicationAlignment of Sd-RanGAP
 duplication from 52 SD chromosomes.Sd-RanGAP_Duplication_GenBank.fasta
DOI: 10.5061/dryad.6140t
title: Data from: Coralline algae in a naturally acidified ecosystem persist by maintaining control of skeletal mineralogy and size

description: To understand the effects of ocean acidification (OA) on marine
 calcifiers, the trade-offs among different sublethal responses within
 individual species and the emergent effects of these trade-offs must be
 determined in an ecosystem setting. Crustose coralline algae (CCA) provide
 a model to test the ecological consequences of such sublethal effects as
 they are important in ecosystem functioning, service provision, carbon
 cycling and use dissolved inorganic carbon to calcify and photosynthesize.
 Settlement tiles were placed in ambient pH, low pH and extremely low pH
 conditions for 14 months at a natural CO2 vent. The size, magnesium (Mg)
 content and molecular-scale skeletal disorder of CCA patches were assessed
 at 3.5, 6.5 and 14 months from tile deployment. Despite reductions in
 their abundance in low pH, the largest CCA from ambient and low pH zones
 were of similar sizes and had similar Mg content and skeletal disorder.
 This suggests that the most resilient CCA in low pH did not trade-off
 skeletal structure to maintain growth. CCA that settled in the extremely
 low pH, however, were significantly smaller and exhibited altered skeletal
 mineralogy (high Mg calcite to gypsum (hydrated calcium sulfate)),
 although at present it is unclear if these mineralogical changes offered
 any fitness benefits in extreme low pH. This field assessment of
 biological effects of OA provides endpoint information needed to generate
 an ecosystem relevant understanding of calcifying system persistence.
description: Kamenos et al
 RSPB-2016-1159
DOI: 10.15468/dl.95heax
title: Occurrence Download

description: A dataset containing 6658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6658 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000561-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7tv20
title: Data from: A synopsis of the saddle fungi (Helvella: Ascomycota) in Europe – species delimitation, taxonomy and typification

description: Helvella is a widespread, speciose genus of large apothecial ascomycetes
 (Pezizomycete: Pezizales) that are found in terrestrial biomes of the
 Northern and Southern Hemispheres. This study represents a beginning on
 assessing species limits and applying correct names for Helvella species
 based on type material and specimens in the university herbaria (fungaria)
 of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and
 phylogenetic evidence from four loci – heat shock protein 90 (hsp),
 translation elongation factor alpha (tef), RNA polymerase II (rpb2) and
 the nuclear large subunit ribosomal DNA (LSU) –to assess species
 boundaries in an expanded sample of Helvella specimens from Europe. We
 combine the morphological and phylogenetic information from 55 Helvella
 species from Europe with a small sample of Helvella species from other
 regions of the world. Little intraspecific variation was detected within
 the species using these molecular markers; hsp and rpb2 markers provided
 useful barcodes for species delimitaion in this genus, while LSU provided
 more variable resolution among the pertinent species. We discuss
 typification issues and identify molecular characteristics for 55 European
 Helvella species, designate neo- and epitypes for 30 species, and describe
 seven Helvella species new to science, i.e., H. alpicola, H. alpina, H.
 carnosa, H. danica, H. nannfeldtii, H. pubescens and H. scyphoides.
description: RPB2_HSP_alignment.nexConcatenated rpb2 and hsp alignment used for ML and bayesian phylogenetic analyses. Nexus format. Rpb2 is bp 1-347, hsp is bp 348-616.RPB2_HSP_alignment.fastaConcatenated rpb2 and hsp alignment used for ML and bayesian phylogenetic analyses. Fasta format. Rpb2 is bp 1-347, hsp is bp 348-616.RPB2_HSP_LSU_alignment.nexConcatenated rpb2, hsp and lsu alignment used for ML and bayesian phylogenetic analyses. Nexus format. Rpb2 is bp 1-347, hsp is bp 348-616, lsu is bp 617-1314.RPB2_HSP_LSU_alignment.fastaConcatenated rpb2, hsp and lsu alignment used for ML and bayesian phylogenetic analyses. Fasta format. Rpb2 is bp 1-347, hsp is bp 348-616, lsu is bp 617-1314.
DOI: 10.15468/dl.xqnber
title: Occurrence Download

description: A dataset containing 6658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6658 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000560-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qt635
title: Data from: Heteroploid Knautia drymeia (Caprifoliaceae) includes K. gussonei and cannot be separated into diagnosable subspecies

description: Premise of the study: Knautia drymeia is a morphologically variable,
 diploid and tetraploid temperate forest understory species distributed in
 southeastern Europe and adjacent areas. The species is an excellent system
 to explore the influence of polypoidy on taxonomic delineations, the role
 of hybridization among genetically distant populations in polyploid
 evolution, as well as the impact of glacial refugia on the evolution of
 polyploids. Methods: Amplified fragment length polymorphism fingerprinting
 and multivariate analyses of morphological characters were performed on 57
 populations spanning the distribution area of K. drymeia. K-means
 clustering, comparison of in-silico tetraploids and observed tetraploids,
 and a phylogeographic analysis using relaxed random walks were used to
 explore the genetic structure within the diploids, to infer the origin of
 the tetraploids and to reconstruct range expansion through time. Further,
 we contrasted morphology and genetic groups with current taxonomy and
 evaluated the status of the tetraploid Apennine endemic K. gussonei and
 the intraspecific taxa of K. drymeia. Key Results: The genetic structure
 was strongly geographically correlated and yielded four genetic groups; K.
 gussonei was inseparable from K. drymeia. Distributions of diploid
 lineages are suggestive of glacial refugia in the northwestern-most and
 southeastern Balkan Peninsula. Polyploids originated at least two times,
 as autopolyploids and probably additionally also as allopolyploids.
 Morphological divergence corresponded with neither genetic groups nor
 current taxonomy. Conclusions: Genetic and morphometric data neither
 confirmed divergence of K. gussonei nor recognition of subspecies within
 K. drymeia. We therefore propose treating K. drymeia as morphologically
 and genetically variable species without infraspecific taxa.
description: Kautia drymeia AFLP data
 matrixAFLP data matrix. IDs of
 individuals (e.g., Kdrym_K023_2_ME_4x) contain the population ID (e.g.,
 "K023") for which further information can be found in Table 1 of
 the manuscript. The next digit (e.g., "_2_) is the individual number,
 followed by the country of origin (e.g., "ME" for Montenegro)
 and the ploidy level (e.g., "4x").Kdrymeia_AFLP_data.xlsxKdrymeia_morphology_dataTable containing raw data of morphometric analysis of Knautia drymeia. For abbreviations of characters and populations see main text of the manuscript.Kdrymeia_morphology.xlsx
DOI: 10.5061/dryad.20cs5
title: Data from: Multi-electrode array for transcutaneous lumbar posterior-root stimulation

description: Interest in transcutaneous electrical stimulation of the lumbosacral
 spinal cord is increasing in human electrophysiological and clinical
 studies. The stimulation effects on lower limb muscles depend on the
 depolarization of segmentally organized posterior root afferents and,
 thus, the rostro-caudal stimulation site. In previous studies, selective
 stimulation was achieved by varying the positions of single self-adhesive
 electrodes over the thoracolumbar spine. Here, we developed a
 multi-electrode surface array consisting of 3 × 8 electrode pads and
 tested its stimulation-site specificity. The array was placed
 longitudinally over the spine covering the T10–L2 vertebrae. Two different
 hydrogel layer configurations were utilized: a single layer adhered to all
 electrode pads of the array and a configuration comprised of eight
 separate strips attached to the three transverse electrode pads of each
 level. Voltage measurements demonstrated that an effectively focused field
 distribution along the longitudinal extent of the array was not
 accomplished when using the single continuous hydrogel layer, and
 segmental selective stimulation of the posterior root afferents was not
 possible. The separate strips produced a focused electric field
 distribution at the rostro-caudal level of the electrode pads selected for
 stimulation. This configuration allowed for the preferential elicitation
 of posterior root-muscle reflexes in either the L2–L4 innervated
 quadriceps or the L5–S2 innervated triceps surae muscle groups. Such
 multi-electrode array for transcutaneous spinal cord stimulation shall
 allow for improved control of stimulation conditions in
 electrophysiological studies and time-dependent and site-specific
 stimulation patterns for neuromodulation applications.
description: Electrode
 arraySchematic (*.sch) and
 board files (*.brd; EAGLE Layout Editor 6.5, CadSoft) of the flexible
 printed circuit (FPC) and the interface board.FPC_and_Interface_Board.zip
DOI: 10.5061/dryad.2q71q2g2
title: Data from: Asymmetric introgression between the M and S molecular forms of the malaria vector, Anopheles gambiae, maintains divergence despite extensive hybridisation.

description: The suggestion that genetic divergence can arise and/or be maintained in
 the face of gene flow, has been contentious since first proposed.
 Partially reproductively isolated taxa have been highlighted as offering
 unique opportunities for identifying the mechanisms underlying the
 maintenance of divergence with gene flow. The African malaria vector,
 Anopheles gambiae s.s., is widely regarded as consisting of two sympatric
 forms, thought by many to represent incipient species, the M and S
 molecular forms. However, there has been much debate about the extent of
 reproductive isolation between M and S, with one view positing that
 divergence may have arisen and is being maintained in the presence of gene
 flow, and the other proposing a more advanced speciation process with
 little realized gene flow due to low fitness of hybrids. These hypotheses
 have been difficult to address because hybrids are typically very rare
 (&lt;1%). Here, we assess samples from an area of high hybridisation
 and demonstrate that hybrids are fit and responsible for extensive
 introgression. Nonetheless, we show that strong divergent selection at a
 subset of loci combined with highly asymmetric introgression has enabled M
 and S to remain genetically differentiated despite extensive gene flow. We
 propose that the extent of reproductive isolation between M and S varies
 across West Africa resulting in a “geographic mosaic of reproductive
 isolation”; a finding which adds further complexity to our understanding
 of divergence in this taxon and which has considerable implications for
 transgenic control strategies.
description: Marsden et al 2011
 Anopheles gambiae Molecular Ecology
DOI: 10.15482/usda.adc/29621762
title: Data from: Towards Sustainable Aquafeeds: Microalgal (<i>Nannochloropsis </i>sp. QH25) Co-Product Biomass Can Fully Replace Fishmeal in the Feeds for Rainbow Trout (<i>Oncorhynchus mykiss</i>)

description: Aquaculture, one of the world’s most rapidly growing food sectors, faces several concerns about its sustainability. A major concern is using fishmeal and fish oil from ocean-derived small pelagic fish (sardine, anchovy, etc.) in aquaculture feed. The aquafeed industry is seeking new sustainable ingredients to replace fish meal. This study focused on microalgal co-product, <i>Nannochloropsis</i> sp. QH25 co-product (leftover after oil extraction for nutraceuticals) is a novel aquafeed ingredient that can replace fishmeal in rainbow trout diets. A nutritional feeding experiment was conducted and compared fishmeal-containing rainbow trout diets with microalgal co-products that replaced fishmeal as follows: 0% replacement in reference diet (fishmeal, no microalgal co-product) and test diets with 33%, 66%, and 100% replacement of fishmeal using microalgal-product. Results showed the complete replacement diet yielded fish growth, feed conversion, and survival similar to the reference diet. Depositions of macronutrients, amino acids, fatty acids, macro minerals, and several trace elements in the filet were not significantly different across diets. Economic conversion ratio (ECR) analysis showed that the rainbow trout fed the 100% replacement diet had the lowest feed cost per kg of fish produced. Microalgal co-products can fully replace fishmeal in trout feed while maintaining fish performance, flesh composition, and cost-effectiveness.
DOI: 10.15482/usda.adc/29621762.v1
title: Data from: Towards Sustainable Aquafeeds: Microalgal (<i>Nannochloropsis </i>sp. QH25) Co-Product Biomass Can Fully Replace Fishmeal in the Feeds for Rainbow Trout (<i>Oncorhynchus mykiss</i>)

description: Aquaculture, one of the world’s most rapidly growing food sectors, faces several concerns about its sustainability. A major concern is using fishmeal and fish oil from ocean-derived small pelagic fish (sardine, anchovy, etc.) in aquaculture feed. The aquafeed industry is seeking new sustainable ingredients to replace fish meal. This study focused on microalgal co-product, <i>Nannochloropsis</i> sp. QH25 co-product (leftover after oil extraction for nutraceuticals) is a novel aquafeed ingredient that can replace fishmeal in rainbow trout diets. A nutritional feeding experiment was conducted and compared fishmeal-containing rainbow trout diets with microalgal co-products that replaced fishmeal as follows: 0% replacement in reference diet (fishmeal, no microalgal co-product) and test diets with 33%, 66%, and 100% replacement of fishmeal using microalgal-product. Results showed the complete replacement diet yielded fish growth, feed conversion, and survival similar to the reference diet. Depositions of macronutrients, amino acids, fatty acids, macro minerals, and several trace elements in the filet were not significantly different across diets. Economic conversion ratio (ECR) analysis showed that the rainbow trout fed the 100% replacement diet had the lowest feed cost per kg of fish produced. Microalgal co-products can fully replace fishmeal in trout feed while maintaining fish performance, flesh composition, and cost-effectiveness.
DOI: 10.5061/dryad.pc14j
title: Data from: Fine-scale local adaptation in an invasive freshwater fish has evolved in contemporary time

description: Adaptive evolutionary change in only a few generations can increase the
 ability of non-native invasive species to spread, and yet adaptive
 divergence is rarely assessed in recently established populations. In this
 paper, we experimentally test for evidence of fine-scale local adaptation
 in juvenile survival and growth among three populations of an invasive
 freshwater fish with reciprocal transplants and common-garden experiments.
 Despite intrinsic differences in habitat quality, in two out of three
 populations we detected evidence of increased survival in ‘home’ vs.
 ‘away’ environments with a Bayesian occupancy model fitted to
 mark-recapture data. We found support for the ‘local vs. foreign’
 criterion of local adaptation as 14 out of 15 pairwise comparisons of
 performance were consistent with local adaptation (p &lt; 0.001).
 Patterns in growth were less clear, though we detected evidence of
 location and population-level effects. Although the agents of divergent
 ecological selection are not known in this system, our results combine to
 indicate that adaptive divergence – reflected by higher relative survival
 of local individuals – can occur in a small number of generations and only
 a few kilometers apart on the landscape.
description: Growth and survival data
 for Westley et al. Proc. BRecapture histories and
 growth data from common garden and reciprocal transplant
 experimentswestley_ProcB_data.xls