cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nt18c
title: Data from: Size-based hydroacoustic measures of within-season fish abundance in a boreal freshwater ecosystem

description: Eleven sequential size-based hydroacoustic surveys conducted with a 200
 kHz split-beam transducer during the summers of 2011 and 2012 were used to
 quantify seasonal declines in fish abundance in a boreal reservoir in
 Manitoba, Canada. Fish densities were sufficiently low to enable single
 target resolution and tracking. Target strengths converted to log2-based
 size-classes indicated that smaller fish were consistently more abundant
 than larger fish by a factor of approximately 3 for each halving of
 length. For all size classes, in both years, abundance (natural log)
 declined linearly over the summer at rates that varied from -0.067.day-1
 for the smallest fish to -0.016.day-1 for the largest (R2 = 0.24–0.97).
 Inter-annual comparisons of size-based abundance suggested that for larger
 fish (&gt;16 cm), mean winter decline rates were an order of magnitude
 lower (-0.001.day-1) and overall survival higher (71%) than in the main
 summer fishing season (mean loss rate -0.038.day-1; survival 33%). We
 conclude that size-based acoustic survey methods have the potential to
 assess within-season fish abundance dynamics, and may prove useful in
 long-term monitoring of productivity and hence management of boreal
 aquatic ecosystems.
description: LDBS1_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on July 26th, 2011.LDBS2_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 2nd, 2011LDBS3_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 3rd, 2011LDBS4_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 15th, 2011LDBS5_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 18th, 2011LDBS6_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 27th, 2011LDBS7_All_ST.csvAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on July 28th, 2012.LDBS8_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 2nd, 2012LDBS9_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 8th, 2012LDBS10_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 11th, 2012LDBS11_All_STAcoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 24th, 2012
DOI: 10.5061/dryad.kr96h
title: Data from: How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Dispersal ability is a key factor in determining insular distributions and
 island community composition, yet non-vagile terrestrial organisms widely
 occur on oceanic islands. The landfowl (pheasants, partridges, grouse,
 turkeys, quails and relatives) are generally poor dispersers, but the Old
 World quail (Coturnix) are a notable exception. These birds evolved small
 body sizes and high-aspect-ratio wing shapes, and hence are capable of
 trans-continental migrations and trans-oceanic colonization. Two monotypic
 partridge genera, Margaroperdix of Madagascar and Anurophasis of alpine
 New Guinea, may represent additional examples of trans-marine dispersal in
 landfowl, but their body size and wing shape are typical of poorly
 dispersive continental species. Here, we estimate historical relationships
 of quail and their relatives using phylogenomics, and infer body size and
 wing shape evolution in relation to trans-marine dispersal events. Our
 results show that Margaroperdix and Anurophasis are nested within the
 Coturnix quail, and are each ‘island giants’ that independently evolved
 from dispersive, Coturnix-like ancestral populations that colonized and
 were subsequently isolated on Madagascar and New Guinea. This evolutionary
 cycle of gain and loss of dispersal ability, coupled with extinction of
 dispersive taxa, can result in the false appearance that non-vagile taxa
 somehow underwent rare oceanic dispersal.
description: Sequences alignments and
 morphological dataNEXUS and PHYLIP format
 .txt files for concatenated UCE alignments. NEXUS format .txt files for
 individual UCE alignments. CSV format .txt file with summary morphological
 data, NEWICK format tree files, and R script used in comparative
 analyses.OWQ-DRAYAD-data.tar.gz
DOI: 10.5061/dryad.m1vt9
title: Data from: Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (Proteaceae)

description: Background: Hotspots of angiosperm species richness and endemism in
 Mediterranean-climate regions are among the most striking, but least
 well-understood, geographic patterns of biodiversity. Recent studies have
 emphasized the importance of rapid diversification within hotspots,
 compared to non-hotspot regions, as a major contributor to these patterns.
 We constructed the first near-complete phylogeny of Banksia (Proteaceae)
 to test whether diversification rates have differed between lineages
 confined to the southwest Australian hotspot and those found throughout
 southern, eastern and northern Australia. We then tested for variation in
 diversification rates among the bioclimatic zones within the southwest
 hotspot itself. Results: Although Banksia species richness in the
 southwest is ten times that of the rest of the continent, we find little
 evidence for more rapid diversification in the southwest, although this
 result is inconclusive. However, we find firmer support for substantial
 rate variation within the southwest hotspot, with more rapid
 diversification in the semi-arid heaths and shrublands, compared to the
 high-rainfall forests. Most of the Banksia diversity of the southwest
 appears to be generated in the heaths and shrublands, with a high
 migration rate out of this zone boosting diversity of the adjacent forest
 zone. Conclusions: The geographic pattern of diversification in Banksia
 appears more complex than can be characterized by a simple hotspot vs.
 non-hotspot comparison, but in general, these findings contrast with the
 view that the high diversity of Mediterranean hotspots is underpinned by
 rapid radiations. Steady accumulation of species at unexceptional rates,
 but over long periods of time, may also have contributed substantially to
 the great botanical richness of these regions.
description: BEAST trees
 fileThis is a
 nexus-formatted text file containing the full posterior set of Banksia
 phylogenies (n=6000) from a bayesian analysis of chloroplast DNA data
 using BEAST.Concatenated alignments
 20.trees.124.txt
DOI: 10.5061/dryad.r7d8h
title: Data from: The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes

description: Within the phylum Nematoda, plant-parasitism is hypothesized to have
 arisen independently on at least four occasions. The most economically
 damaging plant-parasitic nematode species, and consequently the most
 widely studied, are those that feed as they migrate destructively through
 host roots causing necrotic lesions (migratory endoparasites) and those
 that modify host root tissue to create a nutrient sink from which they
 feed (sedentary endoparasites). The false root-knot nematode Nacobbus
 aberrans is the only known species to have both migratory endoparasitic
 and sedentary endoparasitic stages within its life cycle. Moreover, its
 sedentary stage appears to have characteristics of both the root-knot and
 the cyst nematodes. We present the first large-scale genetic resource of
 any false-root knot nematode species. We use RNAseq to describe relative
 abundance changes in all expressed genes across the life cycle to provide
 interesting insights into the biology of this nematode as it transitions
 between modes of parasitism. A multigene phylogenetic analysis of N.
 aberrans with respect to plant-parasitic nematodes of all groups confirms
 its proximity to both cyst and root-knot nematodes. We present a
 transcriptome-wide analysis of both lateral gene transfer events and the
 effector complement. Comparing parasitism genes of typical root-knot and
 cyst nematodes to those of N. aberrans has revealed interesting
 similarities. Importantly, genes that were believed to be either cyst
 nematode, or root-knot nematode, “specific” have both been identified in
 N. aberrans. Our results provide insights into the characteristics of a
 common ancestor and the evolution of sedentary endoparasitism of plants by
 nematodes.
description: Nab_gene_expression_dryadAll expression data for transcripts in the Nacobbus aberrrans de novo assembly, indicating which are in significantly deferentially expressed super clusters (with key), and including the centred log fold change.N.abberans_reference_transcriptsde novo transcriptome assembly - transcriptsN.abberans_reference_no_contam.fastaN.abberans_reference_predicted_proteinsde novo transcriptome assembly - predicted proteinsN.abberans_reference_no_contam.fasta.transdecoder.pepN.abberans_reference_predicted_CDSde novo transcriptome assembly - predicted CDSN.abberans_reference_no_contam.fasta.transdecoder.cds
DOI: 10.5061/dryad.b59qj
title: Data from: A test of the central-marginal hypothesis using population genetics and ecological niche modelling in an endemic salamander (Ambystoma barbouri)

description: The central-marginal hypothesis (CMH) predicts that population size,
 genetic diversity, and genetic connectivity are highest at the core and
 decrease near the edges of species’ geographic distributions. We provide a
 test of the CMH using three replicated core-to-edge transects that
 encompass nearly the entire geographic range of the endemic streamside
 salamander (Ambystoma barbouri). We confirmed that the mapped core of the
 distribution was the most suitable habitat using ecological niche
 modelling (ENM) and via genetic estimates of effective population sizes.
 As predicted by the CMH, we found statistical support for decreased
 genetic diversity, effective population size, and genetic connectivity
 from core to edge in western and northern transects, yet not along a
 southern transect. Based on our niche model, habitat suitability is lower
 towards the southern range edge, presumably leading to conflicting
 core-to-edge genetic patterns. These results suggest that multiple
 processes may influence a species’ distribution based on the heterogeneity
 of habitat across a species’ range and that replicated sampling may be
 needed to accurately test the CMH. Our work also emphasizes the importance
 of identifying the geographic range core with methods other than using the
 Euclidean center on a map, which may help to explain discrepancies among
 other empirical tests of the CMH. Assessing core to edge population
 genetic patterns across an entire species’ range accompanied with ENM can
 inform our general understanding of the mechanisms leading to species’
 geographic range limits.
description: Microsatellite genotype
 data for all individualsThis file contains
 microsatellite genotype data for the 1334 individuals used in the study.
 The columns contain: 1) the individual's ID, 2) the population ID,
 and 3) microsatellite loci split into two alleles per
 locus.microsat.xlsEcological Niche Model Presence PointsThese are latitudes / longitudes of all presence points used in the ecological niche model.barbmax.csvMaxENT Environmental LayersThis file contains all environmental layers (100m resolution) originally tested in the ecological niche model in .asc format.BarbMaxentASC.zipPairwise Fst & Dps tablesPairwise Fst and Dps values for all 3 transects.Pairwise FST & Dps.xlsNEW gpsGPS coordinates for all collection localitiesgps.xls
DOI: 10.5061/dryad.4nt0f
title: Data from: Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in Arabidopsis

description: Plants use light as source of energy and information to detect diurnal
 rhythms and seasonal changes. Sensing changing light conditions is
 critical to adjust plant metabolism and to initiate developmental
 transitions. Here we analyzed transcriptome-wide alterations in gene
 expression and alternative splicing (AS) of etiolated seedlings undergoing
 photomorphogenesis upon exposure to blue, red, or white light. Our
 analysis revealed massive transcriptome reprograming as reflected by
 differential expression of ~20% of all genes and changes in several
 hundred AS events. For more than 60% of all regulated AS events, light
 promoted the production of a presumably protein-coding variant at the
 expense of an mRNA with nonsense-mediated decay-triggering features.
 Accordingly, AS of the putative splicing factor REDUCED RED-LIGHT
 RESPONSES IN CRY1CRY2 BACKGROUND 1 (RRC1), previously identified as a red
 light signaling component, was shifted to the functional variant under
 light. Downstream analyses of candidate AS events pointed at a role of
 photoreceptor signaling only in monochromatic but not in white light.
 Furthermore, we demonstrated similar AS changes upon light exposure and
 exogenous sugar supply, with a critical involvement of kinase signaling.
 We propose that AS is an integration point of signaling pathways that
 sense and transmit information regarding the energy availability in
 plants.
description: Supplemental Dataset
 1Computational Analysis
 of Transcriptome-Wide AS.Supplemental_Data_set_1_AS_analysis.xlsxSupplemental Data Set 2Computational Analysis of Transcriptome-Wide Differential Gene Expression.Supplemental_Data_Set_2_Diff_Expression.xlsxSupplemental Data Set 3Splicing Index Analysis.Supplemental_Data_set_3_SI.xlsxSupplemental Data Set 4Analysis of NMD Target Features and Overlap between NMD- and Light-Regulated AS.Supplemental_Data_Set_4_NMD_Features_Overlap_NMD_set.xlsxSupplemental Data Set 5Categorization of Light-Regulated and Reference Gene Sets into Functional Subgroups.Supplemental_Data_Set_5_GO.xlsxSupplemental Data Set 6Expressed Intergenic Regions.Supplemental_Data_Set_6_Intergenic_regions.xlsxSupplemental Data Set 7Computational Analysis of Transcriptome-Wide AS Changes in Response to Red Light Based on the Data from Shikata et al. (2014).Supplemental_Data_set_7_Shikata.xlsx
DOI: 10.5061/dryad.51sd2p5
title: Data from: Are assortative mating and genital divergence driven by reinforcement?

description: The evolution of assortative mating is a key part of the speciation
 process. Stronger assortment, or greater divergence in mating traits,
 between species pairs with overlapping ranges is commonly observed, but
 possible causes of this pattern of reproductive character displacement are
 difficult to distinguish. We use a multidisciplinary approach to provide a
 rare example where it is possible to distinguish among hypotheses
 concerning the evolution of reproductive character displacement. We build
 on an earlier comparative analysis that illustrated a strong pattern of
 greater divergence in penis form between pairs of sister species with
 overlapping ranges than between allopatric sister-species pairs, in a
 large clade of marine gastropods (Littorinidae). We investigate both
 assortative mating and divergence in male genitalia in one of the
 sister-species pairs, discriminating among three contrasting processes
 each of which can generate a pattern of reproductive character
 displacement: reinforcement, reproductive interference and the Templeton
 effect. We demonstrate reproductive character displacement in assortative
 mating, but not in genital form between this pair of sister species and
 use demographic models to distinguish among the different processes. Our
 results support a model with no gene flow since secondary contact and thus
 favour reproductive interference as the cause of reproductive character
 displacement for mate choice, rather than reinforcement. High gene flow
 within species argues against the Templeton effect. Secondary contact
 appears to have had little impact on genital divergence.
description: Reinforcement in
 Littoraria?The data files covers
 four analyses: ABC modelling, gene flow, genital morphology and mating
 behaviour.Archive
 Littoraria.zip
DOI: 10.5061/dryad.pr7gh
title: Data from: Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes

description: In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and
 the development of an imputation strategy provided an opportunity to
 further investigate the extent of linkage disequilibrium (LD) at short
 distances in the genome of the Spanish Churra dairy sheep breed. A
 population of 1686 animals, including 16 rams and their half-sib
 daughters, previously genotyped for the 50K-chip, was imputed to the
 HD-chip density based on a reference population of 335 individuals. After
 assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2
 (0.921) using a cross-validation approach, the imputed HD-chip genotypes
 obtained with beagle were used to update the estimates of LD and effective
 population size for the studied population. The imputed genotypes were
 also used to assess the degree of homozygosity by calculating runs of
 homozygosity and to obtain genomic-based inbreeding coefficients. The
 updated LD estimations provided evidence that the extent of LD in Churra
 sheep is even shorter than that reported based on the 50K-chip and is one
 of the shortest extents compared with other sheep breeds. Through
 different comparisons we have also assessed the impact of imputation on LD
 and effective population size estimates. The inbreeding coefficient,
 considering the total length of the run of homozygosity, showed an average
 estimate (0.0404) lower than the critical level. Overall, the improved
 accuracy of the updated LD estimates suggests that the HD-chip, combined
 with an imputation strategy, offers a powerful tool that will increase the
 opportunities to identify genuine marker-phenotype associations and to
 successfully implement genomic selection in Churra sheep.
description: DryadRepository_PraveenLD"map" and "ped" files in PLINK format
DOI: 10.5061/dryad.r8q71
title: Data from: Novel conserved genotypes correspond to antibiotic resistance phenotypes of E. coli clinical isolates

description: Current efforts to understand antibiotic resistance on the whole genome
 scale tend to focus on known genes even as high throughput sequencing
 strategies uncover novel mechanisms. To identify genomic variations
 associated with antibiotic resistance, we employed a modified genome-wide
 association study; we sequenced genomic DNA from pools of E. coli clinical
 isolates with similar antibiotic resistance phenotypes using SOLiD
 technology to uncover SNPs unanimously conserved in each pool. The
 multidrug-resistant pools were genotypically similar to SMS-3-5, a
 previously sequenced multidrug-resistant isolate from a polluted
 environment. The similarity was evenly spread across the entire genome and
 not limited to plasmid or pathogenicity island loci. Among the pools of
 clinical isolates, genomic variation was concentrated adjacent to
 previously reported inversion and duplication differences between the
 SMS-3-5 isolate and the drug-susceptible laboratory strain, DH10B. Single
 nucleotide polymorphisms (SNPs) that result in non-synonymous changes in
 gyrA (encoding the well-known S83L allele associated with fluoroquinolone
 resistance), mutM, ligB, and recG were unanimously conserved in every
 fluoroquinolone-resistant pool. Alleles of the latter three genes are
 tightly linked among most sequenced E. coli genomes, and had not been
 implicated in antibiotic resistance previously. The changes in these genes
 map to amino acid positions in alpha helices that are involved in DNA
 binding. Plasmid- encoded complementation of null strains with either
 allelic variant of mutM or ligB resulted in variable responses to
 ultraviolet light or hydrogen peroxide treatment as markers of induced DNA
 damage, indicating their importance in DNA metabolism and revealing a
 potential mechanism for fluoroquinolone resistance. Our approach uncovered
 evidence that additional DNA binding enzymes may contribute to
 fluoroquinolone resistance and further implicate environmental bacteria as
 a reservoir for antibiotic resistance.
description: Raw diBayes SNP calls
 for clinical isolate pools against three different reference E. coli
 genomesThe attached zip file
 contains the raw DiBayes SNP calls for the paper Swick et al,
 PONE-D-12-36402R1. Novel Conserved Genotypes Correspond to Antibiotic
 Resistance Phenotypes of E. coli Clinical Isolates. PLOS ONE. It contains
 16 folders, each of which follows this structure: $PoolID &gt;
 $ReferenceGenome &gt; DB &gt; $PoolID &gt; $PoolID_SNP.gff3. The
 $ReferenceGenome codes correspond to the following NCBI accession numbers:
 NC_010473 - DH10B, NC_010498 - SMS-3-5, NC_012967 -
 REL606SNPCalls_Swicketal_2013.zip
DOI: 10.5061/dryad.m8m6142
title: Data from: The Gambian epauletted fruit bat shows increased genetic divergence in the Ethiopian highlands and in an area of rapid urbanisation

description: The Gambian epauletted fruit bat (Epomophorus gambianus) is an abundant
 species that roosts in both urban and rural settings. The possible role of
 E. gambianus as a reservoir host of zoonotic diseases underlines the need
 to better understand the species movement patterns. So far, neither
 observational nor phylogenetic studies have identified the dispersal range
 or behaviour of this species. Comparative analyses of mitochondrial and
 nuclear markers from 20 localities across the known distribution of E.
 gambianus showed population panmixia, except for the populations in
 Ethiopia and southern Ghana (Accra and Ve-Golokwati). The Ethiopian
 population may be ancestral and is highly divergent to the species across
 the rest of its range, possibly reflecting isolation of an ancient
 colonization along an East-West axis. Mitochondrial haplotypes in the
 Accra population display a strong signature of a past bottleneck event;
 evidence of either an ancient or recent bottleneck using microsatellite
 data, however, was not detected. Demographic analyses identified
 population expansion in most of the colonies, except in the female line of
 descent in the Accra population. The molecular analyses of the colonies
 from Ethiopia and southern Ghana show gender dispersal bias, with the
 mitochondrial DNA fixation values over ten times those of the nuclear
 markers. These findings indicate free mixing of the species across great
 distances, which should inform future epidemiological studies.
description: STRUCTURE output from
 277 bats (Fig_S10)Output data of STRUCTURE
 analyses performed using nuclear microsatellite data from 277 E.
 gambianus14flag0600.zipAlingmentsMitochondrial DNA alignments (.nex and .fasta) of CYTB, DLOOP and Concatenated fragments used in this manuscriptnuclear microsatellitesNuclear microsatellites RAW data (.fsa)microsatellites.zip