cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1164
title: Data from: Genomic diversity, population structure, and migration following rapid range expansion in the balsam poplar, Populus balsamifera

description: Rapid range expansions can cause pervasive changes in the genetic
 diversity and structure of populations. The post-glacial history of the
 Balsam Poplar, Populus balsamifera, involved the colonization of most of
 northern North America, an area largely covered by continental ice sheets
 during the last glacial maximum. To characterize how this expansion shaped
 genomic diversity within and among populations, we developed 412 SNP
 markers that we assayed for a range-wide sample of 474 individuals sampled
 from 34 populations. We complemented the SNP dataset with DNA sequence
 data from 11 nuclear loci from 94 individuals, and used coalescent
 analyses to estimate historical population size, demographic growth, and
 patterns of migration. Bayesian clustering identified three geographically
 separated demes found in the Northern, Central, and Eastern portions of
 the species range. These demes varied significantly in nucleotide
 diversity, the abundance of private polymorphisms, and population
 substructure. Most measures supported the Central deme as descended from
 the primary refuge of diversity. Both SNPs and sequence data suggested
 recent population growth, and coalescent analyses of historical migration
 suggested a massive expansion from the Center to the North and East.
 Collectively, these data demonstrate the strong influence that range
 expansions exert on genomic diversity, both within local populations and
 across the range. Our results suggest that an in-depth knowledge of
 nucleotide diversity following expansion requires sampling within multiple
 populations, and highlight the utility of combining insights from
 different data types in population genomic studies.
description: Balsam Poplar nuclear
 genomic SNP lociThese data are diploid
 SNP genotypes for 412 nuclear genomic regions in Populus balsamifera
 (balsam poplar). Individuals are grouped in Col A according to population
 of origin (pop = ""), and each row is a unique individual (e.g.,
 individual 1 from pop "BOY" = "BOY01"). Each biallelic
 SNP is represented by 2 columns per individual. Alleles symbols are the
 nucleotide bases at that locus; missing data are represented as
 "?". Loci are labeled across row 1 and are named according to
 the transcript I.D. from the Populus trichocarpa
 genome.P_balsamifera_ref_SNPs.xlsx
DOI: 10.5061/dryad.mv88m
title: Data from: Genome-wide association mapping of quantitative traits in a breeding population of sugarcane

description: Background: Molecular markers associated with relevant agronomic traits
 could significantly reduce the time and cost involved in developing new
 sugarcane varieties. Previous sugarcane genome-wide association analyses
 (GWAS) have found few molecular markers associated with relevant traits at
 plant-cane stage. The aim of this study was to establish an appropriate
 GWAS to find molecular markers associated with yield related traits
 consistent across harvesting seasons in a breeding population. Sugarcane
 clones were genotyped with DArT (Diversity Array Technology) and TRAP
 (Target Region Amplified Polymorphism) markers, and evaluated for cane
 yield (CY) and sugar content (SC) at two locations during three successive
 crop cycles. GWAS mapping was applied within a novel mixed-model framework
 accounting for population structure with Principal Component Analysis
 scores as random component. Results: A total of 43 markers significantly
 associated with CY in plant-cane, 42 in first ratoon, and 41 in second
 ratoon were detected. Out of these markers, 20 were associated with CY in
 2 years. Additionally, 38 significant associations for SC were detected in
 plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one
 marker-trait association was found significant for the 3 years of the
 study, while twelve markers presented association for 2 years. In the
 multi-QTL model several markers with large allelic substitution effect
 were found. Sequences of four DArT markers showed high similitude and
 e-value with coding sequences of Sorghum bicolor, confirming the high gene
 microlinearity between sorghum and sugarcane. Conclusions: In contrast
 with other sugarcane GWAS studies reported earlier, the novel methodology
 to analyze multi-QTLs through successive crop cycles used in the present
 study allowed us to find several markers associated with relevant traits.
 Combining existing phenotypic trial data and genotypic DArT and TRAP
 marker characterizations within a GWAS approach including population
 structure as random covariates may prove to be highly successful.
 Moreover, sequences of DArT marker associated with the traits of interest
 were aligned in chromosomal regions where sorghum QTLs has previously been
 reported. This approach could be a valuable tool to assist the improvement
 of sugarcane and better supply sugarcane demand that has been projected
 for the upcoming decades.
description: Additional file
 4Additional file 4: Table
 S4. Dataset of 1,745 polymorphic DArT and TRAP markers scored on the 88
 sugarcane accessions and used to estimate genetic relationship among
 clones. Table S5. Dice distances matrix. Table S6. Ultrametric distances
 matrix.Figure
 1Figure 1.
 Neighbour-joining tree based on the Dice dissimilarity index calculated
 from 1,745 polymorphic markers data (103 TRAP and 1,642 DArT) assembling
 the 88 sugarcane genotypes.
DOI: 10.5061/dryad.165tm
title: Data from: Extinction of South American sparassodontans (Metatheria): environmental fluctuations or complex ecological processes?

description: Sparassodontans are a diverse but now extinct group of metatherians that
 were apex predators in South America during most of the Cenozoic. Studying
 their decline has been controversial mainly due to the scarcity of the
 fossil record, and different methodological approaches have led to
 contradictory hypotheses. In an effort to explore questions about their
 extinction, we developed a novel multi-model statistical approach to
 analyse all of the currently available data at a continental scale. Using
 multiple regression analysis and new advances in beta diversity analysis,
 we used all currently available fossil data at a continental scale to test
 four competing hypotheses to account for the decline of sparassodontans:
 competition with placental carnivorans, competition with avian
 phorusrhacids, non-competitive ecological interactions, and environmental
 fluctuations. Our results show that the sparassodontan extinction was a
 gradual process with species disappearing throughout the Cenozoic.
 Multiple regression analysis supported non-competitive ecological
 interactions as the best extinction model. Native South American
 ungulates, African migrants (caviomorph rodents and platyrrhine primates)
 and didelphimorphians were the groups with the highest statistical
 significance. Sparassodontan beta diversity increased between South
 American Land Mammal Ages after the Paleocene–Eocene boundary. Our results
 demonstrate that ecological modelling techniques illuminate aspects of
 extinction processes whilst mitigating the limitations of the fossil
 record. Our study suggests that non-competitive ecological interactions
 could have been the main driver for sparassodontan extinction rather than,
 as commonly assumed, a result of competition and/or abiotic fluctuations.
description: Data
 matrixEdited data matrix used
 for all statistical analyses including all 33 tested variables, # sites
 and time span for all SALMAsSparAnalysis.csvFile 2Diversity of carnivorans throughout the CenozoicS1.pngFile 3Diversity of different mammal lineages present in SA throughout the CenozoicS2.pngFile 4Diversity of South American ungulates present in SA throughout the CenozoicS3.pngFile 5Diversity of phorusrhacid birds throughout the CenozoicS4.pngFile 6Diversity of rodents throughout the CenozoicS5.pngFile 8Statistical results of the 264 computed multiple linear regressionsS9.docxFile 7Number of LADs for different body-size sparassodontans throughout the CenozoicS6.pngAdditional references and occurences' listSupplement2.xls
DOI: 10.5061/dryad.4df50
title: Data from: Reinforcement and a cline in mating behavior evolve in response to secondary contact and hybridization in shield-back katydids (Orthoptera: Tettigoniidae)

description: In a dispersal-limited species that has evolved reproductive character
 displacement at a contact zone, a cline in mating behavior may result if
 gene flow diffuses alleles out of the contact zone into allopatric
 populations. Prior work has found such a clinal pattern in the shield-back
 katydid Aglaothorax morsei, in which the male calling songs in a sympatric
 population have a displaced, short interpulse interval that increases in
 length with increasing distance from the contact zone. In this study,
 molecular phylogenetic and female preference data show that (1) sympatric
 populations result from secondary contact, (2) hybridization in sympatry
 has resulted in unidirectional mitochondrial introgression, and (3) female
 preferences are consistent with reproductive character displacement, and
 could generate a cline in mating behavior. These data together suggest a
 history of reinforcement, generally considered rare in acoustically
 communicating insects, thus Aglaothorax represents an important example of
 a rarely documented evolutionary process.
description: Aglaothorax cline female
 preference dataFemale preferences in
 populations of shield-back katydids along a song cline in the southern
 California Transverse Ranges. This spreadsheet summarizes results for
 choice testing of pulse number, no-choice testing of interpulse interval,
 and post hoc analyses of preference and male song that support a
 hypothesis of reinforcement.28S MAFFT align GARLI
 bootstrap finalNexus file for maximum
 likelihood estimation of 28S rDNA gene tree for Aglaothorax shield-back
 katydids.AK GARLI
 bootstrapNexus file for maximum
 likelihood estimation of arginine kinase gene tree for Aglaothorax
 shield-back katydids.WG GARLI
 bootstrapNexus file for maximum
 likelihood estimation of wingless gene tree for Aglaothorax shield-back
 katydids.mtDNA Bayesian CIPRES
 final runNexus file for Bayesian
 tree estimation from mt COI and COII for Aglaothorax shield-back
 katydids.concatenated 4SALE align
 Bayesian CIPRES final runNexus file for Bayesian
 estimation of the Aglaothorax shield-back katydid phylogeny from a
 concatenated dataset of six genes.ITS2 4SALE align w gap
 coding Bayesian CIPRES final runNexus file for Bayesian
 estimation of ITS2 gene tree for Aglaothorax shield-back katydids.
 Alignment was aided by secondary structure estimation in 4SALE. Analysis
 includes gap coding.
DOI: 10.5061/dryad.js880
title: Data from: Mutation is a sufficient and robust predictor of genetic variation for mitotic spindle traits in Caenorhabditis elegans

description: Different types of phenotypic traits consistently exhibit different levels
 of genetic variation in natural populations. There are two potential
 explanations: either mutation produces genetic variation at different
 rates, or natural selection removes or promotes genetic variation at
 different rates. Whether mutation or selection is of greater general
 importance is a longstanding unresolved question in evolutionary genetics.
 We report mutational variances (VM) for 19 traits related to the first
 mitotic cell division in C. elegans, and compare them to the standing
 genetic variances (VG) for the same suite of traits in a worldwide
 collection C. elegans. Two robust conclusions emerge. First, the
 mutational process is highly repeatable: the correlation between VM in two
 independent sets of mutation accumulation lines is ~0.9. Second, VM for a
 trait is a good predictor of VG for that trait: the correlation between VM
 and VG is ~0.9. This result is predicted for a population at
 mutation-selection balance; it is not predicted if balancing selection
 plays a primary role in maintaining genetic variation.
description: Mitotic spindle traits
 in C. elegansThe data included in
 this file are the raw measurements for 19 traits associated with the first
 mitotic cell division. The first column is the Species (C. elegans), the
 second column is the Genotype (N2 MA line, PB306 MA line, or wild
 isolate); the third column is the Strain designation, the fourth column is
 the Treatment (MA control, MA line, or wild isolate), the fifth column is
 the Line number, the sixth column is the Replicate number, and the
 remaining columns are the traits. The traits are described in the Methods
 and Materials of the associated publication.19traits_forDryad.csv
DOI: 10.5061/dryad.88pv1
title: Data from: Neurons in primate visual cortex alternate between responses to multiple stimuli in their receptive field

description: A fundamental question concerning representation of the visual world in
 our brain is how a cortical cell responds when presented with more than a
 single stimulus. We find supportive evidence that most cells presented
 with a pair of stimuli respond predominantly to one stimulus at a time,
 rather than a weighted average response. Traditionally, the firing rate is
 assumed to be a weighted average of the firing rates to the individual
 stimuli (response-averaging model) (Bundesen et al., 2005). Here, we also
 evaluate a probability-mixing model (Bundesen et al., 2005), where neurons
 temporally multiplex the responses to the individual stimuli. This
 provides a mechanism by which the representational identity of multiple
 stimuli in complex visual scenes can be maintained despite the large
 receptive fields in higher extrastriate visual cortex in primates. We
 compare the two models through analysis of data from single cells in the
 middle temporal visual area (MT) of rhesus monkeys when presented with two
 separate stimuli inside their receptive field with attention directed to
 one of the two stimuli or outside the receptive field. The spike trains
 were modeled by stochastic point processes, including memory effects of
 past spikes and attentional effects, and statistical model selection
 between the two models was performed by information theoretic measures as
 well as the predictive accuracy of the models. As an auxiliary measure, we
 also tested for uni- or multimodality in interspike interval
 distributions, and performed a correlation analysis of simultaneously
 recorded pairs of neurons, to evaluate population behavior.
description: codeProvides the code for
 data fitting and for producing the figures in the
 paper.R_dataRdata files containing
 spike train data from MT neurons in rhesus monkeys under single or
 multiple random dot pattern stimulimodel_fittingProvides the output from the data fitting. Used to produce the figures.
DOI: 10.5061/dryad.dj82k
title: Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

description: Difficulties in generating nuclear data for polyploids have impeded
 phylogenetic study of these groups. We describe a high-throughput protocol
 and an associated bioinformatics pipeline (PURC: “Pipeline for Untangling
 Reticulate Complexes”) that is able to generate these data quickly and
 conveniently, and demonstrate its efficacy on accessions from the fern
 family Cystopteridaceae. We conclude with a demonstration of the
 downstream utility of these data by inferring a multilabeled species tree
 for a subset of our accessions. We amplified four ~1kb-long nuclear loci
 and sequenced them in a parallel-tagged amplicon sequencing approach using
 the PacBio platform. PURC infers the final sequences from the raw reads
 via an iterative approach that corrects PCR and sequencing errors and
 removes PCR-mediated recombinant sequences (chimeras). We generated data
 for all gene copies (homeologs, paralogs, and segregating alleles) present
 in each of three sets of 50 mostly-polyploid accessions, for four loci, in
 three PacBio runs (one run per set). From the raw sequencing reads PURC
 was able to accurately infer the underlying sequences. This approach makes
 it easy and economical to study the phylogenetics of polyploids, and in
 conjunction with recent analytical advances, facilitates investigation of
 broad patterns of polyploid evolution.
description: PURCvsSanger_treesContains two files (a nexus alignment and a tree file) of the comparison of the alleles inferred by PURC versus those from cloning and Sanger sequencing. See figure S1 in the paper.all_regimes_treesFor each of the four loci, contains a tree that includes all the alleles inferred by each of the six analysis regimes.barcodes_pacbioThe 48 16-base barcodes designed by Pacific Biosciences.PURC_molecularlab_trackingAn example spreadsheet for sample tracking and library preparation (amplicon standardization, etc.)vouchertable_allrunsVoucher data for all three PacBio sequencing runs discussed in the manuscript.scripts_for_figuresPython and R scripts used to generate the figures.extract_specific_accessionsThis script finds the "allele" sequences for a given set of accessions, from all regimes and runs provided. It can be useful to look at the effect of different analysis regimes -- less overwhelming than trying to look at huge trees of all accessions at once. Alternatively, use the merge_allRegimes_and_align.sh bash script to get all the sequences, from all the accessions.merge_allRegimes_and_alignShell script to merge the inferred alleles from multiple analyses (ie, different analysis regimes) into a single alignment.batch_run_purcExample shell script to run purc_recluster.py multiple times, with different analyses settings.
DOI: 10.5061/dryad.s1j6b
title: Data from: A novel mouse segmentation method based on dynamic contrast enhanced micro-CT images

description: With the development of hybrid imaging scanners, micro-CT is widely used
 in locating abnormalities, studying drug metabolism, and providing
 structural priors to aid image reconstruction in functional imaging. Due
 to the low contrast of soft tissues, segmentation of soft tissue organs
 from mouse micro-CT images is a challenging problem. In this paper, we
 propose a mouse segmentation scheme based on dynamic contrast enhanced
 micro-CT images. With a homemade fast scanning micro-CT scanner, dynamic
 contrast enhanced images were acquired before and after injection of
 non-ionic iodinated contrast agents (iohexol). Then the feature vector of
 each voxel was extracted from the signal intensities at different time
 points. Based on these features, the heart, liver, spleen, lung, and
 kidney could be classified into different categories and extracted from
 separate categories by morphological processing. The bone structure was
 segmented using a thresholding method. Our method was validated on seven
 BALB/c mice using two different classifiers: a support vector machine
 classifier with a radial basis function kernel and a random forest
 classifier. The results were compared to manual segmentation, and the
 performance was assessed using the Dice similarity coefficient, false
 positive ratio, and false negative ratio. The results showed high accuracy
 with the Dice similarity coefficient ranging from 0.709 ± 0.078 for the
 spleen to 0.929 ± 0.006 for the kidney.
description: Segmentation
 results
DOI: 10.5061/dryad.32j55
title: Data from: Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

description: Several reviews in the past decade have heralded the benefits of embracing
 high-throughput sequencing technologies to inform conservation policy and
 the management of threatened species, but few have offered practical
 advice on how to expedite the transition from conservation genetics to
 conservation genomics. Here, we argue that an effective and efficient way
 to navigate this transition is to capitalize on emerging synergies between
 conservation genetics and primary industry (e.g., agriculture, fisheries,
 forestry and horticulture). Here, we demonstrate how building strong
 relationships between conservation geneticists and primary industry
 scientists is leading to mutually-beneficial outcomes for both
 disciplines. Based on our collective experience as collaborative New
 Zealand-based scientists, we also provide insight for forging these
 cross-sector relationships.
description: Conservation Genomics
 Literature Search 2005-2015This text file details
 the final list of publications fitting ISI Web of Science conservation
 genomics literature search detailed in Supplement 1 of the publication
 "Building strong relationships between conservation biology and
 primary industry leads to mutually-beneficial genomic advances". All
 final publications included in this literature search are detailed in the
 following text document by authors, year published, publication title,
 journal, and (if available) abstract.ConservationGenomics_2005-2015.txtPrimary Industry Genomics Literature Search 2005-2015This text file details the final list of publications fitting ISI Web of Science primary industry genomics literature search detailed in Supplement 1 of the publication "Building strong relationships between conservation biology and primary industry leads to mutually-beneficial genomic advances". All final publications included in this literature search are detailed in the following text document by year published, authors, publication title, journal, and (if available) abstract.PrimaryIndustry_2005-2015.txt
DOI: 10.5061/dryad.kd835
title: Data from: Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate

description: [No abstract entered]
description: JEB_2016_Genetic
 structure across thermal environmentsAFLP raw
 data.