cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2451q
title: Data from: Speciation dynamics during the global radiation of extant bats

description: Species richness varies widely across extant clades, but the causes of
 this variation remain poorly understood. We investigate the role of
 diversification rate heterogeneity in shaping patterns of diversity across
 families of extant bats. To provide a robust framework for
 macroevolutionary inference, we assemble a time-calibrated, species-level
 phylogeny using a supermatrix of mitochondrial and nuclear sequence data.
 We analyze the phylogeny using a Bayesian method for modeling complex
 evolutionary dynamics. Surprisingly, we find that variation in family
 richness can largely be explained without invoking heterogeneous
 diversification dynamics. We document only a single well-supported shift
 in diversification dynamics across bats, occurring at the base of the
 subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced,
 but - contrary to previous hypotheses - this pattern is unexplained by any
 simple patterns of diversification rate heterogeneity. This discordance
 may indicate that diversification dynamics are more complex than can be
 captured using the statistical tools available for modeling data at this
 scale. We infer that bats as a whole are almost entirely united into one
 macroevolutionary cohort, with decelerating speciation through time. There
 is also a significant relationship between clade age and richness,
 suggesting that global bat diversity may still be expanding.
description: Shi_Rabosky_2015_Evolution.tarThe data include the following sections: (1) PHLAWD alignments per locus and Genbank identifiers/metadata, (2) RAxML input/output and RogueNaRok output for phylogeny construction, (3) treePL input/output for both bootstraps and the ML phylogeny, (4) BAMM input/output for both bootstraps and the ML phylogeny, and (5) code for our phylogeneitc imbalance simulations.
DOI: 10.5061/dryad.s1k47j4
title: Data from: The evolutionary history of dogs in the Americas

description: Dogs were present in the Americas prior to the arrival of European
 colonists, but the origin and fate of these pre-contact dogs are largely
 unknown. We sequenced 71 mitochondrial and seven nuclear genomes from
 ancient North American and Siberian dogs spanning ~9,000 years. Our
 analysis indicates that American dogs were not domesticated from North
 American wolves. Instead, American dogs form a monophyletic lineage that
 likely originated in Siberia and dispersed into the Americas alongside
 people. After the arrival of Europeans, native American dogs almost
 completely disappeared, leaving a minimal genetic legacy in modern dog
 populations. Remarkably, the closest detectable extant lineage to
 pre-contact American dogs is the canine transmissible venereal tumor, a
 contagious cancer clone derived from an individual dog that lived up to
 8,000 years ago.
description: Mitochondrial DNA FASTA
 fileFASTA file containing
 1166 dog mtDNA genomes used in this studyfull_mtDNA_alignment.fastaNEXUS treeMaximum likelihood tree (RAxML) of 1166 dogs mtDNA genomes used in this studyfull_mtDNA_alignment.treExcel sheetPublication source of the 1166 mtDNA genomes used in this studyfull_mtDNA_alignment.xlsxPlink (bed) fileContains genotype for dogs 54 dogsfull_data.bedPlink file (bim)Contains genotype for 54 dogsfull_data.bimPlink file (fam)Contains genotype for 54 dogsfull_data.famNJ tree in Figure 2bNJ tree in Figure 2b (see Table S2 for more info)Figure_b.treNexus fileNexus file used for producing Figure S12 (MKV model in MrBayes)Binary_char_MKV.nexNEXUS treeBayesian tree in Figure S12 (see Table S2 for more info)Figure_S12.tre
DOI: 10.5061/dryad.hm6tt
title: Data from: Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories

description: Anopheles gambiae s.l. are important malaria vectors, but little is known
 about their genomic variation in the wild. Here we present inter- and
 intra- species analysis of genome-wide RADseq data, in three Anopheles
 gambiae s.l. species collected from East Africa. The mosquitoes fall into
 three genotypic clusters representing described species (An. gambiae, An.
 arabiensis, and An. merus) with no evidence of cryptic breeding units. An.
 merus is the most divergent of the three species, supporting a recent new
 phylogeny based on chromosomal inversions. Even though the species
 clusters are well separated, there is extensive shared polymorphism,
 particularly between An. gambiae and An. arabiensis. Divergence between
 An. gambiae and An. arabiensis does not vary across the autosomes, but is
 higher in X-linked inversions than elsewhere on X or on the autosomes,
 consistent with the suggestion that this inversion (or a gene within it)
 is important in reproductive isolation between the species. The 2La/2L+a
 inversion shows no more evidence of introgression between An. gambiae and
 An. arabiensis than the rest of the autosomes. Population differentiation
 within An. gambiae and An. arabiensis is weak over ~190-270km, implying no
 strong barriers to dispersal. Analysis of Tajima's D and the allele
 frequency spectrum is consistent with modest population increases in An.
 arabiensis and An. merus, but a more complex demographic history of
 expansion followed by contraction in An. gambiae. Although they are less
 than 200km apart, the two An. gambiae populations show evidence of
 different demographic histories.
description: RADseq_Gambiae_AllSites_Filtered_to_15xCoverageRADseq_Arabiensis_AllSites_Filtered_to_15xCoverageVCF format, variant and invariant sites for 36 Anopheles arabiensis samples aligned to PEST reference genomeRADseq_Merus_AllSites_Filtered_to_15xCoverageVCF format, variant and invariant sites for 12 Anopheles merus samples aligned with PEST reference genome
DOI: 10.5061/dryad.4nf1c
title: Data from: SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation

description: Blue catfish, Ictalurus furcatus, are valued in the United States as a
 trophy fishery for their capacity to reach large sizes, sometimes
 exceeding 45 kg. Additionally, blue catfish × channel catfish (I.
 punctatus) hybrid food fish production has recently increased the demand
 for blue catfish broodstock. However, there has been little study of the
 genetic impacts and interaction of farmed, introduced and stocked
 populations of blue catfish. We utilized genotyping-by-sequencing (GBS) to
 capture and genotype SNP markers on 190 individuals from five wild and
 domesticated populations (Mississippi River, Missouri, D&B, Rio
 Grande and Texas). Stringent filtering of SNP-calling parameters resulted
 in 4275 SNP loci represented across all five populations. Population
 genetics and structure analyses revealed potential shared ancestry and
 admixture between populations. We utilized the Sequenom MassARRAY to
 validate two multiplex panels of SNPs selected from the GBS data.
 Selection criteria included SNPs shared between populations, SNPs specific
 to populations, number of reads per individual and number of individuals
 genotyped by GBS. Putative SNPs were validated in the discovery population
 and in two additional populations not used in the GBS analysis. A total of
 64 SNPs were genotyped successfully in 191 individuals from nine
 populations. Our results should guide the development of highly
 informative, flexible genotyping multiplexes for blue catfish from the
 larger GBS SNP set as well as provide an example of a rapid, low-cost
 approach to generate and genotype informative marker loci in aquatic
 species with minimal previous genetic information.
description: SNP discovery in wild
 and domesticated populations of blue catfish, Ictalurus furcatus, using
 genotyping-by-sequencing and subsequent SNP validationThe SNPs were called by
 TASSEL 4.0 after mapping the GBS raw reads to the blue catfish genome by
 BWA. The VCF file holding SNP information that retains information on
 depth of coverage for each allele, contains all raw SNP
 calls.all.mergedSNPs.vcf
DOI: 10.5061/dryad.d4d5d
title: Data from: Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae)

description: A well-known issue in phylogenetics is discordance among gene trees,
 species trees, morphology, and other data types. Gene-tree discordance is
 often caused by incomplete lineage sorting, lateral gene transfer, and
 gene duplication. Multispecies-coalescent methods can account for
 incomplete lineage sorting and are believed by many to be more accurate
 than concatenation. However, simulation studies and empirical data have
 demonstrated that concatenation and species tree methods often recover
 similar topologies. We use three popular methods of phylogenetic
 reconstruction (one concatenation, two species tree) to evaluate
 relationships within Teiidae. These lizards are distributed across the
 United States to Argentina and the West Indies, and their classification
 has been controversial due to incomplete sampling and the discordance
 among various character types (chromosomes, DNA, musculature, osteology,
 etc.) used to reconstruct phylogenetic relationships. Recent morphological
 and molecular analyses of the group resurrected three genera and created
 five new genera to resolve non-monophyly in three historically ill-defined
 genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the
 phylogenetic relationships of the Teiidae using “next-generation”
 anchored-phylogenomics sequencing. Our final alignment includes 316 loci
 (488,656 bp DNA) for 244 individuals (56 species of teiids, representing
 all currently recognized genera) and all three methods (ExaML, MP-EST, and
 ASTRAL-II) recovered essentially identical topologies. Our results are
 basically in agreement with recent results from morphology and smaller
 molecular datasets, showing support for monophyly of the eight new genera.
 Interestingly, even with hundreds of loci, the relationships among some
 genera in Tupinambinae remain ambiguous (i.e. low nodal support for the
 position of Salvator and Dracaena).
description: Teiidae Concatenated
 Sequence AlignmentTeiidae_Sequence_Alignment.phyLocus partitions for Teiidae multiple sequence alignmentTeiidae.charSets.txtTeiidae Probe SequencesAHE_Teiidae_ProbeSequences.fastaPairwise Alignments for Probe DesignPairwise_Alignments.fasta
DOI: 10.5061/dryad.15v26
title: Data from: The metabolic cost of changing walking speeds is significant, implies lower optimal speeds for shorter distances, and increases daily energy estimates

description: Humans do not generally walk at constant speed, except perhaps on a
 treadmill. Normal walking involves starting, stopping and changing speeds,
 in addition to roughly steady locomotion. Here, we measure the metabolic
 energy cost of walking when changing speed. Subjects (healthy adults)
 walked with oscillating speeds on a constant-speed treadmill, alternating
 between walking slower and faster than the treadmill belt, moving back and
 forth in the laboratory frame. The metabolic rate for oscillating-speed
 walking was significantly higher than that for constant-speed walking
 (6–20% cost increase for ±0.13–0.27 m s−1 speed fluctuations). The
 metabolic rate increase was correlated with two models: a model based on
 kinetic energy fluctuations and an inverted pendulum walking model,
 optimized for oscillating-speed constraints. The cost of changing speeds
 may have behavioural implications: we predicted that the energy-optimal
 walking speed is lower for shorter distances. We measured preferred human
 walking speeds for different walking distances and found people preferred
 lower walking speeds for shorter distances as predicted. Further,
 analysing published daily walking-bout distributions, we estimate that the
 cost of changing speeds is 4–8% of daily walking energy budget.
description: OscillatingSpeedTrial1_SacralMotionSacral marker motion for oscillating speed trial 1.OscillatingSpeedTrial2_SacralMotionSacral marker motion for oscillating speed trial 2.OscillatingSpeedTrial3_SacralMotionSacral marker motion for oscillating speed trial 3.OscillatingSpeedTrial4_SacralMotionSacral marker motion for oscillating speed trial 4.OscillatingSpeedTrial5_SacralMotionSacral marker motion for oscillating speed trial 5.OscillatingSpeedTrial6_SacralMotionSacral marker motion for oscillating speed trial 6.MetabolicData_AllSubjectsMetabolic data for oscillating speed and constant speed walking + subject propertiesPreferred walking speeds as a function of walking distancePreferred walking speeds for walking different distances, starting and stopping at rest. The "steady state" preferred speed is measured as the average over the middle 1.4 m or the middle 0.75 m of the whole bout. The "average" preferred speed is the average over the whole bout.Dat_PreferredWalkingSpeeds.txtConstantSpeedTrial1_SacralMotionSacral marker motion while walking at a constant speed on a treadmill. Trial 1: 1.12 m/s.ConstantSpeedTrial2_SacralMotionSacral marker motion while walking at a constant speed on a treadmill. Trial 2: 1.56 m/s.readme filereadme file briefly describing the data in this data package.
DOI: 10.5061/dryad.8dk6t78s
title: Data from: Cross-species transferability of SSR loci developed from transcriptome sequencing in lodgepole pine

description: With the advent of next generation sequencing technologies, transcriptome
 level sequence collections are arising as prominent resources for the
 discovery of gene-based molecular markers. In a previous study more than
 15 000 simple sequence repeats (SSRs) in expressed sequence tag (EST)
 sequences resulting from 454 pyrosequencing of Pinus contorta cDNA were
 identified. From these we developed PCR primers for approximately 4000
 candidate SSRs. Here, we tested 184 of these SSRs for successful
 amplification across P. contorta and eight other pine species and examined
 patterns of polymorphism and allelic variability for a subset of these
 SSRs. Cross-species transferability was high, with high percentages of
 loci producing PCR products in all species tested. In addition, 50% of the
 loci we screened across panels of individuals from three of these species
 were polymorphic and allelically diverse. We examined levels of diversity
 in a subset of these SSRs by collecting genotypic data across several
 populations of Pinus ponderosa in northern Wyoming. Our results indicate
 the utility of mining pyrosequenced EST collections for gene-based SSRs
 and provide a source of molecular markers that should bolster evolutionary
 genetic investigations across the genus Pinus.
description: P.contorta_contigs_singletonsConsensus sequences of contigs and singleton sequences used for SSR detection and characterization. Contigs were assembled as described in Parchman et al. (2010, BMC Genomics, 11:180).
DOI: 10.5061/dryad.4c5f9
title: Data from: Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastinae)

description: The prevalence and consequences of genetic introgression between species
 have been intensively debated. I used Hercules beetles as examples to test
 for conditions that may be associated with the occurrence of
 introgression. RADseq data were used to reconstruct the species tree and
 history of introgression between Hercules beetles. Image data from museum
 specimens were used to investigate the phenotypic similarity of two
 adaptive traits between species from two distinct climatic realms
 (Nearctic vs. Neotropical). Genetic introgression was identified between
 Hercules beetles living in geographic proximity (parapatric). Phylogenetic
 relatedness and phenotypic similarity did not predict nor preclude genetic
 introgression between species. Phenotypic assimilation in body coloration
 was evident between distantly related Hercules beetles codistributed in
 Central America, where directional introgression was also statistically
 supported from the putative donor to receiver lineages. The number of
 introgressed loci was significantly higher between species with than
 without phenotypic similarity. I discuss the implications of recent
 studies on adaptive genetic introgression by providing supporting evidence
 from the Hercules beetle system.
description: suplementaryFigsSupplementary FiguresBody_color_image_filesJPG files image data; Dorsal views of male Hercules beetles.Thoracic_horn_LM_image_filesJPG file image data; major adult male Hercules beetles - lateral view - for landmark-based analysestps_&_RGB_inputsinput data for morphological-based analyses.molecular_datainput data for molecular-based analysessample_infocollection information for individual samples included in the molecular analyses.
DOI: 10.5061/dryad.vh5ht
title: Data from: In-vivo imaging of cell migration using contrast enhanced MRI and SVM based post-processing

description: The migration of cells within a living organism can be observed with
 magnetic resonance imaging (MRI) in combination with iron oxide
 nanoparticles as an intracellular contrast agent. This method, however,
 suffers from low sensitivity and specificty. Here, we developed a
 quantitative non-invasive in-vivo cell localization method using contrast
 enhanced multiparametric MRI and support vector machines (SVM) based
 post-processing. Imaging phantoms consisting of agarose with compartments
 containing different concentrations of cancer cells labeled with iron
 oxide nanoparticles were used to train and evaluate the SVM for cell
 localization. From the magnitude and phase data acquired with a series of
 -weighted gradient-echo scans at different echo-times, we extracted
 features that are characteristic for the presence of superparamagnetic
 nanoparticles, in particular hyper- and hypointensities, relaxation rates,
 short-range phase perturbations, and perturbation dynamics. High detection
 quality was achieved by SVM analysis of the multiparametric feature-space.
 The in-vivo applicability was validated in animal studies. The SVM
 detected the presence of iron oxide nanoparticles in the imaging phantoms
 with high specificity and sensitivity with a detection limit of 30 labeled
 cells per mm3, corresponding to 19 μM of iron oxide. As proof-of-concept,
 we applied the method to follow the migration of labeled cancer cells
 injected in rats. The combination of iron oxide labeled cells,
 multiparametric MRI and a SVM based post processing provides high spatial
 resolution, specificity, and sensitivity, and is therefore suitable for
 non-invasive in-vivo cell detection and cell migration studies over
 prolonged time periods.
description: Rat & phantom MRI
 dataThis file contains the
 raw data (not the k-space, but the reconstructed magnitude and phase data)
 of the MR measurements.MRISVM_paper_plosone.zip
DOI: 10.5061/dryad.g579t7k
title: Data from: Macroecology and macroevolution of the latitudinal diversity gradient in ants

description: The latitudinal diversity gradient—the tendency for more species to occur
 toward the equator—is the dominant pattern of life on Earth, yet the
 mechanisms responsible for it remain largely unexplained. Recently, the
 analysis of global data has led to advances in understanding, but these
 advances have been mostly limited to vertebrates and trees and have not
 provided consensus answers. Here, we synthesize large-scale geographic,
 phylogenetic, and fossil data for an exemplar invertebrate group—ants—and
 investigate whether the latitudinal diversity gradient arose due to higher
 rates of net diversification in the tropics, or due to a longer time
 period to accumulate diversity due to Earth’s climatic history. We find
 that latitudinal affinity is highly conserved, temperate clades are young
 and clustered within tropical clades, and diversification rate shows no
 systematic variation with latitude. These results indicate that
 diversification time —and not rate— is the main driver of the diversity
 gradient in ants.
description: Zip archive of data
 filesArchive of data,
 analysis, and results files including control/configuration files used for
 phylogenetic analyses, DNA sequence alignments, phylogenetic tree sets,
 and geographic data.Dryad_archive.zip
DOI: 10.5061/dryad.56f1h
title: Data from: Quantitative analysis of fundus-image sequences reveals phase of spontaneous venous pulsations

description: Purpose: Spontaneous venous pulsation correlates negatively with elevated
 intracranial pressure and papilledema, and it relates to glaucoma. Yet,
 its etiology remains unclear. A key element to elucidate its underlying
 mechanism is the time at which collapse occurs with respect to the heart
 cycle, but previous reports are contradictory. We assessed this question
 in healthy subjects using quantitative measurements of both vein diameters
 and artery lateral displacements; the latter being used as the marker of
 the ocular systole time. Methods: We recorded 5-second fundus sequences
 with a near-infrared scanning laser ophthalmoscope in 12 young healthy
 subjects. The image sequences were coregistered, cleaned from
 microsaccades, and filtered via a principal component analysis to remove
 nonpulsatile dynamic features. Time courses of arterial lateral
 displacement and of diameter at sites of spontaneous venous pulsation or
 proximal to the disk were retrieved from those image sequences and
 compared. Results: Four subjects displayed both arterial and venous
 pulsatile waveforms. On those, we observed venous diameter waveforms
 differing markedly among the subjects, ranging from a waveform matching
 the typical intraocular pressure waveform to a close replica of the
 arterial waveform. Conclusions: The heterogeneity in waveforms and
 arteriovenous phases suggests that the mechanism governing the venous
 outflow resistance differs among healthy subjects. Translational
 relevance: Further characterizations are necessary to understand the
 heterogeneous mechanisms governing the venous outflow resistance as this
 resistance is altered in glaucoma and is instrumental when monitoring
 intracranial hypertension based on fundus observations.
description: Fundus image
 sequences12 Fundus image
 sequences recorded in 12 young (age 22-31) healthy subjects with a
 scanning laser ophthalmoscope under near-infrared illumination. Sequences
 of 5.0 to 5.5 s length, collected at 9 images/s, resulting in 45 to 50
 images trimmed to vertical bands (386 x 768 pixels) centered on optic
 nerve head. Data provided as zipped uncompressed TIFF stacks
 filesMovies_Raw.zip