cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1kr29
title: Data from: Y-chromosome structural diversity in the bonobo and chimpanzee lineages

description: The male specific regions of primate Y-chromosomes (MSY) are enriched for
 multi-copy genes highly expressed in the testis. These genes are located
 in large repetitive sequences arranged as palindromes, inverted-, and
 tandem- repeats termed amplicons. In humans, these genes have critical
 roles in male fertility and are essential for the production of sperm. The
 structure of human and chimpanzee amplicon sequences show remarkable
 difference relative to the remainder of the genome, a difference that may
 be the result of intense selective pressure on male fertility. Four
 subspecies of common chimpanzees have undergone extended periods of
 isolation and appear to be in the early process of subspeciation.. A
 recent study found amplicons enriched for testis-expressed genes on the
 primate X-chromosome the target of hard selective sweeps, and
 male-fertility genes on the Y-chromosome may also be the targets of
 selection. However, little is understood about Y-chromosome amplicon
 diversity within and across chimpanzee populations. Here, we analyze 9
 common chimpanzee (representing three subspecies: Pan troglodytes
 schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and
 two bonobo (Pan paniscus) male whole-genome sequences to assess Y
 ampliconic copy-number diversity across the Pan genus. We observe that the
 copy-number of Y chromosome amplicons is variable amongst chimpanzees and
 bonobos, and identify several lineage-specific patterns, including
 variable copy-number of azoospermia candidates RBMY and DAZ. We detect
 recurrent switchpoints of copy-number change along the ampliconic tracts
 across chimpanzee populations, which may be the result of localized genome
 instability or selective forces.
description: HGDP00222chimp-Y.annotated.kmerFiles accompanying "Y-chromosome structural diversity in the bonobo and chimpanzee lineages" by Oetjens et al. 2016 chimpY and humanY .kmer files are bed files of k-mers referenced in the manuscript used for calculating depth of Y-amplicons. Positions refer to panTro4 and hg19 coordinates for chimp and human k-mers respectively. column 1: chromosome column 2: k-mer start column 3: k-mer end column 4: k-mer sequence column 5: annotationhumanY.annotated.ddPCR.kmerFiles accompanying "Y-chromosome structural diversity in the bonobo and chimpanzee lineages" by Oetjens et al. 2016 chimpY and humanY .kmer files are bed files of k-mers referenced in the manuscript used for calculating depth of Y-amplicons. Positions refer to panTro4 and hg19 coordinates for chimp and human k-mers respectively. column 1: chromosome column 2: k-mer start column 3: k-mer end column 4: k-mer sequence column 5: annotationchimpAndBonobo.vcfVCF files chimpAndBonobo.vcf and HGDP00222.vcf are the final filtered VCF files ( 4.2 Mb of callable sequence).
DOI: 10.15468/sx8cfr
title: Three new centipede species of the genus Newportia Gervais, 1847 from Colombia (Scolopendromorpha, Scolopocryptopidae, Newportiinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Jiménez, Sebastian Galvis, Chagas-Jr, Amazonas (2023): Three new centipede species of the genus Newportia Gervais, 1847 from Colombia (Scolopendromorpha, Scolopocryptopidae, Newportiinae). Zootaxa 5361 (3): 323-344, DOI: 10.11646/zootaxa.5361.3.2, URL: https://www.mapress.com/zt/article/download/zootaxa.5361.3.2/52194AbstractThree new species of the genus Newportia Gervais, 1847 from Colombia are described and illustrated. They were found in the cloud forests of the eastern Andes and in the rainforests of the biogeographical Chocó, ecosystems where the centipede fauna has been little studied. Newportia (Newportia) florezi sp. nov. differs from other Newportia species in the arrangement of the spinous processes on the prefemur of the ultimate legs, while Newportia (Newportia) anopla sp. nov. has a coxopleuron without any trace of a coxopleural process and possesses an atypically small forcipular coxosternite. Newportia (Newportia) tequendama sp. nov. is morphologically similar to Newportia pusilla Pocock, 1893, but differs in having an undivided tarsus 2 in the ultimate legs and the arrangement of the spinous processes on the prefemur and femur. An identification key for the Colombian species of Newportia is provided.
DOI: 10.5061/dryad.vk405
title: Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania’s Appalachian region

description: Informed conservation of stream fishes requires detailed understanding of
 the effects of both natural processes and anthropogenic activities on
 genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to
 eastern North America, typically resides in cold, high-quality stream
 ecosystems. The species has not only faced historical anthropogenic
 pressures, but also confronts current and future pressures. In a genetic
 analysis we used a reduced representation sequencing method (ddRADseq) to
 characterize 63 individuals from 23 streams where Brook Trout are native
 in the Appalachian region of Pennsylvania. A total of 2,590 loci passed
 filtering criteria, and 53% displayed significant association with a major
 stream drainage basin (Susquehanna or Allegheny; mean FST = 0.085).
 Mapping of the sequencing reads to the Atlantic Salmon Salmo salar genome
 revealed no clustering of high interdrainage FST values to specific genome
 regions. Evidence for genetic heterogeneity within each drainage basin was
 also detected. Stepwise regression of observed heterozygosity against
 geographic and environmental features revealed that drainage basin and
 effective area of watersheds were significant predictors of observed
 heterozygosity of Brook Trout within streams. Natural features such as
 waterfalls and major drainage basin, as well as the effects of dams and
 acid-mine drainage have fragmented habitat and shaped genetic diversity
 within Brook Trout populations in the Appalachian region of Pennsylvania,
 overall indicating the vulnerability of this species to increased
 industrialization.
description: Stacks and Genepop
 filesStacks v 1.36 catalog
 files and alleles.tsv, matches.tsv, snps.tsv, and tags.tsv files for each
 individual mapped to Atlantic salmon reference genome. Also included are
 sumstats.tsv file "batch_1.sumstats.tsv" for individuals grouped
 into either Susquehanna or Allegheny river basins, and the final filtered
 GENEPOP file, "batch_1_genepop_HWE001_poolBias.txt" used for
 analysis after filtering for Hardy Weinberg deviations and for loci that
 were associated with library pool.Sfontinalis.tar.gzSupplementFile2R script "tryRollWindows.R" – for performing genome-anchored smoothed FST and diversity significance analysis. Also included is the data file "Fig3_data_forMark.csv" referenced in the script.
DOI: 10.5061/dryad.f6v067r
title: Data from: Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire

description: Animal behavior has been studied for centuries, but few efficient methods
 are available to automatically identify and classify it. Quantitative
 behavioral studies have been hindered by the subjective and imprecise
 nature of human observation, and the slow speed of annotating behavioral
 data. Here, we developed an automatic behavior analysis pipeline for the
 cnidarian Hydra vulgaris using machine learning. We imaged freely behaving
 Hydra, extracted motion and shape features from the videos, and
 constructed a dictionary of visual features to classify pre-defined
 behaviors. We also identified unannotated behaviors with unsupervised
 methods. Using this analysis pipeline, we quantified 6 basic behaviors and
 found surprisingly similar behavior statistics across animals within the
 same species, regardless of experimental conditions. Our analysis
 indicates that the fundamental behavioral repertoire of Hydra is stable.
 This robustness could reflect a homeostatic neural control of
 "housekeeping" behaviors which could have been already present
 in the earliest nervous systems.
description: Hydra behavior
 datasetThis is an annotated
 Hydra behavior dataset collected from 53 Hydra specimens. The dataset
 includes both spontaneous behaviors and induced feeding behavior of Hydra,
 and is annotated with the following 8 labels: silent, elongation, tentacle
 swaying, body swaying, bending, contraction, somersaulting, and
 feeding.Hydra_behavior.zip
DOI: 10.5061/dryad.6r74j69
title: Data from: Modulation of functional activity and connectivity by acupuncture in patients with Alzheimer disease as measured by resting-state fMRI

description: Acupuncture has been used in the therapy of Alzheimer disease (AD);
 however, its neural mechanisms are still unclear. The aim of this study is
 to examine the effect of acupuncture on the functional connectivity in AD
 by using resting-state functional magnetic resonance imaging (rs-fMRI).
 Twenty-eight subjects (14 AD and 14 normal controls) participated in this
 study. The rs-fMRI data were acquired before and after acupuncture
 stimulation at the acupoints of Tai chong (Liv3) and Hegu (LI4). During
 the baseline resting state, by using the amplitude of low-frequency
 fluctuations (ALFF), we found a significantly decreased or increased ALFF
 in the AD patients relative to the controls. These regions were located in
 the right superior frontal gyrus (SFG), left postcentral gyrus, subgenual
 cingulate cortex (SCC), right middle cingulate cortex (MCC), right
 inferior frontal gyrus (IFG), right hippocampus and the right inferior
 temporal gyrus (ITG). Then, we selected these brain regions as seeds to
 investigate whether regional activity and functional connectivity could be
 modulated by acupuncture in the AD patients. When compared to the
 pre-acupuncture stage, several of the above regions showed an increased or
 decreased ALFF after acupuncture in the AD patients. In addition, the
 functional connectivity between the hippocampus and the precentral gyrus
 showed enhancement after acupuncture in the AD patients. Finally, there
 were close correlations between the functional activity, connectivity and
 clinical performance in the AD patients. The current study confirmed that
 acupuncture at Tai chong (Liv3) and He gu (LI4) can modulate functional
 activity and connectivity of specific cognition-related regions in AD
 patients.
description: Before_acupunctureBefor_acupuncture.rarAfter_acupuncture
DOI: 10.5061/dryad.bh52d
title: Data from: Hysteretic dynamics of active particles in a periodic orienting field

description: Active motion of living organisms and artificial self-propelling particles
 has been an area of intense research at the interface of biology,
 chemistry and physics. Significant progress in understanding these
 phenomena has been related to the observation that dynamic
 self-organization in active systems has much in common with ordering in
 equilibrium condensed matter such as spontaneous magnetization in
 ferromagnets. The velocities of active particles may behave similar to
 magnetic dipoles and develop global alignment, although interactions
 between the individuals might be completely different. In this work, we
 show that the dynamics of active particles in external fields can also be
 described in a way that resembles equilibrium condensed matter. It follows
 simple general laws, which are independent of the microscopic details of
 the system. The dynamics is revealed through hysteresis of the mean
 velocity of active particles subjected to a periodic orienting field. The
 hysteresis is measured in computer simulations and experiments on
 unicellular organisms. We find that the ability of the particles to follow
 the field scales with the ratio of the field variation period to the
 particles' orientational relaxation time, which, in turn, is related
 to the particle self-propulsion power and the energy dissipation rate. The
 collective behaviour of the particles due to aligning interactions
 manifests itself at low frequencies via increased persistence of the swarm
 motion when compared with motion of an individual. By contrast, at high
 field frequencies, the active group fails to develop the alignment and
 tends to behave like a set of independent individuals even in the presence
 of interactions. We also report on asymptotic laws for the hysteretic
 dynamics of active particles, which resemble those in magnetic systems.
 The generality of the assumptions in the underlying model suggests that
 the observed laws might apply to a variety of dynamic phenomena from the
 motion of synthetic active particles to crowd or opinion dynamics.
description: experimental_dataPlease see README.txt file.simulation_data_part1Please see README.txt file.simulation_data_part2Please see README.txt file.
DOI: 10.5061/dryad.nb115
title: Data from: Using citizen science monitoring data in species distribution models to inform isotopic assignment of migratory connectivity in wetland birds

description: Stable isotopes have been used to estimate migratory connectivity in many
 species. Estimates are often greatly improved when coupled with species
 distribution models (SDMs), which temper estimates in relation to
 occurrence. SDMs can be constructed using from point locality data from a
 variety of sources including extensive monitoring data typically collected
 by citizen scientists. However, one potential issue with SDM is that these
 data oven have sampling bias. To avoid this potential bias, an approach
 using SDMs based on marsh bird monitoring program data collected by
 citizen scientists and other participants following protocols specifically
 designed to maximize detections of species of interest at locations
 representative of the species range. We then used the SDMs to refine
 isotopic assignments of breeding areas of autumn-migrating and wintering
 Sora (Porzana carolina), Virginia Rails (Rallus limicola), and Yellow
 Rails (Coturnicops noveboracensis) based on feathers collected from
 individuals caught at various locations in the United States from
 Minnesota south to Louisiana and South Carolina. Sora were assigned to an
 area that included much of the western U.S. and prairie Canada, covering
 parts of the Pacific, Central, and Mississippi Flyways. Yellow Rails were
 assigned to a broad area along Hudson and James Bay in northern Manitoba
 and Ontario, as well as smaller parts of Quebec, Minnesota, Wisconsin, and
 Michigan, including parts of the Mississippi and Atlantic Flyways.
 Virginia Rails were from several discrete areas, including parts of
 Colorado, New Mexico, the central valley of California, and southern
 Saskatchewan and Manitoba in the Pacific and Central Flyways. Our study
 demonstrates extensive data from organized citizen science monitoring
 programs are especially useful for improving isotopic assignments of
 migratory connectivity in birds, which can ultimately lead to better
 informed management decisions and conservation actions.
description: SDM Variables Part
 1part
 1 of the input files for SDM creation.sdm_variables_1.zipSDM Variables Part 2part 2 of the input files for SDM creation.sdm_variables_2.zipSDM Variables Part 3part 3 of the input files for SDM creation.sdm_variables_3.zipSora mrange filesZip file of the Sora mrange filess_mrange.zipVirginia Rail mrange filesVirginia Rail mrange filesvira_mrange.zipYellow Rail mrange filesYellow Rail mrange filesy_mrange.zipData Filesinput files for monitoring data, stable isotope data, maping inputs for figures and sdm models saved in .Rdata files.data_files.zipIntermediate FilesIntermediate Files from the data cleaning, SDM and assignment process.intermediate_files.zipShapefilesShapefiles for each speciesshapefiles.zipscriptsR scripts to create all figures, tables, data cleaning, SDM creation and assignment
DOI: 10.5061/dryad.mr3g6
title: Data from: Assessing approaches for inferring species trees from multi-copy genes

description: With the availability of genomic sequence data, there is increasing
 interest in using genes with a possible history of duplication and loss
 for species tree inference. Here we assess the performance of both
 non-probabilistic and probabilistic species tree inference approaches
 using gene duplication and loss and coalescence simulations. We evaluated
 the performance of gene tree parsimony (GTP) based on duplication
 (Only-dup), duplication and loss (Dup-loss), and deep coalescence (Deep-c)
 costs, the NJst distance method, the MulRF supertree method, and PHYLDOG,
 which jointly estimates gene trees and species tree using a hierarchical
 probabilistic model. We examined the effects of gene tree and species
 sampling, gene tree error, and duplication and loss rates on the accuracy
 of phylogenetic estimates. In the 10-taxon duplication and loss simulation
 experiments, MulRF is more accurate than the other methods when the
 duplication and loss rates are low, and Dup-loss is generally the most
 accurate when the duplication and loss rates are high. PHYLDOG performs
 well in 10-taxon duplication and loss simulations, but its run time is
 prohibitively long on larger data sets. In the larger duplication and loss
 simulation experiments, MulRF outperforms all other methods in experiments
 with at most 100 taxa; however, in the larger simulation, Dup-loss
 generally performs best. In all duplication and loss simulation
 experiments with more than 10 taxa, all methods perform better with more
 gene trees and fewer missing sequences, and they are all affected by gene
 tree error. Our results also highlight high levels of error in estimates
 of duplications and losses from GTP methods and demonstrate the usefulness
 of methods based on generic tree distances for large analyses.
description: Simulated-biological-datasetsSimulatedData.zipcoalescenceSIMCoalescence based simulated data setsAppendix-1
DOI: 10.5061/dryad.635ds
title: Data from: Genetic mapping of millions of SNPs in safflower (Carthamus tinctorius L.) via whole-genome resequencing

description: Accurate assembly of complete genomes is facilitated by very high density
 genetic maps. We performed low-coverage, whole-genome shotgun sequencing
 on 96 F6 recombinant inbred lines (RILs) of a cross between safflower
 (Carthamus tinctorius L.) and its wild progenitor (C. palaestinus Eig). We
 also produced a draft genome assembly of C. tinctorius covering 866
 million bp (∼two-thirds) of the expected 1.35 Gbp genome after sequencing
 a single, short insert library to ∼21 × depth. Sequence reads from the
 RILs were mapped to this genome assembly to facilitate SNP identification,
 and the resulting polymorphisms were used to construct a genetic map. The
 resulting map included 2,008,196 genetically located SNPs in 1178 unique
 positions. A total of 57,270 scaffolds, each containing five or more
 mapped SNPs, were anchored to the map. This resulted in the assignment of
 sequence covering 14% of the expected genome length to a genetic position.
 Comparison of this safflower map to genetic maps of sunflower and lettuce
 revealed numerous chromosomal rearrangements, and the resulting patterns
 were consistent with a whole-genome duplication event in the lineage
 leading to sunflower. This sequence-based genetic map provides a powerful
 tool for the assembly of a low-cost draft genome of safflower, and the
 same general approach is expected to work for other species.
description: Supplemental File
 2Fasta file for Safflower
 draft genomeSupplemental File
 4Genetic Map File of
 Recombination BinsSupplemental File
 5Genetic map file of
 consensus genotypes for each contig.Supplemental File
 6Raw
 Data file of genotypes for each SNP.
DOI: 10.5061/dryad.qf916
title: Data from: Substantial differences in bias between single-digest and double-digest RAD-seq libraries: a case study

description: The trade‐offs of using single‐digest vs. double‐digest restriction
 site‐associated DNA sequencing (RAD‐seq) protocols have been widely
 discussed. However, no direct empirical comparisons of the two methods
 have been conducted. Here, we sampled a single population of Gulf pipefish
 (Syngnathus scovelli) and genotyped 444 individuals using RAD‐seq. Sixty
 individuals were subjected to single‐digest RAD‐seq (sdRAD‐seq), and the
 remaining 384 individuals were genotyped using a double‐digest RAD‐seq
 (ddRAD‐seq) protocol. We analysed the resulting Illumina sequencing data
 and compared the two genotyping methods when reads were analysed either
 together or separately. Coverage statistics, observed heterozygosity, and
 allele frequencies differed significantly between the two protocols, as
 did the results of selection components analysis. We also performed an in
 silico digestion of the Gulf pipefish genome and modelled five major
 sources of bias: PCR duplicates, polymorphic restriction sites, shearing
 bias, asymmetric sampling (i.e., genotyping fewer individuals with
 sdRAD‐seq than with ddRAD‐seq) and higher major allele frequencies. This
 combination of approaches allowed us to determine that polymorphic
 restriction sites, an asymmetric sampling scheme, mean allele frequencies
 and to some extent PCR duplicates all contribute to different estimates of
 allele frequencies between samples genotyped using sdRAD‐seq versus
 ddRAD‐seq. Our finding that sdRAD‐seq and ddRAD‐seq can result in
 different allele frequencies has implications for comparisons across
 studies and techniques that endeavour to identify genomewide signatures of
 evolutionary processes in natural populations.
description: sdRADseq vcf
 subsetThis is a vcf file
 containing the individuals genotyped using sdRADseq, analyzed separately.
 Only the pruned set of loci used in the analysis are contained in this
 file.orad.sub.vcfddRADseq vcf subsetA vcf file containing the individuals genotyped using ddRADseq, analyzed separately. This file only contains the pruned subset of loci used in the analyses.drad.sub.vcfBoth sdRADseq and ddRADseq vcf subsetA vcf file containing all individuals, both sdRADseq and ddRADseq, when analyzed together using stacks. This file only contains the pruned subset of loci used in the analysis.both.sub.vcfin silico digest raw dataA compressed file containing all of the raw output from the in silico digestions using different sources of error.insilico_digest_raw.tar.gzBoth sdRADseq and ddRADseq from samtools vcfVariant Call File from the samtools analysis on 60 ddRAD-seq individuals and 60 sdRAD-seq individuals analyzed together.sta.subset.recode.vcfddRADseq from samtools vcfvcf file from the samtools analysis of 60 ddRAD-seq individuals.std.subset.recode.vcfsdRADseq from samtools vcfvcf file from a samtools analysis of the 60 sdRAD-seq individuals.sto.subset.recode.vcf