cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02bf1
title: Data from: 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador

description: Background: Rhodnius ecuadoriensis is the main triatomine vector of Chagas
 disease, American trypanosomiasis, in Southern Ecuador and Northern Peru.
 Genomic approaches and next generation sequencing technologies have become
 powerful tools for investigating population diversity and structure which
 is a key consideration for vector control. Here we assess the
 effectiveness of three different 2b restriction site-associated DNA
 (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient
 genomic resolution to tease apart microevolutionary processes and
 undertake some pilot population genomic analyses. Methodology/Principal
 findings: The 2b-RAD protocol was carried out in-house at a
 non-specialized laboratory using 20 R. ecuadoriensis adults collected from
 the central coast and southern Andean region of Ecuador, from June 2006 to
 July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq
 instrument and analyzed with the STACKS de novo pipeline for loci assembly
 and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population
 genomic analyses (global AMOVA and Bayesian clustering) were implemented.
 Our results showed that the 2b-RAD genotyping protocol is effective for R.
 ecuadoriensis and likely for other triatomine species. However, only BcgI
 and CspCI restriction enzymes provided a number of markers suitable for
 population genomic analysis at the read depth we generated. Our
 preliminary genomic analyses detected a signal of genetic structuring
 across the study area. Conclusions/Significance: Our findings suggest that
 2b-RAD genotyping is both a cost effective and methodologically simple
 approach for generating high resolution genomic data for Chagas disease
 vectors with the power to distinguish between different vector populations
 at epidemiologically relevant scales. As such, 2b-RAD represents a
 powerful tool in the hands of medical entomologists with limited access to
 specialized molecular biological equipment.
description: 2b-RAD raw data of
 Rhodnius ecuadoriensisSequencing A) Clustering
 was done by ‘onboard clustering’ and samples were sequenced on MiSeq (MSC
 2.5.0.5/RTA 1.18.54) with a 1x51 setup using ‘Version2’ chemistry. The Bcl
 to FastQ conversion was performed using bcl2fastq-1.8.4 from the CASAVA
 software suite. The quality scale used is Sanger / phred33 / Illumina
 1.8+.2bRADseq_Recuadoriensis.zip
DOI: 10.34740/kaggle/dsv/14630420
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.n69t3
title: Data from: Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems

description: Sex chromosomes have evolved many times in animals and studying these
 replicate evolutionary “experiments” can help broaden our understanding of
 the general forces driving the origin and evolution of sex chromosomes.
 However this plan of study has been hindered by the inability to identify
 the sex chromosome systems in the large number of species with cryptic,
 homomorphic sex chromosomes. Restriction site-associated DNA sequencing
 (RAD-seq) is a critical enabling technology that can identify the sex
 chromosome systems in many species where traditional cytogenetic methods
 have failed. Using newly generated RAD-seq data from twelve gecko species,
 along with data from the literature, we reinterpret the evolution of
 sex-determining systems in lizards and snakes and test the hypothesis that
 sex chromosomes can routinely act as evolutionary traps. We uncovered
 between 17 and 25 transitions among gecko sex-determining systems. This is
 approximately ½ to ⅔ of the total number of transitions observed among all
 lizards and snakes. We find support for the hypothesis that sex chromosome
 systems can readily become trap-like and show that adding even a small
 number of species from understudied clades can greatly enhance hypothesis
 testing in a model-based phylogenetic framework. RAD-seq will undoubtedly
 prove useful in evaluating other species for male or female heterogamety,
 particularly the majority of fish, amphibian, and reptile species that
 lack visibly heteromorphic sex chromosomes, and will significantly
 accelerate the pace of biological discovery.
description: hemidactylus_frenatus.4.2RADtools output for Hemidactylus frenatus datahemidactylus_turcicus.4.2RADtools output for Hemidactylus turcicus datathecadactylus.4.2RADtools output for Thecadactylus rapicauda dataaristelliger_expectatus_1.4.2RADtools output for Aristelliger expectatus datahemidactylus_mabouia_TT.4.2RADtools output for Hemidactylus mabouia dataheteronotia_1.4.2RADtools output for Heteronotia binoei datasphaero_nicholsi.4.2RADtools output for Sphaerodactylus nicholsi datasphaero_mac_vc.4.2RADtools output for Sphaerodactylus macrolepis datagehyra_mutilata.4.2RADtools output for Gehyra mutilata datacorrelophus_rev14.4.2RADtools output for Correlophus ciliatus datalialis.4.2.ALLRADtools output for Lialis burtonis datachristinus.4.2RADtools output for Christinus marmoratus datarsw.pyPython script to identify sex-specific markers from RADtools outputsquamates_TSD_skinksPruned squamate phylogeny that includes skink species with putative TSDsquamates_NoTSD_skinksPruned squamate phylogeny that excludes skink species with putative TSDsquamates_TSD_skinks_dataSquamate sex determination data that includes skink species with putative TSDsquamates_NoTSD_skinks_dataSquamate sex determination data that excludes skink species with putative TSD
DOI: 10.5061/dryad.hs5jt80
title: Data from: Parallel evolution of gene classes, but not genes: evidence from Hawai’ian honeycreeper populations exposed to avian malaria

description: Adaptation in nature is ubiquitous, yet characterizing its genomic basis
 is difficult because population demographics cause correlations with
 non-adaptive loci. Introduction events provide opportunities to observe
 adaptation over known spatial and temporal scales, facilitating the
 identification of genes involved in adaptation. The pathogen causing avian
 malaria, Plasmodium relictum, was introduced to Hawai’i in the 1930s and
 elicited extinctions and precipitous population declines in native
 honeycreepers. After a sharp initial population decline, the Hawai’i
 ‘amakihi (Chlorodrepanis virens) has evolved tolerance to the parasite at
 low elevations where P. relictum exists, and can sustain infection without
 major fitness consequences. High-elevation, unexposed populations of
 ‘amakihi display little to no tolerance. To explore the genomic basis of
 adaptation to P. relictum in low-elevation ‘amakihi, we genotyped 125
 ‘amakihi from the island of Hawai’i via hybridization capture to 40,000
 oligonucleotide baits containing SNPs, and used the reference ‘amakihi
 genome to identify genes potentially under selection from malaria. We
 tested for outlier loci between low- and high-elevation population pairs
 and identified loci with signatures of selection within low-elevation
 populations. In some cases, genes commonly involved in the immune response
 (e.g., major histocompatibility complex) were associated with malaria
 presence in the population. We also detected several novel candidate loci
 that may be implicated in surviving malaria infection (e.g., beta
 defensin, glycoproteins, and interleukin-related genes). Our results
 suggest that rapid adaptation to pathogens may occur through changes in
 different immune genes, but in the same classes of genes, across
 populations.
description: amakihiN144R1R2_bammerge_081615.vcf
DOI: 10.5061/dryad.f61v3tj
title: Data from: Circadian mood variations in Twitter content

description: Background: Circadian regulation of sleep, cognition, and metabolic state
 is driven by a central clock, which is in turn entrained by environmental
 signals. Understanding the circadian regulation of mood, which is vital
 for coping with day-to-day needs, requires large datasets and has
 classically utilised subjective reporting. Methods: In this study, we use
 a massive dataset of over 800 million Twitter messages collected over 4
 years in the United Kingdom. We extract robust signals of the changes that
 happened during the course of the day in the collective expression of
 emotions and fatigue. We use methods of statistical analysis and Fourier
 analysis to identify periodic structures, extrema, change-points, and
 compare the stability of these events across seasons and weekends.
 Results: We reveal strong, but different, circadian patterns for positive
 and negative moods. The cycles of fatigue and anger appear remarkably
 stable across seasons and weekend/weekday boundaries. Positive mood and
 sadness interact more in response to these changing conditions. Anger and,
 to a lower extent, fatigue show a pattern that inversely mirrors the known
 circadian variation of plasma cortisol concentrations. Most quantities
 show a strong inflexion in the morning. Conclusion: Since circadian rhythm
 and sleep disorders have been reported across the whole spectrum of mood
 disorders, we suggest that analysis of social media could provide a
 valuable resource to the understanding of mental disorder.
description: Twitter Hourly
 WordsTime series of hourly
 frequencies for 9,096 psychometric words sampled between 1st January 2010
 and 31st October 2014 in a represensative set of Twitter Content across
 the United Kingdom.data_CircadianMoodVariationsInTwitterContent.zip
DOI: 10.5061/dryad.jc247v3
title: Data from: ConfeitoGUI: a toolkit for size-sensitive community detection from a correlation network

description: Analysis of the large amounts of data accumulated in public databanks can
 facilitate a more comprehensive understanding of molecular biological
 processes. Community detection from molecular biological data is paramount
 in characterizing evolutionary and functional traits of organisms based on
 gene homology and co-expression, respectively. Although there are common
 tools to detect local communities from a large network, no toolkit exists
 for detecting communities that include an element of interest based on
 size sensitivity, i.e., functionality to obtain local communities with
 preferred sizes. Herein, we present the ConfeitoGUI toolkit for detecting
 local communities from a correlation network involving size sensitivity.
 We compared the toolkit with other common tools for detection in
 reconstructing communities of microarray experiments of mice. In the
 results, ConfeitoGUI was observed to be preferable for detecting
 communities whose sizes are similar to those of original communities
 compared to other common tools. By changing simple parameters representing
 sizes for the toolkit, a user can obtain local communities with preferred
 sizes, which is beneficial for further analysis of members belonging to
 the communities.
description: athgxmatArabidopsis thaliana gene expression datasetConfeitoGUI_1.2.0.2
DOI: 10.5061/dryad.t66ns
title: Data from: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster

description: Sequencing of pools of individuals (Pool-Seq) represents a reliable and
 cost-effective approach for estimating genome-wide SNP and transposable
 element insertion frequencies. However, Pool-Seq does not provide direct
 information on haplotypes so that for example obtaining inversion
 frequencies has not been possible until now. Here, we have developed a new
 set of diagnostic marker SNPs for 7 cosmopolitan inversions in Drosophila
 melanogaster that can be used to infer inversion frequencies from Pool-Seq
 data. We applied our novel marker set to Pool-Seq data from an
 experimental evolution study and from North American and Australian
 latitudinal clines. In the experimental evolution data, we find evidence
 that positive selection has driven the frequencies of In(3R)C and In(3R)Mo
 to increase over time. In the clinal data, we confirm the existence of
 frequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North
 America and Australia and detect a previously unknown latitudinal cline
 for In(3R)Mo in North America. The inversion markers developed here
 provide a versatile and robust tool for characterizing inversion
 frequencies and their dynamics in Pool-Seq data from diverse D.
 melanogaster populations.
description: Haplotype Genomes with
 known karyotypes.The ZIP archive contains
 whole chromosome haplotypes in Multi FASTA format, which were
 reconstructed for 15 individuals with known karyotypes. These were
 randomly picked from populations of a selection experiment. See Material
 and Methods for more details.haplotype_genomes_FASTA.zip
DOI: 10.5061/dryad.75nn5
title: Data from: Steady streaming around a cylinder pair

description: The steady streaming motion that appears around a pair of circular
 cylinders placed in a small-amplitude oscillatory flow is considered.
 Attention is focused on the case where the Stokes layer thickness at the
 surface of the cylinders is much smaller than the cylinder radius, and the
 streaming Reynolds number is of order unity or larger. In that case, the
 steady streaming velocity that persists at the edge of the Stokes layer
 can be imposed as a boundary condition to numerically solve the outer
 streaming motion that it drives in the bulk of the fluid. It is
 investigated how the gap width between the cylinders and the streaming
 Reynolds number affect the flow topology. The results are compared against
 experimental observations.
description: Numerical codes and
 experimental data for steady streaming around a cylinder
 pairThis zip file contains
 FreeFem++ codes to solve the steady Navier-Stokes equations subject to a
 prescribed slip velocity at the cylinder walls, obtained from an
 asymptotic expansion, and the experimental data in the form of photographs
 for the experiment with gap width ga=2.Archive.zip
DOI: 10.5061/dryad.73tj5
title: Data from: Evidence of lasting impact of the Deepwater Horizon oil spill on a deep Gulf of Mexico coral community

description: A coral community 11 km southwest of the site of the Deepwater Horizon
 blowout at 1,370 m water depth was discovered 3.5 months after the well
 was capped on 3 November 2010. Gorgonian corals at the site were partially
 covered by a brown flocculent material (floc) that contained hydrocarbons
 fingerprinted to the oil spill. Here we quantify the visible changes to
 the corals at this site during five visits over 17 months by digitizing
 images of individual branches of each colony and categorizing their
 condition. Most of the floc visible in November 2010 was absent from the
 corals by the third visit in March 2011, and there was a decrease in the
 median proportions of the colonies showing obvious signs of impact after
 the first visit. During our second visit in 2010, about six weeks after
 the first, we documented the onset of hydroid colonization (a sign of
 coral deterioration) on impacted coral branches that increased over the
 remainder of the study. Hydroid colonization of impacted portions of coral
 colonies by the last visit in March 2012 correlated positively with the
 proportion of the colony covered by floc during the first two visits in
 late 2010. Similarly, apparent recovery of impacted portions of the coral
 by March 2012 correlated negatively with the proportion of the coral
 covered with floc in late 2010. A notable feature of the impact was its
 patchy nature, both within and among colonies, suggesting that the
 impacting agent was not homogeneously dispersed during initial contact
 with the corals. While the median level of obvious visible impact
 decreased over time, the onset of hydroid colonization and the probability
 of impacts that were not visually obvious suggest that future visits may
 reveal additional deterioration in the condition of these normally
 long-lived corals.
description: Data from: Evidence of
 lasting impact of the Deepwater Horizon oil spill on a deep Gulf of Mexico
 coral communityThis dataset contains
 digital still images (*.jpg, *.png, or *.tif files) of cold-water coral
 colonies at Mississippi Canyon (MC) 294 in the Gulf of Mexico. They are
 organized into folders by the five visits to the site in November and
 December 2010 (2010-11 and 2010-12), March and October 2011 (2011-03 and
 2011-10), and March 2012 (2012-03). Within the folders for each visit,
 each coral is represented by sub-folders with its ID (e.g. A10) which
 contains the actual image file.Hsing_2013.tar.bz2
DOI: 10.5061/dryad.5fh08
title: Data from: Spatiotemporal rank filtering improves image quality compared to frame averaging in 2-photon laser scanning microscopy

description: Live imaging of biological specimens using optical microscopy is limited
 by tradeoffs between spatial and temporal resolution, depth into intact
 samples, and phototoxicity. Two-photon laser scanning microscopy (2P-LSM),
 the gold standard for imaging turbid samples in vivo, has conventionally
 constructed images with sufficient signal-to-noise ratio (SNR) generated
 by sequential raster scans of the focal plane and temporal integration of
 the collected signals. Here, we describe spatiotemporal rank filtering, a
 nonlinear alternative to temporal integration, which makes more efficient
 use of collected photons by selectively reducing noise in 2P-LSM images
 during acquisition. This results in much higher SNR while preserving image
 edges and fine details. Practically, this allows for at least a four fold
 decrease in collection times, a substantial improvement for time-course
 imaging in biological systems.
description: Stack of VPD 450 T cells
 in Lymph node82 Z slices, 30 time
 points, with each time point corresponding to a single raster scan of the
 sample. Created in ImageJVPD 450 T cell 30 frames 82
 Zslices.tifPS-Speck Beads + Signal
 and noise masks1000 frame time series
 of Yellow PS-Speck beads with each frame corresponding to a single raster
 scan with low excitation power; Also, signal and noise mask images
 generated from thresholding a gaussian filtered averaged image of all 1000
 framesBeads
 + masks.zipXCR1 Venus Dendritic
 cell in explanted lymph node60 frame time series of
 XCR1 Venus Dendritic Cell imaged within explanted lymph node using Nikon
 A1R. Each frame corresponds to a single raster scanXCR1Venus.tif
DOI: 10.5061/dryad.2kn1v
title: Data from: Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

description: The evolutionary mechanisms generating the tremendous biodiversity of
 islands have long fascinated evolutionary biologists. Genetic drift and
 divergent selection are predicted to be strong on islands and both could
 drive population divergence and speciation. Alternatively, strong genetic
 drift may preclude adaptation. We conducted a genomic analysis to test the
 roles of genetic drift and divergent selection in causing genetic
 differentiation among populations of the island fox (Urocyon littoralis).
 This species consists of six subspecies, each of which occupies a
 different California Channel Island. Analysis of 5293 SNP loci generated
 using Restriction-site Associated DNA (RAD) sequencing found support for
 genetic drift as the dominant evolutionary mechanism driving population
 divergence among island fox populations. In particular, populations had
 exceptionally low genetic variation, small Ne (range = 2.1–89.7; median =
 19.4), and significant genetic signatures of bottlenecks. Moreover,
 islands with the lowest genetic variation (and, by inference, the
 strongest historical genetic drift) were most genetically differentiated
 from mainland grey foxes, and vice versa, indicating genetic drift drives
 genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of
 loci as high FST outliers, suggesting that despite strong genetic drift,
 divergent selection contributes to population divergence. Patterns of
 similarity among populations based on high FST outliers mirrored patterns
 based on morphology, providing additional evidence that outliers reflect
 adaptive divergence. Extremely low genetic variation and small Ne in some
 island fox populations, particularly on San Nicolas Island, suggest that
 they may be vulnerable to fixation of deleterious alleles, decreased
 fitness and reduced adaptive potential.
description: README.txtMetadata describing the contents of all data files.grays.tar.gzRaw RAD sequencing data in fastq format for mainland gray foxes.smi.tar.gzRaw RAD sequencing data in fastq format for San Miguel Island foxes.sri.tar.gzRaw RAD sequencing data in fastq format for Santa Rosa Island foxes.sci.tar.gzRaw RAD sequencing data in fastq format for Santa Cruz Island foxes.sca.tar.gzRaw RAD sequencing data in fastq format for Santa Catalina Island foxes.scl.tar.gzRaw RAD sequencing data in fastq format for San Clemente Island foxes.sni.tar.gzRaw RAD sequencing data in fastq format for San Nicolas Island foxes.final_contigs.fafasta file of RAD contigsGP_with_grays.txtSNP genotypes for mainland gray foxes and all island fox populations in Genepop input file format.GP_NO_grays.txtSNP genotypes for all island fox populations (gray foxes NOT included) in Genepop input file format.
DOI: 10.15468/dl.73ebxz
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pampatherium mexicanum"
 ]
}

 The dataset includes 43 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000364-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.