cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j059v
title: Data from: Genomic survey provides insights on the evolutionary changes during invasive European expansion of the mosquitofish (Gambusia holbrooki)

description: Biological invasions rank among the main global threats for biodiversity.
 The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100
 world worst invasive species due to its high adaptation capability to new
 environments. Using the restriction-site-associated DNA tags (RADtags),
 introduced European locations were compared against native US mosquitofish
 populations to analyse genomic changes that occurred during invasive
 process of European locations. After filtering, 7724 RADtags containing
 only one SNP were retained for population studies. Comparative genomics
 indicated that 186 of these RADtags matched sequences in the transcriptome
 of Xyphophorus maculatus, the most closely related genome available.
 Genomic analyses showed that invasive populations show high reductions in
 diversity. Further, analyses of population structuring based on these data
 are concordant with previous analyses based on microsatellites. It is
 concluded that during the invasion process genetic drift was the main
 evolutionary force affecting patterns of diversity and population
 structure. While recognizing that positive selection could be masked by
 the strong drift during founder events, adaptive processes were evidenced
 in a reduced number of RADtags (&lt;2%), with only one of these in a
 putative coding region. Surprisingly, balancing selection was detected in
 several coding RADtags, suggesting that the preservation of polymorphism
 in specific genes could be more important than the average population
 diversity for the population maintenance at any location, particularly for
 the survival of introduced populations.
description: Description of the files
 deposited in Dryad Vera et alDescription of the files
 deposited in Dryad Vera et al for the mansucript "Genomic survey
 provides insights on the evolutionary changes during invasive European
 expansion of the mosquitofish (Gambusia
 holbrooki)"Description_of_files
 _deposited_Dryad_Vera_et_al.txtAll1GambGenepop input file created by populations including all the markers used in the studyADGambGenepop input file created by Populations. Only markers included in Anonymous Database (AD).GDGambGenepop input file created by Populations. Only markers included in Associated-to-Genes Database (GD).BLAST90_mRNABLASTN output file for the VM43 RADtags matching against the Xyphophorus maculatus mRNA sequences retrieved from GenBank using a word size of 90(BLAST90_mRNA.txt).X_mac_mRNAX_mac_mRNA.fasta: Fasta file including the Xyphophorus maculatus mRNA sequences retrieved from Ensembl (23,236 sequences) used for BLASTN analyses.BayeScanGambPRJNA301984Link out to NCBI PRJNA301984. Gambusia holbrooki raw sequence reads. 93 sequence files (.bam files. One file per analysed individual. Each individual is identified with a number and the belonging population code shown on Table 1)
DOI: 10.5061/dryad.fr684
title: Data from: Sound attenuation in the ear of domestic chickens (Gallus gallus domesticus) as a result of beak opening

description: Because the quadrate and the eardrum are connected, the hypothesis was
 tested that birds attenuate the transmission of sound through their ears
 by opening the bill, which potentially serves as an additional protective
 mechanism for self-generated vocalizations. In domestic chickens, it was
 examined if a difference exists between hens and roosters, given the
 difference in vocalization capacity between the sexes. To test the
 hypothesis, vibrations of the columellar footplate were measured ex vivo
 with laser Doppler vibrometry (LDV) for closed and maximally opened beak
 conditions, with sounds introduced at the ear canal. The average
 attenuation was 3.5 dB in roosters and only 0.5 dB in hens. To demonstrate
 the importance of a putative protective mechanism, audio recordings were
 performed of a crowing rooster. Sound pressures levels of 133.5 dB were
 recorded near the ears. The frequency content of the vocalizations was in
 accordance with the range of highest hearing sensitivity in chickens. The
 results indicate a small but significant difference in sound attenuation
 between hens and roosters. However, the amount of attenuation as measured
 in the experiments on both hens and roosters is small and will provide
 little effective protection in addition to other mechanisms such as
 stapedius muscle activity.
description: Muyshondt et al. - Data
 and codeThe file contains the
 Matlab data and code belonging to the manuscript entitled "Sound
 attenuation in the ear of domestic chickens (Gallus gallus domesticus) as
 a result of beak opening" by Muyshondt et al.
DOI: 10.15468/dl.2b9cjc
title: Occurrence Download

description: A dataset containing 3669 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((7.3374 47.19951,14.05884 47.19951,14.05884 49.91333,7.3374 49.91333,7.3374 47.19951))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vipera berus"
 ]
}

 The dataset includes 3669 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000390-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1q994
title: Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes

description: Divergence-time estimation based on molecular phylogenies and the fossil
 record has provided insights into fundamental questions of evolutionary
 biology. In Bayesian node dating, phylogenies are commonly time calibrated
 through the specification of calibration densities on nodes representing
 clades with known fossil occurrences. Unfortunately, the optimal shape of
 these calibration densities is usually unknown and they are therefore
 often chosen arbitrarily, which directly impacts the reliability of the
 resulting age estimates. As possible solutions to this problem, two
 non-exclusive alternative approaches have recently been developed, the
 “fossilized birth-death” model and “total-evidence dating”. While these
 approaches have been shown to perform well under certain conditions, they
 require including all (or a random subset) of the fossils of each clade in
 the analysis, rather than just relying on the oldest fossils of clades. In
 addition, both approaches assume that fossil records of different clades
 in the phylogeny are all the product of the same underlying fossil
 sampling rate, even though this rate has been shown to differ strongly
 between higher-level taxa. We here develop a flexible new approach to
 Bayesian age estimation that combines advantages of node dating and the
 fossilized birth-death model. In our new approach, calibration densities
 are defined on the basis of first fossil occurrences and sampling rate
 estimates that can be specified separately for all clades. We verify our
 approach with a large number of simulated datasets, and compare its
 performance to that of the fossilized birth-death model. We find that our
 approach produces reliable age estimates that are robust to model
 violation, on par with the fossilized birth-death model. By applying our
 approach to a large dataset including sequence data from over 1000 species
 of teleost fishes as well as 147 carefully selected fossil constraints, we
 recover a timeline of teleost diversification that is incompatible with
 previously assumed vicariant divergences of freshwater fishes. Our results
 instead provide strong evidence for trans-oceanic dispersal of cichlids
 and other groups of teleost fishes.
description: Supplementary
 MaterialThis file includes
 Supplementary Texts S1-S2, Supplementary Figures S1-S8, Supplementary
 Tables S1, S3-S15, and Supplementary References.matschiner_et_al_sm.pdfSupplementary Table S2This file includes Supplementary Table S2.accessions.xlsxTime-Calibrated Teleost PhylogenyTeleost phylogeny of Figure 4 and Supplementary Figure S7 in Nexus format.teleost_phylogeny.treSupplementary Data S1This file includes Supplementary Data S1.xmls.tgz
DOI: 10.5061/dryad.qb6b5
title: Data from: Inferring the age of a fixed beneficial allele

description: Estimating the age and strength of beneficial alleles is central to
 understanding how adaptation proceeds in response to changing
 environmental conditions. Several haplotype-based estimators exist for
 inferring the age of segregating beneficial mutations. Here, we develop an
 approximate Bayesian based approach that rather estimates these parameters
 for fixed beneficial mutations in single populations. We integrate a range
 of existing diversity, site frequency spectrum, haplotype and linkage
 disequilibrium based summary statistics. We show that for strong selective
 sweeps on de novo mutations the method can estimate allele age and
 selection strength even in non-equilibrium demographic scenarios. We
 extend our approach to models of selection on standing variation, and
 co-infer the frequency at which selection began to act upon the mutation.
 Finally, we apply our method to estimate the age and selection strength of
 a previously identified mutation underpinning cryptic color adaptation in
 a wild deer mouse population, and compare our findings with previously
 published estimates as well as with geological data pertaining to the
 presumed shift in selective pressure.
description: ABC estimator -
 equilibrium populationR script for running the
 ABC estimator assuming an equilibrium populationABCinference_eqm.RABC estimator - non equilibrium populationR script for running the ABC estimator assuming a non-equilibrium populationABCinference_noneqm.Requilibrium_mouse_simsText file containing 500,000 simulations for the mouse data assuming an equilibrium populationplssummary_mice_eqmText file containing the required information for calculating PLS components for the mouse data assuming an equilibrium populationnon_equilibrium_mouse_simsText file containing 500,000 simulations for the mouse data assuming a non-equilibrium populationplssummary_mice_non_eqmText file containing the required information for calculating PLS components for the mouse data assuming a non-equilibrium populationmousedata80kbText file containing SNP information for the mouse data in msms format (80kb)pythonscript1First python script required for running the ABC estimator in non-equilibrium populationspythonscript2Second python script required for running the ABC estimator in non-equilibrium populations
DOI: 10.5061/dryad.pm7mt
title: Data from: Genome-Wide Analyses Suggest Mechanisms Involving Early B-Cell Development in Canine IgA Deficiency

description: Immunoglobulin A deficiency (IgAD) is the most common primary immune
 deficiency disorder in both humans and dogs, characterized by recurrent
 mucosal tract infections and a predisposition for allergic and other
 immune mediated diseases. In several dog breeds, low IgA levels have been
 observed at a high frequency and with a clinical resemblance to human
 IgAD. In this study, we used genome-wide association studies (GWAS) to
 identify genomic regions associated with low IgA levels in dogs as a
 comparative model for human IgAD. We used a novel percentile
 groups-approach to establish breed-specific cut-offs and to perform
 analyses in a close to continuous manner. GWAS performed in four breeds
 prone to low IgA levels (German shepherd, Golden retriever, Labrador
 retriever and Shar-Pei) identified 35 genomic loci suggestively associated
 (p &lt;0.0005) to IgA levels. In German shepherd, three genomic
 regions (candidate genes include KIRREL3 and SERPINA9) were genome-wide
 significantly associated (p &lt;0.0002) with IgA levels. A ~20kb long
 haplotype on CFA28, significantly associated (p = 0.0005) to IgA levels in
 Shar-Pei, was positioned within the first intron of the gene SLIT1. Both
 KIRREL3 and SLIT1 are highly expressed in the central nervous system and
 in bone marrow and are potentially important during B-cell development.
 SERPINA9 expression is restricted to B-cells and peaks at the time-point
 when B-cells proliferate into antibody-producing plasma cells. The
 suggestively associated regions were enriched for genes in Gene Ontology
 gene sets involving inflammation and early immune cell development.
description: whole-genome SNP data
 from four dog breeds.ped, .map and
 pheno.xlsx files from all dogs included in the GWASArchive.zip
DOI: 10.5061/dryad.26605
title: Data from: Temporal variation in habitat selection breaks the catch-22 of spatially contrasting predation risk from multiple predators

description: Predator avoidance depends on prey being able to discern how risk varies
 in space and time, but this is made considerably more complicated if risk
 is simultaneously present from multiple predators. This is the situation
 for an increasing number of mammalian prey species, as large carnivores
 recover or are reintroduced in ecosystems on several continents. Roe deer
 Capreolus capreolus in southern Norway illustrate a case in which prey
 face two predators with contrasting patterns of predation risk. They face
 a catch-22 situation: spatially avoiding the risk from one predator (lynx
 Lynx lynx in dense habitat) implies exposure to the other (hunters in open
 habitat). Using GPS-data from 29 roe deer, we tested for daily and
 seasonal variation in roe deer selection for habitat with respect to the
 habitats' year-round average risk level. Generally, roe deer altered
 their habitat selection between night and day in a pattern consistent with
 being able to avoid predicted risk from the nocturnal lynx during night
 and predicted risk from human hunters during day. However, seasonal
 variation in habitat selection only partially corresponded with the
 predicted seasonal variation in risk. Whereas roe deer avoided areas with
 high risk from hunters more strongly during the hunting season than in
 other seasons, there was a lack of selection towards areas and time
 periods lowering the risk of lynx predation during winter. It seems likely
 that the risk of starvation and thermal stress constrain roe deer habitat
 selection during this energetically challenging season with cold
 temperatures, snow cover and limited natural forage. The habitat selection
 pattern of roe deer fits thus only partly with the two contrasting risk
 gradients they face. Adjusting risk-avoidance behavior temporally can be
 an adaptive response in the case of several predators whose predation
 patterns differ in space and time.
description: ROE DEER GPS
 DATACLEANED ROE DEER GPS
 DATA. (tab-separated .txt file). ## no locations during migration ## no
 duplicates ## no first 24 hrs after capture ## positions are not
 subsampled to every 6th hour ## Coordinates in WGS84 UTM32N ## Animals
 collared and data collected by The Norwegian Institute for Nature Research
 (NINA), for more information see
 http://scandlynx.nina.no/roegps.txtRisk map huntersRISK TO ROE DEER OF BEING KILLED BY HUNTER. (Georeferenced tiff raster with projection WGS84 UTM32N) ## Study area Hallingdal in Southern Norway ##Map units are "standardized risk"huntZ_131001.tifRisk map lynxRISK TO ROE DEER OF BEING KILLED BY LYNX. (Georeferenced tiff raster with projection WGS84 UTM32N) ## Study area Hallingdal in Southern Norway ##Map units are "standardized risk"lynxZ_131001.tif
DOI: 10.5061/dryad.6ht2c
title: Data from: Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates

description: System-level metabolic network models enable the computation of growth and
 metabolic phenotypes from an organism’s genome. In particular, flux
 balance approaches have been used to estimate the contribution of
 individual metabolic genes to organismal fitness, offering the opportunity
 to test whether such contributions carry information about the
 evolutionary pressure on the corresponding genes. Previous failure to
 identify the expected negative correlation between such computed gene-loss
 cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae
 has been ascribed to a real biological gap between a gene’s fitness
 contribution to an organism “here and now” and the same gene’s historical
 importance as evidenced by its accumulated mutations over millions of
 years of evolution. Here we show that this negative correlation does
 exist, and can be exposed by revisiting a broadly employed assumption of
 flux balance models. In particular, we introduce a new metric that we call
 “function-loss cost”, which estimates the cost of a gene loss event as the
 total potential functional impairment caused by that loss. This new metric
 displays significant negative correlation with evolutionary rate, across
 several thousand minimal environments. We demonstrate that the improvement
 gained using function-loss cost over gene-loss cost is explained by
 replacing the base assumption that isoenzymes provide unlimited capacity
 for backup with the assumption that isoenzymes are completely
 non-redundant. We further show that this change of the assumption
 regarding isoenzymes increases the recall of epistatic interactions
 predicted by the flux balance model at the cost of a reduction in the
 precision of the predictions. In addition to suggesting that the
 gene-to-reaction mapping in genome-scale flux balance models should be
 used with caution, our analysis provides new evidence that evolutionary
 gene importance captures much more than strict essentiality.
description: isoenzymes_flux_balance.tarAll data and scripts to produce the figures and numbers in the paper.
DOI: 10.5061/dryad.1748225
title: Data from: Phylogeography of a widespread eastern North American shrub, Viburnum lantanoides

description: Premise of the Study: There have been relatively few phylogeographic
 studies of eastern North American plants, especially of animal‐dispersed
 shrubby species, and this leaves a significant gap in our understanding of
 how such species were affected by glacial events. Here, we analyzed the
 phylogeography of the widespread understory shrub Viburnum lantanoides.
 Methods: We generated RADseq data and paleoclimatic species distribution
 models (SDMs) to identify the locations of refugia where V. lantanoides
 may have survived the Last Glacial Maximum (LGM) and how its range
 expanded as glaciers receded. Key Results: Genetic diversity falls off
 with increasing latitude and longitude, indicating that range expansion
 likely occurred via serial founder events from southern source
 populations. Samples from the southern Appalachians form a grade, while
 those from the north form a clade, suggesting that a single genetic
 lineage recolonized the north. SDMs indicate that V. lantanoides probably
 survived the LGM in refugia on the mid‐Atlantic Coastal Plain and/or the
 interior Gulf Coastal Plain. Conclusions: Our analyses indicate that V.
 lantanoides survived the LGM in refugia south of the glacier but north of
 the extensive refugium along the Gulf Coast. Following the LGM, a single
 population expanded northward along the Appalachian Mountains and
 eventually into eastern Canada. The patterns observed here suggest that
 range expansion occurred in a stepwise manner, similar to postglacial
 dynamics observed in a number of European plant species.
description: Data used to generate
 distribution models in maxent This file contains the
 GPS coordinates of populations of V. lantanoides that were observed by the
 author (B. Park) during collecting expeditions. These data were used to
 generate species distribution models in maxent. V_LANTANOIDES_MAXENT.csv Results from population genetic analyses This file contains heterozygosity estimates as well as ancestry coefficients estimated using sNMF, tess3R, and DAPC. It also contains PCA scores for PC axes 1, 2, and 3 estimated in LEA. V_LANTANOIDES_HETEROZYGOSITY_CLUSTERING.csv VCF file vcf.gz file of SNPs called using the iPyrad pipeline in 178 samples of *V lantanoides* and 1 sample each of *V. furcatum* and *sympodiale*. base_d6_c88.vcf.gz PRJNA507304 Demultiplexed sequence data is available at the NCBI SRA under SRP170982, or access via BioProject accession PRJNA507304.
DOI: 10.5061/dryad.j0q5m
title: Data from: Intestinal microbiota is influenced by gender and body mass index

description: Intestinal microbiota changes are associated with the development of
 obesity. However, studies in humans have generated conflicting results due
 to high inter-individual heterogeneity in terms of diet, age, and hormonal
 factors, and the largely unexplored influence of gender. In this work, we
 aimed to identify differential gut microbiota signatures associated with
 obesity, as a function of gender and changes in body mass index (BMI).
 Differences in the bacterial community structure were analyzed by 16S
 sequencing in 39 men and 36 post-menopausal women, who had similar dietary
 background, matched by age and stratified according to the BMI. We
 observed that the abundance of the Bacteroides genus was lower in men than
 in women (P&lt;0.001, Q = 0.002) when BMI was &gt; 33. In fact,
 the abundance of this genus decreased in men with an increase in BMI
 (P&lt;0.001, Q&lt;0.001). However, in women, it remained unchanged
 within the different ranges of BMI. We observed a higher presence of
 Veillonella (84.6% vs. 47.2%; X2 test P = 0.001, Q = 0.019) and
 Methanobrevibacter genera (84.6% vs. 47.2%; X2 test P = 0.002, Q = 0.026)
 in fecal samples in men compared to women. We also observed that the
 abundance of Bilophila was lower in men compared to women regardless of
 BMI (P = 0.002, Q = 0.041). Additionally, after correcting for age and
 sex, 66 bacterial taxa at the genus level were found to be associated with
 BMI and plasma lipids. Microbiota explained at P = 0.001, 31.17% variation
 in BMI, 29.04% in triglycerides, 33.70% in high-density lipoproteins,
 46.86% in low-density lipoproteins, and 28.55% in total cholesterol. Our
 results suggest that gut microbiota may differ between men and women, and
 that these differences may be influenced by the grade of obesity. The
 divergence in gut microbiota observed between men and women might have a
 dominant role in the definition of gender differences in the prevalence of
 metabolic and intestinal inflammatory diseases.
description: Microbiota sequences
 dataThis file contains the
 microbiota sequences data from "Intestinal microbiota is influenced
 by gender and body mass index" study.sequences.time_0.R1.fastq.zip