cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s571g
title: Data from: ‘True’ null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties, and survey of possible improvements

description: Null alleles are alleles that for various reasons fail to amplify in a PCR
 assay. The presence of null alleles in microsatellite data is known to
 bias the genetic parameter estimates. Thus, efficient detection of null
 alleles is crucial, but the methods available for indirect null allele
 detection return inconsistent results. Here, our aim was to compare
 different methods for null allele detection, to explain their respective
 performance and to provide improvements. We applied several approaches to
 identify the ‘true’ null alleles based on the predictions made by five
 different methods, used either individually or in combination. First, we
 introduced simulated ‘true’ null alleles into 240 population data sets and
 applied the methods to measure their success in detecting the simulated
 null alleles. The single best-performing method was ML-NullFreq_frequency.
 Furthermore, we applied different noise reduction approaches to improve
 the results. For instance, by combining the results of several methods, we
 obtained more reliable results than using a single one. Rule-based
 classification was applied to identify population properties linked to the
 false discovery rate. Rules obtained from the classifier described which
 population genetic estimates and loci characteristics were linked to the
 success of each method. We have shown that by simulating ‘true’ null
 alleles into a population data set, we may define a null allele frequency
 threshold, related to a desired true or false discovery rate. Moreover,
 using such simulated data sets, the expected null allele homozygote
 frequency may be estimated independently of the equilibrium state of the
 population.
description: Populations_with_simulated_null_allelesAs described in our paper, we used two datasets: control and noisy. Each dataset contained 120 populations. In each population there were 100 individuals with 20 loci. Populations were originally simulated using SPAms program as described by Dąbrowski et al. 2014 (Mol Ecol Res, Volume 14, Issue 2, pages 361-373). In each population we simulated randomly two null alleles using NullAlleleGenerator (NAG) tool. Here we provide 240 populations with simulated 'true' null alleles in the noisy and control dataset. There are genotypes of individuals from each population and summary file where you will find in which loci the null alleles were simulated. For more information about simulating null alleles please download our tool NAG where you will find manual with detailed explanation http://www.lcb.uu.se/papers/dabrowski/NullAlleleGenerator.zip
DOI: 10.5061/dryad.bt7t0
title: Data from: Survival of the fattest? Indices of body condition do not predict viability in the brown anole (Anolis sagrei)

description: 1. Measures of body mass and length are commonly used to derive indices of
 condition, which are often assumed to reflect the energetic state of an
 animal and, by extension, to predict its fitness. However, the
 relationship between condition and fitness is rarely quantified, and the
 appropriate method(s) for deriving indices of condition are frequently
 debated. 2. Data from a decade of mark-recapture studies involving over
 4,600 individual lizards (Anolis sagrei) and 41 replicates of selection
 across seven populations were used to test the common assumption that
 condition, as estimated from body mass and length, is a strong predictor
 of adult survival, an important component of fitness. Inferences about
 natural selection were compared between two alternative indices of
 condition: the popular residual index (Ri), and the scaled mass index
 (Mi), which was recently proposed as a more appropriate method. 3. Linear,
 quadratic, and correlational selection gradients obtained using Ri and Mi
 were highly correlated with one another. Relative to variance in selection
 among replicates and to error associated with the estimation of selection
 gradients, variance due to the use of alternative condition indices was
 minor and effectively negligible. 4. Contrary to the intuitive prediction
 that individuals in better condition should exhibit higher survival, there
 was no evidence for strong or consistent linear (directional) selection
 for higher condition indices in either males or females. Significant
 quadratic (stabilizing or disruptive) selection on condition was similarly
 rare in both sexes. Correlational selection favored combinations of large
 size and high condition in males, but not females. 5. Collectively, these
 results indicate that inferences about natural selection may be robust to
 the choice between indices of condition, but that indices of condition can
 be unreliable as proxies for fitness, particularly when relationships
 between fitness components and condition are contingent upon interactions
 with other traits.
description: Selection analysis for
 female Anolis sagrei lizardsIndividual phenotypes
 (snout-vent length, body mass, and condition indices) and fitness measures
 (survival, relative fitness) for 2338 female Anolis sagrei lizards,
 indexed by population and year of study.Selection analysis for female
 Anolis sagrei.xlsSelection analysis for
 male Anolis sagrei lizardsIndividual phenotypes
 (snout-vent length, body mass, and condition indices) and fitness measures
 (survival, relative fitness) for 2258 male Anolis sagrei lizards, indexed
 by population and year of study.Selection analysis for male
 Anolis sagrei.xls
DOI: 10.82294/dvnxf4pfp
title: COPUS. Territorio: Guainía. Sector: Cultura. Año: 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Guainía.
DOI: 10.5061/dryad.9mj12
title: Data from: An in vivo three-dimensional Magnetic Resonance Imaging-based averaged brain collection of the neonatal piglet (Sus scrofa)

description: Due to the fact that morphology and perinatal growth of the piglet brain
 is similar to humans, use of the piglet as a translational animal model
 for neurodevelopmental studies is increasing. Magnetic resonance imaging
 (MRI) can be a powerful tool to study neurodevelopment in piglets, but
 many of the MRI resources have been produced for adult humans. Here, we
 present an average in vivo MRI-based atlas specific for the 4-week-old
 piglet. In addition, we have developed probabilistic tissue classification
 maps. These tools can be used with brain mapping software packages (e.g.
 SPM and FSL) to aid in voxel-based morphometry and image analysis
 techniques. The atlas enables efficient study of neurodevelopment in a
 highly tractable translational animal with brain growth and development
 similar to humans.
description: Piglet MRI Atlas
 CollectionThis includes the MRI
 data sets of the averaged brain for the 4-week old piglet, prior
 probability maps, and regions of interest files.Piglet_MRI_Atlas.zip
DOI: 10.5061/dryad.70
title: Data from: Influence of alignment on the mtDNA phylogeny of Cetacea: questionable support for a Mysticeti/Physeteroidea clade

description: [No abstract entered]
description: Cerchio and Tucker Data
 Matrix: MALIGN.124.08MALIGN.124.08Cerchio and Tucker Data Matrix: MilinkovitchMilinkovitch.htmCerchio and Tucker Data Matrix: MALIGN.124.07MALIGN.124.07Cerchio and Tucker Data Matrix: MALIGN.124.10MALIGN.124.10Cerchio and Tucker Data Matrix: ClustalClustal.htmCerchio and Tucker Data Matrix: MALIGN.136.02MALIGN.136.02Cerchio and Tucker Data Matrix: MALIGN.124.09MALIGN.124.09Cerchio and Tucker Data Matrix: Conservative-1Conservative-1.htmCerchio and Tucker Data Matrix: Conservative-2Conservative-2.htmCerchio and Tucker Data Matrix: MALIGN.111.02MALIGN.111.02Cerchio and Tucker Data Matrix: MALIGN.111.01MALIGN.111.01Cerchio and Tucker Data Matrix: MALIGN.124.03MALIGN.124.03Cerchio and Tucker Data Matrix: MALIGN.136.06MALIGN.124.06Cerchio and Tucker Data Matrix: MALIGN.136.03MALIGN.136.03Cerchio and Tucker Data Matrix: MALIGN.136.04MALIGN.124.04Cerchio and Tucker Data Matrix: MALIGN.111.03MALIGN.111.03Cerchio and Tucker Data Matrix: MALIGN.136.08MALIGN.136.08Cerchio and Tucker Data Matrix: MALIGN.136.01MALIGN.136.01Cerchio and Tucker Data Matrix: MALIGN.124.05MALIGN.124.05Cerchio and Tucker Data Matrix: MALIGN.124.06MALIGN.124.06Cerchio and Tucker Data Matrix: MALIGN.124.04MALIGN.124.04Cerchio and Tucker Data Matrix: MALIGN.136.05MALIGN.124.05Cerchio and Tucker Data Matrix: MALIGN.124.01MALIGN.124.01Cerchio and Tucker Data Matrix: MALIGN.136.10MALIGN.136.10Cerchio and Tucker Data Matrix: MALIGN.124.02MALIGN.124.02Cerchio and Tucker Data Matrix: MALIGN.136.09MALIGN.136.09Cerchio and Tucker Data Matrix: MALIGN.136.07MALIGN.136.07
DOI: 10.5061/dryad.018g4
title: Data from: Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing

description: The effects of gastrointestinal tract microbiota (GTM) on host physiology
 and health has been the subject of considerable interest in recent years.
 While a variety of captive bred species have been used in experiments, the
 extent to which GTM of captive and/or inbred individuals resembles natural
 composition and variation in wild populations is poorly understood. Using
 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house
 mice (Mus musculus) and wild-derived inbred strain mice belonging to two
 subspecies (M.m.musculus and M.m. domesticus). Sequenced individuals were
 selected according to a 2×2 experimental design: wild (14) vs. inbred
 origin (16) and M. m. musculus (15) vs. M. m. domesticus (15). We compared
 alpha diversity (i.e. number of operational taxonomic units – OTUs), beta
 diversity (i.e. interindividual variability) and microbiota composition
 across the four groups. We found no difference between M. m. musculus and
 M. m. domesticus subspecies, suggesting low effect of genetic
 differentiation between these two subspecies on GTM structure. Both inbred
 and wild populations showed the same level of microbial alpha and beta
 diversity, however, we found strong differentiation in microbiota
 composition between wild and inbred populations. Relative abundance of ~
 16% of OTUs differed significantly between wild and inbred individuals. As
 laboratory mice represent the most abundant model for studying the effects
 of gut microbiota on host metabolism, immunity and neurology, we suggest
 that the distinctness of laboratory-kept mouse microbiota, which differs
 from wild mouse microbiota, needs to be considered in future biomedical
 research.
description: PICRUST_CLUSTERS.tarThis includes clusters of quality filtered sequances that were used for construction of OTU table. Sequences were clustered using CLUSTOM (Hwang et al. 2013, DOI: 10.1371/journal.pone.0062623). Names of sequences correspond to sample IDs in enlisted Table S1.otu_table_DENOVO_CLUSTOM_RThis is the OTU table constructed based on CLUSTOM clustering of quality filtered sequences. Information on taxonomic assignation of individual OTUs is included. Please see the Table S1 for more details concerning individual samples.mapping_vseThis file includes metadata for individual samples.
DOI: 10.5061/dryad.11609
title: Data from: One tree to link them all: a phylogenetic dataset for the European Tetrapoda

description: Since the ever-increasing availability of phylogenetic informative data,
 the last decade has seen an upsurge of ecological studies incorporating
 information on evolutionary relationships among species. However, detailed
 species-level phylogenies are still lacking for many large groups and
 regions, which are necessary for comprehensive large-scale
 eco-phylogenetic analyses. Here, we provide a dataset of 100 dated
 phylogenetic trees for all European tetrapods based on a mixture of
 supermatrix and supertree approaches. Phylogenetic inference was performed
 separately for each of the main Tetrapoda groups of Europe except mammals
 (i.e. amphibians, birds, squamates and turtles) by means of maximum
 likelihood (ML) analyses of supermatrix applying a tree constraint at the
 family (amphibians and squamates) or order (birds and turtles) levels
 based on consensus knowledge. For each group, we inferred 100 ML trees to
 be able to provide a phylogenetic dataset that accounts for phylogenetic
 uncertainty, and assessed node support with bootstrap analyses. Each tree
 was dated using penalized-likelihood and fossil calibration. The trees
 obtained were well-supported by existing knowledge and previous
 phylogenetic studies. For mammals, we modified the most complete supertree
 dataset available on the literature to include a recent update of the
 Carnivora clade. As a final step, we merged the phylogenetic trees of all
 groups to obtain a set of 100 phylogenetic trees for all European
 Tetrapoda species for which data was available (91%). We provide this
 phylogenetic dataset (100 chronograms) for the purpose of comparative
 analyses, macro-ecological or community ecology studies aiming to
 incorporate phylogenetic information while accounting for phylogenetic
 uncertainty.
description: 100 dated supertrees of
 European Tetrapoda100 dated supertrees of
 European Tetrapoda species in newick format. All trees are rooted and
 ultrametric.100Tetrapoda_chronograms.tre100 dated phylogenetic trees of European Squamata and Testudinae100 dated phylogenetic trees of European Squamata and Testudinae species in newick format. All trees are rooted and ultrametric.SquamataTestudinae_100chronograms.tre100 dated phylogenetic trees of European Birds100 dated phylogenetic trees of European Bird species in newick format. All trees are rooted and ultrametric.Birds_100chronograms.tre100 dated phylogenetic trees of European Amphibians100 dated phylogenetic trees of European Amphibian species in newick format. All trees are rooted and ultrametric.Amphibians_100chronograms.tre100 dated supertrees of European Mammals100 dated supertrees of European Mammal species in newick format. All trees are rooted and ultrametric.Mammals_UpdateCarnivora_Europe_100chronograms.tre
DOI: 10.5061/dryad.tm8k3
title: Data from: Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer

description: Introgressive hybridization offers a unique platform for studying the
 molecular basis of natural selection acting on mitogenomes. Most of the
 mtDNA protein-coding genes are extremely conserved; however, some of the
 observed variations have potentially adaptive significance. Here, we
 evaluated whether the evolution of mtDNA in closely related roe deer
 species affected by widespread mtDNA introgression is neutral or adaptive.
 We characterized and compared 16 complete mitogenomes of European
 (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four
 of Siberian origin introgressed into European species. The average
 sequence divergence of species-specific lineages was estimated at 2.8% and
 varied across gene classes. Only 21 of 315 fixed differences identified in
 protein-coding genes represented nonsynonymous changes. Only three of them
 were determined to have arisen in the C. pygargus lineage since the time
 to the most recent common ancestor (TMRCA) of both Capreolus species,
 reflecting a decelerated evolutionary ratio. The almost four-fold higher
 dN/dS ratio described for the European roe deer lineage is constrained by
 overall purifying selection, especially pronounced in the ND4 and ND5
 genes. We suggest that the highly divergent C. capreolus lineage could
 have maintained a capability for genomic incorporation of the
 well-preserved and almost ancestral type of mtDNA present in C. pygargus.
 Our analyses did not indicate any signs of positive selection for Siberian
 roe deer mtDNA, suggesting that the present widespread introgression is
 evolutionarily neutral.
description: mtDNA_-_alignment_filesmtDNA alignment filesTreeSAAP_input_filesTreeSAAP input filesCODEML_-_input_filesCODEML input filesMrBayes_input_fileMrBayes input file
DOI: 10.5878/0nj7-1w57
title: The Gothenburg SOM Survey 2017
title: SOM-undersökningen i Göteborg 2017

description: In the autumn of 2017, the second edition of the Gothenburg SOM survey was conducted. A total of 5000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.

Sample size: 5000
Cause of non response - Respondent unable to participate: 227
Cause of non response - No contact/refusal: 2099
description: Hösten 2017 genomfördes för andra gången en SOM-undersökning i Göteborgs stad, där totalt 5000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär, och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.

Urvalsstorlek: 5000
Anledning till bortfall - Naturligt bortfall: 227
Anledning till bortfall - Ej anträffbar/svarsvägran: 2099
DOI: 10.5878/3ktz-sv77
title: The Gothenburg SOM Survey 2017
title: SOM-undersökningen i Göteborg 2017

description: In the autumn of 2017, the second edition of the Gothenburg SOM survey was conducted. A total of 5000 randomly selected citizens of Gothenburg answered questions about attitudes and habits in relation to society, opinion and media. Many of the questions in the Gothenburg survey are of a regional nature, and concern local politicians and infrastructure initiatives.

Sample size: 5000
Cause of non response - Respondent unable to participate: 227
Cause of non response - No contact/refusal: 2099
description: Hösten 2017 genomfördes för andra gången en SOM-undersökning i Göteborgs stad, där totalt 5000 slumpmässigt utvalda göteborgare fick svara på frågor om attityder och vanor i relation till samhälle, opinion och medier. Många av frågorna i Göteborgsundersökningen är av regional karaktär, och rör lokala politiker, infrastruktursatsningar, och bilden av Göteborg som stad.

Urvalsstorlek: 5000
Anledning till bortfall - Naturligt bortfall: 227
Anledning till bortfall - Ej anträffbar/svarsvägran: 2099
DOI: 10.5061/dryad.b1dt2
title: Data from: Haldane's rule is linked to extraordinary sex ratios and sperm length in stalk-eyed flies.

description: We use three allopatric populations of the stalk-eyed fly Teleopsis
 dalmanni from Southeast Asia to test two predictions made by the sex
 chromosome drive hypothesis for Haldane's rule. The first is that
 modifiers that suppress or enhance drive should evolve rapidly and
 independently in isolated populations. The second is that drive loci or
 modifiers should also cause sterility in hybrid males. We tested these
 predictions by assaying the fertility of 2,066 males derived from
 backcross experiments involving two pairs of populations and found that
 the proportion of mated males that fail to produce any offspring ranged
 from 38-60% among crosses with some males producing strongly female-biased
 or male-biased sex ratios. After genotyping each male at 25-28 genetic
 markers we found quantitative trait loci (QTL) that jointly influence male
 sterility, sperm length and biased progeny sex ratios in each pair of
 populations, but almost no shared QTL between population crosses. We also
 discovered that the extant XSR chromosome has no effect on sex ratio or
 sterility in these backcross males. Whether shared QTL are caused by
 linkage or pleiotropy requires additional study. Nevertheless, these
 results indicate the presence of a "cryptic" drive system that
 is currently masked by suppressing elements that are associated with
 sterility and sperm length within but not between populations and,
 therefore, must have evolved since the populations became isolated, i.e.
 in less than 100,000 years. We discuss how genes that influence sperm
 length may contribute to hybrid sterility.
description: QTL genotype and
 phenotype data for B x G backcross sonsEach row contains
 microsatellite genotype codes and phenotype data for male progeny produced
 in a backcross experiment involving the B and G
 populationsBGdatasubmitted.xlsQTL genotype and phenotype data for S x G backcross sonsEach row contains microsatellite genotype codes and phenotype data for male progeny produced in a backcross experiment involving the S and G populationsSGdatasubmitted.xls
DOI: 10.5061/dryad.943j7
title: Data from: Onshore-offshore gradient in metacommunity turnover emerges only over macroevolutionary time scales

description: Invertebrate lineages tend to originate and become extinct at a higher
 rate in onshore than in offshore habitats over long temporal durations
 (more than 10 Myr), but it remains unclear whether this pattern scales
 down to durations of stages (less than 5 Myr) or even sequences (less than
 0.5 Myr). We assess whether onshore–offshore gradients in long-term
 turnover between the tropical Eocene and the warm-temperate
 Plio-Pleistocene can be extrapolated from gradients in short-term
 turnover, using abundances of molluscan species from bulk samples in the
 northeast Atlantic Province. We find that temporal turnover of
 metacommunities does not significantly decline with depth over short
 durations (less than 5 Myr), but significantly declines with depth between
 the Eocene and Plio-Pleistocene (approx. 50 Myr). This decline is
 determined by a higher onshore extinction of Eocene genera and families,
 by a higher onshore variability in abundances of genera and families, and
 by an onshore expansion of genera and families that were frequent offshore
 in the Eocene. Onshore–offshore decline in turnover thus emerges only over
 long temporal durations. We suggest that this emergence is triggered by
 abrupt and spatially extensive climatic or oceanographic perturbations
 that occurred between the Eocene and Plio-Pleistocene. Plio-Pleistocene
 metacommunities show a high proportion of bathymetric generalists, in
 contrast to Eocene metacommunities. Accordingly, the net cooling and
 weaker thermal gradients may have allowed offshore specialists to expand
 into onshore habitats and maintain their presence in offshore habitats.
description: Supplement-Eocene
 abundance dataSpecies-level abundance
 data from 106 Lower and Middle Eocene stations, assigned to genera and
 families.Supplement-Plio-Pleistocene abundance dataSpecies-level abundance in 48 Pliocene and Pleistocene stations, assigned to genera and families.Supplement-Eocene station dataSupplement-Plio-Pleistocene station data
DOI: 10.34740/kaggle/dsv/14640258
title: BOS Kemdikbud
DOI: 10.5281/zenodo.18389888
title: leptopelis_gramineus_spades_01.fasta.gz
DOI: 10.5281/zenodo.18389889
title: leptopelis_gramineus_spades_01.fasta.gz