cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3m5v5
title: Data from: The representation of prediction error in auditory cortex

description: To survive, organisms must extract information from the past that is
 relevant for their future. How this process is expressed at the neural
 level remains unclear. We address this problem by developing a novel
 approach from first principles. We show here how to generate
 low-complexity representations of the past that produce optimal
 predictions of future events. We then illustrate this framework by
 studying the coding of ‘oddball’ sequences in auditory cortex. We find
 that for many neurons in primary auditory cortex, trial-by-trial
 fluctuations of neuronal responses correlate with the theoretical
 prediction error calculated from the short-term past of the stimulation
 sequence, under constraints on the complexity of the representation of
 this past sequence. In some neurons, the effect of prediction error
 accounted for more than 50% of response variability. Reliable predictions
 often depended on a representation of the sequence of the last ten or more
 stimuli, although the representation kept only few details of that
 sequence.
description: fnames.csvfnames.csv relates unit index with the original data filename, to link back to the raw data. The format of the file is described in readData.m.stim.csvstim.csv contains the sequence of stimuli. The format of the file is described in readData.m.resp.csvresp.csv is the main data file. It contains spike times for all trials of all neurons. Each trial is represented by 700 ms, with stimulus onset at 200 ms after trial onset. Tone duration is 230 ms. The format of the file is described in readData.m.readData.mThis file contains a description of the three files comprising this data set, as well as example matlab code for reading and processing them.
DOI: 10.5061/dryad.ck1m7
title: Data from: Spatiotemporal diversification of the true frogs (Genus Rana): a historical framework for a widely studied group of model organisms

description: True frogs of the genus Rana are widely used as model organisms in studies
 of development, genetics, physiology, ecology, behavior, and evolution.
 Comparative studies among the more than 100 species of Rana rely on an
 understanding of the evolutionary history and patterns of diversification
 of the group. We estimate a well-resolved, time-calibrated phylogeny from
 sequences of six nuclear and three mitochondrial loci sampled from most
 species of Rana, and use that phylogeny to clarify the group’s
 diversification and global biogeography. Our analyses consistently support
 an “Out of Asia” pattern with two independent dispersals of Rana from East
 Asia to North America via Beringian land bridges. The more species-rich
 lineage of New World Rana appears to have experienced a rapid radiation
 following its colonization of the New World, especially with its expansion
 into montane and tropical areas of Mexico, Central America, and South
 America. In contrast, Old World Rana exhibit different trajectories of
 diversification; diversification in the Old World began very slowly and
 later underwent a distinct increase in speciation rate around 29–18 Ma.
 Net diversification is associated with environmental changes and
 especially intensive tectonic movements along the Asian margin from the
 Oligocene to early Miocene. Our phylogeny further suggests that previous
 classifications were misled by morphological homoplasy and plesiomorphic
 color patterns, as well as a reliance primarily on mitochondrial genes. We
 provide a phylogenetic taxonomy based on analyses of multiple nuclear and
 mitochondrial gene loci.
description: Rana Supplementary
 TablesSupplementary Data
 TablesRana Supplementary
 FiguresSupplementary
 FiguresRana Yuan Nexus
 fileNexus file of
 sequencesRana_Yuan_May31.nex
DOI: 10.5061/dryad.8q57v
title: Data from: A demographic ménage à trois: interactions between disturbances both amplify and dampen population dynamics of an endemic plant

description: Natural and anthropogenic disturbances co-occur in most systems, but how
 they interact to shape demographic outcomes remains poorly understood.
 Such interactions may alter dynamics of populations in non-additive ways,
 making demographic predictions challenging when focusing on only one
 disturbance. Thus, understanding the interactive effects of such
 disturbances is critically important to determine the population viability
 of most species under a diversity of stressors. We used a hierarchical
 integral projection model (IPM), parameterized with 13 years of field data
 across 20 populations, encompassing 2435 individuals of an endangered
 herb, Liatris ohlingerae. We examined interactive effects of vertebrate
 herbivory, fire and anthropogenic activities (sand roads) on vital rates
 (e.g. survival, growth, reproduction, recruitment) and ultimately on
 population growth rates (λ), to test the hypothesis that interactions
 amplify or dampen differences in λ depending on environmental contexts. We
 constructed megamatrices to determine coupled dynamics in individuals
 damaged vs. not damaged by herbivores in roadsides and in Florida scrub
 with different times since fire. We identified strong interactive effects
 of fire with herbivory and habitat with herbivory on vital rates and on
 population growth rates in the IPM model. We also found different patterns
 of variation in λ between habitat and time-since-fire scenarios;
 population growth rates were higher in roadside populations compared to
 scrub populations and declined with increasing time since fire. Herbivory
 had interactive effects with both fire and human disturbances on λ.
 Herbivory resulted in decreased differences in λ due to anthropogenic
 disturbance and slightly increased differences in λ due to time since
 fire. Synthesis. The co-occurrence of various disturbances may both
 amplify and dampen the effects of other disturbances on population growth
 rate, thus shaping complex population dynamics that are neither linear nor
 additive. These realistic nonlinearities represent challenges in
 understanding and projecting of population dynamics. Here, we examined the
 effects of various sources of disturbance on the population dynamics of an
 endangered plant species, finding complex interactions affecting
 population growth rates. We argue that integration of multiple,
 interacting stressors in IPMs will allow more accurate estimation of the
 overall effects of ecological processes on species viability.
description: Liatris
 DataData-set containing
 demographic information for Liatris ohlingerae from
 2000-2011Liatrisdata.csv
DOI: 10.5061/dryad.67g0t
title: Data from: Repeated evolution of amphibious behavior in fish and its implications for the colonization of novel environments

description: We know little about on how frequently transitions into new habitats
 occur, especially the colonization of novel environments that are the most
 likely to instigate adaptive evolution. One of the most extreme ecological
 transitions has been the shift in habitat associated with the move from
 water to land by amphibious fish. We provide the first phylogenetic
 investigation of these transitions for living fish. Thirty-three families
 have species reported to be amphibious and these are likely independent
 evolutionary origins of fish emerging onto land. Phylogenetic
 reconstructions of closely related taxa within one of these families, the
 Blenniidae, inferred as many as seven convergences on a highly amphibious
 lifestyle. Taken together, there appear to be few constraints on fish
 emerging onto land given amphibious behavior has evolved repeatedly many
 times across ecologically diverse families. The colonization of novel
 habitats by other taxa resulting in less dramatic changes in environment
 should be equally, if not, more frequent in nature, providing an important
 prerequisite for subsequent adaptive differentiation.
description: Ord_TJ_EVOL_16-0165R2_metaanalysis_nulldistributionData from fishbase.org on the number of genera within particular ecological categories used as the null distribution for meta-analysisOrd_TJ_EVOL_16-0165R2_species_ratingsBehavioral ratings (degree of amphibious behavior) for all blenny species surveyedOrd_TJ_EVOL_16-0165R2_consensus_phylogeniesConsensus phylogenies using Bayesian inference, maximum likelihood or coalescence-based species tree methodsOrd_TJ_EVOL_16-0165R2_BIphylogeny_posteriordistributionEntire posterior distribution (minus burn-in) used to create Bayesian inference consensus treeOrd_TJ_EVOL_16-0165R2_plasticityWithin taxon data for Praealticus labrovittas and Entromacrodus striatus on Guam
DOI: 10.15468/dl.gsr6am
title: Occurrence Download

description: A dataset containing 47510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Polypedates leucomystax, Polypedates megacephalus, Polypodium hydriforme)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Living Specimen, Unknown evidence, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1500",
 "Year is less than or equal to 2026",
 "HasCoordinate is true"
 ]
}

 The dataset includes 47510 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001464-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mj714
title: Data from: Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data

description: Estimating contemporary genetic structure and population connectivity in
 marine species is challenging, often compromised by genetic markers that
 lack adequate sensitivity, and unstructured sampling regimes. We show how
 these limitations can be overcome via the integration of modern genotyping
 methods and sampling designs guided by LiDAR and SONAR data sets. Here we
 explore patterns of gene flow and local genetic structure in a
 commercially harvested abalone species (Haliotis rubra) from southeastern
 Australia, where the viability of fishing stocks is believed to be
 dictated by recruitment from local sources. Using a panel of
 microsatellite and genomewide SNP markers, we compare allele frequencies
 across a replicated hierarchical sampling area guided by bathymetric LiDAR
 imagery. Results indicate high levels of gene flow and no significant
 genetic structure within or between benthic reef habitats across 1400 km
 of coastline. These findings differ to those reported for other regions of
 the fishery indicating that larval supply is likely to be spatially
 variable, with implications for management and long-term recovery from
 stock depletion. The study highlights the utility of suitably designed
 genetic markers and spatially informed sampling strategies for gaining
 insights into recruitment patterns in benthic marine species, assisting in
 conservation planning and sustainable management of fisheries.
description: SNP and msat
 datasetsMicrosatellite genotypes
 for broad geographic sampling, and three fine scale replicates as outlined
 in the paper. Also the 3 SNP datasets derived from alternative parameter
 settings.
DOI: 10.34810/data1247
title: Partitura i enregistrament d' "Amavit Eum Dominus Motete a solo con violines para la Ascensión" (Francesc Queralt, 1740-1825)

description: Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical, aquest dataset conté dos arxius: 
&lt;br&gt; Transcripció del manuscrit original de Francesc Queralt
&lt;br&gt; Enregistrament de la peça interpretada per: 
&lt;br&gt; - Eva del Campo, orgue positiu. Orgue positiu construït per Gerrit Klop el
2022
&lt;br&gt; - Ricart Renart, violí I. Violí construït per Joseph Massaguer el 1753
&lt;br&gt; - Marta Guillen, violí II. Violí construït per Giuseppe Tenneriello el 2009
&lt;br&gt; - Guillermo Turina, violoncel. Violoncel construït per Marchal a finals del
segle XVIII
&lt;br&gt; - Martí Doñate (tenor)
DOI: 10.5061/dryad.p3p4p
title: Data from: Recovery from hybrid breakdown in a marine invertebrate is faster, stronger and more repeatable under environmental stress

description: Understanding how environmental stress alters the consequences of
 hybridization is important, because the rate of hybridization and the
 likelihood of hybrid speciation both appear elevated in harsh, disturbed
 or marginal habitats. We assessed fitness, morphometrics and molecular
 genetic composition over 14 generations of hybridization between two
 highly divergent populations of the marine copepod Tigriopus californicus.
 Replicated, experimental hybrid populations in both control and high
 salinity conditions showed a decline in fitness, followed by a recovery.
 Recovery was faster in the salinity stress treatment, returning to
 parental levels up to two generations earlier than in the control. This
 recovery was stable in the high salinity treatment, while in the control
 treatment fitness dropped back below parental levels at the final time
 point. Recovery in the high salinity treatment was also stronger in terms
 of competitive fitness and heat shock tolerance. Finally, consequences of
 hybridization were more repeatable under salinity stress, where
 among-replicate variance for survivorship and molecular genetic
 composition was lower than in the control treatment. In a system with low
 effective population sizes (estimates ranged from 17 to 63), where genetic
 drift might be expected to be the predominate force, strong selection
 under harsh environmental conditions apparently promoted faster, stronger
 and more repeatable recovery from depressed hybrid fitness.
description: Fitness
 dataData on hatching,
 survival and metamorphosis across 13 generationsfitness.xls
DOI: 10.5061/dryad.26j38
title: Data from: Phylogenomics from whole genome sequences using aTRAM

description: Novel sequencing technologies are rapidly expanding the size of data sets
 that can be applied to phylogenetic studies. Currently the most commonly
 used phylogenomic approaches involve some form of genome reduction. While
 these approaches make assembling phylogenomic data sets more economical
 for organisms with large genomes, they reduce the genomic coverage and
 thereby the long-term utility of the data. Currently, for organisms with
 moderate to small genomes (&lt;1000 Mbp) it is feasible to sequence
 the entire genome at modest coverage (10−30×). Computational challenges
 for handling these large data sets can be alleviated by assembling
 targeted reads, rather than assembling the entire genome, to produce a
 phylogenomic data matrix. Here we demonstrate the use of automated Target
 Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog
 genes from whole genome sequencing of sucking lice (Anoplura) and
 out-groups. We developed a pipeline to extract exon sequences from the
 aTRAM assemblies by annotating them with respect to the original target
 protein. We aligned these protein sequences with the inferred amino acids
 and then performed phylogenetic analyses on both the concatenated matrix
 of genes and on each gene separately in a coalescent analysis. Finally, we
 tested the limits of successful assembly in aTRAM by assembling 100 genes
 from close- to distantly related taxa at high to low levels of coverage.
description: Concatenated alignment
 and treeAlignment and
 phylogenetic tree of the concatenated 1,101 exon DNA alignment from 15
 louse taxa. Genes were assembled from raw genomic DNA with aTRAM and exons
 extracted and stitched together. Third codon position was removed due to
 base composition bias, and tree build in RAxML.Dataset_1.zipIndividual Gene Trees and AlignmentsAll 1,101 gene trees and alignments for the 15 taxon dataset. Each gene was aligned using PASTA and UPP for fragmentary sequences. Each gene tree was built using ASTRAL.Dataset_2.zipSupplementaryTableDNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis.Supplementary FigureBox plot of the standard deviations away from mean for each codon position for each of the GTR rate parameters. The majorities of the extreme outliers fell above 10 standard deviations from the mean and were removed from the analysis.SupplementalFigure1.pdf
DOI: 10.5061/dryad.12d36
title: Data from: Accuracy of assignment of Atlantic salmon (Salmo salar L.) to rivers and regions in Scotland and northeast England based on single nucleotide polymorphism (SNP) markers.

description: Understanding the habitat use patterns of migratory fish, such as Atlantic
 salmon (Salmo salar L.), and the natural and anthropogenic impacts on
 them, is aided by the ability to identify individuals to their stock of
 origin. Presented here are the results of an analysis of informative
 single nucleotide polymorphic (SNP) markers for detecting genetic
 structuring in Atlantic salmon in Scotland and NE England and their
 ability to allow accurate genetic stock identification. 3,787 fish from
 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order
 to identify a cost-effective subset of SNPs, they were ranked according to
 their ability to differentiate between fish from different rivers. A panel
 of 288 SNPs was used to examine both individual assignments and mixed
 stock fisheries and eighteen assignment units were defined. The results
 improved greatly on previously available methods and, for the first time,
 fish caught in the marine environment can be confidently assigned to
 geographically coherent units within Scotland and NE England, including
 individual rivers. As such, this SNP panel has the potential to aid
 understanding of the various influences acting upon Atlantic salmon on
 their marine migrations, be they natural environmental variations and/or
 anthropogenic impacts, such as mixed stock fisheries and interactions with
 marine power generation installations.
description: Scottish Baseline SNP
 PanelRaw genotypes for the
 baseline SNP panel developed for Scotland and NE
 England.
DOI: 10.5061/dryad.2qv8n
title: Data from: Genetic variation in variability: phenotypic variability of fledging weight and its evolution in a songbird population

description: Variation in traits is essential for natural selection to operate and
 genetic and environmental effects can contribute to this phenotypic
 variation. From domesticated populations, we know that families can differ
 in their level of within-family variance, which leads to the intriguing
 situation that within-family variance can be heritable. For offspring
 traits, such as birth weight, this implies that within-family variance in
 traits can vary among families and can thus be shaped by natural
 selection. Empirical evidence for this in wild populations is however
 lacking. We investigated whether within-family variance in fledging weight
 is heritable in a wild great tit (Parus major) population and whether
 these differences are associated with fitness. We found significant
 evidence for genetic variance in within-family variance. The genetic
 coefficient of variation (GCV) was 0.18 and 0.25, when considering
 fledging weight a parental or offspring trait, respectively. We found a
 significant quadratic relationship between within-family variance and
 fitness: families with low or high within-family variance had lower
 fitness than families with intermediate within-family variance. Our
 results show that within-family variance can respond to selection and
 provides evidence for stabilizing selection on within-family variance.
description: data1This file was used for
 the analysis of variability; the file itself contains the description of
 the columnsdata2This file was used for
 the fitness analysis; the file itself contains the description of the
 columnspedigreeThis file contains the pedigree data used for the genetic analysis of fledging weight and its variability
DOI: 10.15468/dl.js9yr3
title: Occurrence Download

description: A dataset containing 1026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Rhopalosiphum maidis",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2026"
 ]
}

 The dataset includes 1026 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001467-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rg22j
title: Data from: Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

description: Background: Transcriptomics in non-model plant systems has recently
 reached a point where the examination of nuclear genome-wide patterns in
 understudied groups is an achievable reality. This progress is especially
 notable in evolutionary studies of ferns, for which molecular resources to
 date have been derived primarily from the plastid genome. Here, we utilize
 transcriptome data in the first genome-wide comparative study of molecular
 evolutionary rate in ferns. We focus on the ecologically diverse family
 Pteridaceae, which comprises about 10 % of fern diversity and includes the
 enigmatic vittarioid ferns—an epiphytic, tropical lineage known for
 dramatically reduced morphologies and radically elongated phylogenetic
 branch lengths. Using expressed sequence data for 2091 loci, we perform
 pairwise comparisons of molecular evolutionary rate among 12 species
 spanning the three largest clades in the family and ask whether previously
 documented heterogeneity in plastid substitution rates is reflected in
 their nuclear genomes. We then inquire whether variation in evolutionary
 rate is being shaped by genes belonging to specific functional categories
 and test for differential patterns of selection. Results: We find
 significant, genome-wide differences in evolutionary rate for vittarioid
 ferns relative to all other lineages within the Pteridaceae, but we
 recover few significant correlations between faster/slower vittarioid loci
 and known functional gene categories. We demonstrate that the faster rates
 characteristic of the vittarioid ferns are likely not driven by positive
 selection, nor are they unique to any particular type of nucleotide
 substitution. Conclusions: Our results reinforce recently reviewed
 mechanisms hypothesized to shape molecular evolutionary rates in
 vittarioid ferns and provide novel insight into substitution rate
 variation both within and among fern nuclear genomes.
description: Additional_file_10
DOI: 10.34740/kaggle/dsv/14638190
title: Global Genomic Neurofibromatosis Neoplasia