cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98470
title: Data from: A classification system for zebrafish adipose tissues

description: The zebrafish model system offers significant utility for in vivo imaging
 of adipose tissue (AT) dynamics and for screening to identify chemical and
 genetic modifiers of adiposity. In particular, AT can be quantified
 accurately in live zebrafish using fluorescent lipophilic dyes. Although
 this methodology offers considerable promise, the comprehensive
 identification and classification of zebrafish ATs has not been performed.
 Here, we use fluorescent lipophilic dyes and in vivo imaging
 systematically to identify, classify and quantify the zebrafish AT pool.
 We identify 34 regionally distinct zebrafish ATs, including five visceral
 ATs and 22 subcutaneous ATs. For each of these ATs, we describe detailed
 morphological characteristics to aid their identification in future
 studies. Furthermore, we quantify the areas for each AT and construct
 regression models to allow prediction of expected AT size and variation
 across a range of developmental stages. Finally, we demonstrate the
 utility of this resource for identifying effects of strain variation and
 high-fat diet on AT growth. Altogether, this resource provides
 foundational information on the identity, dynamics and expected quantities
 of zebrafish ATs for use as a reference for future studies.
description: minchin_rawls_2017_dryad_uploadtif files for the EKW and WIK cohorts. Image # corresponds to Dryad # in Table S4.
DOI: 10.5061/dryad.pp176
title: Data from: Taxonomic, phylogenetic and ecological diversity of Niphargus (Amphipoda: Crustacea) in the Hölloch cave system (Switzerland)

description: Groundwater belongs to the spatially most extensive, but least explored
 freshwater systems. On a global scale, the species richness of several
 subterranean invertebrate taxa parallels species richness found in surface
 waters, while on a local scale species richness hardly exceeds 20 species.
 This results in a high contribution of groundwater ecosystems to regional
 β- and γ-diversity, and to a smaller degree to α-diversity, and deserves
 focused attention. In general, more species are to be found in large cave
 systems. The second largest cave system in Europe is Hölloch in
 Switzerland. In this paper we revised the taxonomic, phylogenetic and
 ecological diversity of the amphipod community in the Hölloch cave system.
 While previous records listed five geographically widespread species of
 the genus Niphargus for this cave system, we could not confirm the
 presence of any of those species, but rather found three highly distinct
 species new to science. In this paper we describe Niphargus styx sp. nov.,
 Niphargus murimali sp. nov., and Niphargus muotae sp. nov., and suggest
 that previous records from that cave were probably misidentifications.
 Although amphipod species richness in this cave system seems to be lower
 than previously thought in terms of absolute numbers, the cave retained
 its regional and international importance in terms of nature conservation
 for multiple reasons. First, all newly described species are probably
 endemic to this cave system. Second, they are phylogenetically distantly
 related and exhibit moderate to high phylogenetic diversity. Third, the
 species, as inferred from their functional morphology, are also
 ecologically highly divergent. Based on geographic distribution of their
 nearest relatives, we hypothesize that the cave system was most likely
 independently colonized from North, West and South and that the
 pre-adapted ancestors occupied different ecological niches within the
 system.
description: 28S_alignmentAlignment of 169 partial 28S rDNA nucleotide sequences from amphipods in genus Niphargus. Sequences were highly variable in their length and were aligned in MAFFT ver. 6 using the E-INS-i option for sequences with multiple conserved domains and long gaps.COI_alignmentAlignment of 117 nucleotide sequences of mitochondrial gene cytochrome oxidase subunit I (COI), partial cds, from amphipods in genus Niphargus. Sequences were aligned with a simple alghoritm (Geneious alignment).H3_alignmentAlignment of 109 nucleotide sequences of nuclear gene histone H3, partial cds, from amphipods in genus Niphargus. All sequences were the same length and were aligned using a simple alghoritm (Geneious alignment).Concatenated alignmentsConcatenated alignments of all three genes (28S, H3, COI).MrBayes outputOutput files from MRBAYES for each gene(28S, H3, COI) analysed separately and a concatenated analysis.
DOI: 10.5061/dryad.2p7ns
title: Data from: The mouse universal genotyping array: from substrains to subspecies

description: Genotyping microarrays are an important resource for genetic mapping,
 population genetics, and monitoring of the genetic integrity of laboratory
 stocks. We have developed the third generation of the Mouse Universal
 Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina
 Infinium II array for the house mouse (Mus musculus). The bulk of the
 content of GigaMUGA is optimized for genetic mapping in the Collaborative
 Cross and Diversity Outbred populations, and for substrain-level
 identification of laboratory mice. In addition to 141,090 single
 nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy
 number concentrated in structurally polymorphic regions of the mouse
 genome. The performance of the array is characterized in a set of 500
 high-quality reference samples spanning laboratory inbred strains,
 recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA
 is highly informative across a wide range of genetically diverse samples,
 from laboratory substrains to other Mus species. In addition to describing
 the content and performance of the array, we provide detailed probe-level
 annotation and recommendations for quality control.
description: Genotypes and
 hybridization intensities for 522 reference samples.This file is an Rdata
 file containing a single object, 'geno'. That object contains
 genotypes and hybridization intensities for 522 samples used in this
 paper, of which 500 passed quality controls and were used for most of the
 analyses. See the README file for further information.refsamples.Rdata
DOI: 10.5061/dryad.rm574
title: Data from: QST FST comparisons with unbalanced half-sib designs

description: QST, a measure of quantitative genetic differentiation among populations,
 is an index that can suggest local adaptation if QST for a trait is
 sufficiently larger than the mean FST of neutral genetic markers. A
 previous method by Whitlock and Guillaume derived a simulation resampling
 approach to statistically test for a difference between QST and FST, but
 that method is limited to balanced data sets with offspring related as
 half-sibs through shared fathers. We extend this approach to (1) allow for
 a model more suitable for some plant populations or breeding designs in
 which offspring are related through mothers (assuming independent fathers
 for each offspring; half-sibs by dam), and (2) by explicitly allowing for
 unbalanced data sets. The resulting approach is made available through the
 R package QstFstComp.
description: SourceCode_DamModelSource code used when doing type I error testing of balanced or unbalanced half-sib dam modelDamModel_WorkingCopy.RSireModel_WorkingCopySource code used when doing type I error testing of unbalanced half-sib sire modelTypeI_ErrorTest_DamBalancedR code to run the error testing of the balanced half-sib dam model over 1000 replicate datasets.TypeI_ErrorTest_DamUnbalancedR code to run the error testing of the unbalanced half-sib dam model over 1000 replicate datasets.TypeI_ErrorTest_SireUnbalancedR code to run the error testing of the unbalanced half-sib sire model over 1000 replicate datasets.NemoReplicatesZipped file containing the 1000 simulated replicate datasets from Nemo used for type I error testing.
DOI: 10.5061/dryad.34gm6
title: Data from: A DNA barcode library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae)

description: Although members of the crambid subfamily Pyraustinae are frequently
 important crop pests, their identification is often difficult because many
 species lack conspicuous diagnostic morphological characters. DNA
 barcoding employs sequence diversity in a short standardized gene region
 to facilitate specimen identifications and species discovery. This study
 provides a DNA barcode reference library for North American pyraustines
 based upon the analysis of 1589 sequences recovered from 137 nominal
 species, 87% of the fauna. Data from 125 species were barcode compliant
 (&gt;500bp, &lt;1% n), and 99 of these taxa formed a distinct
 cluster that was assigned to a single BIN. The other 26 species were
 assigned to 56 BINs, reflecting frequent cases of deep intraspecific
 sequence divergence and a few instances of barcode sharing, creating a
 total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were
 examined to check the correspondence between current taxonomy and sequence
 clusters. The BIN system performed better than ABGD in delimiting closely
 related species, while OTU counts with ABGD were influenced by the value
 employed for relative gap width. Different species with low or no
 interspecific divergence may represent cases of unrecognized synonymy,
 whereas those with high intraspecific divergence require further taxonomic
 scrutiny as they may involve cryptic diversity. The barcode library
 developed in this study will also help to advance understanding of
 relationships among species of Pyraustinae.
description: DS-ZYPAN_trace_filesTrace File packageDS-ZYPAN_specimens_sequencesSpecimen Data and COI-5P sequences in json format
DOI: 10.5061/dryad.fp4vv8s
title: Data from: Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is linked to behavioral differentiation

description: Biogeographic barriers are thought to be important in initiating
 speciation through geographic isolation, but they rarely indiscriminately
 and completely reduce gene flow across the entire community. Understanding
 which species’ attributes regulate a barrier could help elucidate how
 speciation is initiated and isolation maintained. Here, we investigated
 the association of behavioral isolation on population differentiation in
 Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise
 Filter Barrier, a region of transitional habitat which separates the
 Sonoran and Chihuahuan deserts of North America. Using genome-wide
 markers, we modeled demographic history by fitting the data to isolation
 and isolation-with-migration models. The best-fit model indicated that
 desert populations diverged in the Pleistocene with low, historic, and
 asymmetric gene flow across the barrier. We then tested behavioral
 isolation using reciprocal call-broadcast experiments to compare song
 recognition between deserts, controlling for song dialect changes within
 deserts. We found that male Northern Cardinals in both deserts were most
 aggressive to local songs and failed to recognize across-barrier songs. A
 correlation of genomic differentiation despite historic introgression and
 strong song discrimination is consistent with a model where speciation is
 initiated across a barrier and maintained by behavioral isolation.
description: Provost_etal_cardinalis_data This ZIP file contains multiple files of data, including data associated with the playback experiments, generalized linear mixed models, fastsimcoal demography, and STRUCTURE.     Provost_etal_cardinalis_scripts This file contains the scripts used to generate and process the data for the playback experiments and STRUCTURE analyses.
DOI: 10.5281/zenodo.18380343
title: Using Digital Prompts to Support Physics Students Self-Regulated Learning

description: csv file pre-post student survey data and learning outcome in a business-as-usual condition (student id starting in SP23) and intervention condition (student id starting in SP24).
DOI: 10.5061/dryad.qp578
title: Data from: Deep sequencing of the olfactory epithelium reveals specific chemosensory receptors are expressed at sexual maturity in the European eel Anguilla anguilla

description: Vertebrate genomes encode a diversity of G protein-coupled receptors
 (GPCR) that belong to large gene families and are used by olfactory
 systems to detect chemical cues found in the environment. It is not clear
 however, if individual receptors from these large gene families have
 evolved roles that are specific to certain life stages. Here, we used deep
 sequencing to identify differentially expressed receptor transcripts in
 the olfactory epithelia (OE) of freshwater, seawater and sexually mature
 male eels (Anguilla anguilla). This species is particularly intriguing
 because of its complex life cycle, extreme long distance migrations and
 early-branching position within the teleost phylogeny. In the A. anguilla
 OE, we identified full-length transcripts for 13, 112, 6 and 38
 trace-amine associated receptors (TAAR), odorant receptors (OR) and type I
 and type II vomeronasal receptors (V1R and V2R). Most of these receptors
 were expressed at similar levels at different life stages and that a
 subset of OR and V2R-like transcripts were more abundant in sexually
 mature males suggesting that ORs and V2R-like genes are important for
 reproduction. We also identified a set of GPCR signal transduction genes
 that were differentially expressed indicating that eels make use of
 different GPCR signal transduction genes at different life stages. The
 finding that a diversity of chemosensory receptors are expressed in the
 olfactory epithelium and that a subset are differentially expressed
 suggest that most receptors belonging to large chemosensory gene families
 have functions that are important at multiple life stages while a subset
 have evolved specific functions at different life stages.
description: Aanguilla olfactory
 epithelium transcriptome assemblyThis is the Trinity
 assembled olfactory epithelium transcriptome (Illiumna HiSeq 2000) for
 Anguilla anguilla.Aanguilla_olfactory_epithelium_transcriptome_assembly.fastaAanguilla_olfactory_expression_dataThese are the expression data for the olfactory epithelium of freshwater (FW), seawater (SW) and sexually mature (SM) male A. anguilla. The expression values are condition means and the protein descriptions for the transcriptome assembly contigs are based on a BLAST search of RefSeq proteins. For further details, please see the associated publication
DOI: 10.5061/dryad.p63jh
title: Data from: Assortative social learning and its implications for human (and animal?) societies

description: Choosing from whom to learn is an important element of social learning. It
 affects learner success and the profile of behaviors in the population.
 Because individuals often differ in their traits and capabilities, their
 benefits from different behaviors may also vary. Homophily, or assortment,
 the tendency of individuals to interact with other individuals with
 similar traits, is known to affect the spread of behaviors in humans. We
 introduce models to study the evolution of assortative social learning
 (ASL), where assorting on a trait acts as an individual-specific mechanism
 for filtering relevant models from which to learn when that trait varies.
 We show that when the trait is polymorphic, ASL may maintain a stable
 behavioral polymorphism within a population (independently of coexistence
 with individual learning in a population). We explore the evolution of ASL
 when assortment is based on a nonheritable or partially heritable trait,
 and when ASL competes with different non-ASL strategies: oblique (learning
 from the parental generation) and vertical (learning from the parent). We
 suggest that the tendency to assort may be advantageous in the context of
 social learning, and that ASL might be an important concept for the
 evolutionary theory of social learning.
description: Code for simulations of
 model 1Matlab code for
 simulating model 1. Here, starting conditions are of invasion of NASL to a
 population of ASL at equilibrium (data included). Starting frequencies can
 be changed for any other starting conditions.model1Code.zipCode for simulations of model 2Matlab code for simulating model 2. Here, starting conditions are of invasion of NASL to a population of ASL at equilibrium (data included). Starting frequencies can be changed for any other starting conditions.model2Code.zipFigure dataMatlab .mat files with the figure datafigureData.zip
DOI: 10.5061/dryad.t7f3rc8
title: Data from: Compound- and context-dependent effects of antibiotics on greenhouse gas emissions from livestock

description: The use of antibiotics in livestock production may trigger ecosystem
 disservices, including increased emissions of greenhouse gases. To
 evaluate this, we conducted two separate animal experiments, administering
 two widely used antibiotic compounds (benzylpenicillin and tetracycline)
 over a 4 or 5-day period locally and/or systemically. We then recorded
 enteric methane production, total gas production from dung decomposing
 under aerobic versus anaerobic conditions, prokaryotic community
 composition in rumen and dung, and accompanying changes in nutrient
 intake, rumen fermentation, and digestibility resulting from antibiotic
 administration in dairy cows. The focal antibiotics had no detectable
 effect on gas emissions from enteric fermentation or dung in aerobic
 conditions, while it decreased total gas production from anaerobic dung.
 Microbiome-level effects of benzylpenicillin proved markedly different
 from those previously recorded for tetracycline. Antibiotic effects on gas
 production differed substantially between dung maintained under aerobic
 versus anaerobic conditions and between compounds, but not by mode of
 administration, under anaerobic conditions. These findings demonstrate
 compound- and context-dependent impacts of antibiotics on methane
 emissions and underlying processes, and highlight the need for a global
 synthesis of data on agricultural antibiotic use before we can understand
 their climatic impacts.
description: Primary data used in the
 analyses reported in the paper and its Supplementary Online
 Material.See README file included
 in zip archive.Danielsson_et_al_DataS1.zipMolecular data used in analyses of prokaryotic community compositionSee README file included in the zip archive.Danielsson_et_al_DataS2.zip
DOI: 10.5061/dryad.91j93
title: Data from: Topological data analysis of biological aggregation models

description: We apply tools from topological data analysis to two mathematical models
 inspired by biological aggregations such as bird flocks, fish schools, and
 insect swarms. Our data consists of numerical simulation output from the
 models of Vicsek and D'Orsogna. These models are dynamical systems
 describing the movement of agents who interact via alignment, attraction,
 and/or repulsion. Each simulation time frame is a point cloud in
 position-velocity space. We analyze the topological structure of these
 point clouds, interpreting the persistent homology by calculating the
 first few Betti numbers. These Betti numbers count connected components,
 topological circles, and trapped volumes present in the data. To interpret
 our results, we introduce a visualization that displays Betti numbers over
 simulation time and topological persistence scale. We compare our
 topological results to order parameters typically used to quantify the
 global behavior of aggregations, such as polarization and angular
 momentum. The topological calculations reveal events and structure not
 captured by the order parameters.
description: Vicsek Simulation
 1Raw
 data for Vicsek simulation #1. Parameter values are given in manuscript.
 Columns are time, x position, y position, x velocity, y
 velocity.vicsek1.csvVicsek Simulation 2Raw data for Vicsek simulation #2. Parameter values are given in manuscript. Columns are time, x position, y position, x velocity, y velocity.vicsek2.csvVicsek Simulation 3Raw data for Vicsek simulation #3. Parameter values are given in manuscript. Columns are time, x position, y position, x velocity, y velocity.vicsek3.csvD'Orsogna SimulationRaw data for D'Orsogna simulation. Parameter values are given in manuscript. Columns are time, x position, y position, x velocity, y velocity.dorsogna.csv
DOI: 10.5061/dryad.084g8
title: Data from: Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies

description: There are three described subspecies of fin whales (Balaenoptera
 physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p.
 quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described
 pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution
 in the North Pacific and North Atlantic raises the question of whether a
 single Northern Hemisphere subspecies is valid. We assess phylogenetic
 patterns using ~16 K base pairs of the complete mitogenome for 154 fin
 whales from the North Pacific, North Atlantic - including the
 Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the
 resulting 136 haplotypes revealed several well-supported clades
 representing each ocean basin, with no haplotypes shared among ocean
 basins. The North Atlantic haplotypes (n = 12) form a sister clade to
 those from the Southern Hemisphere (n = 42). The estimated time to most
 recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade
 and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14
 of the remaining North Pacific samples formed a well-supported clade
 within the Southern Hemisphere. The TMRCA for this node suggests that at
 least one female from the Southern Hemisphere immigrated to the North
 Pacific approximately 0.37 Ma. These results provide strong evidence that
 North Pacific and North Atlantic fin whales should not be considered the
 same subspecies, and suggest the need for revision of the global taxonomy
 of the species.
description: CDS data set - BEAST
 inputcds.sasaki.strict.xmlMITO data set - BEAST inputmito.sasaki.strict.xmlCDS data set - TREES outputcds.sasaki.strict.treesMITO data set - TREES outputmito.sasaki.strict.treesCDS data set - LOG outputcds.sasaki.strict.logMITO data set - LOG outputmito.sasaki.strict.logBalaenoptera physalus sample informationBphy sample info.csvCDS data set - annotated treecds.sasaki.strict.anno.treMITO data set - annotated treemito.sasaki.strict.anno.tre