cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p7g5p
title: Data from: Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data

description: Species divergence is typically thought to occur in the absence of gene
 flow, but many empirical studies are discovering that gene flow may be
 more pervasive during species formation. Although many examples of
 divergence with gene flow have been identified, only few clades have been
 investigated in a comparative manner, and fewer have been studied using
 genome-wide sequence data. We contrast species divergence genetic
 histories across eight triplets of North American Sceloporus lizards using
 a maximum likelihood implementation of the isolation–migration (IM) model.
 Gene flow at the time of species divergence is modeled indirectly as
 variation in species divergence time across the genome or explicitly using
 a migration rate parameter. Likelihood ratio tests (LRTs) are used to test
 the null model of no gene flow at speciation against these two alternative
 gene flow models. We also use the Akaike information criterion to rank the
 models. Hundreds of loci are needed for the LRTs to have statistical
 power, and we use genome sequencing of reduced representation libraries to
 obtain DNA sequence alignments at many loci (between 340 and 3,478; mean
 1⁄4 1,678) for each triplet. We find that current species distributions
 are a poor predictor of whether a species pair diverged with gene flow.
 Interrogating the genome using the triplet method expedites the
 comparative study of species divergence history and the estimation of
 genetic parameters associated with speciation.
description: Triplet
 DataPhylip alignments for
 Sceloporus triplets.TripletData.zip
DOI: 10.5061/dryad.6h5v1
title: Data from: Comparative analysis reveals that polyploidy does not decelerate diversification in fish

description: While the proliferation of the species-rich teleost fish has been ascribed
 to an ancient genome duplication event at the base of this group, the
 broader impact of polyploidy on fish evolution and diversification remains
 poorly understood. Here, we investigate the association between polyploidy
 and diversification in several fish lineages: the sturgeons
 (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae:
 Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the
 salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary
 methodologies, we co-estimate speciation and extinction rates associated
 with polyploid vs. diploid fish lineages. Family-level analysis of
 Acipenseridae and Botiidae revealed no significant difference in
 diversification rates between polyploid and diploid relatives, while
 analysis of the subfamily Cyprininae revealed higher polyploid
 diversification. Additionally, order-level analysis of the polyploid
 Salmoniformes and its diploid sister clade, the Esociformes, did not
 support a significantly different net diversification rate between the two
 groups. Taken together, our results suggest that polyploidy is generally
 not associated with decreased diversification in fish – a pattern that
 stands in contrast to that previously observed in plants. While there are
 notable differences in the time frame examined in the two studies, our
 results suggest that polyploidy is associated with different
 diversification patterns in these two major branches of the eukaryote tree
 of life.
description: fish_polyploidyPhylogenetic and ploidy level data of 4 fish groups examined: Acipenseridae, Botiidae, Cyprininae, and Salmoniformes.
DOI: 10.5061/dryad.qp747
title: Data from: Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

description: Molecular phylogenetic and phylogeographic reconstructions generally
 assume time-homogeneous substitution processes. Motivated by computational
 convenience, this assumption sacrifices biological realism and offers
 little opportunity to uncover the temporal dynamics in evolutionary
 histories. Here, we propose an evolutionary approach that explicitly
 relaxes the time-homogeneity assumption by allowing the specification of
 different infinitesimal substitution rate matrices across different time
 intervals, called epochs, along the evolutionary history. We focus on an
 epoch model implementation in a Bayesian inference framework that offers
 great modeling flexibility in drawing inference about any discrete data
 type characterized as a continuous-time Markov chain, including
 phylogeographic traits. To alleviate the computational burden that the
 additional temporal heterogeneity imposes, we adopt a massively parallel
 approach that achieves both fine- and coarse-grain parallelization of the
 computations across branches that accommodate epoch transitions, making
 extensive use of graphics processing units. Through synthetic examples, we
 assess model performance in recovering evolutionary parameters from data
 generated according to different evolutionary scenarios that comprise
 different numbers of epochs for both nucleotide and codon substitution
 processes. We illustrate the usefulness of our inference framework in two
 different applications to empirical data sets: the selection dynamics on
 within-host HIV populations throughout infection and the seasonality of
 global influenza circulation. In both cases, our epoch model captures key
 features of temporal heterogeneity that remained difficult to test using
 ad hoc procedures.
description: SupplementEpochModelSupplementary InfromationXMLBEAST XML files used for the data analysis.
DOI: 10.5061/dryad.97j4b
title: Data from: Heterochrony, dental ontogenetic diversity and the circumvention of constraints in marsupial mammals and extinct relatives

description: In marsupial mammals and their extinct relatives -collectively,
 metatherians- only the last premolar is replaced, but the timing of dental
 eruption is variable within the group. Our knowledge of fossils
 metatherians is limited, but is critical to understanding several aspects
 of the evolution and morphological diversification of this clade. We
 analyzed the sequence of eruption of 76 specimens of metatherians,
 including Sparassodonta, an extinct clade of specialized carnivores from
 South America. In Sparassodonta (1) the P3/p3 erupt simultaneously, in
 common with some didelphids (in other didelphids, p3 erupts before P3,
 whereas in the remaining didelphids, some peramelids, one caenolestid, and
 Pucadelphys this order is reversed); (2) the upper and lower molars at the
 same locus erupt more in synchrony than in other carnivorous metatherians
 in which the lower molars clearly precede the upper equivalents; (3) the
 upper canine in thylacosmilids and proborhyaenids is hypselodont; (4)
 species with similar molar morphologies have different morphologies of the
 deciduous premolars, suggesting diverse diets among the juveniles of
 different taxa; (5) deciduous teeth are functional for a long period of
 time, with thylacosmilids even retaining a functional DP3 in the permanent
 dentition. The retention of the DP3 and the hypertrophied and hypselodont
 upper canine of thylacosmilids represent clear heterochronic shifts.
 Specializations in the timing of dental eruption and in the deciduous
 tooth shape of sparassodonts are evolutionary mechanisms that circumvent
 constraints imposed by the metatherian replacement pattern and increase
 morphological disparity during ontogeny.
description: Supplementary Appendix
 1Supplementary material,
 Appendix 1. Table 1, rough data with the stage of tooth eruption of living
 marsupials and extinct stem taxa. Table 2, reduced data with 76 specimens.
 Table 3, ranking of tooth eruption sumarized per genera. Table 4, sequence
 of tooth eruption per genera used in the event-pairing
 analysis.Supplementary Appendix
 2Description of tooth
 eruption timing in the Sparassodonta, morphology of the deciduous premolar
 of sparassodonts and Prothylacynus patagonicus: the taxonomy of specimen
 MACN-A 642.
DOI: 10.5061/dryad.1qp80
title: Data from: Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos) and black bears (U. americanus) derived from genome sequences

description: We assessed the relationships of polar bears (Ursus maritimus), brown
 bears (U. arctos), and black bears (U. americanus) with high throughput
 genomic sequencing data with an average coverage of 25X for each species.
 A total of 1.4 billion 100-bp paired-end reads was assembled using the
 polar bear and annotated giant panda (Ailuropoda melanoleuca) genome
 sequences as references. We identified 13.8 million single nucleotide
 polymorphisms (SNP) in the three species aligned to the polar bear genome.
 These data indicate that polar bears and brown bears share more SNP with
 each other than either does with black bears. Concatenation and
 coalescence-based analysis of consensus sequences of approximately one
 million base pairs of ultra-conserved elements (UCE) in the nuclear genome
 resulted in a phylogeny with black bears as the sister group to brown and
 polar bears, and all brown bears are in a separate clade from polar bears.
 Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed
 that the species are genetically differentiated and there is geographic
 population structure of brown and black bears but not polar bears.
description: BearUCE_with_PartitionsRobNexus file of 996,381 nucleotides of concatenated Ultra Conserved Elements sequences from polar, brown, and black bears and other carnivora.162 SNP genotpesGenotypes for 162 sngle nucleotide polymorphisms for 336 bears.
DOI: 10.5061/dryad.j15q6
title: Data from: Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus)

description: Pleistocene climate cycles and glaciations had profound impacts on taxon
 diversification in the Boreal Forest Biome. Using population genetic
 analyses with multilocus data we examined diversification, isolation, and
 hybridization in two sibling species of tree squirrels (Tamiasciurus
 douglasii and T. hudsonicus) with special attention to the geographically
 and genetically enigmatic population of T. hudsonicus on Vancouver Island,
 Canada. The two species differentiated only about 500,000 years ago, in
 the late Pleistocene. The island population is phylogenetically nested
 within T. hudsonicus according to our nuclear analysis but within T.
 douglasii according to mtDNA. This conflict is more likely due to
 historical hybridization than to incomplete lineage sorting, and it
 appears that bidirectional gene flow occurred between the island
 population and both species on the mainland. This interpretation of our
 genetic analyses is consistent with our bioclimatic modeling, which
 demonstrates that both species were able to occupy this region throughout
 the late Pleistocene. The divergence of the island population 40,000 years
 ago suggests that tree squirrels persisted in a refugium on Vancouver
 Island at the Last Glacial Maximum, 20,000 years ago. Our observations
 demonstrate how Pleistocene climate change and habitat shifts have created
 incipient divergence in the presence of gene flow.
description: IMa2IMa2 file used for
 analyses of isolation with migration. Data includes DNA sequences from 15
 nuclear introns and 1 mtDNA locus.BEAST_mtDNAmtDNA xml file used for phylogenetic analyses in BEAST.BEAST_15-nuclear-intronsXML file for *BEAST (Species Tree) analyses using 15 nuclear intronic markers.STRUCTURE_Tam-huds_15IntronsMultilocus genotype dataset from 15 nuclear introns from samples of Tamiasciurus hudsonicus. Dataset was used in population structure/assignment analysis using STRUCTURE.STRUCTURE_Tam-doug_15IntronsMultilocus genotype dataset from 15 nuclear introns from samples of Tamiasciurus douglasii. Dataset was used in population structure/assignment analysis using STRUCTURE.
DOI: 10.5061/dryad.6gd87
title: Data from: Artificial selection on relative brain size reveals a positive genetic correlation between brain size and proactive personality in the guppy

description: Animal personalities range from individuals that are shy, cautious, and
 easily stressed (a ‘reactive’ personality type) to individuals that are
 bold, innovative and quick to learn novel tasks, but also prone to routine
 formation (a ‘proactive’ personality type). Although personality
 differences should have important consequences for fitness, their
 underlying mechanisms remain poorly understood. Here, we investigated how
 genetic variation in brain size affects personality. We put selection
 lines of large- and small-brained guppies (Poecilia reticulata), with
 known differences in cognitive ability, through three standard personality
 assays. First, we found that large-brained animals were faster to
 habituate to, and more exploratory in, open field tests. Large-brained
 females were also bolder. Second, large-brained animals excreted less
 cortisol in a stressful situation (confinement). Third, large-brained
 animals were slower to feed from a novel food source, which we interpret
 as being caused by reduced behavioral flexibility rather than lack of
 innovation in the large-brained lines. Overall, the results point towards
 a more proactive personality type in large-brained animals. Thus, this
 study provides the first experimental evidence linking brain size and
 personality, an interaction which may affect important fitness-related
 aspects of ecology such as dispersal and niche exploration.
description: Kotrschaletal.DataforDRYADthis file contains spreadsheets covering the original data used to analyze OPEN FIELD, FOOD TRIALS, and CORTISOL dataKotrschaletal.DataforDRYAD_burstspeedKotrschaletal.DataforDRYAD_criticalspeed
DOI: 10.5281/zenodo.18390705
title: RAQAMLI DAVRDA YOSHLAR TAFAKKURINING SHAKLLANISHI VA O'ZGARISH TENDENSIYALARI

description:  Mazkur ilmiy maqolada sun’iy intellekt asosidagi raqamli muhit sharoitida kognitiv jarayonlarning yangi ko‘rinishlari, ijtimoiy tarmoqlar va media oqimining yoshlar dunyoqarashi hamda qadriyatlar tizimiga ta’siri, shuningdek raqamli axborot makonida shaxs ongining transformatsiyasi va ijtimoiy xulq-atvordagi o‘zgarishlar kompleks tarzda tahlil qilinadi. Tadqiqotda raqamli texnologiyalar, ayniqsa sun’iy intellekt algoritmlarining axborotni qabul qilish, qayta ishlash va baholash jarayonlariga ta’siri ko‘rib chiqilib, bu jarayonlar inson tafakkuri va qaror qabul qilish mexanizmlarini qanday o‘zgartirayotgani ochib beriladi.
DOI: 10.5281/zenodo.18390706
title: RAQAMLI DAVRDA YOSHLAR TAFAKKURINING SHAKLLANISHI VA O'ZGARISH TENDENSIYALARI

description:  Mazkur ilmiy maqolada sun’iy intellekt asosidagi raqamli muhit sharoitida kognitiv jarayonlarning yangi ko‘rinishlari, ijtimoiy tarmoqlar va media oqimining yoshlar dunyoqarashi hamda qadriyatlar tizimiga ta’siri, shuningdek raqamli axborot makonida shaxs ongining transformatsiyasi va ijtimoiy xulq-atvordagi o‘zgarishlar kompleks tarzda tahlil qilinadi. Tadqiqotda raqamli texnologiyalar, ayniqsa sun’iy intellekt algoritmlarining axborotni qabul qilish, qayta ishlash va baholash jarayonlariga ta’siri ko‘rib chiqilib, bu jarayonlar inson tafakkuri va qaror qabul qilish mexanizmlarini qanday o‘zgartirayotgani ochib beriladi.
DOI: 10.5061/dryad.j5925
title: Data from: High resolution mapping of community structure in three glass sponge reefs (Porifera, Hexactinellida).

description: ABSTRACT: Glass sponge reefs (Porifera, Hexactinellida) are unique to the
 Pacific coast of Canada. To date, the locations and extents of reefs have
 only been assessed by multibeam echosounders, a method that does not
 resolve where live, dead and buried sponges are within a reef. We
 performed fine-scale (25 and 12.5 m grids) photographic surveys using
 remote operated vehicles and carried out GIS and semivariogram analysis to
 produce high resolution maps of the spatial distribution and abundance of
 glass sponges among 3 reefs in the Strait of Georgia and also to determine
 the community structure of animals associated with the reefs. Within a
 reef, glass sponges are clustered in spatially dependent patches 35 to 72
 m in diameter, which we interpret to result from growth and reproduction
 processes. Reefs occur within a narrow range of depths (30 to 50 m), which
 may be explained by suspension feeding requirements for flow, which is
 accelerated over the underlying elevated bedrock mounds and ridges. The
 local abundance of fish and crustaceans was significantly higher in the
 presence of glass sponges while significantly lower abundances of molluscs
 and other sponges were found within the reefs. Also, we determined that a
 dense population of reef sponges can process water at 83000 l s–1,
 removing carbon at a rate of 0.96 g C m–2 d–1. Our high resolution mapping
 establishes a biological baseline for 3 glass sponge reefs in the Strait
 of Georgia.
description: 2008 - Phantom ROV
 Animal countsCounts of animals in
 images captured by the Department of Fisheries and Oceans ROV
 Phantom2008
 - Phantom Animals.xlsx2009 -
 DSC-SurveysAnalysis of images from
 the sponge reefs captured by the ROV ROPOS in 2009GALIANO-ROPOS&PHANTOMReef area cover - analysis of images captured by both ROVs Phantom and ROPOS
DOI: 10.5061/dryad.88233
title: Data from: Cryptic differences in colour among Müllerian mimics: how can the visual capacities of predators and prey shape the evolution of wing colours?

description: Antagonistic interactions between predators and prey often lead to
 co-evolution. In the case of toxic prey, aposematic colours act as warning
 signals for predators and play a protective role. Evolutionary convergence
 in colour patterns among toxic prey evolves due to positive
 density-dependent selection and the benefits of mutual resemblance in
 spreading the mortality cost of educating predators over a larger prey
 assemblage. Comimetic species evolve highly similar colour patterns, but
 such convergence may interfere with intraspecific signalling and
 recognition in the prey community, especially for species involved in
 polymorphic mimicry. Using spectrophotometry measures, we investigated the
 variation in wing coloration among comimetic butterflies from distantly
 related lineages. We focused on seven morphs of the polymorphic species
 Heliconius numata and the seven corresponding comimetic species from the
 genus Melinaea. Significant differences in the yellow, orange and black
 patches of the wing were detected between genera. Perceptions of these
 cryptic differences by bird and butterfly observers were then estimated
 using models of animal vision based on physiological data. Our results
 showed that the most strikingly perceived differences were obtained for
 the contrast of yellow against a black background. The capacity to
 discriminate between comimetic genera based on this colour contrast was
 also evaluated to be higher for butterflies than for birds, suggesting
 that this variation in colour, likely undetectable to birds, might be used
 by butterflies for distinguishing mating partners without losing the
 benefits of mimicry. The evolution of wing colour in mimetic butterflies
 might thus be shaped by the opposite selective pressures exerted by
 predation and species recognition.
description: Color spectra for all
 individuals (raw data)Here are the spectra for
 each measures: on each individual and on each color
 patch.Llaurens-Spectra-Rawdata.xlsx
DOI: 10.5061/dryad.1h0n1
title: Data from: Diagnostic gene expression biomarkers of coral thermal stress

description: Gene expression biomarkers can enable rapid assessment of physiological
 conditions in situ, providing a valuable tool for reef managers interested
 in linking organism physiology with large-scale climatic conditions. Here,
 we assessed the ability of quantitative PCR (qPCR) based gene expression
 biomarkers to evaluate (1) the immediate cellular stress response (CSR) of
 Porites astreoides to incremental thermal stress and (2) the magnitude of
 CSR and cellular homeostasis response (CHR) during a natural bleaching
 event. Expression levels largely scaled with treatment temperature, with
 the strongest responses occurring in heat shock proteins. This is the
 first demonstration of a “tiered” CSR in a coral, where the magnitude of
 expression change is proportional to stress intensity. Analysis of a
 natural bleaching event revealed no signature of an acute CSR in normal or
 bleached corals, indicating that the bleaching stressor(s) had abated by
 the day of sampling. Another long-term stress CHR-based indicator assay
 was significantly elevated in bleached corals; though assay values overall
 were low, suggesting good prospects for recovery. This study represents
 the first step in linking variation in gene expression biomarkers to
 stress tolerance and bleaching thresholds in situ by quantifying the
 severity of ongoing thermal stress and its accumulated long-term impacts.
description: Expression Analysis R
 fileThis file contains the
 annotated R scripts necessary to conduct all gene expression analyses
 described in the accompanying paper, from initial normalization of raw Ct
 values to creating figures.QPCRanalysis.RData for Heat Gradation ExperimentThis folder contains all the input data files for gene expression analysis (including raw Ct and normalized expression data) in addition to temperature/light logger data (and associated R scripts for generating figures) and sample processing notes.HeatGrad.zipin situ Bleaching DataThis folder contains all data for gene expression analysis (including raw and normalized Ct data), sequencing data from Symbiodinium genotyping and the raw PAM data and associated R scripts for analysis and figure generation.BNB.zip
DOI: 10.15468/dl.spcz2f
title: Occurrence Download

description: A dataset containing 3418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Calligonum"
 ]
}

 The dataset includes 3418 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001606-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.