cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.50tq3
title: Data from: Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

description: Carnivorous plants exploit animals as a nutritional source and have
 inspired long-standing questions about the origin and evolution of
 carnivory-related traits. To investigate the molecular bases of carnivory,
 we sequenced the genome of the heterophyllous pitcher plant Cephalotus
 follicularis, in which we succeeded in regulating the developmental switch
 between carnivorous and non-carnivorous leaves. Transcriptome comparison
 of the two leaf types and gene repertoire analysis identified genetic
 changes associated with prey attraction, capture, digestion and nutrient
 absorption. Analysis of digestive fluid proteins from C. follicularis and
 three other carnivorous plants with independent carnivorous origins
 revealed repeated co-options of stress-responsive protein lineages coupled
 with convergent amino acid substitutions to acquire digestive physiology.
 These results imply constraints on the available routes to evolve plant
 carnivory.
description: BadiRate_analysisBadiRate.zipconvergence_detectiongene_modelgenome_sequenceGO_annotationmaximum_likelihood_phylogenyorthoMCL_analysisorthoMCL.zipprotein_structuretranscriptome_comparison
DOI: 10.5061/dryad.51110
title: Data from: Correlations of behavioral deficits with brain pathology assessed through longitudinal MRI and histopathology in the HDHQ150/Q150 mouse model of Huntington's disease

description: A variety of mouse models have been developed that express mutant
 huntingtin (mHTT) leading to aggregates and inclusions that model the
 molecular pathology observed in Huntington’s disease. Here we show that
 although homozygous HdhQ150 knock-in mice developed motor impairments
 (rotarod, locomotor activity, grip strength) by 36 weeks of age, cognitive
 dysfunction (swimming T maze, fear conditioning, odor discrimination,
 social interaction) was not evident by 94 weeks. Concomitant to behavioral
 assessments, T2-weighted MRI volume measurements indicated a slower
 striatal growth with a significant difference between wild type (WT) and
 HdhQ150 mice being present even at 15 weeks. Indeed, MRI indicated
 significant volumetric changes prior to the emergence of the “clinical
 horizon” of motor impairments at 36 weeks of age. A striatal decrease of
 27% was observed over 94 weeks with cortex (12%) and hippocampus (21%)
 also indicating significant atrophy. A hypothesis-free analysis using
 tensor-based morphometry highlighted further regions undergoing atrophy by
 contrasting brain growth and regional neurodegeneration. Histology
 revealed the widespread presence of mHTT aggregates and cellular
 inclusions. However, there was little evidence of correlations between
 these outcome measures, potentially indicating that other factors are
 important in the causal cascade linking the molecular pathology to the
 emergence of behavioral impairments. In conclusion, the HdhQ150 mouse
 model replicates many aspects of the human condition, including an
 extended pre-manifest period prior to the emergence of motor impairments.
description: MRI - in
 vivoHdhQ150
 MRI.zip
DOI: 10.15468/dl.2trknv
title: Occurrence Download

description: A dataset containing 1179494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Psittaciformes",
 "Year 2000-2026"
 ]
}

 The dataset includes 1179494 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000315-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h13jv
title: Data from: Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa

description: Ecological diversification through divergent selection is thought to be a
 major force during the process of adaptive radiations. However, the large
 sizes and complexity of most radiations such as those of the cichlids in
 the African Great Lakes make it impossible to infer the exact evolutionary
 history of any population divergence event. The genus Alcolapia, a small
 cichlid lineage endemic to Lakes Magadi and Natron in East Africa,
 exhibits phenotypes similar to some of those found in cichlids of the
 radiations of the African Great Lakes. The simplicity within Alcolapia
 makes it an excellent model system to investigate ecological
 diversification and speciation. We used an integrated approach including
 population genomics based on RAD-seq data, geometric morphometrics, and
 stable isotope analyses to investigate the eco-morphological
 diversification of tilapia in Lake Magadi and its satellite lake Little
 Magadi. Additionally, we reconstructed the demographic history of the
 species using coalescent simulations based on the joint site frequency
 spectrum. The population in Little Magadi has a characteristically
 upturned mouth - possibly an adaptation to feeding on prey from the water
 surface. Eco-morphological differences between populations within Lake
 Magadi are more subtle, but are consistent with known ecological
 differences between its lagoons such as high concentrations of nitrogen
 attributable to extensive guano deposits in Rest of Magadi relative to
 Fish Springs Lagoon. All populations diverged simultaneously only about
 1,100 generations ago. Differences in levels of gene flow between
 populations and the effective population sizes have likely resulted in the
 inferred heterogeneous patterns of genome-wide differentiation.
description: Stacks catalog and
 variant filesAll catalog and variant
 files produced by STACKS that formed the basis of the population genomic
 analyses. Note that additional individuals and populations were used to
 create the catalog, but were not used for this project.stacks_files.tar.gzVariant Call Format (VCF) fileData file containing the final (filtered) variants for all individuals that were used to build the site frequency spectrum and the population cluster analyses. Only one SNP per RAD-tag locus was included in this file.batch_1.vcfBayeScan resultsFull BayeScan output and data file.BayeScan.zipStable_isotope_dataStable isotope data file containing all relevant quantities.Magadi morphometrics input filesInput data file containing the two dimensional coordinates of the twelve landmarks used in the morphometric analysis
DOI: 10.5061/dryad.d95j4
title: Data from: Transcriptome analysis of predator- and prey-induced phenotypic plasticity in the Hokkaido salamander (Hynobius retardatus)

description: Predator- and prey-induced phenotypic plasticity is widely observed among
 amphibian species. Although ecological factors inducing diverse phenotypic
 responses have been extensively characterized, we know little about the
 molecular bases of variation in phenotypic plasticity. Larvae of the
 Hokkaido salamander, Hynobius retardatus, exhibit two distinct morphs: the
 presence of their prey, Rana pirica tadpoles, induces a broad-headed
 attack morph, and the presence of predatory dragonfly nymphs (Aeshna
 nigroflava) induces a defence morph with enlarged external gills and a
 high tail. To compare the genes involved in predator- and prey-induced
 phenotypic plasticity, we carried out a de novo transcriptome analysis of
 Hokkaido salamander larvae exposed to either prey or predator individuals.
 First, we found that the number of genes involved in the expression of the
 defence morph was approximately five times the number involved in the
 expression of the attack morph. This result is consistent with the fact
 that the predator-induced plasticity involves more drastic morphological
 changes than the prey-induced plasticity. Second, we found that particular
 sets of genes were upregulated during the induction of both the attack and
 defence morphs, but others were specific to the expression of one or the
 other morph. Because both shared and unique molecular mechanisms were used
 in the expression of each morph, the evolution of a new plastic phenotype
 might involve both the co-option of pre-existing molecular mechanisms and
 the acquisition of novel regulatory mechanisms.
description: PRJDB2409BioProjecct of transcriptome of Hokkaido salamander include raw sequencing files, a de novo assembly file, and gene expression files.EzoSal.transcriptome.annotationAn Annotation file of de novo assembled contigsEzosal.transcriptome.Trinity_components.countsCounting data of each library which is an input file of DEG analysisDEG.piarwise.outputRaw output files of pairwise DEG analysisDEG.GLM.outputRaw output files of GLM DEG analysisMorphological.measurementsData of morphological measurementsTranscriptome assembly of Hokkaido salamanderTrinity.EzoSal.fasta
DOI: 10.5061/dryad.r1921
title: Data from: Collective behaviour in vertebrates: a sensory perspective

description: Collective behaviour models can predict behaviours of schools, flocks, and
 herds. However, in many cases, these models make biologically unrealistic
 assumptions in terms of the sensory capabilities of the organism, which
 are applied across different species. We explored how sensitive collective
 behaviour models are to these sensory assumptions. Specifically, we used
 parameters reflecting the visual coverage and visual acuity that determine
 the spatial range over which an individual can detect and interact with
 conspecifics. Using metric and topological collective behaviour models, we
 compared the classic sensory parameters, typically used to model birds and
 fish, with a set of realistic sensory parameters obtained through
 physiological measurements. Compared with the classic sensory assumptions,
 the realistic assumptions increased perceptual ranges, which led to fewer
 groups and larger group sizes in all species, and higher polarity values
 and slightly shorter neighbour distances in the fish species. Overall,
 classic visual sensory assumptions are not representative of many species
 showing collective behaviour and constrain unrealistically their
 perceptual ranges. More importantly, caution must be exercised when
 empirically testing the predictions of these models in terms of choosing
 the model species, making realistic predictions, and interpreting the
 results.
description: Simulation
 DataRaw data for the
 modeling simulations for each of the four species (European Starling,
 Red-winged Blackbird, Golden Shiner and Zebrafish).
DOI: 10.5061/dryad.ds21fv5
title: Data from: Evolution of sex-biased gene expression and dosage compensation in the eye and brain of Heliconius butterflies

description: Differences in behavior and life history traits between females and males
 are the basis of divergent selective pressures between sexes. It has been
 suggested that a way for the two sexes to deal with different life history
 requirements is through sex-biased gene expression. In this study, we
 performed a comparative sex-biased gene expression analysis of the
 combined eye and brain transcriptome from five Heliconius species, H.
 charithonia, H. sara, H. erato, H. melpomene and H. doris, representing
 five of the main clades from the Heliconius phylogeny. We found that the
 degree of sexual dimorphism in gene expression is not conserved across
 Heliconius. Most of the sex-biased genes identified in each species are
 not sex-biased in any other, suggesting that sexual selection might have
 driven sexually dimorphic gene expression. Only three genes shared
 sex-biased expression across multiple species: ultraviolet opsin UVRh1 and
 orthologs of Drosophila Krüppel-homolog 1 and CG9492. We also observed
 that in some species female-biased genes have higher evolutionary rates,
 but in others, male-biased genes show the fastest rates when compared with
 unbiased genes, suggesting that selective forces driving sex-biased gene
 evolution in Heliconius act in a sex- and species-specific manner.
 Furthermore, we found dosage compensation in all the Heliconius tested,
 providing additional evidence for the conservation of dosage compensation
 across Lepidoptera. Finally, sex-biased genes are significantly enriched
 on the Z, a pattern that could be a result of sexually antagonistic
 selection.
description: HSA_heads_denovoDe novo transcriptome made from heads of 1 male and 1 female Heliconius melpomeneHDO_heads_denovoDe novo transcriptome made from heads of 1 male and 1 female Heliconius dorisHCH_heads_denovoDe novo transcriptome made from heads of 1 male and 1 female Heliconius charithoniaHER_new_headsDe novo transcriptome made from 1 male and 1 female Heliconius eratoBH_full_annotation_HSABH_full_annotation_HMEBH_full_annotation_HERBH_full_annotation_HDOBH_full_annotation_HCHAnnotation file for H. charithonia de novo trancriptome
DOI: 10.5061/dryad.5g1k6
title: Data from: Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin

description: The mechanism(s) by which fatty acids are sequestered and transported in
 muscle have not been fully elucidated. A potential key player in this
 process is the protein myoglobin (Mb). Indeed, there is a catalogue of
 empirical evidence supporting direct interaction of globins with fatty
 acid metabolites; however, the binding pocket and regulation of the
 interaction remains to be established. In this study, we employed a
 computational strategy to elucidate the structural determinants of fatty
 acids (palmitic & oleic acid) binding to Mb. Sequence analysis and
 docking simulations with a horse (Equus caballus) structural Mb reference
 reveals a fatty acid-binding site in the hydrophobic cleft near the heme
 region in Mb. Both palmitic acid and oleic acid attain a “U” shaped
 structure similar to their conformation in pockets of other fatty
 acid-binding proteins. Specifically, we found that the carboxyl head group
 of palmitic acid coordinates with the amino group of Lys45, whereas the
 carboxyl group of oleic acid coordinates with both the amino groups of
 Lys45 and Lys63. The alkyl tails of both fatty acids are supported by
 surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67,
 Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail
 moves freely and occasionally penetrates deeper inside the hydrophobic
 cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our
 simulations reveal a dynamic and stable binding pocket in which the oxygen
 molecule and heme group in Mb are required for additional hydrophobic
 interactions. Taken together, these findings support a mechanism in which
 Mb acts as a muscle transporter for fatty acid when it is in the
 oxygenated state and releases fatty acid when Mb converts to deoxygenated
 state.
description: 2V1K_horse_deoxyhorse_oxyhorse_oxy_10nshorse_oxy_only_wbi_10nshorse_oxy-OLE_wbi_100nshorse_oxy-PLM_wbi_100nsmutant_complex_wbipar_all27top_hemescript_construction_deoxyscript_construction_oxyscript_construction_oxy-FA-complexhorse_oxy_only_wbi_10ns_compressedhorse_oxy-OLE_wbi_100ns_compressedmutant_complex_wbi_compressedhorse_oxy-PLM_wbi_100ns_compressedhorse_oxy-PLM_wbi_100ns_compresses.dcdRead_Metop_heme_oxy_optimized_chargesTopology file for the updated oxygen and heme parameters calculated from Quantum Mechanics calculations
DOI: 10.5061/dryad.34569
title: Data from: Strong coupling of plant and fungal community structure across western Amazonian rainforests

description: The Amazon basin harbors a diverse ecological community that has a
 critical role in the maintenance of the biosphere. Although plant and
 animal communities have received much attention, basic information is
 lacking for fungal or prokaryotic communities. This is despite the fact
 that recent ecological studies have suggested a prominent role for
 interactions with soil fungi in structuring the diversity and abundance of
 tropical rainforest trees. In this study, we characterize soil fungal
 communities across three major tropical forest types in the western Amazon
 basin (terra firme, seasonally flooded and white sand) using 454
 pyrosequencing. Using these data, we examine the relationship between
 fungal diversity and tree species richness, and between fungal community
 composition and tree species composition, soil environment and spatial
 proximity. We find that the fungal community in these ecosystems is
 diverse, with high degrees of spatial variability related to forest type.
 We also find strong correlations between α- and β-diversity of soil fungi
 and trees. Both fungal and plant community β-diversity were also
 correlated with differences in environmental conditions. The correlation
 between plant and fungal richness was stronger in fungal lineages known
 for biotrophic strategies (for example, pathogens, mycorrhizas) compared
 with a lineage known primarily for saprotrophy (yeasts), suggesting that
 this coupling is, at least in part, due to direct plant–fungal
 interactions. These data provide a much-needed look at an understudied
 dimension of the biota in an important ecosystem and supports the
 hypothesis that fungal communities are involved in the regulation of
 tropical tree diversity.
description: GPV8ECL04SFF file with raw fungal ITS sequencesPrimer_Map_12May2014Primer map for 454 data
DOI: 10.5061/dryad.02tf9
title: Data from: Computational performance and statistical accuracy of *BEAST and comparisons with other methods

description: Under the multispecies coalescent model of molecular evolution, gene trees
 have independent evolutionary histories within a shared species tree. In
 comparison, supermatrix concatenation methods assume that gene trees share
 a single common genealogical history, thereby equating gene coalescence
 with species divergence. The multispecies coalescent is supported by
 previous studies which found that its predicted distributions fit
 empirical data, and that concatenation is not a consistent estimator of
 the species tree. *BEAST, a fully Bayesian implementation of the
 multispecies coalescent, is popular but computationally intensive, so the
 increasing size of phylogenetic data sets is both a computational
 challenge and an opportunity for better systematics. Using simulation
 studies, we characterize the scaling behavior of *BEAST, and enable
 quantitative prediction of the impact increasing the number of loci has on
 both computational performance and statistical accuracy. Follow-up
 simulations over a wide range of parameters show that the statistical
 performance of *BEAST relative to concatenation improves both as branch
 length is reduced and as the number of loci is increased. Finally, using
 simulations based on estimated parameters from two phylogenomic data sets,
 we compare the performance of a range of species tree and concatenation
 methods to show that using *BEAST with tens of loci can be preferable to
 using concatenation with thousands of loci. Our results provide insight
 into the practicalities of Bayesian species tree estimation, the number of
 loci required to obtain a given level of accuracy and the situations in
 which supermatrix or summary methods will be outperformed by the fully
 Bayesian multispecies coalescent.
description: Supplementary Data
 FilesSpecies tree, gene tree
 and BEAST 2 XML files used for simulation studiessuppl-data.tar.gzNew Supplementary InformationSupplementary tables, figures and descriptions of experiments.
DOI: 10.5061/dryad.fp1bg
title: Data from: Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments

description: Assays to accurately estimate relative fitness of bacteria growing in
 multistrain communities can advance our understanding of how selection
 shapes diversity within a lineage. Here, we present a variant of the
 “evolve and resequence” approach both to estimate relative fitness and to
 identify genetic variants responsible for fitness variation of symbiotic
 bacteria in free-living and host environments. We demonstrate the utility
 of this approach by characterizing selection by two plant hosts and in two
 free-living environments (sterilized soil and liquid media) acting on
 synthetic communities of the facultatively symbiotic bacterium Ensifer
 meliloti. We find (i) selection that hosts exert on rhizobial communities
 depends on competition among strains, (ii) selection is stronger inside
 hosts than in either free-living environment, and (iii) a positive
 host-dependent relationship between relative strain fitness in multistrain
 communities and host benefits provided by strains in single-strain
 experiments. The greatest changes in allele frequencies in response to
 plant hosts are in genes associated with motility, regulation of nitrogen
 fixation, and host/rhizobia signaling. The approach we present provides a
 powerful complement to experimental evolution and forward genetic screens
 for characterizing selection in bacterial populations, identifying gene
 function, and surveying the functional importance of naturally occurring
 genomic variation.
description: Select and resequence
 data packageThis zipped set of files
 includes all intermediate data sets and major scripts used to create the
 results and figures in the paper. See Readme file for additional
 info.public_data_release_final.zip
DOI: 10.5061/dryad.nr1td
title: Data from: A phylogeny of the treehopper subfamily Heteronotinae reveals convergent pronotal traits (Hemiptera: Auchenorrhyncha: Membracidae)

description: Even within an insect family famous for its morphological diversity, the
 treehopper subfamily Heteronotinae is a microcosm of pronotal variation,
 displaying remarkably dissimilar thoracic ornamentations among its ten
 included genera. Presented here is a reconstruction of heteronotine
 relationships based on DNA nucleotide sequence data from five nuclear and
 two mitochondrial genes from a comprehensive sample of ingroup taxa
 (including exemplars of all genera except for the monotypic Dysyncritus
 Fowler, 1895). Concordant phylogenetic estimates support the monophyly of
 Heteronotinae sensu stricto (i.e. excluding Darnoides Fairmaire, 1846), as
 well as the monophyly of the included genera Heteronotus Laporte, 1832,
 Nassunia Stål, 1862, Omolon Walker, 1862, Rhexia Stål, 1867, and
 Smiliorachis Fairmaire, 1846. Conversely, Anchistrotus Buckton, 1902,
 Allodrilus Evangelista, 2014 and Iria Stål, 1867 were not recovered as
 monophyletic, although topology comparison tests failed to reject the
 nonmonophyly of the latter two genera, nor Heteronotinae, as currently
 circumscribed. These results are interpreted in the context of available
 morphological evidence, which generally supports these findings. Also
 addressed here is the evolution of selected pronotal features representing
 major aspects of heteronotine morphology. Bayesian stochastic mapping of
 pronotal traits estimated multiple character state transitions, suggesting
 repeated acquisition of pronotal features, most of which have evolved
 independently within the diverse genus Heteronotus. These convergences may
 provide insight into the role of the pronotum in heteronotine groups that
 appear to serve different adaptive strategies, such as mimicry, crypsis
 and defence against predators. Furthermore, our results show a substantial
 diversity in need of formal description, including possible new genera,
 and several unique sexually dimorphic syndromes that may constitute a
 species complex within Heteronotus delineatus Walker, 1858. Nomenclatural
 changes are proposed for Nassunia nigromacula (Funkhouser, 1940) new
 combination and Smiliorachis inornata Stål, 1862 combination reinstated,
 which were found to be misplaced at the generic and subfamily levels
 according to our analyses.
description: DNA
 MatricesDNA matrices for the
 concatenated dataset and single gene fragments.Matrices.zipVoucher ImagesPhotographs for DNA voucher specimens included in the phylogenetic analysesCharacters scoresMatrices used in the stochastic mapping of pronotal traisCharacters scored.zipTable S1 - Voucher DataVoucher information for specimens included in the phylogenetic analyses.Table S1.pdf