cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tj428
title: Data from: The earliest bird-line archosaurs and the assembly of the dinosaur body plan

description: The relationship between dinosaurs and other reptiles is well established,
 but the sequence of acquisition of dinosaurian features has been obscured
 by the scarcity of fossils with transitional morphologies. The closest
 extinct relatives of dinosaurs either have highly derived morphologies or
 are known from poorly preserved or incomplete material. Here we describe
 one of the stratigraphically lowest and phylogenetically earliest members
 of the avian stem lineage (Avemetatarsalia), Teleocrater rhadinus gen. et
 sp. nov., from the Middle Triassic epoch. The anatomy of T. rhadinus
 provides key information that unites several enigmatic taxa from across
 Pangaea into a previously unrecognized clade, Aphanosauria. This clade is
 the sister taxon of Ornithodira (pterosaurs and birds) and shortens the
 ghost lineage inferred at the base of Avemetatarsalia. We demonstrate that
 several anatomical features long thought to characterize Dinosauria and
 dinosauriforms evolved much earlier, soon after the bird–crocodylian
 split, and that the earliest avemetatarsalians retained the
 crocodylian-like ankle morphology and hindlimb proportions of stem
 archosaurs and early pseudosuchians. Early avemetatarsalians were
 substantially more species-rich, widely geographically distributed and
 morphologically diverse than previously recognized. Moreover, several
 early dinosauromorphs that were previously used as models to understand
 dinosaur origins may represent specialized forms rather than the ancestral
 avemetatarsalian morphology.
description: Teleocrater matrix
 Nesbitt 2011 dataset final with ScleromochlusPhylogenetic dataset
 file in tnt format.Teleocrater matrix
 Nesbitt 2011 dataset finalPhylogenetic dataset
 file in tnt format.Teleocrater matrix
 Ezcurra 2016 dataset final with ScleromochlusPhylogenetic dataset
 file in nexus format.Teleocrater matrix
 Ezcurra 2016 dataset finalPhylogenetic dataset
 file in tnt format.Teleocrater matrix
 Ezcurra 2016 dataset final with ScleromochlusPhylogenetic dataset
 file in tnt format.Teleocrater matrix
 Ezcurra 2016 dataset finalPhylogenetic dataset
 file in nexus format.Hindlimb_data_ternaryplot_FINALHindlimb data from the ternary plot. Can be opened in excel.Hindlimb_data_ternaryplot_Rscript_FINALR script used to analyze the hindlimb data.Disparity_analysis_input_data_FINALDisparity analysis results. Can be opened in excel.Disparity_analysis_Rscript_FINALR script used tin the disparity analysis.Metatarsal_estimate_inputdata_FINALData used to estimate the metatarsal length of Teleocrater. Can be opened in Excel.Metatarsal_estimate_Rscript_FINALR script used to estimate the metatarsal length of Teleocrater.Teleocrater matrix Nesbitt 2011 dataset finalPhylogenetic dataset file in nexus format.Teleocrater matrix Nesbitt 2011 dataset final with Scleromochlus
DOI: 10.5061/dryad.n511h
title: Data from: Cultural evolution of military camouflage

description: While one has evolved and the other been consciously created, animal and
 military camouflage are expected to show many similar design principles.
 Using a unique database of calibrated photographs of camouflage uniform
 patterns, processed using texture and colour analysis methods from
 computer vision, we show that the parallels with biology are deeper than
 design for effective concealment. Using two case studies we show that,
 like many animal colour patterns, military camouflage can serve multiple
 functions. Following the dissolution of the Warsaw Pact, countries that
 became more Western-facing in political terms converged on NATO patterns
 in camouflage texture and colour. Following the break-up of the former
 Yugoslavia, the resulting states diverged in design, becoming more similar
 to neighbouring countries than the ancestral design. None of these
 insights would have been obtained using extant military approaches to
 camouflage design, which focus solely on concealment. Moreover, our
 computational techniques for quantifying pattern offer new tools for
 comparative biologists studying animal coloration.
description: Data for texture,
 average colour and quantised colour for camouflage
 uniforms.RData file contents:
 PatternNames - camouflage pattern identifier; SumMaxResponses - sum of
 maximum responses per pixels (across logical maps) for each Log-Gabor
 filter (described by spatial frequency and orientation); ColDistAvgColours
 - pairwise distances of average colours of patterns; ColDistQntColours -
 pairwise distances of quantised colours of patternsCamouflageUniformsAll_Data.RData
DOI: 10.5061/dryad.10g95
title: Data from: Social learning and the demise of costly cooperation in humans

description: Humans have a sophisticated ability to learn from others, termed social
 learning, which has allowed us to spread over the planet, construct
 complex societies, and travel to the moon. It has been hypothesized that
 social learning has played a pivotal role in making human societies
 cooperative, by favouring cooperation even when it is not favoured by
 genetical selection. However, this hypothesis lacks direct experimental
 testing, and the opposite prediction has also been made, that social
 learning disfavours cooperation. We experimentally tested how different
 aspects of social learning affect the level of cooperation in public-goods
 games. We found that: (i) social information never increased cooperation
 and usually led to decreased cooperation; (ii) cooperation was lowest when
 individuals could observe how successful individuals behaved; and (iii)
 cooperation declined because individuals preferred to copy successful
 individuals, who cooperated less, rather than copy common behaviours.
 Overall, these results suggest that individuals use social information to
 try and improve their own success, and that this can lead to lower levels
 of cooperation.
description: SL_ms_final_Variables_PUBLIC_COPYData set including all the variables used in analyses for this paperSL_ms_final_results_a_baseline_cooperation copyCopy of SPSS analyses for Results section ASL_ms_final_results_b_social_learning_and_cooperationCopy of SPSS analyses for Results Section BSL_ms_final_results_c_using_social_informationCopy of SPSS analyses for Results Section CSL_ms_final_results_d_mechanisms_of_social_learningCopy of SPSS analyses for Results Section DSL_ms_final_results_e_learning_about_people_or_about_payoffsCopy of SPSS analyses for Results Section ESL_ms_final_results_f_alternative_testsCopy of SPSS analyses for Results Section FSL_ms_final_results_Si_ESMCopy of SPSS analyses for Results Section ESMSL_ms_final_results_Supp_info_correlations_TableS1Copy of SPSS analyses for Results Section ESM TABLE 1SL_ms_final_results_Supp_info_correlations_TableS2Copy of SPSS analyses for Results Section ESM TABLE 2SL_ms_final_results_Si_ESM_calculating_attractionCopy of SPSS code and analyses for calculating attraction variablesSL_Ms_public_datasetExcel copy version of SPSS dataset
DOI: 10.5061/dryad.jq32s
title: Data from: Mapping and exploring variation in post-fire vegetation recovery following mixed severity wildfire using airborne LiDAR

description: There is a public perception that large high severity wildfires decrease
 biodiversity and increase fire hazard by homogenising vegetation
 composition and increasing the cover of mid-story vegetation. But a
 growing literature suggests that vegetation responses are nuanced. LiDAR
 technology provides a promising remote sensing tool to test hypotheses
 about post-fire vegetation regrowth because vegetation cover can be
 quantified within different height strata at fine-scales over large areas.
 We assess the usefulness of airborne LiDAR data for measuring post-fire
 mid-story vegetation regrowth over a range of spatial resolutions (10x10m,
 30x30m, 50x50m, 100x100m cell size) and investigate the effect of fire
 severity on regrowth amount and spatial pattern following a mixed severity
 wildfire in Warrumbungle National Park, Australia. We predicted that
 recovery would be more vigorous in areas of high fire severity, because
 park managers observed dense post-fire regrowth in these areas. Moderate
 to strong positive associations were observed between LiDAR and field
 surveys of mid-story vegetation cover between 0.5–3m. Thus our LiDAR
 survey was an apt representation of on-ground vegetation cover.
 LiDAR-derived mid-story vegetation cover was 22–40% higher in areas of low
 and moderate than high fire severity. Linear mixed-effects models showed
 that fire severity was among the strongest biophysical predictors of
 mid-story vegetation cover irrespective of spatial resolution. However
 much of the variance associated with these models was unexplained,
 presumably because soil seedbanks varied at finer-scales than our LiDAR
 maps. Dense patches of mid-story vegetation regrowth were small (median
 size 0.01ha) and evenly distributed between areas of low, moderate and
 high fire severity, demonstrating that high severity fires do not
 homogenise vegetation cover. Our results are relevant for ecosystem
 conservation and fire management because they: indicate that native
 vegetation are responsive and resilient to high severity fire, and show
 the usefulness of remote sensing tools such as LiDAR to monitor post-fire
 vegetation recovery over large area in situ.
description: Gordonetal_2017_EcolApp_DataData presented in the manuscript "Mapping and exploring variation in post-fire vegetation recovery following mixed severity wildfire using airborne LiDAR"
DOI: 10.5061/dryad.21tm5
title: Data from: An RGB colour image steganography scheme using overlapping block-based pixel-value differencing

description: This paper presents a steganographic scheme based on the RGB colour cover
 image. The secret message bits are embedded into each colour pixel
 sequentially by the pixel-value differencing (PVD) technique. PVD
 basically works on two consecutive non-overlapping components; as a
 result, the straightforward conventional PVD technique is not applicable
 to embed the secret message bits into a colour pixel, since a colour pixel
 consists of three colour components, i.e. red, green and blue. Hence, in
 the proposed scheme, initially the three colour components are represented
 into two overlapping blocks like the combination of red and green colour
 components, while another one is the combination of green and blue colour
 components, respectively. Later, the PVD technique is employed on each
 block independently to embed the secret data. The two overlapping blocks
 are readjusted to attain the modified three colour components. The notion
 of overlapping blocks has improved the embedding capacity of the cover
 image. The scheme has been tested on a set of colour images and
 satisfactory results have been achieved in terms of embedding capacity and
 upholding the acceptable visual quality of the stego-image.
description: RGB_RSOSAll figuresMatlab codecode.rar
DOI: 10.5061/dryad.q713h
title: Data from: Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata

description: Seed germination is an important developmental and life history stage.
 Yet, the evolutionary impact of germination has mainly been studied in the
 context of dormancy, or for its role in reproductive isolation between
 species. Here, we aim to examine multiple consequences of genetic
 divergence on germination traits between two Arabidopsis lyrata
 subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North-America).
 Post-dormancy germination time, a potentially adaptive trait, showed
 differentiation between the populations, and quantitative trait loci (QTL)
 mapping revealed that the trait variation is mainly controlled by two
 antagonistic loci. These QTL areas contain several candidate genes with
 known function in post-dormancy germination in A. thaliana. The sequence
 variation of three genes was consistent with differential selection, and
 they also included fixed nonsynonymous substitutions with potential to
 account for the phenotypic differentiation. We further show that the
 divergence between the subspecies has led to a slight but significant
 reduction in hybrid germination proportions, indicating incipient
 reproductive isolation. Comparison of reciprocal F1 and F2 progenies
 suggest that Bateson-Dobzhansky-Muller-incompatibilities likely act
 through uniparentally inherited factors. Examination of genome-wide
 transmission ratio distortion further revealed that cytonuclear
 interactions cause substantial pregermination inviability in the hybrids.
 These results confirm that seed germination has adaptive potential beyond
 the dormancy stage and that hybrid seed inviability can be one of the
 first reproductive barriers to arise during divergence.
description: Measurements of seed
 germination in Arabidopsis lyrataMeasurements of
 germination time and germination success in controlled conditions. Block
 and place mark the seed position within a plate. Crosstype defines the
 reciprocal crosses. Group is the ID number of the mother plant. Ripening-
 and stratdays refer to lengths of the after-ripening and stratification
 treatments. Germination is the binary representation of whether seed
 germinated during the experiment (1) or not (0). Germdays is number of
 days from the start of the experiment until
 germination.Germlist.txtGenotypes and phenotypes of QTL mapping family 1Family1.csvGenotypes and phenotypes of QTL mapping family 2Family2.csvPhenotype_scriptR commands used to analyze the phenotype dataQTL_scriptR/qtl commands used in the QTL analysis
DOI: 10.5061/dryad.619t0
title: Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

description: Genomic studies of invasive species can reveal both invasive pathways and
 functional differences underpinning patterns of colonization success. The
 European green crab (Carcinus maenas) was initially introduced to eastern
 North America nearly 200 years ago where it expanded northwards to eastern
 Nova Scotia. A subsequent invasion to Nova Scotia from a northern European
 source allowed further range expansion, providing a unique opportunity to
 study the invasion genomics of a species with multiple invasions. Here, we
 use restriction-site-associated DNA sequencing-derived SNPs to explore
 fine-scale genomewide differentiation between these two invasions. We
 identified 9137 loci from green crab sampled from 11 locations along
 eastern North America and compared spatial variation to mitochondrial COI
 sequence variation used previously to characterize these invasions.
 Overall spatial divergence among invasions was high (pairwise FST ~0.001
 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of
 loci examined characterized by FST values &gt;0.05. The majority of
 the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal
 clines in allele frequency highlighting extensive genomic divergence among
 the invasions. Discriminant analysis of principal components (both neutral
 and outlier loci) clearly resolved the two invasions spatially and was
 highly correlated with mitochondrial divergence. Our results reveal
 extensive cryptic intraspecific genomic diversity associated with
 differing patterns of colonization success and demonstrates clear utility
 for genomic approaches to delineating the distribution and colonization
 success of aquatic invasive species.
description: green_crab_RAD_FilteredAll RAD loci in Genepop format after filtering for missing data and prior to linkage disequilibrium filters.COI_alignmentAligned nucleotides of the COI mitochondrial gene in FASTA format.
DOI: 10.5061/dryad.p9b8k
title: Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic

description: Invasive species have been associated with significant negative impacts in
 their introduced range often outcompeting native species, yet the
 long-term evolutionary dynamics of biological invasions are not well
 understood. Hybridization, either among waves of invasion or between
 native and introduced populations, could alter the ecological and
 evolutionary impacts of invasions yet has rarely been studied in marine
 invasive species. The European green crab (Carcinus maenas) invaded
 eastern North America twice from northern and southern locations in its
 native range. Here we examine the frequency of hybridization among these
 two distinct invasions at locations from New Jersey, USA to Newfoundland,
 Canada using restriction-site associated DNA sequencing (RAD-seq),
 microsatellite loci, and COI mtDNA sequences. We used Bayesian clustering
 and hybrid assignment analyses to investigate hybridization between the
 northern and southern populations. Of the samples analyzed, six locations
 contained at least one hybrid individual, while two locations were
 characterized by extensive hybridization, with 95% of individuals
 collected from Placentia Bay, Newfoundland being hybrids (mostly F2), and
 90% of individuals from Kejimkujik, Nova Scotia being classified as
 hybrids, mostly backcrosses to the northern ecotype. The presence of both
 F2 hybrids and backcrossed individuals suggests that these hybrids are
 viable and introgression is occurring between invasions. Our results
 provide insight into the demographic and evolutionary consequences of
 hybridization between independent invasions, and will inform the
 management of green crabs in eastern North America.
description: Microsat_GenepopGenepop file of all microsatellite alleles for green crabgreen_crab_RAD_FilteredGenepop file of RAD-seq derived loci after filtering for missing data and individuals with low coverage.FinalMicrosat_Renamed_Genepop_ForSim_S1R1_NHNewHybrids file of simulated individuals for power analyses using microsatellite dataSimulated_RAD_Data_ForNewHybridsSimulated Pure 1, Pure 2, F1, F2, and BC1 and BC2 individuals using the top 200 high Fst low linkage disequilibrium loci for testing power of the SNP panel.Final_Renamed_Genepop_ForSim_200_Loci_Panel_S1R1_NH.txt
DOI: 10.5061/dryad.pp837
title: Data from: Gene-tree reconciliation with MUL-trees to resolve polyploidy events

description: Polyploidy can have a huge impact on the evolution of species, and it is a
 common occurrence, especially in plants. The two types of polyploids -
 autopolyploids and allopolyploids - differ in the level of divergence
 between the genes that are brought together in the new polyploid lineage.
 Because allopolyploids are formed via hybridization, the homoeologous
 copies of genes within them are at least as divergent as orthologs in the
 parental species that came together to form them. This means that common
 methods for estimating the parental lineages of allopolyploidy events are
 not accurate, and can lead to incorrect inferences about the number of
 gene duplications and losses. Here, we have adapted an algorithm for
 topology-based gene-tree reconciliation to work with multi-labeled trees
 (MUL-trees). By definition, MUL-trees have some tips with identical
 labels, which makes them a natural representation of the genomes of
 polyploids. Using this new reconciliation algorithm we can: accurately
 place allopolyploidy events on a phylogeny, identify the parental lineages
 that hybridized to form allopolyploids, distinguish between allo-, auto-,
 and (in most cases) no polyploidy, and correctly count the number of
 duplications and losses in a set of gene trees. We validate our method
 using gene trees simulated with and without polyploidy, and revisit the
 history of polyploidy in data from the clades including both baker's
 yeast and bread wheat. Our re-analysis of the yeast data confirms the
 allopolyploid origin and parental lineages previously identified for this
 group. The method presented here should find wide use in the growing
 number of genomes from species with a history of polyploidy.
description: Supplemental_referencesSupplemental ReferencesSupplemental Figures 1-9Figures_S1-9.pdfSupplemental Tables 1-5Tables_S1-5.xlsx
DOI: 10.5061/dryad.5rm68
title: Data from: De novo transcriptome analysis of the excretory tubules of Carausius morosus (Phasmatodea) and possible functions of the midgut 'appendices'

description: The Malpighian tubules are the insect excretory organs, responsible for
 ion and water homeostasis and elimination of nitrogenous wastes.
 Post-genomic assays suggest they also metabolize and detoxify xenobiotic
 compounds and have antimicrobial properties. The Phasmatodea have an
 additional, unique set of excretory organs referred to predominantly as
 midgut appendices. Their function and how it compares to phasmid and other
 insect Malpighian tubules is unknown. Hypotheses include carbonic
 anhydrase activity, calcium and metal cation sequestration, and xenobiotic
 transport. This work presents the first comparative transcriptomic
 analysis of the Phasmatodean excretory organs, using the model insect
 Carausius morosus. I produced de novo transcriptomes of the midgut
 appendices, midgut wall, and Malpighian tubules, and looked for
 differentially expressed genes associated with putative organ functions.
 The appendices differentially and highly express lipid transport and
 metabolism proteins, and the biomineralization gene otopetrin. The
 Malpighian tubules differentially and highly express acid phosphatases and
 multiple transporter types, while appendices express fat-soluble vitamin
 and peptide transporters. Many defense proteins such as multidrug
 resistance proteins, ABC transporters, cytochrome P450's, and
 glutathione-S-transferases were differentially expressed in specific
 excretory organs. I hypothesize that the appendices and Malpighian tubules
 both have defensive / xenobiotic metabolism functions, but each likely
 target different substrates. Phasmid Malpighian tubules excrete as in
 other insects, while the appendices may predominantly regulate amino
 acids, fats, and fat-soluble compounds. Lipid metabolism in insects is
 poorly understood, and the Phasmatodea may thus serve as a model for
 studying this further.
description: Carausius morosus
 excretory system transcriptomede novo Assembly of
 Carausius morosus [Insecta: Phamatodea] transcriptome [tissues: posterior
 midgut with appendices and Malpighian tubules], assembled using CLC
 Genomics Workbench v8.0 (Qiagen®), tested for duplications, and with
 contigs fused using CAP3 with standard parameters.Carausius_cap3_assembly.fasta