cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7ds27
title: Data from: Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)

description: Honey bees are exposed to many damaging pathogens and parasites. The most
 devastating is Varroa destructor, which mainly affects the brood. A
 promising approach for preventing its spread is to breed Varroa-resistant
 honey bees. One trait that has been shown to provide significant
 resistance against the Varroa mite is hygienic behavior, which is a
 behavioral response of honeybee workers to brood diseases in general. Here
 we report the use of an Affymetrix 44K SNP array to analyze SNPs
 associated with detection and uncapping of Varroa-parasitized brood by
 individual worker bees (Apis mellifera). For this study, 22,000
 individually labeled bees were video-monitored and a sample of 122 cases
 and 122 controls was collected and analyzed to determine the dependence /
 independence of SNP genotypes from hygienic and non-hygienic behavior on a
 genome-wide scale. After false-discovery rate correction of the p-values,
 six SNP markers had highly significant associations with the trait
 investigated (alpha &lt; 0.01). Inspection of the genomic regions
 around these SNPs led to the discovery of putative candidate genes.
description: SNP data, family
 structure and SNP positionsThe zip-file contains
 the SNP data ( 2 files), the identification of the queens (families) and
 the SNP map used.zip.zip
DOI: 10.5061/dryad.31g1b
title: Data from: Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium

description: Species delimitation has seen a paradigm shift as increasing accessibility
 of genomic-scale data enables separation of lineages with convergent
 morphological traits and the merging of recently diverged ecotypes that
 have distinguishing characteristics. We inferred the process of lineage
 formation among Australian species in the widespread and highly variable
 genus Pelargonium by combining phylogenomic and population genomic
 analyses along with breeding system studies and character analysis.
 Phylogenomic analysis and population genetic clustering supported seven of
 the eight currently described species but provided little evidence for
 differences in genetic structure within the most widely distributed group
 that containing P. australe. In contrast, morphometric analysis detected
 three deep lineages within Australian Pelargonium; with P. australe
 consisting of five previously unrecognized entities occupying separate
 geographic ranges. The genomic approach enabled elucidation of parallel
 evolution in some traits formerly used to delineate species, as well as
 identification of ecotypic morphological differentiation within recognized
 species. Highly variable morphology and trait convergence each contribute
 to the discordance between phylogenomic relationships and morphological
 taxonomy. Data suggest that genetic divergence among species within the
 Australian Pelargonium may result from allopatric speciation while
 morphological differentiation within and among species may be more
 strongly driven by environmental differences.
description: Nicotra et al MEC data
 archive part 1Data from phenotype
 analyses, crossing and autogamy experiments as well as herbarium accession
 data.Nicotra et al MEC data
 archive part 2Data and supporting
 files for DAPC, STRUCTURE, SNAPP analysesPART 2
 archive.zip
DOI: 10.5061/dryad.g6s2k
title: Data from: Mek1 down regulates Rad51 activity during yeast meiosis by phosphorylation of Hed1

description: During meiosis, programmed double strand breaks (DSBs) are repaired
 preferentially between homologs to generate crossovers that promote proper
 chromosome segregation at Meiosis I. In many organisms, there are two
 strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required
 for interhomolog (IH) bias. This bias requires the presence, but not the
 strand exchange activity of Rad51, while Dmc1 is responsible for the bulk
 of meiotic recombination. How these activities are regulated is less well
 established. In dmc1Δ mutants, Rad51 is actively inhibited, thereby
 resulting in prophase arrest due to unrepaired DSBs triggering the meiotic
 recombination checkpoint. This inhibition is dependent upon the
 meiosis-specific kinase Mek1 and occurs through two different mechanisms
 that prevent complex formation with the Rad51 accessory factor Rad54: (i)
 phosphorylation of Rad54 by Mek1 and (ii) binding of Rad51 by the
 meiosis-specific protein Hed1. An open question has been why inhibition of
 Mek1 affects Hed1 repression of Rad51. This work shows that Hed1 is a
 direct substrate of Mek1. Phosphorylation of Hed1 at threonine 40 helps
 suppress Rad51 activity in dmc1Δ mutants by promoting Hed1 protein
 stability. Rad51-mediated recombination occurring in the absence of Hed1
 phosphorylation results in a significant increase in non-exchange
 chromosomes despite wild-type levels of crossovers, confirming previous
 results indicating a defect in crossover assurance. We propose that Rad51
 function in meiosis is regulated in part by the coordinated
 phosphorylation of Rad54 and Hed1 by Mek1.
description: RecSeq_files_for_Callender_et_al_2016
DOI: 10.5061/dryad.59s7t
title: Data from: Simulated annealing approach to vascular structure with application to the coronary arteries

description: Do the complex processes of angiogenesis during organism development
 ultimately lead to a near optimal coronary vasculature in the organs of
 adult mammals? We examine this hypothesis using a powerful and universal
 method, built on physical and physiological principles, for the
 determination of globally energetically optimal arterial trees. The method
 is based on simulated annealing, and can be used to examine arteries in
 hollow organs with arbitrary tissue geometries. We demonstrate that the
 approach can generate in silico vasculatures which closely match porcine
 anatomical data for the coronary arteries on all length scales, and that
 the optimized arterial trees improve systematically as computational time
 increases. The method presented here is general, and could in principle be
 used to examine the arteries of other organs. Potential applications
 include improvement of medical imaging analysis and the design of vascular
 trees for artificial organs.
description: dataData for various parts
 of the paper are contained in appropriate directories, and include matlab
 files for plotting where appropriate.
DOI: 10.5061/dryad.562ft
title: Data from: Thermal plasticity in farmed, wild and hybrid Atlantic salmon during early development: has domestication caused divergence in low temperature tolerance?

description: Background: In the past three decades, millions of domesticated Atlantic
 salmon Salmo salar L. have escaped from farms into the wild. Their
 offspring display reduced survival in the natural environment, which
 demonstrates that gene-flow is likely to have a negative effect on wild
 populations. However, inter-population differences in introgression of
 farmed salmon have been observed, and the underlying ecological mechanisms
 remain enigmatic. We hypothesised that domestication-driven divergence in
 tolerance to low temperatures during early development may contribute to
 lower survival of farmed salmon offspring in the wild, which in turn, may
 influence patterns of introgression among populations exposed to different
 temperature regimes. We reared the offspring of 35 families of wild,
 farmed and hybrid origin at three temperatures (3.9, 5.6 and 12 °C) from
 the onset of exogenous feeding and throughout their first summer. Thermal
 reaction norms for growth and survival were investigated along the
 gradient. Results: The main results of this study, which is based upon the
 analysis of juvenile salmon from five wild strains, two farmed strains and
 two hybrid strains, can be summarised as; (i) salmon of all origins were
 able to successfully initiate feeding at all temperatures and similar
 survival reaction norms were detected in all strains across the
 temperature gradient; (ii) deviating growth reaction norms were detected
 between strains, although this result was most likely due to an overall
 lack of growth in the lower temperature treatments. Conclusions: This
 study revealed no evidence of domesticated-driven divergence in low
 temperature tolerance in Atlantic salmon during early development.
 Although the potential interaction between low temperature and other
 river-specific factors cannot be excluded, our results indicate that the
 reduced survival of farmed offspring in the wild is not explained by
 farmed salmon displaying impaired abilities to initiate feeding at low
 temperatures. We therefore suggest that the observed inter-population
 patterns of introgression are not low-temperature driven and that other
 ecological or biological factors may explain why detection of farmed
 salmon in wild rivers is not synonymous with introgression. In general,
 our results support the literature indicating that phenotypic plasticity
 instead of thermal adaption has been selected for in Atlantic salmon.
description: Solberg et al 2016 BMC
 Evolutionary BiologySurvival and growth data
 for Atlantic salmon of farmed, hybrid and wild origin.
DOI: 10.5061/dryad.k974s
title: Data from: Inferring bounded evolution in phenotypic characters from phylogenetic comparative data

description: Our understanding of phenotypic evolution over macroevolutionary
 timescales largely relies on the use of stochastic models for the
 evolution of continuous traits over phylogenies. The two most widely used
 models, Brownian motion and the Ornstein–Uhlenbeck (OU) process, differ in
 that the latter includes constraints on the variance that a trait can
 attain in a clade. The OU model explicitly models adaptive evolution
 toward a trait optimum and has thus been widely used to demonstrate the
 existence of stabilizing selection on a trait. Here we introduce a new
 model for the evolution of continuous characters on phylogenies: Brownian
 motion between two reflective bounds, or Bounded Brownian Motion (BBM).
 This process also models evolutionary constraints, but of a very different
 kind. We provide analytical expressions for the likelihood of BBM and
 present a method to calculate the likelihood numerically, as well as the
 associated R code. Numerical simulations show that BBM achieves good
 performance: parameter estimation is generally accurate but more
 importantly BBM can be very easily discriminated from both BM and OU. We
 then analyze climatic niche evolution in diprotodonts and find that BBM
 best fits this empirical data set, suggesting that the climatic niches of
 diprotodonts are bounded by the climate available in Australia and the
 neighboring islands but probably evolved with little additional
 constraints. We conclude that BBM is a valuable addition to the
 macroevolutionary toolbox, which should enable researchers to elucidate
 whether the phenotypic traits they study are evolving under hard
 constraints between bounds.
description: Boucher&Démery_Online_Appendix
DOI: 10.5061/dryad.d4p98
title: Data from: Global patterns in threats to vertebrates by biological invasions

description: Biological invasions as drivers of biodiversity loss have recently been
 challenged. Fundamentally, we must know where species that are threatened
 by invasive alien species (IAS) live, and the degree to which they are
 threatened. We report the first study linking 1,372 vertebrates threatened
 by more than 200 IAS from the completely revised Global Invasive Species
 Database. New maps of the vulnerability of threatened vertebrates to IAS
 permit assessments of whether IAS have a major influence on biodiversity,
 and if so, which taxonomic groups are threatened and where they are
 threatened. We found that centres of IAS-threatened vertebrates are
 concentrated in the Americas, India, Indonesia, Australia, and New
 Zealand. The areas in which IAS-threatened species are located do not
 fully match the current hotspots of invasions, or the current hotspots of
 threatened species. The relative importance of biological invasions as
 drivers of biodiversity loss clearly varies across regions and taxa, and
 changes over time, with mammals from India, Indonesia, Australia, and
 Europe are increasingly being threatened by IAS. The chytrid fungus
 primarily threatens amphibians, whereas invasive mammals primarily
 threaten other vertebrates. The differences in IAS threats between regions
 and taxa can help efficiently target IAS, which is essential for achieving
 the Strategic Plan 2020 of the Convention on Biological Diversity.
description: Amphibians Inv
 threatenedExcel list of amphibian
 species threatened by IASBirds Inv
 ThreatenedExcel list of bird
 species threatened by IASMammals Inv
 threatenedExcel list of mammal
 species threatened by IASReptiles Inv
 threatenedExcel list of reptile
 species threatened by IASAmphibians_invasive_sumCRENVUraster of amphibian species threatened by IASbirds_invasive_sumCRENVUraster of bird species threatened by IASMammals Inv threatenedraster of mammal species threatened by IASmammals_invasive_sumCRENVU.tifreptiles_invasive_sumCRENVUraster of reptiles threatened by IAS
DOI: 10.5061/dryad.d6bc7
title: Data from: Transcriptomic response to injury sheds light on the physiological costs of reproduction in ant queens

description: The trade-off between reproduction and longevity is widespread among
 multicellular organisms. As an important exception, the reproductive
 females of perennial social insects (ants, honeybees, termites) are
 simultaneously highly fertile and very long-lived relative to their
 nonreproductive nestmates. The observation that increased fecundity is not
 coupled with decreased lifespan suggests that social insect queens do not
 have to reallocate resources between reproduction and self-maintenance. If
 queens have to compensate for the costs of reproduction on the level of
 the individual, the activation of other energy-demanding physiological
 processes might force them to reduce the production of eggs. To test this
 hypothesis in ant queens, we increased immunity costs by injury and
 measured the effect of this treatment on egg-laying rates and genomewide
 gene expression. Amputation of both middle legs led to a temporary
 decrease in egg-laying rates and affected the expression of 947 genes
 corresponding to 9% of the transcriptome. The changes comprised the
 upregulation of the immune and wound healing response on the one hand, and
 the downregulation of germ cell development, central nervous system
 development and learning ability on the other hand. Injury strongly
 influenced metabolism by inducing catabolism and repressing amino acid and
 nitrogen compound metabolism. By comparing our results to similar
 transcriptomic studies in insects, we found a highly consistent
 upregulation of immune genes due to sterile and septic wounding. The gene
 expression changes, complemented by the temporary decline of egg-laying
 rates, clearly reveal a trade-off between reproduction and the immune
 response in social insect queens.
description: FecundityEgg counts from RNA-seq queens and queens which were monitored for 4 weeksScript_RNA-seqR script for RNA-seq analysisRNA-seqGene counts and DESeq2 analysis resultCross_species_comparisonsCross-species comparison matrix (Camponotus & Drosophila studies)
DOI: 10.5061/dryad.1qt12
title: Data from: Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

description: DNA metabarcoding on soil samples is increasingly used for large-scale and
 multi-taxa biodiversity studies. However, DNA extraction may be a major
 bottleneck for such wide uses. It should be cost/time effective and allow
 dealing with large sample volumes so as to maximise the representativeness
 of both micro- and macro-organisms diversity. Here, we compared the
 performances of a fast and cheap extracellular DNA extraction protocol
 with a total DNA extraction method in retrieving bacterial, eukaryotic and
 plant diversity from tropical soil samples of ca. 10 g. The total DNA
 extraction protocol yielded more high-quality DNA. Yet, the extracellular
 DNA protocol provided similar diversity assessments although it presented
 some differences in clades relative abundance and undersampling biases. We
 argue that extracellular DNA is a good compromise between cost, labor, and
 accuracy for high-throughput DNA metabarcoding studies of soil
 biodiversity.
description: Zinger_et_al_SBB_extracellular_samplesThis file contains geographic coordinates and other characteristics of each sampleZinger_et_al_SBB_extracellular_rawdata_uniq.tarThis tar.gz file contains 3 zipped fasta files of unfiltered sequencing data (i.e. assembled reads assigned to their original sample), corresponding each to Bacteria, Eukaryota and Plants amplicons.Nouragues2013_Plants_GH_uniqThis fasta file contains sequence references of the trnL P6 loop from plant specimens occurring in the Nouragues Reserve (French Guiana).Zinger_et_al_SBB_extracellular_filtered.tarThis tar.gz file contains 3 txt files (tab delim) of filtered sequencing data (i.e. after sequence clustering and spurious OTUs removal) and associated characteristics, corresponding each to Bacteria, Eukaryota and Plants amplicons. A full description of data curation is provided in the Supplementary Methods of Zinger et al. (2016) Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA.
DOI: 10.5061/dryad.2sk24
title: Data from: Proteroctopus ribeti in coleoid evolution

description: Palaeontological data are key elements for inferring ancestral character
 states and the assembly of character complexes, but cephalopod fossils
 preserving soft tissues are very rare. The exceptionally well-preserved,
 unique specimen of Jurassic Proteroctopus ribeti Fischer & Riou
 from the Lagerstätte of La-Voulte-sur-Rhône (c. 165 Ma, France) is one of
 the few fossil octopod related taxa, but is rarely considered in
 evolutionary studies. In this paper, we used synchrotron microtomography
 to reappraise its external characters and for the first time, to reveal
 its internal structures. A unique character association is found with two
 fins, head fused to the body, eight well-developed arms with cirri and two
 rows of oblique suckers, a gladius and absence of an ink sac. The
 phylogenetic analysis indicates that Proteroctopus is a basal member of
 the Vampyropoda. However, this result should be interpreted with caution
 due to the number of unknown character states in the matrix. Contrary to
 previous assumptions, the phylogenetic position of Proteroctopus, as well
 as its stratigraphic occurrence, suggest that the arrangement of biserial
 suckers may be the ancestral condition in Vampyropoda.
description: Proteroctopus in coleoid
 evolution supplementary materialThe supplementary
 material includes CT scan data acquisition, table of measurements,
 phylogenetic analysis data, characters list, list of synapomorphies and 2
 figures (tree with nodes and image of the gills).Dryad_palaeontology.docx
DOI: 10.5061/dryad.0bn55
title: Data from: Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set

description: A diversity reference set has been constructed for the Gossypium
 accessions in the U.S. National Cotton Germplasm Collection to facilitate
 more extensive evaluation and utilization of accessions held in the
 Collection. A set of 105 mapped simple sequence repeat markers were used
 to study the allelic diversity of 1,933 tetraploid Gossypium accessions
 representative of the range of diversity of the improved and wild
 accessions of G. hirsutum and G. barbadense. The reference set contained
 410 G. barbadense accessions and 1,523 G. hirsutum accessions. Observed
 numbers of polymorphic and private bands indicated a greater diversity in
 G. hirsutum as compared to G. barbadense as well as in wild type
 accessions as compared to improved accessions in both species. The markers
 clearly differentiated the two species. Patterns of diversity within
 species were observed but not clearly delineated, with much overlap
 occurring between races and regions of origin for wild accessions and
 between historical and geographic breeding pools for cultivated
 accessions. Although the percentage of accessions showing introgression
 was higher among wild accessions than cultivars in both species, the
 average level of introgression within individual accessions, as indicated
 by species-specific bands, was much higher in wild accessions of G.
 hirsutum than in wild accessions of G. barbadense. The average level of
 introgression within individual accessions was higher in improved G.
 barbadense cultivars than in G. hirsutum cultivars. This molecular
 characterization reveals the levels and distributions of genetic diversity
 that will allow for better exploration and utilization of cotton genetic
 resources.
description: Molecular Data Scores
 for G. hirsutum and G. barbadenseSSR fragment
 presence/absence matrix of molecular data originally collected from 1971
 G. hirsutum and G. barbadense accessions obtained from the US National
 Cotton Germplasm Collection (NCGC) using 105 SSR markers. Please see
 ReadMe file for further information.HirsBarbSSRDataset.xlsx
DOI: 10.5061/dryad.8gm85
title: Data from: Bayes factors unmask highly variable information content, bias, and extreme influence in phylogenomic analyses

description: As the application of genomic data in phylogenetics has become routine, a
 number of cases have arisen where alternative data sets strongly support
 conflicting conclusions. This sensitivity to analytical decisions has
 prevented firm resolution of some of the most recalcitrant nodes in the
 tree of life. To better understand the causes and nature of this
 sensitivity, we analyzed several phylogenomic data sets using an
 alternative measure of topological support (the Bayes factor) that both
 demonstrates and averts several limitations of more frequently employed
 support measures (such as Markov chain Monte Carlo estimates of posterior
 probabilities). Bayes factors reveal important, previously hidden,
 differences across six “phylogenomic” data sets collected to resolve the
 phylogenetic placement of turtles within Amniota. These data sets vary
 substantially in their support for well-established amniote relationships,
 particularly in the proportion of genes that contain extreme amounts of
 information as well as the proportion that strongly reject these
 uncontroversial relationships. All six data sets contain little
 information to resolve the phylogenetic placement of turtles relative to
 other amniotes. Bayes factors also reveal that a very small number of
 extremely influential genes (less than 1% of genes in a data set) can
 fundamentally change significant phylogenetic conclusions. In one example,
 these genes are shown to contain previously unrecognized paralogs. This
 study demonstrates both that the resolution of difficult phylogenomic
 problems remains sensitive to seemingly minor analysis details and that
 Bayes factors are a valuable tool for identifying and solving these
 challenges.
description: AlignmentsIndividual gene alignments from six phylogenomic studies.alignments.zipSupplementary Code, Tables, and FiguresBrown_Thomson_SystBiol_SI.pdf