cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9v852
title: Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae)

description: Biogeographic patterns displayed by obligate freshwater organisms are
 intimately related to the nature and extent of connectivity between
 suitable habitats. Two of the more significant barriers to freshwater
 connections are seawater and major drainage divides. South-eastern
 Australia provides a contrast between these barriers as it has discrete
 areas that are likely influenced to a greater or lesser extent by each
 barrier type. We use continental shelf width as a proxy for the potential
 degree of river coalescence during low sea levels. Our specific hypothesis
 is that the degree of phylogeographic divergence between coastal river
 basins should correspond to the continental shelf width of each region.
 This predicts that genetic divergences between river basins should be
 lowest in regions with a wider continental shelf and that regions with
 similar continental shelf width should have similar genetic divergences.
 Pygmy perches (Nannoperca australis and Nannoperca ‘flindersi’) in
 south-eastern Australia provide an ideal opportunity to test these
 biogeographic hypotheses. Phylogeographic patterns were examined based on
 range-wide sampling of 82 populations for cytochrome b and 23 polymorphic
 allozyme loci. Our results recovered only limited support for our
 continental shelf width hypothesis, although patterns within Bass clade
 were largely congruent with reconstructed low sea-level drainage patterns.
 In addition, we identified several instances of drainage divide crossings,
 typically associated with low elevational differences. Our results
 demonstrate high levels of genetic heterogeneity with important
 conservation implications, especially for declining populations in the
 Murray–Darling Basin and a highly restricted disjunct population in Ansons
 River, Tasmania.
description: 5699 bp of mtDNA
 datafileNexus file for sequence
 data for 5699 bp of mtDNA.mtdna.dryad.submission.nexNannoperca cytb data for unique haplotypesNexus file for sequence data for cytochrome b gene by haplotype.spp.byhap.haponly2.nexNannoperca cytb data for all individualsNexus file for sequence data for cytochrome b gene for all individuals.spp.cytb.all.final.paper.nexNannoperca cytb data for all individuals grouped by lineageMega file for sequence data for cytochrome b gene for all individuals grouped by lineage.spp.cytb.all.group.by.lineage.final.paper.megNannoperca cytb data for continental shelf hypothesis grouped by lineageMega file for sequence data for cytochrome b gene for testing the continental shelf hypothesis grouped by lineage. This contains a subset of the complete datafiles.spp.shelf.hyp.bygroup.megInput data file to BEAST based on 5699 bp of mtDNAspp.allgenes.StarBEAST.upgma.xmlSPP_Molec_Ecol_raw_allozyme_dataRaw allozyme data
DOI: 10.15468/dl.c2xp9g
title: Occurrence Download

description: A dataset containing 391537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Marchantiophyta",
 "HasCoordinate is true",
 "Geometry POLYGON((-180 60, 180 60, 180 90, -180 90, -180 60))"
 ]
}

 The dataset includes 391537 records from 228 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001567-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.354cpr
title: Occurrence Download

description: A dataset containing 8014 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Ficus religiosa L."
 ]
}

 The dataset includes 8014 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004186-250123221155621/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6j9r7
title: Data from: Anatomical enablers and the evolution of C4 photosynthesis in grasses

description: C4 photosynthesis is a series of anatomical and biochemical modifications
 to the typical C3 pathway that increases the productivity of plants in
 warm, sunny, and dry conditions. Despite its complexity, it evolved more
 than 62 times independently in flowering plants. However, C4 origins are
 absent from most plant lineages and clustered in others, suggesting that
 some characteristics increase C4 evolvability in certain phylogenetic
 groups. The C4 trait has evolved 22–24 times in grasses, and all origins
 occurred within the PACMAD clade, whereas the similarly sized BEP clade
 contains only C3 taxa. Here, multiple foliar anatomy traits of 157 species
 from both BEP and PACMAD clades are quantified and analyzed in a
 phylogenetic framework. Statistical modeling indicates that C4
 evolvability strongly increases when the proportion of vascular bundle
 sheath (BS) tissue is higher than 15%, which results from a combination of
 short distance between BS and large BS cells. A reduction in the distance
 between BS occurred before the split of the BEP and PACMAD clades, but a
 decrease in BS cell size later occurred in BEP taxa. Therefore, when
 environmental changes promoted C4 evolution, suitable anatomy was present
 only in members of the PACMAD clade, explaining the clustering of C4
 origins in this lineage. These results show that key alterations of foliar
 anatomy occurring in a C3 context and preceding the emergence of the C4
 syndrome by millions of years facilitated the repeated evolution of one of
 the most successful physiological innovations in angiosperm history.
description: datasetDataset of anatomical data used for comparative analyses. Details and definition of abbreviations can be found in the manuscript.matrixAlignment of the plastid markers rbcL, ndhF and matK used for phylogenetic analyses, in nexus format.phylogenyCalibrated phylogenetic tree inferred with Beast based on the three plastid markers rbcL, ndhF and matK.
DOI: 10.5061/dryad.pd658
title: Data from: A virus responds instantly to the presence of the vector on the host and forms transmission morphs

description: Many plant and animal viruses are spread by insect vectors. Cauliflower
 mosaic virus (CaMV) is aphid-transmitted, with the virus being taken up
 from specialized transmission bodies (TB) formed within infected plant
 cells. However, the precise events during TB-mediated virus acquisition by
 aphids are unknown. Here, we show that TBs react instantly to the presence
 of the vector by ultra-rapid and reversible redistribution of their key
 components onto microtubules throughout the cell. Enhancing or inhibiting
 this TB reaction pharmacologically or by using a mutant virus enhanced or
 inhibited transmission, respectively, confirming its requirement for
 efficient virus-acquisition. Our results suggest that CaMV can perceive
 aphid vectors, either directly or indirectly by sharing the host
 perception. This novel concept in virology, where viruses respond directly
 or via the host to the outside world, opens new research horizons, that
 is, investigating the impact of ‘perceptive behaviors’ on other steps of
 the infection cycle.
description: Figure2AConfocal image stackFigure2BConfocal image stackFigure2CConfocal image stackFigure2DConfocal image stackFigure2EConfocal image stackFigure2FConfocal image stackFigure5AConfocal image stackFigure5BConfocal image stackFigure6AConfocal image projectionFigure6BConfocal image sectionFigure6CConfocal image sectionFigure8AConfocal image stackFigure8BConfocal image stackFigure8DConfocal image stackFigure9FConfocal image stackFigure10BConfocal image stackFigure10FConfocal image stack
DOI: 10.5061/dryad.4h554
title: Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin

description: Across heterogeneous landscapes, populations may have adaptive differences
 in gene regulation that adjust their physiologies to match local
 environments. Such differences could have origins in acclimation or in
 genetically fixed variation between habitats. Here we use common garden
 experiments to evaluate differences in gene expression between populations
 of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km
 and average temperature differences of 5 °C to 8 °C. Across expression
 profiles from 18,883 genes after three years of common conditions, we find
 highly correlated expression patterns (Pearson’s r = 0.992) among most
 genes. However, sixty-six genes were differentially expressed, including
 many ribosomal protein and biomineralization genes, all of which had
 higher expression in urchins originally from the southern population. Gene
 function analyses revealed slight but pervasive expression differences in
 genes related to ribosomal function, metabolism, transport, “bone”
 development, and response to stimuli. In accord with gene expression
 patterns, a post-hoc spine re-growth experiment revealed that urchins of
 southern origin re-grew spines at a faster rate than northern urchins.
 These results suggest that there may be genetically controlled,
 potentially adaptive differences in gene regulation across habitats and
 that gene expression differences may be under strong enough selection to
 overcome high dispersal-mediated gene flow in this marine species.
description: Pespeni_SpurpuratusAdultCommonGardenGeneExpressionDataGene expression data from Strongylocentrotus purpuratus adult tube foot tissue. Animals were collected from the field (Boiler Bay, Oregon and San Diego, California) and common garden acclimated for 3 years in outdoor flow-through aquaria at the Hopkins Marine Station of Stanford University in Pacific Grove, California. See README file for additional information.
DOI: 10.5061/dryad.d08h9
title: Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping

description: Threespine stickleback populations are model systems for studying adaptive
 evolution and the underlying genetics. In lakes on the Haida Gwaii
 archipelago (off western Canada), stickleback have undergone a remarkable
 local radiation and show phenotypic diversity matching that seen
 throughout the species distribution. To provide a historical context for
 this radiation, we surveyed genetic variation at &gt;1000 single
 nucleotide polymorphism (SNP) loci in stickleback from over 100
 populations. SNPs included markers evenly distributed throughout genome
 and candidate SNPs tagging adaptive genomic regions. Based on evenly
 distributed SNPs, the phylogeographic pattern differs substantially from
 the disjunct pattern previously observed between two highly divergent
 mtDNA lineages. The SNP tree instead shows extensive within watershed
 population clustering and different watersheds separated by short branches
 deep in the tree. These data are consistent with separate colonizations of
 most watersheds, despite underlying genetic connections between some
 independent drainages. This supports previous suppositions that
 morphological diversity observed between watersheds has been shaped
 independently, with populations exhibiting complete loss of lateral plates
 and giant size each occurring in several distinct clades. Throughout the
 archipelago, we see repeated selection of SNPs tagging candidate
 freshwater adaptive variants at several genomic regions differentiated
 between marine–freshwater populations on a global scale (e.g. EDA, Na/K
 ATPase). In estuarine sites, both marine and freshwater allelic variants
 were commonly detected. We also found typically marine alleles present in
 a few freshwater lakes, especially those with completely plated
 morphology. These results provide a general model for postglacial
 colonization of freshwater habitat by sticklebacks and illustrate the
 tremendous potential of genome-wide SNP data sets hold for resolving
 patterns and processes underlying recent adaptive divergences.
description: Genotype
 dataGenotype data at 1170
 loci for all 467 individual sticklebackHaidaGwaiiStickleSNP.csv
DOI: 10.5061/dryad.bg40m
title: Data from: Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings

description: Conservation programmes aim at minimising the loss of genetic diversity,
 which allows populations to adapt to potential environmental changes. This
 can be achieved by calculating how many offspring every individual should
 contribute to the next generation to minimise global coancestry. However,
 an undesired consequence of this strategy is that it maintains deleterious
 mutations, compromising the viability of the population. In order to avoid
 this, optimal contributions could be combined with inbred matings, to
 expose and eliminate recessive deleterious mutations by natural selection
 in a process known as purging. Although some populations that have
 undergone purging experienced reduced inbreeding depression, this effect
 is not consistent across species. Whether purging by inbred matings is
 efficient in conservation programmes depends on the balance between the
 loss of diversity, the initial decrease in fitness and the reduction in
 mutational load. Here we perform computer simulations to determine whether
 managing a population by combining optimal contributions with inbred
 matings improves its long-term viability while keeping reasonable levels
 of diversity. We compare the management based on genealogical information
 with management based on molecular data to calculate coancestries. In the
 scenarios analysed, inbred matings never led to higher fitness and usually
 maintained lower diversity than random or minimum coancestry matings.
 Replacing genealogical with molecular coancestry can maintain a larger
 genetic diversity but can also lead to a lower fitness. Our results are
 strongly dependent on the mutational model assumed for the trait under
 selection, the population size during management and the reproductive
 rate.
description: Dryad_data.tarFour sets of genotypes used for population management, for populations of 1000 diploid individuals with 20 chromosomes of 1 Morgan each. For S=100 (1000), each chromosome has 2000 neutral loci, 100 (1000) selected loci and 1000 markers. Each row is one individual, and within row the two alleles per position.
DOI: 10.5061/dryad.bt658
title: Data from: Costs of growing up as a subordinate sibling are passed to the next generation in blue-footed boobies

description: As stresses in early development may generate costs in adult life, sibling
 competition and conflict in infancy are expected to diminish the
 reproductive value of surviving low-status members of broods and litters.
 We analysed delayed costs to blue-footed booby fledglings, Sula nebouxii,
 of junior status in the brood, which involves aggressive subordination,
 food deprivation and elevated corticosterone, but little or no deficit in
 size at fledging. In ten cohorts observed for up to 16 years, juniors
 showed no deficit in breeding success at any age, independent of lifespan,
 including in a sample of sibling pairs. Among females, juniors actually
 outreproduced seniors across the 16-year span. However, offspring produced
 by juniors in the first 3 years of life were less likely to recruit into
 the breeding population than offspring of seniors. Since junior fledglings
 survive, recruit and compete as well as seniors (shown earlier), and breed
 as successfully as seniors across the lifespan, it appears the delayed
 cost of subordination is passed to offspring, and only to those few
 offspring produced in the first 3 years of life. These correlational
 results indicate that systematic competition-related differences in
 developmental conditions of infant siblings can alter their reproductive
 value by affecting the viability of their eventual offspring.
description: Data of JEB
 12087Data of JEB 12087. The
 excel file has multiple sheets; each sheet is the database of the
 different analysis.
DOI: 10.5061/dryad.m83r0
title: Data from: How does evolutionary variation in basal metabolic rates arise? A statistical assessment and a mechanistic model

description: Metabolic rates are related to the pace of life. Hence, research into
 their variability at global scales is of vital importance for several
 contemporary theories in physiology, ecology and evolution. Here we
 evaluated the effect of latitude, climate, primary productivity, habitat
 aridity, and species trophic habits, on mass-independent basal metabolic
 rates (BMR) for 195 rodent species. The aims of this paper were two-fold.
 First, we evaluated the predictive power of different statistical models
 (via a model selection approach), using a dimensional reduction technique
 on the exogenous factor matrix to achieve a clear interpretation of the
 selected models. Second, we evaluated three specific predictions derived
 from a recently proposed hypothesis, herein called the “obligatory heat”
 model (OHM), for the evolution of BMR. Obtained results indicate that mean
 / minimum environmental temperature, rainfall / primary productivity and,
 finally, species trophic habits are, in this order, the major determinants
 of mass-independent BMR. Concerning the mechanistic causes behind this
 variation, obtained data agree with the predictions of the OHM: (i) mean
 annual environmental temperature was the best single predictor of residual
 variation in BMR, (ii) herbivorous species have greater mass-independent
 metabolic rates, and tend to be present at high-latitude cold
 environments, than species in other trophic categories.
description: TableS1Data on basal metabolic rate, body mass, and geographic, climatic and ecological variables for 195 rodent species.TableS2Parameter estimation (and standard deviation) for models including exogenous factors in addition to body mass.TableS3Data on basal metabolic rate and intestinal length for 30 rodent species.
DOI: 10.5061/dryad.p7s88
title: Data from: Feeding-induced rearrangement of green leaf volatiles reduces moth oviposition

description: The ability to decrypt volatile plant signals is essential if herbivorous
 insects are to optimize their choice of host plants for their offspring.
 Green leaf volatiles (GLVs) constitute a widespread group of defensive
 plant volatiles that convey a herbivory-specific message via their
 isomeric composition: feeding of the tobacco hornworm Manduca sexta
 converts (Z)-3- to (E)-2-GLVs thereby attracting predatory insects. Here
 we show that this isomer-coded message is monitored by ovipositing M.
 sexta females. We detected the isomeric shift in the host plant Datura
 wrightii and performed functional imaging in the primary olfactory center
 of M. sexta females with GLV structural isomers. We identified two
 isomer-specific regions responding to either (Z)-3- or (E)-2-hexenyl
 acetate. Field experiments demonstrated that ovipositing Manduca moths
 preferred (Z)-3-perfumed D. wrightii over (E)-2-perfumed plants. These
 results show that (E)-2-GLVs and/or specific (Z)-3/(E)-2-ratios provide
 information regarding host plant attack by conspecifics that ovipositing
 hawkmoths use for host plant selection.
description: Volatile collection
 results for field and climate chamber, to accompany Fig
 1.Datura wrightii
 volatiles collected in field and climate chamber. Quantification of (Z)-3-
 and (E)-2-isomers of hexenal, hexenol and hexenyl acetate. Data processing
 for Figure 1.F1AB_AllmannSpaethe2012_volatiles.xlsxSpectral irradiance and illuminance during volatile collection in climate chamber, to accompany Fig 2.F2_AllmannSpaethe2012_light.xlsxCorrelation of field GLV emission to flowernumber and percentaged plant damage, to accompany Fig 3.F3_AllmannSpaethe2012_ correlation.xlsxCorrelation coefficients calculated from change in flourescence, to accompany Fig 4C.Maximum change in fluorescence (delta F max) in response to odor stimulation calculated for correlations of (Z)-3- and (E)-2-isomers and of repeated measurements of the same isomer of each GLV.F4C_AllmannSpaethe2012_correlationcoefficientsGlvs.xlsxChange in flourescence in response to odor stimulation with GLVs, to accompany Fig 4B.F4B_AllmannSpaethe2012_timetracesGlvs.xlsxChange in flourescence in response to odor stimulation with isomeric mixtures of hexenal acetate, to accompany Fig 5A.F5A_AllmannSpaethe2012_timetraceshexenylacetate.xlsxChange in flourescence in response to odor stimulation with isomeric mixtures of hexenal acetate, to accompany Fig 5BCD.Calculation of maximum change in fluorescence (delta F max) and change of fluorescence normalized to the strongest response. Data processing for graphs and calculation of ROI signal ratios.F5BCE_AllmannSpaethe2012_imaginghexenylacetate.xlsxField oviposition data, to accompany Fig 6.F6B_AllmannSpaethe2012_oviposition.xlsxCalcium signals recorded in response to stimulation with (Z)-3- and (E)-2-hexenyl acetate.eLIFE_480p_low.mp4
DOI: 10.5061/dryad.bc0v0
title: Data from: Genomic basis for coral resilience to climate change

description: Recent advances in DNA-sequencing technologies now allow for in-depth
 characterization of the genomic stress responses of many organisms beyond
 model taxa. They are especially appropriate for organisms such as
 reef-building corals, for which dramatic declines in abundance are
 expected to worsen as anthropogenic climate change intensifies. Different
 corals differ substantially in physiological resilience to environmental
 stress, but the molecular mechanisms behind enhanced coral resilience
 remain unclear. Here, we compare transcriptome-wide gene expression (via
 RNA-Seq using Illumina sequencing) among conspecific thermally sensitive
 and thermally resilient corals to identify the molecular pathways
 contributing to coral resilience. Under simulated bleaching stress,
 sensitive and resilient corals change expression of hundreds of genes, but
 the resilient corals had higher expression under control conditions across
 60 of these genes. These “frontloaded” transcripts were less up-regulated
 in resilient corals during heat stress and included thermal tolerance
 genes such as heat shock proteins and antioxidant enzymes, as well as a
 broad array of genes involved in apoptosis regulation, tumor suppression,
 innate immune response, and cell adhesion. We propose that constitutive
 frontloading enables an individual to maintain physiological resilience
 during frequently encountered environmental stress, an idea that has
 strong parallels in model systems such as yeast. Our study provides broad
 insight into the fundamental cellular processes responsible for enhanced
 stress tolerances that may enable some organisms to better persist into
 the future in an era of global climate change.
description: 33496_Ahyacinthus_CoralContigs.fastaContigs with putative Cnidarian origin from a de novo transcriptome assembly of Acropora hyacinthus. 16 individual A hyacinthus adult colonies were exposed to control and elevated thermal exposures, mRNA was isolated and sequenced using the Illumina GA IIX platform, assembled, and resulting contigs were screened against known cnidarian databases for strong matches to isolate sequences likely to be coral in origin.33496_MasterCombinedAnnotationTablewHGNC.txtCombined annotation information for the 33,496 coral contigs from the Acropora hyacinthus de novo assembly. Annotations are based on BLASTx matches to the ncbi nr and uniprot swissprot and TrEMBL databases.