cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3mg69k5
title: Data from: Non-stationary climate-salmon relationships in the Gulf of Alaska

description: Studies of climate effects on ecology often account for non-stationarity
 in individual physical and biological variables, but rarely allow for
 non-stationary relationships among variables. Here, we show that
 non-stationary relationships among physical and biological variables are
 central to understanding climate effects on salmon (Onchorynchus spp.) in
 the Gulf of Alaska during 1965-2012. The relative importance of two
 leading patterns in North Pacific climate, the Pacific Decadal Oscillation
 (PDO) and North Pacific Gyre Oscillation (NPGO), changed around 1988/89 as
 reflected by changing correlations with leading axes of sea surface
 temperature variability. Simultaneously, relationships between the PDO and
 Gulf of Alaska environmental variables weakened, and long-standing
 temperature-salmon and PDO-salmon covariance declined to zero. We propose
 a mechanistic explanation for changing climate-salmon relationships in
 terms of non-stationary atmosphere-ocean interactions coinciding with
 changing PDO-NPGO relative importance. We also show that regression models
 assuming stationary climate-salmon relationships are inappropriate over
 the multidecadal time scale we consider. Relaxing assumptions of
 stationary relationships markedly improved modeling of climate effects on
 salmon catches and productivity. Attempts to understand the implications
 of changing climate patterns in other ecosystems might also be aided by
 the application of models that allow associations among environmental and
 biological variables to change over time.
description: GOA_salmon_covariatesSix climate variables related to salmon production.sockeye_SR_dataSockeye salmon spawner-recruit data.chum_SR_dataChum salmon spawner-recruit data.pink_SR_dataPink salmon spawner-recruit data.winter_npgo_pdoWinter values of the PDO and NPGO.npgoNPGO values.pdoPDO values.long_area_salmon_catchGOA salmon commercial catch data.GOA_non-analogue_code_Fig_1Code for Fig. 1.GOA_non-analogue_code_Figs_2-6Code for Figs. 2-6.code for Fig. S2Code for Fig. S2.readmeDetails concerning data sources, data accession, and code hosting.dryad readme.txt
DOI: 10.5061/dryad.63g17
title: Data from: Advancing Precambrian palaeomagnetism with the PALEOMAGIA and PINT(QPI) databases

description: State-of-the-art measurements of the direction and intensity of Earth’s
 ancient magnetic field have made important contributions to our
 understanding of the geology and palaeogeography of Precambrian Earth. The
 PALEOMAGIA and PINT(QPI) databases provide thorough public collections of
 important palaeomagnetic data of this kind. They comprise more than 4,100
 observations in total and have been essential in supporting our
 international collaborative efforts to understand Earth's magnetic
 history on a timescale far longer than that of the present Phanerozoic
 Eon. Here, we provide an overview of the technical structure and
 applications of both databases, paying particular attention to recent
 improvements and discoveries.
description: PALEOMAGIA and PINT(QPI)
 databasesThis package contains
 static copies (as of July 15, 2016) of PALEOMAGIA
 (http://www.helsinki.fi/paleomagia/) and PINT(QPI)
 (http://earth.liv.ac.uk/pint/) palaeomagnetic databases as Open Document
 spreadsheet files (ods) as follows: - PALEOMAGIA spreadsheet
 (PALEOMAGIA_web.ods) contains sheets corresponding to each actual database
 table (agerefs, countries, data, pmagrefs, terranes). - PINT(QPI)
 spreadsheet (PINT_Qpi_web.ods) contains sheets corresponding to each
 actual database table (Refs, PINTdata, PIMethods and Information). For
 additional information, and to access the most recent versions of
 databases, users are advised to access the PALEOMAGIA and PINT(QPI)
 websites (http://www.helsinki.fi/paleomagia/,
 http://earth.liv.ac.uk/pint/).paleomag_databases.zip
DOI: 10.5061/dryad.38nd7
title: Data from: Among-lake reciprocal transplants induce convergent expression of immune genes in threespine stickleback

description: Geographic variation in parasite communities can drive evolutionary
 divergence in host immune genes. However, biotic and abiotic environmental
 variation can also induce plastic differences in immune function among
 populations. At present, there is little information concerning the
 relative magnitudes of heritable vs. induced immune divergence in natural
 populations. We examined immune gene expression profiles of threespine
 stickleback (Gasterosteus aculeatus) from six lakes on Vancouver Island,
 British Columbia. Parasite community composition differs between lake
 types (large or small, containing limnetic- or benthic-like stickleback)
 and between watersheds. We observed corresponding differences in immune
 gene expression profiles among wild-caught stickleback, using a set of
 seven immune genes representing distinct branches of the immune system. To
 evaluate the role of environmental effects on this differentiation, we
 experimentally transplanted wild-caught fish into cages in their native
 lake, or into a nearby foreign lake. Transplanted individuals' immune
 gene expression converged on patterns typical of their destination lake,
 deviating from their native expression profile. Transplant
 individuals' source population had a much smaller effect, suggesting
 relatively weak genetic underpinning of population differences in
 immunity, as viewed through gene expression. This strong environmental
 regulation of immune gene expression provides a counterpoint to the large
 emerging literature documenting microevolution and genetic diversification
 of immune function. Our findings illustrate the value of studying immunity
 in natural environmental settings where the immune system has evolved and
 actively functions.
description: Expression and trait
 dataA
 .csv file containing all data relevant to gene expression and fish
 morphology (condition, size, growth) necessary to recreate the results of
 the study. See the ReadMe file for metadata detailsfull_data_long.csvParasitedataA .txt file containing parasite load data on wild-caught stickleback, collected in 2009 from 6 lakes on Vancouver Island British Columbia. These data are used in the publication to establish that parasite communities differ between lakes, habitat types, and watersheds.
DOI: 10.5061/dryad.sg2d3
title: Data from: Study of mixed mode fracture toughness and fracture trajectories in gypsum interlayers in corrosive environment

description: Based on the engineering background of water dissolving mining for
 hydrocarbon storage in multi-laminated salt stratum, the mixed mode
 fracture toughness and fracture trajectory of gypsum interlayers soaked in
 half-saturated brine at various temperatures (20°C, 50°C and 80°C) were
 studied by using CSNBD (centrally straight-notched Brazilian disc)
 specimens with required inclination angles (0°, 7°, 15°, 22°, 30°, 45°,
 60°, 75°, 90°) and SEM (scanning electron microscopy). The results showed:
 (i) The fracture load of gypsum specimens first decreased then increased
 with increasing inclination angle, due to the effect of friction
 coefficient. When soaked in brine, the fracture toughness of gypsum
 specimens gradually decreased with increasing brine temperature. (ii) When
 soaked in brine, the crystal boundaries of gypsum separated and became
 clearer, and the boundaries became more open between the crystals with
 increasing brine temperature. Besides, tensile micro-cracks appeared on
 the gypsum crystals when soaked in 50°C brine, and the intensity of
 tensile cracks became more severe when soaking in 80°C brine. (iii) The
 experimental fracture envelopes derived from the conventional fracture
 criteria and lay outside these conventional criteria. The experimental
 fracture envelopes were dependent on the brine temperature and gradually
 expanded outward as brine temperature increases. (iv) The size of FPZ
 (fracture process zone) was greatly dependent on the damage degree of
 materials and gradually increased with increase of brine temperature. The
 study has important implication for the control of shape and size of salt
 cavern.
description: The data of all the
 figures
DOI: 10.5061/dryad.hh6342f
title: Data from: Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta

description: Background: The Sb supergene in the fire ant Solenopsis invicta determines
 the form of colony social organization, with colonies whose inhabitants
 bear the element containing multiple reproductive queens and colonies
 lacking it containing only a single queen. Several features of this
 supergene — including suppressed recombination, presence of deleterious
 mutations and abundant transposable elements, association with a large
 centromere, and “green-beard” behavior — suggest that it may be a selfish
 genetic element that engages in transmission ratio distortion (TRD),
 defined as significant departures in progeny allele frequencies from
 Mendelian inheritance ratios. We tested this possibility by surveying
 segregation ratios in embryo progenies of 101 queens of the “polygyne”
 social form (3512 embryos) using three supergene-linked markers and twelve
 markers not associated with the supergene. Results: Significant departures
 from Mendelian ratios were observed at the supergene loci in 3-5 times
 more progenies than expected in the absence of TRD and than found, on
 average, among non-supergene loci. Also, supergene loci displayed the
 greatest mean deviations from Mendelian ratios among all study loci,
 although these typically were modest. A surprising feature of the observed
 inter-progeny variation in TRD was that significant deviations involved
 not only excesses of supergene alleles but also similarly frequent
 excesses of the alternate alleles on the homologous chromosome. As
 expected given the common occurrence of such “drive reversal,” alleles
 associated with the supergene evidently gain no consistent transmission
 advantage over their alternate alleles at the population level. Finally,
 we observed low levels of recombination and incomplete gametic
 disequilibrium across the supergene, including between adjacent markers
 within a single inversion. Conclusions: Our data confirm the prediction
 that the Sb supergene is a selfish genetic element capable of biasing its
 own transmission during reproduction, yet counterselection for suppressor
 loci evidently has produced an evolutionary stalemate in TRD between the
 variant homologous haplotypes on the “social chromosome”. Evidence
 implicates prezygotic segregation distortion as responsible for the TRD we
 document, with “true” meiotic drive the most likely mechanism. Low levels
 of recombination and incomplete gametic disequilibrium across the
 supergene suggest that selection does not act to preserve a single uniform
 supergene haplotype.
description: Genotypes for Gp-9 and
 14 microsatellite markers in polygyne Solenopsis invicta embryo progenies
 and reproductive queensRaw genotypic data used
 to study transmission ratio distortion in Solenopsis invicta. Genotypes
 are from 14 microsatellite loci and the protein-coding gene
 Gp-9.Ross
 & Shoemaker- DRYAD raw data.xlsx
DOI: 10.15468/dl.s3v3gv
title: Occurrence Download

description: A dataset containing 129174 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Uta stansburiana"
 ]
}

 The dataset includes 129174 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000452-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.92vh2
title: Data from: A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world

description: There is an increasing interest to combine phylogenetic data with
 distributional and ecological records to assess how natural communities
 arrange under an evolutionary perspective. In the microbial world there is
 also a need to go beyond the problematic species definition to deeply
 explore ecological patterns using genetic data. We explored links between
 evolution/phylogeny and community ecology using bacterial 16S rRNA gene
 information from a high altitude lakes district dataset to describe
 phylogenetic community composition, spatial distribution, and β-diversity
 and biogeographical patterns applying evolutionary relatedness without
 relying on any particular operational taxonomic unit definition. High
 altitude lakes districts usually contain a large mosaic of highly diverse
 small water bodies and conform a fine biogeographical model of spatially
 close but environmentally heterogeneous ecosystems. We sampled eighteen
 lakes in the Pyrenees with a selection criteria focused on capturing the
 maximum environmental variation within a small geographical area. The
 results showed highly diverse communities non-randomly distributed with
 phylogenetic β-diversity patterns mainly shaped by the environment and not
 by the spatial distance. Community similarity based on both bacterial
 taxonomic composition and phylogenetic β-diversity approach shared similar
 patterns and were primarily structured by similar environmental drivers.
 We observed a positive relationship between lake area and phylogenetic
 diversity with a slope consistent with highly dispersive planktonic
 organisms. The phylogenetic approach incorporated patterns of common
 ancestry into bacterial community analysis and emerged as a very
 convenient analytical tool for direct inter- and intrabiome biodiversity
 comparisons and sorting out microbial habitats with potential application
 in conservation studies for microorganisms.
description: Aligned fasta
 filesPyNAST-aligned fasta
 files for each lakePyrennes_bacteria.zipPhylogenetic treePhylogenetic tree of PyNAST aligned 16S rRNA bacterial sequences from Pyrenean lakespyrenees_aligned_pfiltered.tre
DOI: 10.5061/dryad.q7p1126
title: Data from: Selection for pollen competitive ability in mixed-mating systems

description: Co-expression of genes in plant sporophytes and gametophytes allows
 correlated gametic and sporophytic selection. Theory predicts that, under
 outcrossing, an allele conferring greater pollen competitive ability
 should fix within a population unless antagonistic pleiotropy with the
 sporophyte stage is strong. However, under strong selfing, pollen
 competitiveness is immaterial as superior and inferior competitors are
 deposited on opposite stigmas, producing assortative competition. Because
 many plant species have mixed-mating systems, selfing should be critical
 in the spread and maintenance of pollen-expressed genes affecting
 competitiveness. We present two one-locus, two-allele population genetic
 models for the evolution of a locus controlling pleiotropic antagonism
 between pollen competitiveness and diploid fitness. Analytical solutions
 provide minimum and maximum selfing rates allowing invasion of alleles
 with greater diploid and haploid fitness respectively. Further,
 polymorphism is only maintained when diploid selection is recessive.
 Fixation of the allele conferring greater pollen competitiveness may be
 prevented, even with weak sporophytic counter-selection, with sufficiently
 high selfing. Finally, selfing expands and limits the range of
 haploid-diploid selection coefficients allowing polymorphism, depending on
 dominance and selfing mode.
description: SelectionMixedMating_dataExcel file containing series for each figure found in both the main text and in the appendices.
DOI: 10.5061/dryad.3fp5c
title: Data from: Transgenerational interactions between pesticide exposure and warming in a vector mosquito

description: While transgenerational plasticity may buffer ectotherms to warming and
 pesticides separately, it remains unknown how combined exposure to warming
 and pesticides in the parental generation shapes the vulnerability to
 these stressors in the offspring. We studied the transgenerational effects
 of single and combined exposure to warming (4°C increase) and the
 pesticide chlorpyrifos on life history traits of the vector mosquito Culex
 pipiens. Parental exposure to a single stressor, either warming or the
 pesticide, had negative effects on the offspring: both parental exposure
 to warming and to the pesticide resulted in an overall lower offspring
 survival, and a delayed offspring metamorphosis. Parental exposure to a
 single stressor did, however, not alter the vulnerability of the offspring
 to the same stressor in terms of survival. Parental pesticide exposure
 resulted in larger offspring when the offspring experienced the same
 stressor as the parents. Within both the parental and offspring
 generations, warming made the pesticide more toxic in terms of survival.
 Yet, this synergism disappeared in the offspring of parents exposed to
 both stressors simultaneously because in this condition the pesticide was
 already more lethal at the lower temperature. Our results indicate that
 transgenerational effects will not increase the ability of this vector
 species to deal with pesticides in a warming world. Bifactorial
 transgenerational experiments are crucial to understand the combined
 impact of warming and pesticides across generations, hence to assess the
 efficacy of vector control in a warming world.
description: Survival, sex ratio,
 development time and size in the parental generationThis data file contains
 5 sheets including data of all response variables in the parental
 generation. EmergencesuccessF0 contains emergence success data for each
 insectary. SexratioF0 provides numbers of males and females that
 successfully emerged from each insectary. DevtimeF0 contains development
 time of each larva from the start of the fourth larval stage until
 emergence. SizeadultF0 contains data on size (winglength) of the adults.
 LarvalsurF0 is survival data during the five day pesticide exposure
 period.F0_all_variables.xlsxSurvival, sex ratio, development time and size in the offspring generationThis data file contains 5 sheets including data of all response variables in the offspring generation. EmergencesuccessF1 contains emergence success data for each insectary. SexratioF1 provides numbers of males and females that successfully emerged from each insectary. DevtimeF1 contains development time of each larva from the start of the fourth larval stage until emergence. SizeadultF1 contains data on size (winglength) of the adults. LarvalsurvivalF1 is survival data during the five day pesticide exposure period.F1_all_variables.xlsx
DOI: 10.5061/dryad.1862
title: Data from: Evolutionary history of chimpanzees inferred from complete mitochondrial genomes

description: Investigations into the evolutionary history of the common chimpanzee, Pan
 troglodytes, have produced inconsistent results, due to differences in the
 types of molecular data considered, the model assumptions employed, and
 the quantity and geographical range of samples used. We amplified and
 sequenced 24 complete P. troglodytes mitochondrial genomes from fecal
 samples collected at multiple study sites throughout sub-Saharan Africa.
 Using a ‘relaxed molecular clock,’ fossil calibrations, and 12 additional
 complete primate mitochondrial genomes, we analyzed the pattern and timing
 of primate diversification in a Bayesian framework. Our results support
 the recognition of four chimpanzee subspecies. Within P. troglodytes, we
 report a mean (95% highest posterior density (HPD)) time since most recent
 common ancestor (tMRCA) of 1.026 (0.811-1.263) MYA for the four proposed
 subspecies, with two major lineages. One of these lineages (tMRCA = 0.510
 [0.387-0.650] MYA) contains P. t. verus (tMRCA = 0.155 [0.101-0.213] MYA)
 and P. t. ellioti (formerly P. t. vellerosus; tMRCA = 0.157 [0.102-0.215]
 MYA), both of which are monophyletic. The other major lineage contains P.
 t. schweinfurthii (tMRCA = 0.111 [0.077-0.146] MYA), a monophyletic clade
 nested within the P. t. troglodytes lineage (tMRCA = 0.380 [0.296-0.476]
 ¬MYA). We utilized two analysis techniques that may be of widespread
 interest. First, we implemented a Yule speciation prior across the entire
 primate tree with separate coalescent priors on each of the chimpanzee
 subspecies. The validity of this approach was confirmed by estimates based
 on more traditional techniques. We also suggest that accurate tMRCA
 estimates from large, computationally difficult sequence alignments may be
 obtained by implementing our novel method of bootstrapping smaller,
 randomly sub-sampled alignments.
description: bootstrapped-chimpanzee
 example xml filebootstrapped-chimpanzeeexample.xmlchimpanzee-plus example xml filechimpanzee-plusexample.xmlchimpanzee-only example xml filechimpanzee-onlyexample.xml
DOI: 10.5061/dryad.rp8mp68
title: Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes

description: Dispersal is fundamental to population dynamics and hence extinction risk.
 The dispersal success of animals depends on the biophysical structure of
 their environments and their biological traits; however, comparatively
 little is known about how evolutionary trade-offs among suites of
 biological traits affect dispersal potential. We developed a spatially
 explicit agent-based simulation model to evaluate the influence of
 trade-offs among a suite of biological traits on the dispersal success of
 vagile animals in fragmented landscapes. We specifically chose traits
 known to influence dispersal success: speed of movement, perceptual range,
 risk of predation, need to forage during dispersal, and amount of suitable
 habitat required for successful settlement in a patch. Using the metric of
 relative dispersal success rate, we assessed how the costs and benefits of
 evolutionary investment in these biological traits varied with landscape
 structure. In heterogeneous environments with low habitat availability and
 scattered habitat patches, individuals with more equal allocation across
 the trait spectrum dispersed most successfully. Our analyses suggest that
 the dispersal success of animals in heterogeneous environments is highly
 dependent on hierarchical interactions between trait trade-offs and the
 geometric configurations of the habitat patches in the landscapes through
 which they disperse. In an applied sense, our results indicate potential
 for ecological mis-alignment between species’ evolved suites of
 dispersal-related traits and altered environmental conditions as a result
 of rapid global change. In many cases identifying the processes that shape
 patterns of animal dispersal, and the consequences of abiotic changes for
 these processes, will require consideration of complex relationships among
 a range of organism-specific and environmental factors.
description: Final model version
 1.3NetLogo file containing
 model code for the final patch dispersal model that was used to run
 simulation experiments and generate the data presented in the results of
 this manuscript.Trade-off analysis data
 filesAll model output showing
 dispersal success under a range of habitat amount, habitat aggregation and
 intrinsic trait trade-off scenarios. All results and figures in the
 manuscript were generated from these data.Quantile regression
 resultsTwo files containing the
 results of the quantile regression analysis, which were used to generate
 figures 5 & 6.