cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gc981
title: Data from: Community assembly of a euryhaline fish microbiome during salinity acclimation

description: Microbiomes play a critical role in promoting a range of host functions.
 Microbiome function, in turn, is dependent on its community composition.
 Yet, how microbiome taxa are assembled from their regional species pool
 remains unclear. Many possible drivers have been hypothesized, including
 deterministic processes of competition, stochastic processes of
 colonization and migration, and physiological ‘host-effect’ habitat
 filters. The contribution of each to assembly in nascent or perturbed
 microbiomes is important for understanding host–microbe interactions and
 host health. In this study, we characterized the bacterial communities in
 a euryhaline fish and the surrounding tank water during salinity
 acclimation. To assess the relative influence of stochastic versus
 deterministic processes in fish microbiome assembly, we manipulated the
 bacterial species pool around each fish by changing the salinity of
 aquarium water. Our results show a complete and repeatable turnover of
 dominant bacterial taxa in the microbiomes from individuals of the same
 species after acclimation to the same salinity. We show that changes in
 fish microbiomes are not correlated with corresponding changes to abundant
 taxa in tank water communities and that the dominant taxa in fish
 microbiomes are rare in the aquatic surroundings, and vice versa. Our
 results suggest that bacterial taxa best able to compete within the unique
 host environment at a given salinity appropriate the most niche space,
 independent of their relative abundance in tank water communities. In this
 experiment, deterministic processes appear to drive fish microbiome
 assembly, with little evidence for stochastic colonization.
description: OTU
 tableRaw 97% OTU table
 showing the number of sequences clustered into each UCLUST OTU. Each OTU
 is identified according to a unique OTU number, followed by its GAST
 taxonomy. Metadata on salinity treatment, total raw sequence count, and
 sample ID is also given.FileS2.xlsxDNA sequencesRaw demultiplexed Fastq files generated on an Illumina HiSeq 1000.MIMARKS sequence metadataMIMARKS-formatted metadata for sequences generated as part of this study. All sequences are available in NCBI's Sequence Read Archive (SRA) under accession number SRP047374.TableS1.xls
DOI: 10.5061/dryad.8330
title: Data from: Local and global abundance associated with extinction risk in late Paleozoic and early Mesozoic gastropods

description: Ecological theory predicts an inverse association between population size
 and extinction risk, but most previous paleontological studies have not
 confirmed this relationship. The reasons for this discrepancy between
 theory and observation remain poorly understood. In this study, we
 compiled a global database of gastropod occurrences and collection-level
 abundances spanning the Early Permian through Early Jurassic
 (Pliensbachian). Globally, the database contains 5469 occurrences of 496
 genera and 2156 species from 839 localities. Within the database, 30
 collections distributed across 7 stages contain at least 75 specimens and
 10 genera – our minimum criteria for within-collection analysis of
 extinction selectivity. We use logistic regression analysis to assess the
 relationship between abundance and extinction risk using global and local
 measures of population size and stage-level extinction patterns in Early
 Permian through Early Jurassic marine gastropods. We find that global
 genus occurrence frequency is inversely associated with extinction risk
 (i.e., positively associated with survival) in 15 of 16 stages examined,
 statistically significantly so in 6 stages. Although correlation between
 geographic range and occurrence frequency may account for some of this
 association, results from multivariable regression analysis suggest that
 the association between occurrence frequency and extinction risk is
 largely independent of geographic range. Within local assemblages,
 abundance (number of individuals) is also inversely associated with
 extinction risk. The strength of association is consistent across time and
 modes of fossil preservation. Effect strength is poorly constrained,
 particularly in analyses of local collections. In addition to limited
 power due to small sample size, this poor constraint may result from
 confounding by ecological variables not controlled for in the analyses, by
 taphonomic or collection biases, or from non-monotonic relationships
 between abundance and extinction risk. Two factors are likely to account
 for the difference between our results and those of most previous studies.
 First, many previous studies focused on the end-Cretaceous mass extinction
 event; the extent to which these results can be generalized to other
 intervals remains unclear. Second, previous findings of non-selective
 extinction could result from insufficient statistical power rather than
 the absence of an underlying effect because non-selective extinction is
 generally used as the null hypothesis for statistical convenience.
 Survivorship patterns in late Paleozoic and early Mesozoic gastropods
 suggest that abundance has been a more important influence on extinction
 risk through the Phanerozoic than previously appreciated.
description: payne_collectionspayne_collections_genuspayne_global_genuspayne_occurrences
DOI: 10.5061/dryad.rj5fk
title: Data from: Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches

description: Premise of the study: Heterokont algae of the class Synurophyceae,
 characterized by distinctive siliceous scales that cover the surface of
 the cell, are ecologically important in inland waters, yet their
 evolutionary history remains enigmatic. We explore phylogenetic
 relationships within this group of algae relative to geologic time, with a
 focus on evolution of siliceous components. Methods: We combined an
 expansive five-gene and time-calibrated molecular phylogeny of synurophyte
 algae with an extensive array of fossil specimens from the middle Eocene
 to infer evolutionary trends within the group. Key results: The group
 originated in the Jurassic approximately 157 million years ago (Ma), with
 the keystone genera Mallomonas and Synura diverging during the Early
 Cretaceous at 130 Ma. Mallomonas further splits into two major subclades,
 signaling the evolution of the V-rib believed to aid in the spacing and
 organization of scales on the cell covering. Synura also diverges into two
 primary subclades, separating taxa with forward-projecting spines on the
 scale from those with a keel positioned on the scale proper. Approximately
 one third of the fossil species are extinct, whereas the remaining taxa
 are linked to modern congeners. Conclusions: The taxonomy of synurophytes,
 which relies extensively on the morphology of the siliceous components, is
 largely congruent with molecular analyses. Scales of extinct synurophytes
 were significantly larger than those of modern taxa and may have played a
 role in their demise. In contrast, many fossil species linked to modern
 lineages were smaller in the middle Eocene, possibly reflecting growth in
 the greenhouse climatic state that characterized this geologic interval.
description: Fig2 Five gene data
 matrix.nexFive gene data set
 (nuclear SSU, nuclear LSU, plastid LSU, plastid psaA, plastid
 rbcL)Fig 2
 Five gene data matrix.nex.txtFig2 Time-calibrated
 phylogenetic tree.treFigure 2.
 Time-calibrated phylogenetic tree for the Synurophyceae based on a
 five-gene dataset.
DOI: 10.5061/dryad.3k8c0
title: Data from: Offspring provisioning explains clone specific maternal age effects on life history and lifespan in the water flea, Daphnia pulex

description: Genetic inheritance underpins evolutionary theories of aging, but the role
 that nongenetic inheritance plays is unclear. Parental age reduces the
 life span of offspring in a diverse array of taxa but has not been
 explained from an evolutionary perspective. We quantified the effect that
 maternal age had on the growth and maturation decisions, life history,
 rates of senescence, and life span of offspring from three Daphnia pulex
 clones collected from different populations. We then used those data to
 test general hypotheses proposed to explain maternal age effects on
 offspring life span. Three generations of breeding from young or old
 mothers produced dramatic differences in the life histories of
 fourth-generation offspring, including significant reductions in life
 span. The magnitude of the effect differed between clones, which suggests
 that genetic and nongenetic factors ultimately underpin trait inheritance
 and shape patterns of aging. Older parents did not transmit a senescent
 state to their offspring. Instead, offspring from older ancestors had
 increased early-life reproductive effort, which resulted in an earlier
 onset of reproductive senescence, and an increased rate of actuarial
 senescence, which shortened their life span. Our results provide a clear
 example of the need to consider multiple inheritance mechanisms when
 studying trait evolution.
description: Electronic supplementary
 files for Plaistow et al. - Offspring provisioning explains clone specific
 maternal age effects on life history and lifespan in the water flea,
 Daphnia pulex1. Table S1 - details of
 the 57 models fitted to the PMRN data in experiment 2. 2. Data used in the
 multivariate analyses in experiment 1. 3. Data used for the age-specific
 reproduction analysis used in experiment 1. 4. Data used for comparing
 age-specific mortality rates in experiment 1. 5. Data used for the growth
 analysis in experiment 2. 6. Data used for the PMRN analysis in experiment
 2.
DOI: 10.5061/dryad.3p147
title: Data from: Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

description: We tested the hypothesis that the rate of marsupial cranial evolution is
 dependent on the distribution of genetic variation in multivariate space.
 To do so, we carried out a genetic analysis of cranial morphological
 variation in laboratory strains of Monodelphis domestica and used
 estimates of genetic covariation to analyze the morphological
 diversification of the Monodelphis brevicaudata species group. We found
 that within-species genetic variation is concentrated in only a few axes
 of the morphospace and that this strong genetic covariation influenced the
 rate of morphological diversification of the brevicaudata group, with
 between-species divergence occurring fastest when occurring along the
 genetic line of least resistance. Accounting for the geometric
 distribution of genetic variation also increased our ability to detect the
 selective regimen underlying species diversification, with several
 instances of selection only being detected when genetic covariances were
 taken into account. Therefore, this work directly links patterns of
 genetic covariation among traits to macroevolutionary patterns of
 morphological divergence. Our findings also suggest that the limited
 distribution of Monodelphis species in morphospace is the result of a
 complex interplay between the limited dimensionality of available genetic
 variation and strong stabilizing selection along two major axes of genetic
 variation.
description: Priors_Posterior_and_MeasurementsBSFG model input data and resulting posterior distributions. File names follow the convention established by the BSFG model (Runcie & Mukherjee, 2013). A file containing the 30 linear measurements collected in the skull of each strain specimen is also attached.MatricesVariance/covariance matrices used in this study, separated by species. The BSFG G-matrix is named G_Bayes. The BSFG P-matrix is named P_Bayes.Posterior_and_matrices_GnoiseBSFG model priors and posterior distributions, when estimating G based on random noise. File names follow the convention established by the BSFG model (Runcie & Mukherjee, 2013).Species_and_node_informationInformation on species' trait means and branch lengths used when estimating rate of morphological evolution. Branch names correspond to the names reported in the main text.Species_and_node_info.rar
DOI: 10.5061/dryad.8343
title: Data from: Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

description: Geographic characters---traits relating to the spatial distribution of a
 species---may both affect and be affected by processes associated with
 lineage birth and death. This is potentially confounding to comparative
 analyses of species distributions because current models do not allow
 reciprocal interactions between the evolution of traits and the growth of
 phylogenetic trees. Here we introduce a likelihood-based approach to
 estimating region-dependent rates of speciation, extinction, and range
 evolution from a phylogeny, using a new model in which these processes are
 interdependent. We demonstrate the method with simulation tests that
 accurately recover parameters relating to the mode of speciation and
 source-sink dynamics. We then apply it to the evolution of habitat
 occupancy in Californian plant communities, where we find higher rates of
 speciation in chaparral than in forests and evidence for expanding habitat
 tolerances.
description: habitat character states
 for Arctostaphylos1 = chaparral, 2 =
 forest, 0 = botharc-states.csvhabitat character states for Ceanothus1 = chaparral, 2 = forest, 0 = bothcea-states.csvphylogenetic trees for Arctostaphylos1000 trees from the posterior set produced by BEASTarc-trees.trephylogenetic trees for Ceanothus1000 trees from the posterior set produced by BEASTcea-trees.trechaparral analysis scriptFitting the GeoSSE model with this script requires the R package diversitree, written by Rich FitzJohn. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (diversitreeGSE_0.4-5.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. This package is presently undergoing rapid development, so for any new applications, please use the current, improved version of the package, available from: http://cran.r-project.org/web/packages/diversitree/ and http://www.zoology.ubc.ca/prog/diversitree/.chaparral-analysis.Rsimulation analysis scriptSimulating trees under the GeoSSE model requires the C program SimTreeSDD. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (SimTreeSDD-2009.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. Extensive further development is not planned, but the current version of the package is available from: http://tigger.uic.edu/~eeg/code/code.html. The R package diversitree is also required by this script. See Description for chaparral-analysis.R.simulation-analysis.Ralignment for Arctostaphylosalso contains habitat states and maximum clade credibility treeArctostaphylos.nexalignment for Ceanothusalso contains habitat states and maximum clade credibility treeCeanothus.nexBEAST input file for ArctostaphylosArctostaphylosBeastfile.xmlBEAST input file for CeanothusCeanothusBeastfile.xmlarc & cea supplementary tableGenBank accession numbers and habitat encoding notes and referencesArcCeaSupplementaryTable.xls
DOI: 10.5061/dryad.jn81h
title: Data from: Variation of xylem vessel diameters across a climate gradient: insight from a reciprocal transplant experiment with a widespread boreal tree

description: Xylem vessel diameters represent an important plant hydraulic trait to
 ensure sufficient water supply from the roots to the leaves. The ability
 to adjust the hydraulic pathway to environmental cues is key in order to
 satisfy transpirational demands and maximize growth and survival. We
 evaluated the variability of vessel diameters in trembling aspen in a
 reciprocal transplant experiment. We tested six provenances from three
 ecological regions of North America planted at four test sites in western
 Canada. All test sites were established at the same time with the same
 provenances arranged in a randomized complete block design. Vessel
 diameter showed a strong interaction of population and test site
 suggesting a high degree of phenotypic plasticity in this trait. Gaussian
 kernel density estimates support plastic as well as genetic contributions
 in vessel diameter control trending from bimodal distributions at the most
 northern test site towards unimodal distributions at the warmest and
 mildest test site. Furthermore, we used test site-specific climate data in
 form of a 2-year, 5-year and 10-year average of 21 directly and derived
 climatic variables and found that average site-specific vessel diameters
 correlated strongly with summer moisture availability. A previously found
 negative relationship with vessel diameter and tree height in central
 Alberta was also found at two other boreal test sites but reversed at a
 wetter and milder sub-boreal test site. In summary, vessel diameters were
 highly plastic in response to different environments and varied with
 summer moisture availability. The variability of vessel diameter and tree
 height correlations suggests that vessel diameter alone cannot serve as a
 reliable proxy for long-term growth performance beyond boreal
 environments. Instead, selecting aspen populations with a high degree of
 plasticity in this trait appears to be the safest option for assisted
 migration and seed transfer programmes under climate change.
description: Vessel diameter
 measurementsThis file contains xylem
 vessel diameters (µm) for trembling aspen collected at four test sites in
 western Canada. These test sites were located in northeastern British
 Columbia, northern Alberta, central Alberta and the Alberta
 foothills.Vessel_diameter.csvAnnual climate dataThis file contains annual climate data for the northeastern British Columbia (BC), northern Alberta (nAB), central Alberta (cAB) and Alberta foothills (ABf) test site. The data was generated using the ClimateWNA software (http://www.climatewna.com/).Climate_annual.csvSeasonal climate dataThis file contains seasonal climate data for the northeastern British Columbia (BC), northern Alberta (nAB), central Alberta (cAB) and Alberta foothills (ABf) test site. The data was generated using the ClimateWNA software (http://www.climatewna.com/).Climate_seasonal.csv
DOI: 10.5061/dryad.2v7kr
title: Data from: MHC-similarity and sexual selection: different doesn't always mean attractive

description: Females that mate multiply have the possibility to exert postcopulatory
 choice and select more compatible sperm to fertilize eggs. Prior work
 suggests that dissimilarity in major histocompatibility complex (MHC)
 plays an important role in determining genetic compatibility between
 partners. Favouring a partner with dissimilar MHC alleles would result in
 offspring with high MHC diversity and therefore with enhanced survival
 thanks to increased resistance to pathogens and parasites. The high
 variability of MHC genes may further allow discrimination against the
 sperm from related males, reducing offspring homozygosity and inbreeding
 risk. Despite the large body of work conducted at precopulatory level, the
 role of MHC similarity between partners at postcopulatory level has been
 rarely investigated. We used an internal fertilizing fish with high level
 of multiple matings (Poecilia reticulata) to study whether MHC similarity
 plays a role in determining the outcome of fertilization when sperm from
 two males compete for the same set of eggs. We also controlled for
 genomewide similarity by determining similarity at 10 microsatellite loci.
 Contrary to prediction, we found that the more MHC-similar male sired more
 offspring while similarity at the microsatellite loci did not predict the
 outcome of sperm competition. Our results suggest that MHC discrimination
 may be involved in avoidance of hybridization or outbreeding rather than
 inbreeding avoidance. This, coupled with similar findings in salmon,
 suggests that the preference for MHC-dissimilar mates is far from being
 unanimous and that pre- and postcopulatory episodes of sexual selection
 can indeed act in opposite directions.
description: datasetPlease see paper for details on data collection, experimental design and data analysis.aligned sequencesMHC aligned sequencesMHCRaw data (1st sheet) and band sharing-similarity (2nd sheet)Microsatellites dataraw data (1st sheet) and genalex summary-similarity (2nd sheet)Microsatellites.xlsx
DOI: 10.5061/dryad.h4dt0
title: Data from: When the going gets tough: behavioral type dependent space use in the sleepy lizard changes as the season dries

description: Understanding space use remains a major challenge for animal ecology, with
 implications for species interactions, disease spread, and conservation.
 Behavioural type (BT) may shape the space use of individuals within animal
 populations. Bolder or more aggressive individuals tend to be more
 exploratory and disperse further. Yet, to date we have limited knowledge
 on how space use other than dispersal depends on BT. To address this
 question we studied BT-dependent space-use patterns of sleepy lizards
 (Tiliqua rugosa) in southern Australia. We combined high-resolution global
 positioning system (GPS) tracking of 72 free-ranging lizards with repeated
 behavioural assays, and with a survey of the spatial distributions of
 their food and refuge resources. Bayesian generalized linear mixed models
 (GLMM) showed that lizards responded to the spatial distribution of
 resources at the neighbourhood scale and to the intensity of space use by
 other conspecifics (showing apparent conspecific avoidance). BT
 (especially aggressiveness) affected space use by lizards and their
 response to ecological and social factors, in a seasonally dependent
 manner. Many of these effects and interactions were stronger later in the
 season when food became scarce and environmental conditions got tougher.
 For example, refuge and food availability became more important later in
 the season and unaggressive lizards were more responsive to these
 predictors. These findings highlight a commonly overlooked source of
 heterogeneity in animal space use and improve our mechanistic
 understanding of processes leading to behaviourally driven disease
 dynamics and social structure.
description: Lizards space use data
 for the Bayesian GLMM modelsThis file includes all
 the data used for modeling the space use by the lizards. It contains
 separates sheets for the Early and Late season and columns names are
 explained in a metadata sheet.LizardsDataForProcBForDryad.xlsx