cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7f1h767
title: Data from: Large-effect mutations generate trade-off between predatory and locomotor ability during arms race coevolution with deadly prey

description: Adaptive evolution in response to one selective challenge may disrupt
 other important aspects of performance. Such evolutionary trade-offs are
 predicted to arise in the process of local adaptation, but it is unclear
 if these phenotypic compromises result from the antagonistic effects of
 simple amino acid substitutions. We tested for trade-offs associated with
 beneficial mutations that confer tetrodotoxin (TTX) resistance in the
 voltage-gated sodium channel (NaV1.4) in skeletal muscle of the common
 garter snake (Thamnophis sirtalis). Separate lineages in California and
 the Pacific Northwest independently evolved TTX-resistant changes to the
 pore of NaV1.4 as a result of arms race coevolution with toxic prey, newts
 of the genus Taricha. Snakes from the California lineage that were
 homozygous for an allele known to confer large increases in toxin
 resistance (NaV1.4LVNV) had significantly reduced crawl speed compared to
 individuals with the ancestral TTX-sensitive channel. Heterologous
 expression of native snake NaV1.4 proteins demonstrated that the same
 NaV1.4LVNV allele confers a dramatic increase in TTX resistance and a
 correlated decrease in overall channel excitability. Our results suggest
 the same mutations that accumulate during arms race coevolution and
 beneficially interfere with toxin-binding also cause changes in
 electrophysiological function of the channel that may affect organismal
 performance. This trade-off was only evident in the predator lineage where
 coevolution has led to the most extreme resistance phenotype, determined
 by four critical amino acid substitutions. If these biophysical changes
 also translate to a fitness cost—for example, through the inability of T.
 sirtalis to quickly escape predators—then pleiotropy at this single locus
 could contribute to observed variation in levels of TTX resistance across
 the mosaic landscape of coevolution.
description: Dryad_CA_neonatesCrawl speed and DIV genotypic data for California neonate snakesDryad_PNW_neonatesCrawl speed and DIV genotypic data for Pacific Northwest neonate snakesTs1.4_cl1.1_Illinois_FIFast inactivation data for Nav1.4 Illinois cloneTs1.4_cl1.1_Illinois_IVActivation data for Nav1.4 Illinois cloneTTXcalc_Ts1.4_IL_Cl-1.1_UDBTTX data for Nav1.4 Illinois cloneTs1.4_cl2_LVNV_FIFast inactivation data for Nav1.4 LVNV cloneTs1.4_cl2_LVNV_IVActivation data for Nav1.4 LVNV cloneTTXcalc_Ts1.4_LVNV_cl2_UDBTTX data for Nav1.4 LVNV cloneTs1.4_cl3_V_FIFast inactivation data for Nav1.4 V cloneTs1.4_cl3_V_IVActivation data for Nav1.4 V cloneTTXcalc_Ts1.4_V_cl3_UDBTTX data for Nav1.4 V clone
DOI: 10.5061/dryad.13ks6
title: Data from: The crouching of the shrew: mechanical consequences of limb posture in small mammals

description: An important trend in the early evolution of mammals was the shift from a
 sprawling stance, whereby the legs are held in a more abducted position,
 to a parasagittal one, in which the legs extend more downward. After that
 transition, many mammals shifted from a crouching stance to a more upright
 one. It is hypothesized that one consequence of these transitions was a
 decrease in the total mechanical power required for locomotion, because
 side-to-side accelerations of the body have become smaller, and thus less
 costly with changes in limb orientation. To test this hypothesis we
 compared the kinetics of locomotion in two mammals of body size close to
 those of early mammals (&lt; 40 g), both with parasagittally oriented
 limbs: a crouching shrew (Blarina brevicauda; 5 animals, 17 trials) and a
 more upright vole (Microtus pennsylvanicus; 4 animals, 22 trials). As
 predicted, voles used less mechanical power per unit body mass to perform
 steady locomotion than shrews did (P = 0.03). However, while lateral
 forces were indeed smaller in voles (15.6 ± 2.0% body weight) than in
 shrews (26.4 ± 10.9%; P = 0.046), the power used to move the body from
 side-to-side was negligible, making up less than 5% of total power in both
 shrews and voles. The most power consumed for both species was that used
 to accelerate the body in the direction of travel, and this was much
 larger for shrews than for voles (P = 0.01). We conclude that side-to-side
 accelerations are negligible for small mammals–whether crouching or more
 upright–compared to their sprawling ancestors, and that a more upright
 posture further decreases the cost of locomotion compared to crouching by
 helping to maintain the body’s momentum in the direction of travel.
description: Force Plate Recordings
 for the 39 trials in the studykey_to_all_trials.csv
 gives metadata for each force plate recording (which individual, its mass,
 initial velocity, etc.). The 39 other files are each recordings from an
 individual force plate trial, truncated from left hind footfall to left
 hind footfall (one stride cycle).Riskin_Kendall_Hermanson_2016_PeerJ_Force_Plate_Recordings.zip
DOI: 10.5061/dryad.n7n170m
title: Data from: Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

description: Roots provide plants mineral nutrients and stability in soil; while doing
 so, they come into contact with diverse soil microbes that affect plant
 health and productivity. Despite their ecological and agricultural
 relevance, the factors that shape the root microbiome remain poorly
 understood. We grew a worldwide panel of replicated Arabidopsis thaliana
 accessions outdoors and over winter to characterize their root-microbial
 communities. Although studies of the root microbiome tend to focus on
 bacteria, we found evidence that fungi have a strong influence on the
 structure of the root microbiome. Moreover, host effects appear to have a
 stronger influence on plant-fungal communities than plant-bacterial
 communities. Mapping the host genes that affect microbiome traits
 identified a priori candidate genes with roles in plant immunity; the root
 microbiome also appears to be strongly affected by genes that impact root
 and root hair development. Our results suggest that future analyses of the
 root microbiome should focus on multiple kingdoms, and that the root
 microbiome is shaped not only by genes involved in defense, but also by
 genes involved in plant form and physiology.
description: Root microbiome
 phenotypesThis tar-gz file
 contains phenotypes related to alpha-diversity (species richness) and
 beta-diversity (modeled using PCA). In the case of richness, we estimated
 species richness in the bacterial, fungal, and combined (bacterial and
 fungal) communities. In the paper, we also introduced the phenotype
 'bacterial preference', which measures whether an
 accession's roots form a better habitat for either bacteria or fungi
 (or diversity within these communities; the estimates are in the phenotype
 file: slant.1.tn2.ranef_diff_exps.txt). The phenotype files for PCA are
 also included.phenotypes.tgzArabidopsis thaliana root microbiome, GWAS resultsResults from GWAS of species richness (the folder gwas_alpha) and beta diversity (modeled using PCA; the folder is gwas_pca). The tar gz file includes 'reports' (e.g. the top SNPs after GWAS) and image files (manhattan plots). The Methods section of the paper describes the procedure(s) used in GWAS. For more information about the phenotypes, please see the description for the phenotypes.tgz file.results.tgz
DOI: 10.5061/dryad.pm4m5
title: Data from: Gas exchange and leaf anatomy of a C3-CAM hybrid, Yucca gloriosa (Asparagaceae)

description: While the majority of plants use the typical C3 carbon metabolic pathway,
 ~6% of angiosperms have adapted to carbon limitation as a result of water
 stress by employing a modified form of photosynthesis known as
 Crassulacean acid metabolism (CAM). CAM plants concentrate carbon in the
 cells by temporally separating atmospheric carbon acquisition from
 fixation into carbohydrates. CAM has been studied for decades, but the
 evolutionary progression from C3 to CAM remains obscure. In order to
 better understand the morphological and physiological characteristics
 associated with CAM photosynthesis, phenotypic variation was assessed in
 Yucca aloifolia, a CAM species, Yucca filamentosa, a C3 species, and Yucca
 gloriosa, a hybrid species derived from these two yuccas exhibiting
 intermediate C3–CAM characteristics. Gas exchange, titratable leaf
 acidity, and leaf anatomical traits of all three species were assayed in a
 common garden under well-watered and drought-stressed conditions. Yucca
 gloriosa showed intermediate phenotypes for nearly all traits measured,
 including the ability to acquire carbon at night. Using the variation
 found among individuals of all three species, correlations between traits
 were assessed to better understand how leaf anatomy and CAM physiology are
 related. Yucca gloriosa may be constrained by a number of traits which
 prevent it from using CAM to as high a degree as Y. aloifolia. The
 intermediate nature of Y. gloriosa makes it a promising system in which to
 study the evolution of CAM.
description: Leaf phenotype
 dataData from all genotypes
 from all three species including measures of leaf succulence, cross
 sectional data, and stomatal densities. See second tab for information on
 units.leaf_phenotype_data.xlsxRaw cross section dataData collected from cross section replicates from all three species and all genotypes.crosssections.xlsxLiCOR 6400XT dataGas exchange, etc data from all species for all days/timespoints and all experimental months (July and Oct 2014, Feb 2015). First five tabs are all data from a given day in an experiment, followed by tabs for species specific and genotype specific values.licor_data_alldays_allspecies.xlsxTitratable acidityTitratable acidity values (and raw pH values where measured) for all samples, all species.leaf_acidity.xlsx
DOI: 10.5061/dryad.682ns
title: Data from: Indirect genetic effects underlie oxygen-limited thermal tolerance within a coastal population of chinook salmon

description: With global temperatures projected to surpass the limits of thermal
 tolerance for many species, evaluating the heritable variation underlying
 thermal tolerance is critical for understanding the potential for
 adaptation to climate change. We examined the evolutionary potential of
 thermal tolerance within a population of chinook salmon (Oncorhynchus
 tshawytscha) by conducting a full-factorial breeding design and measuring
 the thermal performance of cardiac function and the critical thermal
 maximum (CTmax) of offspring from each family. Additive genetic variation
 in offspring phenotype was mostly negligible, although these direct
 genetic effects explained 53% of the variation in resting heart rate (fH).
 Conversely, maternal effects had a significant influence on resting fH,
 scope for fH, cardiac arrhythmia temperature and CTmax. These maternal
 effects were associated with egg size, as indicated by strong
 relationships between the mean egg diameter of mothers and offspring
 thermal tolerance. Because egg size can be highly heritable in chinook
 salmon, our finding indicates that the maternal effects of egg size
 constitute an indirect genetic effect contributing to thermal tolerance.
 Such indirect genetic effects could accelerate evolutionary responses to
 the selection imposed by rising temperatures and could contribute to the
 population-specific thermal tolerance that has recently been uncovered
 among Pacific salmon populations.
description: Electronic Supplementary
 Material (data)The heart rate and CTmax
 data from all individuals used in this study. These data were collected
 from 25 different families of chinook salmon (5 females and 5 males mated
 in all combinations). Heart rates were counted from electrocardiograms and
 recorded along with the corresponding temperature. These data were then
 analyzed to find the Arrhenius break temperature of heart rate, which
 corresponds to a drop in the temperature sensitivity (Q10) of heart rate.
 The additive genetic, non-additive genetic, and maternal effects
 contributing to cardiac performance and CTmax were calculated by
 partitioning the variation in these phenotypes to Sire (i.e. father) and
 Dam (i.e. mother) ID and their interaction using a two-way
 ANOVA.
DOI: 10.5066/p13e4pmt
title: Mark recapture data for loggerhead sea turtles in St. Joseph Bay, FL from 2011-2024

description: This dataset includes information on total loggerhead sea turtle captures, recaptures, and their size ranges upon capture by year (2011–2024) in St. Joseph Bay, FL.
DOI: 10.5061/dryad.58d51
title: Data from: Experimental manipulation of female reproduction demonstrates its fitness costs in kangaroos

description: 1. When resources are scarce, female mammals should face a trade-off
 between lactation and other life-history traits such as growth, survival
 and subsequent reproduction. Kangaroos are ideal to test predictions about
 reproductive costs because they may simultaneously lactate and carry a
 young, and have indeterminate growth and a long breeding season. 2. An
 earlier study in three of our five study populations prevented female
 eastern grey kangaroos (Macropus giganteus) from reproducing during one
 reproductive season by either inserting contraceptive implants or removing
 very small pouch young. We explored how individual and environmental
 variables affect the costs of reproduction over time, combining this
 experimental reduction of reproductive effort with multi-year monitoring
 of 270 marked females. Experimental manipulation should control for
 individual heterogeneity, revealing the costs of reproduction and their
 likely sources. We also examined the fitness consequences of reproductive
 effort and offspring sex among unmanipulated individuals to test if sex
 allocation strategies affected trade-offs. 3. Costs of reproduction
 included longer inter-birth intervals and lower probability of producing a
 young that survived to 7 months in the subsequent reproductive event.
 Weaning success, however, did not differ significantly between manipulated
 and control females. By reducing reproductive effort, manipulation
 appeared to increase individual condition and subsequent reproductive
 success. 4. Effects of offspring sex upon subsequent reproductive success
 varied according to year and study population. Mothers of sons were
 generally more likely to have a young that survived to 7 months, compared
 to mothers of daughters. 5. The fitness costs of reproduction arise from
 constraints in both acquisition and allocation of resources. To meet these
 costs, females delay subsequent parturition and may manipulate offspring
 sex. Reproductive tactics thus vary according to the amount of resource
 available to each individual, promoting a wide range in reproductive
 performance within and among individuals and populations.
description: data_reproduction-kangaroocollected in the field
DOI: 10.5061/dryad.vq31g
title: Data from: Transoceanic origin of microendemic and flightless New Caledonian weevils

description: The origin of the astonishing New Caledonian biota continues to fuel a
 heated debate among advocates of a Gondwanan relict scenario and defenders
 of late oceanic dispersal. Here, we study the origin of New Caledonian
 Trigonopterus flightless weevils using a multimarker molecular phylogeny.
 We infer two independent clades of species found in the archipelago. Our
 dating estimates suggest a Late Miocene origin of both clades long after
 the re-emergence of New Caledonia about 37 Ma. The estimation of ancestral
 ranges supports an ancestral origin of the genus in a combined region
 encompassing Australia and New Guinea with subsequent colonizations of New
 Caledonia out of New Guinea in the mid-Miocene. The two New Caledonian
 lineages have had very different evolutionary trajectories. Colonizers
 belonging to a clade of foliage dwellers greatly diversified, whereas
 species inhabiting leaf-litter have been less successful.
description: Trigonopterus with focus
 on New CaledoniaNexus file of aligned
 DNA sequence data.NC.nex
DOI: 10.5061/dryad.1045
title: Data from: The ontogeny of plant defense and herbivory: characterizing general patterns using meta-analysis

description: Defense against herbivores often changes dramatically as plants develop.
 Hypotheses based on allocation theory and herbivore selection patterns
 predict that defense should either increase or decrease, respectively,
 across ontogeny, and previous research partly supports both predictions.
 Thus, it remains unclear which pattern is more common and what factors
 contribute to variability among studies. We conducted a meta-analysis of
 116 published studies reporting ontogenetic patterns in plant defense
 traits and herbivory. Patterns varied depending on plant life form (woody,
 herbaceous, grass), type of herbivore (insect, mollusk, mammal), and type
 of defense trait (secondary chemistry, physical defense, tolerance). In
 woody plants, chemical defense increased during the seedling stage,
 followed by an increase in physical defenses during the vegetative
 juvenile stage. Mammalian herbivores showed a strong preference for mature
 compared to juvenile tissues in woody plants. Herbs experienced a
 significant increase in secondary chemistry across the entire ontogenetic
 trajectory, although the magnitude of increase was greatest during the
 seedling stage. Correspondingly, mollusks preferred young compared to
 older herbs. Future research investigating growth/defense trade-offs,
 allometry, herbivore selection patterns, and ecological costs, would shed
 light on the mechanisms driving the ontogenetic patterns observed.
description: Metadata
 BibliographyMetadata_Bibliography.docComplete Meta DatabaseComplete datasets analyzed by meta-analysis (Tables 1-8)Complete_Meta_Database.doc
DOI: 10.15468/dl.3zvgcc
title: Occurrence Download

description: A dataset containing 7120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is Kenya",
 "Geometry POLYGON((39.77467 -3.51376,40.05945 -3.51376,40.05945 -3.16084,39.77467 -3.16084,39.77467 -3.51376))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 7120 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000518-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mk159
title: Data from: Patterns, causes, and consequences of defensive microbiome dynamics across multiple scales

description: The microbiome can significantly impact host phenotypes and serve as an
 additional source of heritable genetic variation. While patterns across
 eukaryotes are consistent with a role for symbiotic microbes in host
 macroevolution, few studies have examined symbiont-driven host evolution
 or the ecological implications of a dynamic microbiome across temporal,
 spatial or ecological scales. The pea aphid, Acyrthosiphon pisum, and its
 eight heritable bacterial endosymbionts have served as a model for studies
 on symbiosis and its potential contributions to host ecology and
 evolution. But we know little about the natural dynamics or ecological
 impacts of the heritable microbiome of this cosmopolitan insect pest. Here
 we report seasonal shifts in the frequencies of heritable defensive
 bacteria from natural pea aphid populations across two host races and
 geographic regions. Microbiome dynamics were consistent with symbiont
 responses to host-level selection and findings from one population
 suggested symbiont-driven adaptation to seasonally changing parasitoid
 pressures. Conversely, symbiont levels were negatively correlated with
 enemy-driven mortality when measured across host races, suggesting
 important ecological impacts of host race microbiome divergence. Rapid
 drops in symbiont frequencies following seasonal peaks suggest microbiome
 instability in several populations, with potentially large costs of
 ‘superinfection’ under certain environmental conditions. In summary, the
 realization of several laboratory-derived, a priori expectations suggests
 important natural impacts of defensive symbionts in host-enemy
 eco-evolutionary feedbacks. Yet negative findings and unanticipated
 correlations suggest complexities within this system may limit or obscure
 symbiont-driven contemporary evolution, a finding of broad significance
 given the widespread nature of defensive microbes across plants and
 animals.
description: AppendixSIThis file is an excel database that includes data and data collection information.MolEcolSmithAppendixS1.xlsxHamiltonella sequence alignmentThis is a text file of DNA sequence alignments in FASTA formatHamiltonella defensaRegiella insecticola alignmentThis is a text file of sequence alignments in FASTA format.Regiella insecticolaSerratia symbiotica alignmentThis is a text file of a DNA sequence alignment in FASTA format.Serratia symbioticaX-type alignmentThis is a text file of a DNA sequence alignment in FASTA format.X-typeRickettsiella viridis alignmentThis is a text file of a DNA sequence alignment in FASTA format.RickettsiellaRickettsia alignmentThis is a text file of a DNA sequence alignment in FASTA format.RickettsiaSpiroplasma alignmentThis is a text file of a DNA sequence alignment in FASTA format.Spiroplasma
DOI: 10.15468/dl.zf8mqq
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mamíferos pequeños en el municipio de Medina, Cundinamarca - Proyecto Colombia Bio"
 ]
}

 The dataset includes 44 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000516-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.