cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9b5q2pv
title: Data from: Long-term evolution on complex fitness landscapes when mutation is weak

description: Understanding evolution on complex fitness landscapes is difficult both
 because of the large dimensionality of sequence space and the
 stochasticity inherent to population-genetic processes. Here I present an
 integrated suite of mathematical tools for understanding evolution on
 time-invariant fitness landscapes when mutations occur sufficiently rarely
 that the population is typically monomorphic and evolution can be modeled
 as a sequence of well-separated fixation events. The basic intuition
 behind this suite of tools is that surrounding any particular genotype
 lies a region of the fitness landscape that is easy to evolve to, while
 other pieces of the fitness landscape are difficult to evolve to (due to
 distance, being across a fitness valley, etc.). I propose a rigorous
 definition for this ``dynamical neighborhood' of a genotype which
 captures several aspects of the distribution of waiting times to evolve
 from one genotype to another. The neighborhood structure of the landscape
 as a whole can be summarized as a matrix, and I show how this matrix can
 be used to approximate the expected waiting time for certain evolutionary
 events to occur and to provide an intuitive interpretation to existing
 formal results on the index of dispersion of the molecular clock.
description: McCandlishHeredityCodeWolfram Mathematica 10.2.0.0 notebook
DOI: 10.5061/dryad.7vf45
title: Data from: Maiasaura, a model organism for extinct vertebrate population biology: a large sample statistical assessment of growth dynamics and survivorship

description: Fossil bone microanalyses reveal the ontogenetic histories of extinct
 tetrapods, but incomplete fossil records often result in small sample sets
 lacking statistical strength. In contrast, a histological sample of 50
 tibiae of the hadrosaurid dinosaur Maiasaura peeblesorum allows
 predictions of annual growth and ecological interpretations based on more
 histologic data than any previous large sample study. Tibia length
 correlates well (R2&gt;0.9) with diaphyseal circumference, cortical
 area, and bone wall thickness, thereby allowing longitudinal predictions
 of annual body size increases based on growth mark circumference
 measurements. With an avian level apposition rate of 86.4 μm/day,
 Maiasaura achieved over half of asymptotic tibia diaphyseal circumference
 within its first year. Mortality rate for the first year was 89.9% but a
 seven year period of peak performance followed, when survivorship (mean
 mortality rate=12.7%) was highest. During the third year of life,
 Maiasaura attained 36% (x=1260 kg) of asymptotic body mass, growth rate
 was decelerating (18.2 μm/day), cortical vascular orientation changed, and
 mortality rate briefly increased. These transitions may indicate onset of
 sexual maturity and corresponding reallocation of resources to
 reproduction. Skeletal maturity and senescence occurred after 8 years, at
 which point the mean mortality rate increased to 44.4%. Compared with
 Alligator, an extant relative, Maiasaura exhibits rapid cortical increase
 early in ontogeny, while Alligator cortical growth is much lower and
 protracted throughout ontogeny. Our life history synthesis of Maiasaura
 utilizes the largest histological sample size for any extinct tetrapod
 species thus far, demonstrating how large sample microanalyses strengthen
 paleobiological interpretations.
description: R code for Maiasaura
 growth curvesA modified version of
 the R script from Cooper et al. 2008 used to construct Maiasaura growth
 curves.Supplementary Document
 1.docxSupplementary Figures
 and TablesSupplementary Figures
 1-3 and Supplementary Tables 1-7.
DOI: 10.5061/dryad.r3sh7
title: Data from: Deterministic processes vary during community assembly for ecologically dissimilar taxa

description: The continuum hypothesis states that both deterministic and stochastic
 processes contribute to the assembly of ecological communities. However,
 the contextual dependency of these processes remains an open question that
 imposes strong limitations on predictions of community responses to
 environmental change. Here we measure community and habitat turnover
 across multiple vertical soil horizons at 183 sites across Scotland for
 bacteria and fungi, both dominant and functionally vital components of all
 soils but which differ substantially in their growth habit and dispersal
 capability. We find that habitat turnover is the primary driver of
 bacterial community turnover in general, although its importance decreases
 with increasing isolation and disturbance. Fungal communities, however,
 exhibit a highly stochastic assembly process, both neutral and non-neutral
 in nature, largely independent of disturbance. These findings suggest that
 increased focus on dispersal limitation and biotic interactions are
 necessary to manage and conserve the key ecosystem services provided by
 these assemblages.
description: Bacterial community data
 from the second National Soils Inventory of ScotlandBacterial community data
 from the second National Soils Inventory of Scotland.
 'SAMPLE.ID' refers to the unique sample identifier associated
 with the NSIS2 database (to be released publically by the James Hutton
 Institute); 'LAYER' refers to the paedological horizon sampled
 (L1: topsoil horizon; L2-4: second, third, and fourth horizon in depth
 from the topsoil horizon); all columns with prefix S16 represent OTUs
 derived from T-RFLP analysis, with the value representing the proportional
 abundance of that OTU in that sample based on peak height (the sum of
 these columns equals 1).NSIS2_bacteriaTRFs.csvFungal community data from the second National Soils Inventory of ScotlandFungal community data from the second National Soils Inventory of Scotland. 'SAMPLE.ID' refers to the unique sample identifier associated with the NSIS2 database (to be released publically by the James Hutton Institute); 'LAYER' refers to the paedological horizon sampled (L1: topsoil horizon; L2-4: second, third, and fourth horizon in depth from the topsoil horizon); all columns with prefix ITS represent OTUs derived from T-RFLP analysis, with the value representing the proportional abundance of that OTU in that sample based on peak height (the sum of these columns equals 1).NSIS2_fungiTRFs.csv
DOI: 10.7910/dvn/he4aaq
title: Replication Data for: A Detailed Historical and Statistical Analysis of the Influence of Hardware Artifacts on SPEC Integer Benchmark Performance

description: This dataset includes the Standard Performance Evaluation Corporation (SPEC)
CPU benchmark since 1995. This dataset is used for analysis in the paper "A Detailed Historical and Statistical Analysis of the Influence of Hardware Artifacts on SPEC Integer Benchmark Performance." DOI: 10.1109/TC.2024.3365941
description: The four files below include the benchmark score from SPEC95,
SPEC2000, SPEC2006, SPEC2017 respectively.
DOI: 10.5061/dryad.km484
title: Data from: Medical expenditure for chronic diseases in Mexico: the case of selected diagnoses treated by the largest care providers

description: Background: Chronic diseases (CD) are a public health emergency in Mexico.
 Despite concern regarding the financial burden of CDs in the country,
 economic studies have focused only on diabetes, hypertension, and cancer.
 Furthermore, these estimated financial burdens were based on hypothetical
 epidemiology models or ideal healthcare scenarios. The present study
 estimates the annual expenditure per patient and the financial burden for
 the nine most prevalent CDs, excluding cancer, for each of the two largest
 public health providers in the country: the Ministry of Health (MoH) and
 the Mexican Institute of Social Security (IMSS). Methods: Using the
 Mexican National Health and Nutrition Survey 2012 (ENSANUT) as the main
 source of data, health services consumption related to CDs was obtained
 from patient reports. Unit costs for each provided health service (e.g.
 consultation, drugs, hospitalization) were obtained from official reports.
 Prevalence data was obtained from the published literature. Annual
 expenditure due to health services consumption was calculated by
 multiplying the quantity of services consumed by the unit cost of each
 health service. Results: The most expensive CD in both health institutions
 was chronic kidney disease (CKD), with an annual unit cost for MoH per
 patient of US$ 8,966 while for IMSS the expenditure was US$ 9,091. Four
 CDs (CKD, arterial hypertension, type 2 diabetes, and chronic ischemic
 heart disease) accounted for 88% of the total CDs financial burden (US$
 1.42 billion) in MoH and 85% (US$ 3.96 billion) in IMSS. The financial
 burden of the nine CDs analyzed represents 8% and 25% of the total annual
 MoH and IMSS health expenditure, respectively. Conclusions/Significance:
 The financial burden from the nine most prevalent CDs, excluding cancer,
 is already high in Mexico. This finding by itself argues for the need to
 improve health promotion and disease detection, diagnosis, and treatment
 to ensure CD primary and secondary prevention. If the status quo remains,
 the financial burden could be higher.
description: Figueroa-Lara A,
 Gonzalez-Block M, Alarcón-Irigoyen J_PLoS_26_12_2015
DOI: 10.5061/dryad.89qp4
title: Data from: Prey state alters trait-mediated indirect interactions in rocky tide pools

description: Several studies on trait-mediated indirect interactions (TMIIs) have shown
 that predators can initiate trophic cascades by altering prey behaviour.
 Although it is well recognized that individual prey state alters
 antipredator and foraging behaviour, few studies explore whether this
 state-dependent prey behaviour can alter the strength of the ensuing
 tritrophic cascade. Here, we link state-dependent individual behaviour to
 community processes by experimentally testing whether hunger level and
 body size of prey altered antipredator behaviour and thus changed the
 strength of trophic cascades between predators and primary producers. In
 rocky intertidal tide pools on the California Coast, waterborne cues from
 the predatory seastar Leptasterias spp. (Stimpson) can cause the
 herbivorous snail Tegula (Chlorostoma) funebralis (A. Adams) to reduce
 grazing and flee tide pools, resulting in positive indirect effects on
 tide pool microalgae. However, we show that the strength of this
 behaviourally-mediated cascade may be contingent on prey hunger level and
 body size. During short field experiments at low tide, medium-sized snails
 that were either newly collected from the field or fed for 1 week in the
 laboratory mediated strong TMIIs because they grazed less when seastars
 were present. In contrast, no TMIIs occurred when medium-sized snails had
 been starved for 1 week because they continued grazing regardless of
 seastar presence. Newly collected small snails fled from seastars but did
 not mediate cascades because they ate little algae. Despite reaching an
 apparent size refuge from predation, many newly collected large snails
 fled from seastars, but those individuals that remained tended to graze
 the algae more quickly, resulting in unexpected negative indirect effects
 of seastars on algae cover. The implication of this pattern for the
 natural system is unclear. Because average hunger level and size of snails
 vary over time and space in nature, a mosaic of TMII strength may exist.
 Overall, the strength of tritrophic TMIIs in tide pools depended on
 individual prey state, supporting model predictions and adding to sparse
 empirical evidence. This outcome suggests that patterns occurring
 system-wide over the long term may be influenced by the state-dependent
 decisions made by the individuals present.
description: Dryad_Gravem and
 Morgan_Prey traits alter TMIIsExcel workbook
 containing, raw data, metadata, data used for figures and other reported
 means
DOI: 10.5061/dryad.1th6k
title: Data from: Aerobic power and flight capacity in birds: a phylogenetic test of the heart-size hypothesis

description: Flight capacity is one of the most important innovations in animal
 evolution; it only evolved in insects, birds, mammals and the extinct
 pterodactyls. Given that powered flight represents a demanding aerobic
 activity, an efficient cardiovascular system is essential for the
 continuous delivery of oxygen to the pectoral muscles during flight. It is
 well known that the limiting step in the circulation is stroke volume (the
 volume of blood pumped from the ventricle to the body during each beat),
 which is determined by the size of the ventricle. Thus, the fresh mass of
 the heart represents a simple and repeatable anatomic measure of aerobic
 power of an animal. Although several authors have already compared heart
 masses across bird species, a phylogenetic comparative analysis of these
 comparisons is still lacking. Compiling heart sizes for 915 species and
 applying several statistical procedures controlling for body size and/or
 testing for adaptive trends in the dataset (e.g., model selection
 approaches, phylogenetic generalized linear models), we found that
 (residuals of) heart sizes are consistently associated with four
 categories of flight capacity. In general, our results indicate that
 species exhibiting continuous hovering flight (i.e., hummingbirds) have
 substantially larger hearts than do other groups, that species that use
 flapping flight and gliding show intermediate values, and that species
 categorized as poor flyers show the smallest values. Our study shows that
 at a broad scale, routine flight modes seem to have shaped the energetic
 requirements of birds sufficiently to be anatomically detected at the
 comparative level.
description: Supplementary
 MaterialClassification criteria
 for flight mode (extended) and complete list of species including flight
 mode, migration class, body mass (BM) and heart mass (HM) and the
 respective source of information.
DOI: 10.5061/dryad.56bb4
title: Data from: Adaptation to temporally fluctuating environments by the evolution of maternal effects

description: All organisms live in temporally fluctuating environments. Theory predicts
 that the evolution of deterministic maternal effects (i.e., anticipatory
 maternal effects or transgenerational phenotypic plasticity) underlies
 adaptation to environments that fluctuate in a predictably alternating
 fashion over maternal-offspring generations. In contrast, randomizing
 maternal effects (i.e., diversifying and conservative bet-hedging), are
 expected to evolve in response to unpredictably fluctuating environments.
 Although maternal effects are common, evidence for their adaptive
 significance is equivocal since they can easily evolve as a correlated
 response to maternal selection and may or may not increase the future
 fitness of offspring. Using the hermaphroditic nematode Caenorhabditis
 elegans, we here show that the experimental evolution of maternal glycogen
 provisioning underlies adaptation to a fluctuating normoxia–anoxia
 hatching environment by increasing embryo survival under anoxia. In
 strictly alternating environments, we found that hermaphrodites evolved
 the ability to increase embryo glycogen provisioning when they experienced
 normoxia and to decrease embryo glycogen provisioning when they
 experienced anoxia. At odds with existing theory, however, populations
 facing irregularly fluctuating normoxia–anoxia hatching environments
 failed to evolve randomizing maternal effects. Instead, adaptation in
 these populations may have occurred through the evolution of fitness
 effects that percolate over multiple generations, as they maintained
 considerably high expected growth rates during experimental evolution
 despite evolving reduced fecundity and reduced embryo survival under one
 or two generations of anoxia. We develop theoretical models that explain
 why adaptation to a wide range of patterns of environmental fluctuations
 hinges on the existence of deterministic maternal effects, and that such
 deterministic maternal effects are more likely to contribute to adaptation
 than randomizing maternal effects.
description: READMERead me text file with
 information concerning all deposited filesassay.fecundityfecundity raw dataassay.genotypesgenotypes raw dataassay.growth.ratefitness raw dataassay.hatchabilityhatchability raw dataassay.size.glycogenoocyte and embryo raw size and glycogen content data. contains data for unstained controlsee.designationexperimental evolution replicate population nomenclatureee.growth.rategrowth rate raw data during experimental evolutionee.sequences.codeQBasic code employed to design environmental sequencesee.sequencessequences of normoxia-anoxia environment employed for experimental evolutionfix.prob.simulationWolfram Mathematica code employed to determine the probability of fixation of maternal effects
DOI: 10.5061/dryad.t4jd0
title: Data from: PaleoENM: applying ecological niche modeling to the fossil record

description: Ecological niche modeling (ENM) is a quantitative approach to predict
 species’ abiotic requirements. It is a correlative technique, requiring
 geographically explicit information on species occurrences and the suites
 of environmental conditions experienced at each occurrence point. The
 output of these models is a set of environmental suitability rules that
 can be projected geographically and through time to test biogeographic,
 ecologic, and evolutionary hypotheses. Although developed by biologists
 and used extensively in the modern, ENM is in its early stages of
 application to the deep-time fossil record (hence PaleoENM). In part its
 limited use in the fossil record thus far reflects the methodological
 challenge of constructing paleoenvironmental layers needed for PaleoENM
 analysis, whereas in the modern these layers are available from large
 public databases (e.g., WorldClim). This paper provides a contextual and
 methodological framework for appropriately applying PaleoENM, including
 best practices for developing species occurrence and paleoenvironmental
 data sets for PaleoENM analyses.
description: Myers_etal_SuppTextSupplemental text with additional information regarding ENM/paleoENM methodology.Myers_etal_SuppTable1Supplemental table including stratigraphic correlations and associated references for fossil-bearing formations in the Late Cretaceous Western Interior Seaway of the US.
DOI: 10.5061/dryad.r2445
title: Data from: Fragment size affects plant herbivory via predator loss

description: Fragmentation and resultant changes in patch size are predicted to alter
 species diversity and community composition, yet the consequences of these
 differences for species interactions are poorly understood. Theory
 predicts that predators are more sensitive to fragmentation than their
 prey, resulting in greater predator loss in small patches. Predator loss,
 in turn, is predicted to 1) increase herbivory rates overall, and 2) cause
 herbivores to shift feeding from plants that act as refugia to those that
 are preferred forage. We tested these predictions in an old-field
 community using two experiments. The first was a large-scale experiment
 that included hundreds of arthropod species in fragments of various sizes,
 and used goldenrod and switchgrass to assess herbivory. Our second
 experiment manipulated densities of a focal predator species and a focal
 prey species to determine if changes in densities, rather than other
 characteristics of fragments, were sufficient to cause the trends observed
 in the first experiment. We found that predator densities declined in
 small fragments whereas herbivore densities showed the opposite trend.
 Total herbivory mirrored herbivore densities by increasing in small
 patches, and this mean increase was driven by large increases in goldenrod
 herbivory but declines in switchgrass herbivory. Experimental manipulation
 of densities confirmed that herbivores preferentially feed on goldenrod,
 and that predators depress herbivory on goldenrod but have a negligible
 effect on switchgrass. Our results suggest that fragmentation alters
 trophic interactions by causing declines in predator densities and
 increases in herbivore densities, but that feeding preferences of
 herbivores may generate unequal impacts among plant species.
description: Arthropod survey
 dataA
 species matrix of arthropods observed on focal plants.
DOI: 10.5061/dryad.k83b8
title: Data from: Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue

description: We report a method for Selective Depletion of abundant RNA (SDRNA) species
 from Human total RNA isolated from formalin-fixed, paraffin-embedded
 (FFPE) tissue, here demonstrating removal of ribosomal and mitochondrial
 transcripts from clinical FFPE tissue RNA archived up to 20 years.
 Importantly, SDRNA removes 98% of targeted RNAs while preserving relative
 abundance profiles of non-targeted RNAs, enabling routine whole
 transcriptome analysis of clinically valuable archival tissue specimens by
 Next-Generation Sequencing.
description: gene_countsGene level read counts for the eight libraries reported in the manuscript.
DOI: 10.5061/dryad.1bj51s9
title: Data from: Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations

description: Environmental gradients constrain physiological performance and thus
 species’ ranges, suggesting that species occurrence in diverse
 environments may be associated with local adaptation. Genome-environment
 association analyses (GEAA) have become central for studies of local
 adaptation, yet they are sensitive to the spatial orientation of
 historical range expansions relative to landscape gradients. To test
 whether potentially adaptive genotypes occur in varied climates in
 wide-ranged species, we implemented GEAA on the basis of genome-wide data
 from the anole lizards Anolis ortonii and A. punctatus, which expanded
 from Amazonia, presently dominated by warm and wet settings, into the
 cooler and less rainy Atlantic Forest. To examine whether local adaptation
 has been constrained by population structure and history, we estimated
 effective population sizes, divergence times, and gene flow under a
 coalescent framework. In both species, divergence between Amazonian and
 Atlantic Forest populations dates back to the mid-Pleistocene, with
 subsequent gene flow. We recovered eleven candidate genes involved with
 metabolism, immunity, development, and cell signaling in A. punctatus, and
 found no loci whose frequency is associated with environmental gradients
 in A. ortonii. Distinct signatures of adaptation between these species are
 not associated with historical constraints or distinct climatic space
 occupancies. Similar patterns of spatial structure between selected and
 neutral SNPs along the climatic gradient, as supported by patterns of
 genetic clustering in A. punctatus, may have led to conservative GEAA
 performance. This study illustrates how tests of local adaptation can
 benefit from knowledge about species histories to support hypothesis
 formulation, sampling design, and landscape gradient characterization.
description: Figure
 S1Histograms of corrected
 p-values from genome-environment association analyses using
 LFMM.FigS1.pdfFigure S2Genetic PCA based on the entire SNP dataset (A) or on the candidate SNPs only (B) for Anolis punctatus. Red arrows indicate A. punctatus sample MTR 20798 from Pacaraima, a mid-elevation site (820 m above sea level) in the Guiana Shield region that overlaps climatically with Atlantic Forest sites (see Fig. 3).FigS2.pdfTable S1Sampled specimens and locality information.Table_S1.pdfTable S2Specimens used in climatic space occupancy analyses.Table_S2.pdfTable S3Loadings of each climatic variable on PC1, and correlations among climate variables and PC1 scores.Table_S3.pdf