cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.119
title: Data from: Step matrices and the interpretation of homoplasy

description: Assumptions about the costs of character change, coded in the form of a
 step matrix, determine most-parsimonious inferences of character evolution
 on phylogenies. We present a graphical approach to exploring the
 relationship between cost assumptions and evolutionary inferences from
 character data. The number of gains and losses of a binary trait on a
 phylogeny can be plotted over a range of cost assumptions, to reveal the
 inflection point at which there is a switch from more gains to more losses
 and the point at which all changes are inferred to be in one direction or
 the other. Phylogenetic structure in the data, the tree shape, and the
 relative frequency of states among the taxa influence the shape of such
 graphs and complicate the interpretation of possible permutation-based
 tests for directionality of change. The costs at which the
 most-parsimonious state of each internal node switches from one state to
 another can also be quantified by iterative ancestral-state reconstruction
 over a range of costs. This procedure helps identify the most robust
 inferences of change in each direction, which should be of use in
 designing comparative studies.
description: Ree and Donoghue C
 Source CodeRee.c.codeSource Code Readme Filec.readme.txt
DOI: 10.5061/dryad.g370c
title: Data from: Should I change or should I go? phenotypic plasticity and matching habitat choice in the adaptation to environmental heterogeneity

description: It can be challenging for organisms to achieve a good match between their
 phenotypic characteristics and environmental requirements that vary in
 space and time. The evolution of adaptive phenotypes can result from
 genetic differentiation at the population level. Individuals, however,
 could also change their phenotype (adaptive plasticity) or select an
 environment because it matches with their phenotype (matching habitat
 choice). It is poorly known under which conditions these different
 solutions to environmental heterogeneity evolve and whether they operate
 together. Using an individual-based simulation model, we assessed which
 solutions evolved depending on degree of temporal variation, costs of
 multiple underlying traits, and order of dispersal and development.
 Population genetic divergence was superseded by plasticity or matching
 habitat choice as temporal variation increased. Plasticity and matching
 habitat choice were limited by their trait costs, even when this involved
 only a part of the underlying traits. Independent of the order of
 dispersal and development, plasticity evolved more commonly than matching
 habitat choice, in part because the match a phenotype can achieve by
 matching habitat choice is limited by the types of environments available.
 Our results explain the apparent relative rarity of matching habitat
 choice in nature. At the same time, our results can be used to look for
 matching habitat choice in those biological systems where the conditions
 for other solutions seem unfavorable.
description: Supplementary Material -
 model codeThe Netlogo code for the
 program used to run the simulations. This program was developed using
 NetLogo 5.0 (http://ccl.northwestern.edu/netlogo). The program is free of
 use for research and education. If you use this program or model for your
 own research, please refer to our paper “Pim Edelaar, Roger Jovani &
 Ivan Gomez-Mestre 2017. Should I change or should I go? Phenotypic
 plasticity and matching habitat choice in the adaptation to environmental
 heterogeneity. The American Naturalist”.Am Nat - plasticity and
 MHC - NetLogo model online v. 45The model code in
 Netlogo format. Download (http://ccl.northwestern.edu/netlogo) and install
 NetLogo for free, and you can open and run the model
 directly.
DOI: 10.5061/dryad.g7qs2
title: Data from: Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium?

description: Heterozygosity-fitness correlations (HFCs) have been observed for several
 decades, but their causes are often elusive. Tests for identity
 disequilibrium (ID, correlated heterozygosity between loci) are commonly
 used to determine if inbreeding depression is a possible cause of HFCs. We
 used computer simulations to determine how often ID is detected when HFCs
 are caused by inbreeding depression. We also used ID in conjunction with
 HFCs to estimate the proportion of variation (r2) in fitness explained by
 the individual inbreeding coefficient (F). ID was not detected in a large
 proportion of populations with statistically significant HFCs (sample size
 = 120 individuals) unless the variance of F was high (σ2(F) ≥ 0.005) or
 many loci were used (100 microsatellites or 1000 SNPs). For example, with
 25 microsatellites, ID was not detected in 49% of populations when HFCs
 were caused by six lethal equivalents and σ2(F) was typical of vertebrate
 populations (σ2(F) ≈ 0.002). Estimates of r2 between survival and F based
 on ID and HFCs were imprecise unless ID was strong and highly
 statistically significant (P ≈ 0.01). These results suggest that failing
 to detect ID in HFC studies should not be taken as evidence that
 inbreeding depression is absent. The number of markers necessary to
 simultaneously detect HFC and ID depends strongly on σ2(F). Thus the
 mating system and demography of populations, which influence σ2(F), should
 be considered when designing HFC studies. ID should be used in conjunction
 with HFCs to estimate the correlation between fitness and F, because HFCs
 alone reveal little about the strength of inbreeding depression.
description: kardos_HFC_ID_simModel_11September2013R script for simulation used in our paper
DOI: 10.15468/dl.gd9xrp
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Latua pubiflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 23 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000939-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.503ds62
title: Data from: Evolution of nutrient resorption across the herbaceous genus Helianthus

description: Foliar nutrient resorption is a key modulator of plant nutrient use.
 However, evolutionary patterns for nutrient resorption remain unclear,
 especially in herbs. We measured nitrogen and phosphorus resorption on
 pre-selected leaves across the Helianthus (sunflower) genus in a common
 garden in Athens, GA. We analyzed our data with published leaf traits and
 native habitat environmental data. Using phylogenetically-controlled
 analyses, we tested if (1) nutrient resorption correlates with leaf
 economic, vasculature, and defense traits through evolutionary time, and
 2) native habitat environment predicts nutrient resorption evolution. For
 Helianthus, nutrient resorption capacity is greater in
 resource-conservative species, as previously defined for Helianthus with a
 principle components analysis of leaf economic spectrum traits
 (photosynthetic rate, respiration rate, leaf lifespan, leaf mass per area,
 and green-leaf N and P concentration). Nutrient resorption capacity also
 evolutionarily correlates with individual leaf economic traits, though not
 always as expected based on broad species surveys. Greater nutrient
 resorption is also positively associated with leaf chemical defenses, but
 not leaf vasculature or senescence rate. Finally, nitrogen resorption
 evolution increases with native habitat precipitation, but native habitat
 soil fertility does not predict nitrogen or phosphorus resorption. Our
 results suggest nutrient resorption evolution is more closely tied to
 resource economic strategy than native habitat.
description: Rea_EVOLUTION OF
 NUTRIENT RESORPTION ACROSS THE HERBACEOUS GENUS
 HELIANTHUS_Area-based_leaf_data_20180806Area-based leaf data and
 climate and soil fertility data for 27 Helianthus species and 1
 Phoebanthus species.Rea_EVOLUTION OF
 NUTRIENT RESORPTION ACROSS THE HERBACEOUS GENUS
 HELIANTHUS_Massbased_leaf_data_20180806Mass-based leaf data and
 climate and soil fertility data for 27 Helianthus species and 1
 Phoebanthus species.
DOI: 10.5061/dryad.3pt7b
title: Data from: Systematics and taxonomy of the Snubnose Darter, Etheostoma simoterum (Cope)

description: A taxonomic revision of Etheostoma simoterum (Cope) published in 2007
 resulted in the recognition of six species, with two species distributed
 in the Tennessee River system. A newly defined Etheostoma simoterum was
 restricted to populations in the Holston River above the confluence of the
 North and South Forks, and the Russell Fork system of the Ohio River
 drainage. A newly described species, Etheostoma tennesseense Powers
 & Mayden, included all other populations historically considered
 Etheostoma simoterum in the Tennessee River system from near the mouth of
 the Duck River upstream to the Clinch River, including the Holston River
 below the forks. A subsequent study utilizing molecular phylogenetics and
 analysis of male nuptial coloration did not support the recognition of
 Etheostoma tennesseense. Molecular phylogenies resolve both Etheostoma
 simoterum and Etheostoma tennesseense as paraphyletic. In addition, it was
 determined that male coloration patterns are not diagnostic for the more
 restricted and new definition of Etheostoma simoterum. In this study, we
 examine the systematics of Etheostoma simoterum using meristic traits
 sampled from more than 1,000 specimens, including Cope's syntype
 series of Hyostoma simoterum and Powers and Mayden's paratopotype
 series of Etheostoma tennesseense. Our results show a pattern of clinal
 variation, where meristic traits are higher in the in the lower Tennessee
 River system. Comparisons of populations above and below the forks of the
 Holston River show no differences in meristic traits, but populations
 sampled from the Watauga River system exhibit scale counts lower than any
 other population of Etheostoma simoterum. We cannot reject the hypothesis
 that Etheostoma tennesseense is conspecific with the specimens that
 comprise the Hyostoma simoterum syntype series. Based on both
 morphological and molecular species delimitation strategies, we treat
 Etheostoma tennesseense as a synonym of Etheostoma simoterum.
description: Etheostoma
 simoterum_meristic_dataMeristic data from
 specimens of Etheostoma simoterumE_simoterum_meristics.csvE_simoterum_localitiesLocality data of specimens included in the morphological analyses.
DOI: 10.5061/dryad.s8045
title: Data from: Maternal oxidative stress and reproduction: testing the constraint, cost and shielding hypotheses in a wild mammal

description: 1. Oxidative stress has been proposed as a central causal mechanism
 underlying the life history trade-off between current and future
 reproduction and survival in wild animals. 2. Whereas mixed evidence
 suggests that maternal oxidative stress may act both as a constraint and a
 cost to reproduction, some studies have reported a lack of association
 between reproduction and maternal oxidative stress. 3. The oxidative
 shielding hypothesis offers an alternative explanation, suggesting that
 mothers may pre-emptively mitigate the oxidative costs of reproduction by
 increasing antioxidant defences prior to reproduction. 4. We tested the
 oxidative constraint, cost, and shielding hypotheses using a longitudinal
 field study of oxidative stress levels in a species that breeds using
 daily energy income, the Columbian ground squirrel (Urocitellus
 columbianus). 5. Elevated maternal oxidative damage prior to reproduction
 was associated with higher maternal investment in litter mass at birth,
 but not at weaning. 6. Breeding females increased their antioxidant
 capacity and decreased their oxidative damage from birth to lactation
 compared to non-breeding females measured at the same time periods.
 However, lower maternal oxidative stress during lactation was not
 associated with higher offspring survival or mass growth over this period.
 7. Our results provide little evidence for maternal oxidative stress
 acting as a constraint on, or cost to, reproduction in Columbian ground
 squirrels, but partially support the idea that oxidative shielding
 occurred to buffer potential oxidative costs of reproduction.
description: Columbian ground
 squirrel oxidative stress dataData collected from a
 2016 field study on Columbian ground squirrels conducted by Viblanc,
 Dobson and collaborators.Viblanc et
 al._FEC_2018_DRYAD.xlsx
DOI: 10.5061/dryad.mj0hn
title: Data from: Understanding past population dynamics: Bayesian coalescent-based modeling with covariates

description: Effective population size characterizes the genetic variability in a
 population and is a parameter of paramount importance in population
 genetics and evolutionary biology. Kingman's coalescent process
 enables inference of past population dynamics directly from molecular
 sequence data, and researchers have developed a number of flexible
 coalescent-based models for Bayesian nonparametric estimation of the
 effective population size as a function of time. Major goals of
 demographic reconstruction include identifying driving factors of
 effective population size, and understanding the association between the
 effective population size and such factors. Building upon Bayesian
 nonparametric coalescent-based approaches, we introduce a flexible
 framework that incorporates time-varying covariates that exploit Gaussian
 Markov random fields to achieve temporal smoothing of effective population
 size trajectories. To approximate the posterior distribution, we adapt
 efficient Markov chain Monte Carlo algorithms designed for highly
 structured Gaussian models. Incorporating covariates into the demographic
 inference framework enables the modeling of associations between the
 effective population size and covariates while accounting for uncertainty
 in population histories. Furthermore, it can lead to more precise
 estimates of population dynamics. We apply our model to four examples. We
 reconstruct the demographic history of raccoon rabies in North America and
 find a significant association with the spatiotemporal spread of the
 outbreak. Next, we examine the effective population size trajectory of the
 DENV-4 virus in Puerto Rico along with viral isolate count data and find
 similar cyclic patterns. We compare the population history of the HIV-1
 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find
 that the effective population size is more reflective of incidence rate.
 Finally, we explore the hypothesis that the population dynamics of musk ox
 during the Late Quaternary period were related to climate change.
description: BEAST XML input files
 used for the data analysisSkygridXMLs.tar.gz
DOI: 10.5061/dryad.qd88b
title: Data from: Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster

description: [No abstract entered]
description: eworoRL514BC_QTLPhenotype and genotype data for QTL mapping between strains e, wo, ro and RAL514.eworoRL514BC.xlsstsse_ORER_QTL_mapMap information for QTL mapping between strains st, ss, e and oregon R.ssste_ORER_QTL_crossCross information for QTL mapping between strains st, ss, e and oregon R.
DOI: 10.5061/dryad.2j0h3
title: Data from: Design- and model-based strategies for detecting and quantifying an amphibian pathogen in environmental samples

description: Accurate pathogen detection is essential for developing management
 strategies to address emerging infectious diseases, an increasingly
 prominent threat to wildlife. Sampling for free-living pathogens outside
 of their hosts has benefits for inference and study efficiency, but is
 still uncommon. We used a laboratory experiment to evaluate the influences
 of pathogen concentration, water type, and qPCR inhibitors on the
 detection and quantification of Batrachochytrium dendrobatidis (Bd) using
 water filtration. We compared results pre- and post-inhibitor removal, and
 assessed inferential differences when single versus multiple samples were
 collected across space or time. We found that qPCR inhibition influenced
 both Bd detection and quantification in natural water samples, resulting
 in biased inferences about Bd occurrence and abundance. Biases in
 occurrence could be mitigated by collecting multiple samples in space or
 time, but biases in Bd quantification were persistent. Differences in Bd
 concentration resulted in variation in detection probability, indicating
 that occupancy modeling could be used to explore factors influencing
 heterogeneity in Bd abundance among samples, sites, or over time. Our work
 will influence the design of studies involving amphibian disease dynamics
 and studies utilizing environmental DNA (eDNA) to understand species
 distributions.
description: single_samples_occ_prePre-purification detection data from triplicate wells under the single samples scenario.single_samples_occ_postPost-purification detection data from triplicate wells under the single samples scenario.multi_samples_occ_prePre-purification detection data from triplicate wells under the multiple samples scenario.multi_samples_occ_postPost-purification detection data from triplicate wells under the multiple samples scenario.quant_data_prePre-purification quantity estimates from triplicate qPCR wells.quant_data_postPost-purification quantity estimates from triplicate qPCR wells.
DOI: 10.5061/dryad.v1t54
title: Data from: Repetitive concussive traumatic brain injury interacts with post-injury foot shock stress to worsen social and depression-like behavior in mice

description: The debilitating effects of repetitive concussive traumatic brain injury
 (rcTBI) have been increasingly recognized in both military and civilian
 populations. rcTBI may result in significant neurological, cognitive, and
 affective sequelae, and is often followed by physical and/or psychological
 post-injury stressors that may exacerbate the effects of the injury and
 prolong the recovery period for injured patients. However, the
 consequences of post-injury stressors and their subsequent effects on
 social and emotional behavior in the context of rcTBI have been relatively
 little studied in animal models. Here, we use a mouse model of rcTBI with
 two closed-skull blunt impacts 24 hours apart and social and emotional
 behavior testing to examine the consequences of a stressor (foot shock
 fear conditioning) following brain injury (rcTBI). rcTBI alone did not
 affect cued or contextual fear conditioning or extinction compared to
 uninjured sham animals. In the sucrose preference test, rcTBI animals had
 decreased preference for sucrose, an anhedonia-like behavior, regardless
 of whether they experienced foot shock stress or were non-shocked
 controls. However, rcTBI and post-injury foot shock stress had synergistic
 effects in tests of social recognition and depression-like behavior. In
 the social recognition test, animals with both injury and shock were more
 impaired than either non-shocked injured mice or shocked but uninjured
 mice. In the tail suspension test, injured mice had increased
 depression-like behavior compared with uninjured mice, and shock stress
 worsened the depression-like behavior only in the injured mice with no
 effect in the uninjured mice. These results provide a model of subtle
 emotional behavioral deficits after combined concussive brain injury and
 stress, and may provide a platform for testing treatment and prevention
 strategies for social behavior deficits and mood disorders that are
 tailored to patients with traumatic brain injury.
description: rcTBI Behavior
 ArchiveThis zip file includes
 the raw behavioral and histological data reported in the paper
 "Repetitive concussive traumatic brain injury interacts with
 post-injury foot shock stress to worsen social and depression-like
 behavior in mice". Behavioral tests include cued fear conditioning,
 contextual fear conditioning, social recognition, tail suspension, and
 sucrose preference. The histological data consists of counts of Iba1
 positive cells in the corpus callosum. Abbreviations: rcTBI - repetitive
 concussive traumatic brain injuryrcTBI_behavior_archive.zip
DOI: 10.5061/dryad.d6p27
title: Data from: Spatial patterns of neutral and functional genetic variation reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies

description: Local adaptation is necessary for population survival and depends on the
 interplay between responses to selective forces and demographic processes
 that introduce or retain adaptive and maladaptive attributes.
 Host-parasite systems are dynamic, varying in space and time, where both
 host and parasites must adapt to their ever-changing environment in order
 to survive. We investigated patterns of local adaptation in raccoon
 populations with varying temporal exposure to the raccoon rabies virus
 (RRV). RRV infects approximately 85% of the population when epizootic and
 has been presumed to be completely lethal once contracted; however,
 disease challenge experiments and varying spatial patterns of RRV spread
 suggest some level of immunity may exist. We first assessed patterns of
 local adaptation in raccoon populations along the eastern seaboard of
 North America by contrasting spatial patterns of neutral (microsatellite
 loci) and functional, major histocompatibility complex (MHC) genetic
 diversity and structure. We explored variation of MHC allele frequencies
 in light of temporal population exposure to RRV (0-60 years) and specific
 RRV strains in infected raccoons. Our results revealed high levels of MHC
 variation (66 DRB exon 2 alleles) and pronounced genetic structure
 relative to neutral microsatellite loci, indicative of local adaptation.
 We found a positive association linking MHC genetic diversity and temporal
 RRV exposure, but no association with susceptibility and resistance to RRV
 strains. These results have implications for landscape epidemiology
 studies seeking to predict the spread of RRV and present an example of how
 population demographics influence the degree to which populations adapt to
 local selective pressures.
description: Microsatellite and MHC
 genetic dataFirst sheet: Neutral
 microsatellite data for 10 loci in 203 raccoon samples analyzed from four
 regions (Ontario, New York, Alabama and Florida). Second sheet: MHC
 alleles identified in 203 raccoon samples including information of animals
 positive or negative to rabies virus, years of exposure per region, and
 alleles identified as resistance or susceptible to rabies and within their
 corresponding lineage 1 (L1) or lineage 3 (L3). Third sheet: number of
 alleles associated to lineage 1 and 3 per individual and
 regionKyle
 et al_genodata_RRV Spatial MHC.xlsx