cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t137
title: Data from: Invasiveness, chimerism and genetic diversity

description: Adaptation for invasiveness should comprise the capability to exploit and
 prosper in a wide range of ecological conditions, and is therefore
 expected to be associated with a certain level of genetic diversity.
 Paradoxically, however, invasive populations are established by only a few
 founders, resulting in low genetic diversity. As a conceivable way of
 attaining high genetic diversity and high variance of gene expression even
 when a small number of founders is involved in invasiveness, I suggest
 here chimerism, a fusion between different individuals—a common phenomenon
 found in numerous phyla. The composite entity offers the chimeric organism
 genetic flexibility and higher inclusive fitness that depends on the joint
 genomic fitness of the original partners. The ability to form a chimeric
 entity is also applied to subsequent generations and, consequently, the
 level of genetic diversity does not decline over generations of population
 establishment following invasion.
description: 0. All populations - 4
 LociSampling locations and
 microsatellite genotypes
DOI: 10.5061/dryad.cr6k97r
title: Data from: The cover uncovered: bark control over wood decomposition

description: 1. Woody debris (WD) represents a globally significant carbon stock and
 its decomposition returns nutrients to the soil while providing habitat to
 microbes, plants and animals. Understanding what drives WD decomposition
 is therefore important. 2. WD decomposition rates differ greatly among
 species. However, the role of bark in the process remains poorly known. 3.
 We ask how, and how much, interspecific variation in bark functional
 traits related to growth and protection have afterlife effects on the
 decomposition of wood, partly mediated by animals. We examine the roles of
 bark cover and bark traits throughout the wood decomposition process. 4.
 Synthesis. We find that: (i) bark effects on WD decomposition are species-
 and wood size-specific, (ii) bark can enhance coarser WD decomposition but
 slows twig decomposition in some species, and (iii) bark acts as an
 environmental filter to faunal assemblages in the early stage of wood
 decomposition. We highlight the need to account for bark effects on WD
 decomposition and offer an important complementary contribution to
 including woody species identity effects in biogeochemical and
 climate-change models via species bark traits.
description: Case study twig with and
 no bark R script fileThis file is the R
 script recording analyses conducted on the case study.Dossa et al the cover uncover
 bark role in wood decomposition case study twig with and no
 bark.RCase study twig
 decomposition dataThis represents the data
 set for the twigs decomposition reported in the case study. In total, 15
 species were used and details are in the paper supplementary
 material.Chongqing_twig_data.csvCase study bark decomposition dataThis represents the data of the bark removed from twig used for bark decomposition. The bark litter was collected from 15 different species.Chongqing_bark_data.csvCase study twig decay rate k valuesThis data is a compilation of twig data from the case study with the decay rate (k) values obtained after using non-least -squared (nls) functiontwig_k.csvCase study bark decay rate k valuesThis data is a compilation of twig's bark data from the case study with bark's decay rate (k) values obtained after from using non-least -squared (nls) functionbark_k.csvTwig with bark and twig without bark decomposition Figure 4AThis represents the decay rate k values of twig with bark and twig without bark obtained after least squared means (lsmeans) based on best model.Twig_with_tiwg_without_bark_lmeans_posthoc_results_reduced_for_plotting.csvBark and twig without bark lmeans posthoc results reduced for plotting Figure 4BThis represents the decay rate k values of bark and twig without bark obtained after least squared means (lsmeans).Bark_twig_without_bark_lmeans_posthoc_results_reduced_for_plotting.csv
DOI: 10.5061/dryad.st5rk
title: Data from: Factors associated with pulmonary impairment in HIV-infected South African adults

description: Background: HIV-infected individuals have increased risk of developing
 obstructive lung disease (OLD). Studies from developed countries report
 high viral load, low CD4 counts, and anti-retroviral therapy (ART) to be
 associated with OLD; but these findings may not be generalizable to
 populations in resource-limited settings. Methods: We conducted a
 prospective cohort study of lung function in 730 HIV-infected black South
 African adults. Pre-bronchodilator spirometry was performed at enrollment
 and repeated annually for three years. Logistic regression models were
 used to identify factors associated with OLD, defined as
 FEV1/FVC&lt;0.70, at enrollment. Excess annual declines in FEV1 and
 FVC were modelled as the product-term of follow-up time and exposures
 using random effects regression. Results: Median (IQR) age at enrollment
 was 36 (32-41) years, 85% were female and 30% ever-smoked with a median
 (IQR) exposure of 3 (1-6) pack-years. Median (IQR) CD4 count and viral
 load at enrollment were 372 (261-518) cells/mm3 and 2655 (91-13,548)
 copies/mL respectively. Overall, 25% were receiving ART at enrollment, 16%
 of whom reported at least 6 months of ART receipt. OLD was found in 35
 (5%) at enrollment. Increasing age (aOR=2.08 per 10-years [95%CI
 1.22-3.57], p=0.007), current smoking (aOR=3.55 [95%CI 1.20-10.53],
 p=0.02), and CRP (aOR=1.01 per unit-increase [95%CI 1.00-1.03], p=0.04)
 were significantly associated with OLD at enrollment; while increasing CD4
 count (aOR=1.02 per-100 cells/mm3 [95%CI 0.85-1.22], p=0.82), viral load
 (aOR=0.67 per log-increase [95%CI 0.43-1.10], p=0.12) and receipt of ART
 (aOR=0.57 [95%CI 0.18-1.75], p=0.32) were not. The median (IQR) follow-up
 time was 18 (12-24) months. Participants with a history of tuberculosis
 (TB) had a 35 mL (95%CI 2-68, p=0.03) and 57 mL (95%CI 19-96, p=0.003) per
 year excess loss of FEV1 and FVC respectively. Conclusion: Prevalent OLD
 was associated with older age, current smoking and higher CRP levels, but
 not CD4 counts and ART, in HIV-infected South African adults. Better
 understanding of the long-term effects of TB, smoking and inflammation on
 lung function in HIV-infected populations is urgently needed.
description: PONE-D-17-17716
DOI: 10.5061/dryad.h1m02nc
title: Data from: Estimating feral cat densities using distance sampling in an urban environment

description: 1. Estimating feral cat population densities in urban environments can be
 difficult due to lack of public space and human interference. The purpose
 of this study was to use distance sampling in a citywide landscape to
 determine population size and areas of high abundance to inform
 trap-neuter-release management programs. 2. Line transect distance
 sampling was used to estimate density of the feral cat population in
 Windsor, Ontario from June to July 2014. Windsor has a human population of
 217,188 and is about 146 km2 in size. Most transects were placed along
 local roads. 3. Density was estimated at about 13.3 (95% CI 9.7 – 18.1)
 cats per km2, and an estimated population size of 1858 cats (95% CI 1361 –
 2537) with the highest relative density occurring in West and Central
 Windsor. 4. Urban wildlife managers could utilize these methods to monitor
 feral cat populations and evaluate the effectiveness of
 trap-neuter-release programs.
description: Feral Cat Distance 6.0
 DataThis is the data file
 for Distance 6.0 containing feral cat distance sampling data, along with
 the density analysis.catthesis.dstRaw Cat Distance Sampling DataThis is the excel file of raw feral cat distance sampling data that was used for entry into Distance 6.0.Cat_Data.xlsx
DOI: 10.5061/dryad.ng8mn
title: Data from: Age and gender differential relationship between employment status and body mass index among middle aged and elderly adults: a cross-sectional study

description: Objective: To determine the influence of age and gender respectively on
 the association between employment status and body mass index (BMI) in
 Korean adults using a large, nationally representative sample. Design:
 Cross-sectional study. Setting: South Korea. Participants: 7,228 from
 fourth wave of the Korean Longitudinal Study of Aging (KLoSA), the survey
 short form and year: “KLoSA 2012”. Main outcome measures: body mass index.
 Results: BMI among the employed was higher than among the unemployed for
 those under 60. In terms of gender, employed males reported higher BMI
 than their unemployed counterparts, whereas employed females reported
 lower BMI than did unemployed females. Conclusions: Employment status
 showed varying impacts on obesity by age and gender. Both unemployment at
 or after 60, as well as unemployment among females, is associated with
 increased BMI compared with unemployment among younger individuals or
 males, respectively.
description: KLoSA2012_subdata_agegenderemploy_BMIThis data file includes a subset from the KLoSA 2012 data. This data was used in the study entitled "Age and gender differential relationship between employment status and body mass index among middle aged and elderly adults: A cross-sectional study" that was published in BMJ Open. In the data set, variables coded as following: age_gr (0: &lt;60; 1: 60~74; 2: &gt;=75), alcohol (0: normal; 1: addictive or excessive drinking), w04edu (1&lt;=elementary school grad.; 2: junior high grad.; 3: high school grad.; 4: college grad. or higher).
DOI: 10.15468/dl.b46tku
title: Occurrence Download

description: A dataset containing 14711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Adinetidae, Brachionidae, Gastropodidae, Dicranophoridae, Asplanchnidae, Euchlanidae, Proalidae, Notommatidae, Philodinidae, Collothecidae, Lepadellidae, Conochilidae, Trichocercidae, Epiphanidae, Trochosphaeridae, Flosculariidae, Habrotrochidae, Hexarthridae, Ituridae, Lecanidae, Lindiidae, Mytilinidae, Trichotriidae, Microcodidae, Philodinavidae, Synchaetidae, Testudinellidae, Scaridiidae, Tetrasiphonidae, Centropagidae, Diaptomidae, Cyclopidae, Halicyclopidae, Lernaeidae, Canthocamptidae, Ameiridae, Laophontidae, Phyllognathopodidae, Miraciidae, Ergasilidae, Daphniidae, Moinidae, Bosminidae, Chydoridae, Macrothricidae, Ilyocryptidae, Neothricidae)",
 "Geometry POLYGON ((-181.131592 -37.12775, -187.78141 -33.078885, -189.068184 -33.987495, -186.411552 -37.925243, -192.774353 -44.251839, -195.387383 -46.345032, -192.379532 -48.31083, -188.062592 -45.989329, -183.377609 -41.69727, -180.416107 -38.542795, -181.131592 -37.12775))"
 ]
}

 The dataset includes 14711 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000607-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6642j2s
title: Data from: What happens to offspring when parents are inbred, old or had a poor start in life? : Interactions between multiple causes of parental effects

description: Parental effects on offspring performance have been attributed to many
 factors such as parental age, size, and condition. However, we know little
 about how these different parental characteristics interact to determine
 parental effects, or the extent to which their effect on offspring depends
 on either the sex of the parent or that of the offspring. Here we
 experimentally tested for main effects of variation in parents' early
 diet and inbreeding levels, as well as effects of parental age, and for
 potential interactive effects of these three factors on key aspects of
 offspring development in the mosquitofish (Gambusia holbrooki). Older
 mothers produced offspring that were significantly smaller at birth. This
 negative effect of maternal age on offspring size was still evident at
 maturation as older mothers had smaller daughters, but not smaller sons.
 The daughters of older mothers did, however, reach maturity sooner.
 Paternal age did not affect offspring body size, but it had a complex
 effect on their sons' relative genital size. When initially raised on
 a food-restricted diet, older fathers sired sons with relatively smaller
 genitalia, but when fathers were initially raised on a control diet their
 sons had relatively larger genitalia. The inbreeding status of mothers and
 fathers had no significant effects on any of the measured offspring
 traits. Our results indicate that the manifestation of parental effects
 can be complex. It can vary with both parent and offspring sex; can change
 over an offspring's life; and is sometimes evident as an interaction
 between different parental traits. Understanding this complexity will be
 important to predict the role of parental effects in adaptation.
description: Vega_Trejo
 etal_MaternalPaternalfish_DryadData from What happens
 to offspring when parents are inbred, old or had a poor start in life?
 Evidence for sex-specific parental effects, Vega-Trejo, Regina, Kruuk,
 Loeske, Jennions, Michael, Head, Megan. Raw data in sheet 1 and labels in
 sheet 2.
DOI: 10.5061/dryad.tq8c2
title: Data from: Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry Valleys

description: Altered temperature profiles resulting in increased warming and
 freeze–thaw cycle (FTC) frequency pose great ecological challenges to
 organisms in alpine and polar ecosystems. We performed a laboratory
 microcosm experiment to investigate how temperature variability affects
 soil bacterial cell numbers, and abundance and traits of soil microfauna
 (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys,
 Antarctica. FTCs and constant freezing shifted nematode body size
 distribution towards large individuals, driven by higher mortality among
 smaller individuals. FTCs reduced both bacterial and nematode abundance,
 but bacterial cell numbers also declined under warming, demonstrating
 decoupled consumer–prey responses. We predict that higher occurrence of
 FTCs in cold ecosystems will select for large body size within soil
 microinvertebrates and overall reduce their abundance. In contrast, warm
 temperatures without FTCs could lead to divergent responses in soil
 bacteria and their microinvertebrate consumers, potentially affecting
 energy and nutrient transfer rates in soil food webs of cold ecosystems.
description: Knox et al.
 dataFull dataset for Knox et
 al. (2017) Ecology Letters
DOI: 10.5061/dryad.6s80j
title: Data from: Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat

description: Background: Among the understudied fungi found in nature are those living
 in close association with social and solitary bees. The bee-specialist
 genera Bettsia, Ascosphaera and Eremascus are remarkable not only for
 their specialized niche but also for their simple fruiting bodies or
 ascocarps, which are morphologically anomalous in Pezizomycotina. Bettsia
 and Ascosphaera are characterized by a unicellular cyst-like
 cleistothecium known as a spore cyst, while Eremascus is characterized by
 completely naked asci, or asci not formed within a protective ascocarp.
 Before molecular phylogenetics the placement of these genera within
 Pezizomycotina remained tentative; morphological characters were
 misleading because they do not produce multicellular ascocarps, a defining
 character of Pezizomycotina. Because of their unique fruiting bodies, the
 close relationship of these bee-specialist fungi and their monophyly
 appeared certain. However, recent molecular studies have shown that
 Bettsia is not closely related to Ascosphaera. In this study, I isolated
 the very rare fungus Eremascus fertilis (Ascomycota, Pezizomycotina) from
 the bee bread of honey bees. These isolates represent the second report of
 E. fertilis both in nature and in the honey bee hive. To establish the
 systematic position of E. fertilis and Bettsia alvei, I performed
 phylogenetic analyses of nuclear ribosomal LSU + SSU DNA sequences from
 these species and 63 additional ascomycetes. Results: The phylogenetic
 analyses revealed that Eremascus is not monophyletic. Eremascus albus is
 closely related to Ascosphaera in Eurotiomycetes while E. fertilis belongs
 in Myxotrichaceae, a putative member of Leotiomycetes. Bettsia is not
 closely related to Ascosphaera and like E. fertilis apparently belongs in
 Leotiomycetes. These results indicate that both the naked ascus and spore
 cyst evolved twice in the Pezizomycotina and in distantly related
 lineages. The new genus Skoua is described to accommodate E. fertilis.
 Conclusions: The naked ascus and spore cyst are both shown to have evolved
 convergently within the bee habitat. The convergent evolution of these
 unusual ascocarps is hypothesized to be adaptive for bee-mediated
 dispersal. Elucidating the dispersal strategies of these fungal symbionts
 contributes to our understanding of their interaction with bees and
 provides insight into the factors which potentially drive the evolution of
 reduced ascocarps in Pezizomycotina.
description: combined SSU + LSU nrDNA
 matrixLSU_SSU_combined_dataset_convergent_evol.nexnrDNA LSU + SSUcombined_SSU_LSU_25_April_15.nex
DOI: 10.5061/dryad.h9541
title: Data from: Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics

description: Since their advent, supertrees have been increasingly used in large-scale
 evolutionary studies requiring a phylogenetic framework and substantial
 efforts have been devoted to developing a wide variety of supertree
 methods (SMs). Recent advances in supertree theory have allowed the
 implementation of maximum likelihood (ML) and Bayesian SMs, based on using
 an exponential distribution to model incongruence between input trees and
 the supertree. Such approaches are expected to have advantages over
 commonly used non-parametric SMs, e.g. matrix representation with
 parsimony (MRP). We investigated new implementations of ML and Bayesian
 SMs and compared these with some currently available alternative
 approaches. Comparisons include hypothetical examples previously used to
 investigate biases of SMs with respect to input tree shape and size, and
 empirical studies based either on trees harvested from the literature or
 on trees inferred from phylogenomic scale data. Our results provide no
 evidence of size or shape biases and demonstrate that the Bayesian method
 is a viable alternative to MRP and other non-parametric methods.
 Computation of input tree likelihoods allows the adoption of standard
 tests of tree topologies (e.g. the approximately unbiased test). The
 Bayesian approach is particularly useful in providing support values for
 supertree clades in the form of posterior probabilities.
description: Carnivore_and_Metazoan_datasetsThis zip file contain the input trees, in newick format, used in a supertree analysis to infer the metazoan phylogenetic supertree. It also contains 10 carnivore input tree datasets, in newick format, that were used in a supertree analysis to reconstruct the phylogenetic supertree for the Carnivores.
DOI: 10.5061/dryad.fh6d9
title: Data from: Genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population

description: There is ample evidence for inbreeding depression manifested as a
 reduction in fitness or fitness-related traits in the focal individual. In
 many organisms, fitness is not only affected by genes carried by the
 individual, but also by genes carried by their parents, for example if
 receiving parental care. While maternal effects have been described in
 many systems, the extent to which inbreeding affects fitness directly
 through the focal individual, or indirectly through the inbreeding
 coefficients of its parents, has rarely been examined jointly. The Soay
 sheep study population is an excellent system in which to test for both
 effects, as lambs receive extended maternal care. Here, we tested for both
 maternal and individual inbreeding depression in three fitness-related
 traits (birthweight and weight and hindleg length at 4 months of age) and
 three fitness components (first-year survival, adult annual survival and
 annual breeding success), using either pedigree-derived inbreeding or
 genomic estimators calculated using ~37 000 SNP markers. We found evidence
 for inbreeding depression in 4-month hindleg and weight, first-year
 survival in males, and annual survival and breeding success in adults.
 Maternal inbreeding was found to depress both birthweight and 4-month
 weight. We detected more instances of significant inbreeding depression
 using genomic estimators than the pedigree, which is partly explained
 through the increased sample sizes available. In conclusion, our results
 highlight that cross-generational inbreeding effects warrant further
 exploration in species with parental care and that modern genomic tools
 can be used successfully instead of, or alongside, pedigrees in natural
 populations.
description: Inbreeding coefficients
 and all fitness and phenotypic data: genomic analysis reveals depression
 due to both individual and maternal inbreeding in a free-living mammal
 population.data
 dryad.zip
DOI: 10.5066/p13lspgv
title: Data Describing the Presence of Live Trees for Three Years in Sentinel-2 Pixels Across Four Fires in California, USA

description: This dataset represents photointerpretation of live tree presence and raw pixel values from 500 randomly selected Sentinel-2 pixels across four fires in the state of California. This dataset was used to run random forest models to predict live tree presence in the Cabin Fire, Rough Fire, Pier Fire, and Schaeffer Fire at 1, 3, and 5 years post fire.
DOI: 10.5061/dryad.8sb02
title: Data from: Female preference for male courtship effort can drive the evolution of male mate choice

description: The evolution of male mate choice is constrained by costs of choice in
 species with a male-biased operational sex ratio. Previous theoretical
 studies have shown that significant benefits of male choice are required,
 e.g., by mating with more fecund females, in order for these costs to be
 offset and a male preference to spread. In a series of population genetic
 models we show the novel effect that male mating preference, expressed as
 a bias in courtship, can spread when females prefer, and thus are more
 likely to mate with, males who court more. We explore two female
 preference functions for levels of male courtship, one representing a
 threshold and the other a weighted female preference. The basic finding
 generally holds for both preference functions. However, the preference
 function greatly affects the spread of a male preference allele after the
 addition of competing males who can court more in total. Our results thus
 stress that a thorough understanding of the response of females to male
 courtship is a critical component to understanding male preference
 evolution in polygynous species.
description: analytical
 filesWolfram Mathematica
 Notebook filesC code for
 simulationsCreated in Xcode. Also
 includes a parameter file.