cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2s71b
title: Data from: Model-data assimilation of multiple phenological observations to constrain and predict leaf area index

description: Our limited ability to accurately simulate leaf phenology is a leading
 source of uncertainty in models of ecosystem carbon cycling. We evaluate
 if continuously updating canopy state variables with observations is
 beneficial for predicting phenological events. We employed ensemble
 adjustment Kalman filter (EAKF) to update predictions of leaf area index
 (LAI) and leaf extension using tower-based photosynthetically active
 radiation (PAR) and moderate resolution imaging spectrometer (MODIS) data
 for 2002–2005 at Willow Creek, Wisconsin, USA, a mature, even-aged,
 northern hardwood, deciduous forest. The ecosystem demography model
 version 2 (ED2) was used as the prediction model, forced by offline
 climate data. EAKF successfully incorporated information from both the
 observations and model predictions weighted by their respective
 uncertainties. The resulting estimate reproduced the observed leaf
 phenological cycle in the spring and the fall better than a parametric
 model prediction. These results indicate that during spring the
 observations contribute most in determining the correct bud-burst date,
 after which the model performs well, but accurately modeling fall leaf
 senesce requires continuous model updating from observations. While the
 predicted net ecosystem exchange (NEE) of CO2 precedes tower observations
 and unassimilated model predictions in the spring, overall the prediction
 follows observed NEE better than the model alone. Our results show state
 data assimilation successfully simulates the evolution of plant leaf
 phenology and improves model predictions of forest NEE.
description: modisModis observations from
 2002 forward, first column is the day of year, second column the
 observation and third column observation uncertaintyED2Model estimate for four
 hour time windows. First column is the running day of year since January
 1st 2002 and second column if the model prediction for that
 day.estState estimation for
 eight day time window. First column is the running day of year since
 January 1st 2002, second column is the prior estimate value for that time
 window, third column is the posterior estimate, fourth column is the prior
 uncertainty and fifth column is the posterior
 uncertainty.fluxFlux tower observed data
 for eight day time window. First column is the running day of year since
 January 1st 2002, second column is the observed value for that time window
 and third column is the observation uncertainty.f_fluxFlux tower observed data
 for four day time window. First column is the running day of year since
 January 1st 2002, second column is the observed value for that time window
 and third column is the observation uncertainty.f_estState estimation for
 four day time window. First column is the running day of year since
 January 1st 2002, second column is the prior estimate value for that time
 window, third column is the posterior estimate, fourth column is the prior
 uncertainty and fifth column is the posterior
 uncertainty.
DOI: 10.5061/dryad.7p1d3
title: Data from: Organic farming enhances parasitoid diversity at the local and landscape scale

description: 1. The magnitude of the benefits derived from organic farming within
 contrasting managed landscapes remains unclear and, in particular, the
 potential scale-dependent response of insect parasitoids is relatively
 unexplored. Identifying the scale at which parasitoids are affected by
 organic farming will be an important step to enhance their conservation.
 2. We sampled tachinid parasitoids at the centre and margin of arable and
 grassland fields on paired organic and conventional farms located in
 landscapes with different proportions of organic land. A total of 192
 fields were sampled in two biogeographical regions of the UK. 3. We found
 that the positive effect of organic farming on tachinid parasitoid
 diversity can be observed at multiple spatial scales. At the local scale,
 we found higher abundance and species richness of tachinid parasitoids on
 organic than on conventional farms and on field margins than on field
 centres. At the landscape scale, the diversity of tachinids was higher in
 landscapes with higher proportions of organic land. At both scales, the
 positive effect of organic farming was clear for arable fields, while it
 was almost neutral for grasslands. 4. Synthesis and applications. Any
 attempt to enhance parasitoid diversity in agricultural landscapes needs
 to consider the local management in relation to the habitat type, location
 within the field and agricultural management in the surrounding landscape.
 To restore parasitoid diversity, the promotion of organic agriculture
 should aim to increase both the total extent of organic farming and the
 connectivity of individual farms. As the benefits of organic farming to
 biodiversity clearly spread beyond individual farm boundaries, any
 assessment of organic farming should consider these positive
 externalities.
description: Tachinid abundance and
 species richness in organic and conventional farmsThe file contains all
 data used in the statistical analyses described in the materials and
 methods section of the article. The dataset includes: “Region” (“S” =
 Central South West and “N” = North Midlands), “Cluster” (the cluster of
 paired landscapes), “Landscape” (“hotspot” = landscapes with high
 proportion of land under organic farming and “coldspot” = landscapes with
 low proportion of land under organic farming), “Management” (“Organic” and
 “Conventional” farm management), “Habitat” (“arable” = mainly winter wheat
 fields and “grassland” = mainly grazed permanent pastures), “Field” (three
 replicates A-C), “Location” (“margin” and “centre” trap position within
 each field), “Abundance” and “Species Richness” (total per each
 site).Inclán et al 2015 Tachinid
 species richness and abundance by
 site.txt
DOI: 10.5061/dryad.f06t6
title: Data from: Determinants of male floating behaviour and floater reproduction in a threatened population of the hihi (Notiomystis cincta)

description: Floating males are usually thought of as non-breeders. However, some
 floating individuals are able to reproduce through extra-pair copulations.
 Floater reproductive success can impact breeders’ sex-ratio, reproductive
 variance, multiple paternity and inbreeding, particularly in small
 populations. Changes in reproductive variance alter the rate of genetic
 drift and loss of genetic diversity. Therefore, genetic management of
 threatened species requires an understanding of floater reproduction and
 determinants of floating behaviour to effectively conserve species. Here,
 we used a pedigreed, free-living population of the endangered New Zealand
 hihi (Notiomystis cincta) to assess variance in male reproductive success
 and test the genetic (inbreeding and heritability) and conditional (age
 and size) factors that influence floater behaviour and reproduction.
 Floater reproduction is common in this species. However, floater
 individuals have lower reproductive success and variance in reproductive
 success than territorial males (total and extra-pair fledglings), so their
 relative impact on the population's reproductive performance is low.
 Whether an individual becomes a floater, and if so then how successful
 they are, is determined mainly by individual age (young and old) and to
 lesser extents male size (small) and inbreeding level (inbred). Floating
 males have a small, but important role in population reproduction and
 persistence of threatened populations.
description: Mixed models input file
 ARSRaw data used in male
 annual reproductive success analysis.Evol app dryad data
 ARS.txtMixed models input file
 for AMTRaw data input file used
 for mixed models for male annual mating behaviour
 analysis.Evol app dryad data
 AMT.txt
DOI: 10.5061/dryad.2qd2g
title: Data from: Intraspecific competition, not predation, drives lizard tail loss on islands

description: Tail autotomy is mainly considered an antipredator mechanism. Theory
 suggests that predation pressure relaxes on islands, subsequently reducing
 autotomy rates. Intraspecific aggression, which may also cause tail loss,
 probably intensifies on islands due to the higher abundance. We studied
 whether tail autotomy is mostly affected by predation pressure or by
 intraspecific competition. We further studied whether predator abundance
 or predator richness is more important in this context. To test our
 predictions, we examined multiple populations of two gecko species:
 Kotschy's gecko (Mediodactylus kotschyi; mainland and 41 islands) and
 the Mediterranean house gecko (Hemidactylus turcicus; mainland and 17
 islands), and estimated their abundance together with five indices of
 predation. In both species, autotomy rates are higher on islands and
 decline with most predation indices, in contrast with common wisdom, and
 increase with gecko abundance. In M. kotschyi, tail-loss rates are higher
 on predator and viper-free islands, but increase with viper abundance. We
 suggest that autotomy is not simply, or maybe even mainly, an
 antipredatory mechanism. Rather, such defence mechanisms are a response to
 complex direct and indirect biotic interactions and perhaps, in the case
 of tail autotomy in insular populations, chiefly to intraspecific
 aggression.
description: Data used in the
 cross-population analysesSheet 1: Data of studied
 populations. n is number of individual geckos examined. Abundance of M.
 kotschyi is the number of geckos found per hour of search by YI.
 Abundances of H. turcicus and vipers are the numbers of animals found per
 day of search per person searching. Viper abundance is given in
 parentheses in the viper presence column. Predator richness includes all
 potential mammalian, avian, and reptilian gecko-predators, given in
 parentheses from left to right, respectively. Sheet 2: Data for
 non-significant predictors and sex-specific autotomy
 frequencies.data deposited in
 Dryad.xlsx
DOI: 10.5061/dryad.b1q15
title: Data from: Parasites contribute to ecologically dependent postmating isolation in the adaptive radiation of three spined stickleback

description: Spatial variation in parasitic infections is common, and has the potential
 to drive population divergence and the reproductive isolation of hosts.
 However, despite support from theory and model laboratory systems, little
 strong evidence has been forthcoming from the wild. Here, we show that
 parasites are likely to cause reproductive isolation in the adaptive
 radiation of three-spined stickleback. Adjacent wild populations on the
 Scottish island of North Uist differ greatly and consistently in the
 occurrence of different parasites that have substantial effects on
 fitness. Laboratory-reared fish are more resistant to experimental
 infection by parasite species from their own population. Furthermore,
 hybrid backcrosses between the host populations are more resistant to
 parasites from the parental population to which they are more closely
 related. These patterns provide strong evidence that parasites can cause
 ecological speciation, by contributing to selection against migrants and
 ecologically dependent postmating isolation.
description: El Nagar & MacColl
 stickleback parasite dataIn order, the four
 worksheets contain: (1) Data on the occurrence of parasites in CHRU and
 OBSM in years 2011 and 2013; (2) Diplostomum abundance and hepatosomatic
 index of individual wild fish from CHRU; (3) Gyrodactylus counts from
 artificially infected, lab-raised fish of different cross types ('Day
 28' = count of parasites on the 28th day following infection;
 'AUC28' = sum of all counts to day 28; 'Max' = maximum
 count during the whole infection period.Dryad_data_PRSB.xlsx
DOI: 10.5061/dryad.538jd
title: Data from: Atypical experiences of captive chimpanzees (Pan troglodytes) are associated with higher hair cortisol concentrations as adults

description: Experiences during early development are influential on the lives of human
 and non-human primates into adulthood. The population of captive
 chimpanzees in the United States can provide insight into this
 relationship, as collectively they have experienced a wide range of early
 exposure to both conspecifics (those raised in natal groups) and humans
 (those raised as personal pets or performers). Our study investigated
 chimpanzee exposure to humans using a continuous measure of
 categorization, the Chimpanzee Human Index (CHI), and the relationship
 between this experience and cortisol concentrations in adulthood.
 Historical records and hair samples were collected from 60 chimpanzees who
 were socially-housed in 13 zoos and sanctuaries. We found that more human
 exposure throughout the life of a chimpanzee was associated with higher
 hair cortisol concentrations in adulthood. Sex was also a significant
 factor affecting cortisol concentration, with male chimpanzees having
 higher cortisol concentrations than female chimpanzees. These results
 build upon the extensive literature about aversive effects of atypical
 early social histories for chimpanzees and emphasize to managers the
 importance of monitoring potential negative health consequences and social
 deficits these individuals may exhibit.
description: Chimp cortisol
 datasetCortisol samples and CHI
 values for each subjectChimp cort
 dataset.xlsx
DOI: 10.5061/dryad.218n0
title: Data from: Informative plot sizes in presence-absence sampling of forest floor vegetation

description: 1. Plant communities are attracting increased interest in connection with
 forest and landscape inventories due to society’s interest in ecosystem
 services. However, the acquisition of accurate information about plant
 communities poses several methodological challenges. Here we investigate
 the use of presence-absence sampling with the aim to monitor state and
 change of plant density. We study what plot sizes are informative, i.e.
 the estimators should have as high precision as possible. 2. Plant
 occurrences were modeled through different Poisson processes and tests
 were developed for assessing the plausibility of the model assumptions.
 Optimum plot sizes were determined by minimizing the variance of the
 estimators. While state estimators of similar kind as ours have been
 proposed in previous studies, our tests and change estimation procedures
 are new. 3. We found that the most informative plot size for state
 estimation is 1.6 divided by the plant density, i.e. if the true density
 is 1 plant per square meter the optimum plot size is 1.6 square meters.
 This is in accordance with previous findings. More importantly, the most
 informative plot size for change estimation was smaller and depended on
 the change patterns. We provide theoretical results as well as some
 empirical results based on data from the Swedish National Forest
 Inventory. 4. Use of too small or too large plots resulted in poor
 precision of the density (and density change) estimators. As a
 consequence, a range of different plot sizes would be required for jointly
 monitoring both common and rare plants using presence-absence sampling in
 monitoring programmes.
description: PAsampling_dataThis dataset contains data from presence-absence registrations on the permanent plots of the Swedish National Forest Inventory. On each plot, registrations are made for two subplots. The data file is separated into three parts: the first contain information about the first subplot, the second about the second subplot, and the third about the union of the two subplots. Descriptions of the variables are given inside the data file.
DOI: 10.5061/dryad.36df0
title: Data from: A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data

description: Studies of evolutionary correlations commonly utilize phylogenetic
 regression (i.e., independent contrasts and phylogenetic generalized least
 squares) to assess trait covariation in a phylogenetic context. However,
 while this approach is appropriate for evaluating trends in one or a few
 traits, it is incapable of assessing patterns in highly-multivariate data,
 as the large number of variables relative to sample size prohibits
 parametric test statistics from being computed. This poses serious
 limitations for comparative biologists, who must either simplify how they
 quantify phenotypic traits, or alter the biological hypotheses they wish
 to examine. In this article, I propose a new statistical procedure for
 performing ANOVA and regression models in a phylogenetic context that can
 accommodate high-dimensional datasets. The approach is derived from the
 statistical equivalency between parametric methods utilizing covariance
 matrices and methods based on distance matrices. Using simulations under
 Brownian motion, I show that the method displays appropriate Type I error
 rates and statistical power, whereas standard parametric procedures have
 decreasing power as data dimensionality increases. As such, the new
 procedure provides a useful means of assessing trait covariation across a
 set of taxa related by a phylogeny, enabling macroevolutionary biologists
 to test hypotheses of adaptation and phenotypic change in high-dimensional
 datasets.
description: Mean phenotypes (head
 shape) for each speciesMean head shape
 phenotypes for each species of Plethodon used in the empirical
 examplePlethMeans.csvProcD.PGLSR script for implementing D-PGLSPower-D-PGLS-PIC-Iso-BifurPower simulation code part 1Power-D-PGLS-PIC-Iso-RandPower simulation code part 2Power-D-PGLS-PIC-NonIso-BifurPower simulation code part 3Power-D-PGLS-PIC-NonIso-RandPower simulation code part 4
DOI: 10.5061/dryad.d20qc
title: Data from: The genetic architecture of methotrexate toxicity is similar in Drosophila melanogaster and humans

description: The severity of the toxic side effects of chemotherapy varies among
 patients, and much of this variation is likely genetically based. Here, we
 use the model system Drosophila melanogaster to genetically dissect the
 toxicity of methotrexate (MTX), a drug used primarily to treat childhood
 acute lymphoblastic leukemia and rheumatoid arthritis. We use the
 Drosophila Synthetic Population Resource, a panel of recombinant inbred
 lines derived from a multiparent advanced intercross, and quantify MTX
 toxicity as a reduction in female fecundity. We identify three
 quantitative trait loci (QTL) affecting MTX toxicity; two colocalize with
 the fly orthologs of human genes believed to mediate MTX toxicity and one
 is a novel MTX toxicity gene with a human ortholog. A fourth suggestive
 QTL spans a centromere. Local single-marker association scans of candidate
 gene exons fail to implicate amino acid variants as the causative
 single-nucleotide polymorphisms, and we therefore hypothesize the
 causative variation is regulatory. In addition, the effects at our mapped
 QTL do not conform to a simple biallelic pattern, suggesting multiple
 causative factors underlie the QTL mapping results. Consistent with this
 observation, no single single-nucleotide polymorphism located in or near a
 candidate gene can explain the QTL mapping signal. Overall, our results
 validate D. melanogaster as a model for uncovering the genetic basis of
 chemotoxicity and suggest the genetic basis of MTX toxicity is due to a
 handful of genes each harboring multiple segregating regulatory factors.
description: MTX toxicity
 measurementsThe file contains
 fecundity measurements for females dosed with methotrexate using the DSPR
 panel of recombinant inbred lines and an ABcross design (see
 http://FlyRILs.org for details about the DSPR and the cross design). There
 are 3 replicate measures for each cross. Column names are as follows:
 patRIL: paternal RIL number matRIL: maternal RIL number mtx1: replicate 1
 fecundity mtx2: replicate 2 fecundity mtx3: replicate 3 fecundity SP:
 subpopulation 12 = paternal pA1 x maternal pB2, 21 = paternal pA2 x
 maternal pB1 chWeek: Week (block effect) Condo: rearing condo (connected
 set of Drosophila vials 6 x 8)MTX_phenotype_ms.txt
DOI: 10.15468/dl.rbyc5k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Checklist of Coleoptera Belgium"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001278-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.r8f04fk2
title: Data from: A new method for handling missing species in diversification analysis applicable to randomly or non-randomly sampled phylogenies

description: Chronograms from molecular dating are increasingly being used to infer
 rates of diversification and their change over time. A major limitation in
 such analyses is incomplete species sampling that moreover is usually
 non-random. While the widely used γ statistic with the MCCR test or the
 birth-death likelihood analysis with the ∆AICrc test statistic are
 appropriate for comparing the fit of different diversification models in
 phylogenies with random species sampling, no objective, automated method
 has been developed for fitting diversification models to non-randomly
 sampled phylogenies. Here we introduce a novel approach, CorSiM, which
 involves simulating missing splits under a constant-rate birth-death model
 and allows the user to specify whether species sampling in the phylogeny
 being analyzed is random or non-random. The completed trees can be used in
 subsequent model-fitting analyses. This is fundamentally different from
 previous diversification rate estimation methods, which were based on null
 distributions derived from the incomplete trees. CorSiM is automated in an
 R package and can easily be applied to large data sets. We illustrate the
 approach in two Araceae clades, one with a random species sampling of 52%
 and one with a non-random sampling of 55%. In the latter clade, the CorSiM
 approach detects and quantifies an increase in diversification rate while
 classic approaches prefer a constant rate model, whereas in the former
 clade, results do not differ among methods (as indeed expected since the
 classic approaches are valid only for randomly sampled phylogenies). The
 CorSiM method greatly reduces the type I error in diversification
 analysis, but type II error remains a methodological problem.
description: CorSIM_v0.3Zipped archive of the CorSiM package described in this paper.