cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.59185
title: Data from: WSL5, a pentatricopeptide repeat protein, is essential for chloroplast biogenesis in rice under cold stress

description: Chloroplasts play an essential role in plant growth and development, and
 cold has a great effect on chloroplast development. Although many genes or
 regulators involved in chloroplast biogenesis and development have been
 isolated and characterized, many components affecting chloroplast
 biogenesis in the cold conditions have not yet been
 discovered.identification of novel components associated with cold is
 still lacking. In this study, we reported the functional characterization
 of white stripe leaf 5 (wsl5) mutant in rice. The mutant developed
 white-striped leaves during early leaf development and was albinic when
 planted under cold stress. Genetic and molecular analysis revealed that
 WSL5 encodes a novel chloroplast-targeted pentatricopeptide repeat
 protein. RNA-seq analysis showed that expression of nuclear-encoded
 photosynthetic genes in the mutant was significantly repressed, and
 expression of many chloroplast-encoded genes was also significantly
 changed. Notably, the WSL5 mutation caused defects in editing of rpl2 and
 atpA, and in splicing of rpl2 and rps12. Chloroplast ribosome biogenesis
 was impaired under cold stress. We propose that WSL5 is required for
 normal chloroplast development to maintaining the retrograde signaling
 from the plastids to the nucleus in rice under cold stress.
description: Data
 S2Genes differentially
 expressed in wild type and wsl5 under different temperature
 conditions.Data
 S1Genes differentially
 expressed in wild type and wsl5.Supplementary
 informationTable S1, S2 and Fig.
 S1-S10
DOI: 10.5061/dryad.3v590
title: Data from: Modelling mobile agent-based ecosystem services using kernel weighted predictors

description: 1. Agriculture benefits from ecosystem services provided by mobile agents,
 such as biological pest control by natural enemies and pollination by
 bees. However, methods that can generate spatially explicit predictions
 and maps of these ecosystem services based on empirical data are still
 scarce. 2. Here we propose a generic statistical model to derive kernel
 functions to characterize the spatial distribution of ecosystem services
 provided by mobile agents. The model is similar in spirit to a generalized
 linear model, and uses data of landscape composition and ecosystem
 services assessed at target sites to estimate parameters of the kernel.
 The approach is tested in a simulation study and illustrated by an
 empirical case study on parasitism rates of the diamondback moth Plutella
 xylostella. 3. The simulation study shows that the scale parameter of the
 exponential power kernel can be estimated with limited bias, whereas
 estimation of the shape parameter is difficult. For the case study the
 model provides biologically relevant estimates for the kernel associated
 with parasitism of Plutella xylostella. These estimates can be used to
 generate ecosystem service maps for existing or planned landscapes. The
 case study reveals that predictions can be sensitive to the parameter
 values for the width and shape of the kernel, and to the link function
 used in the statistical model. 4. In the last two decades numerous
 empirical studies assessed ecosystem services at target sites and related
 these to the surrounding landscape. Our method can take advantage of these
 data by estimating underlying kernels that can be used to map the spatial
 distribution of ecosystem services. However, empirical data that can
 discriminate between alternative kernel shapes remain critical.
description: R script to fit the
 kernel logistic regression model to the empirical case
 study(1) Parasitism rates of
 larvae of the diamond black moth in 22 organic Brussels sprout fields
 across the Netherlands. (2) Area of forest and area of forest edge in 20
 rings around the 22 target sites. (3) R code to fit the kernel logistic
 regression model model for the empirical case study.FitModel.RData with amount of forest edge for a 10 x 10 km area in the NetherlandsAmount of source of forest edge within 25x25 m grid cells, expressed as a percentage of the area of a grid cell, for a 10 x 10 km area from the Dutch national map. See Figure 1 in the publication. The data can be used to generate Figure 2 with predicted parasitism rates following the fit of a kernel logistic regression model for the empirical case study.ForestEdge.txtReproduces Figures 1 and 2 of the publicationR script to map the amount of forest edge for a 10 x 10 area in the Netherlands, and to map the predicted parasitism rates following the fit of a kernel logistic regression model for the empirical case studyMapModel.R
DOI: 10.17632/58bcswpwcx
title: A multicriteria model to assessing the environmental risk for municipal solid waste incineration residues

description: The dataset consists of a spreadsheet used to calculate the Cumulative Metal Toxicity Index (CMTI) and Synthetic Risk Indicator (SRI), which together constitute an original model for determining risk assessment for various management methods of municipal solid waste incineration residues.
DOI: 10.5061/dryad.j7401
title: Data from: Migratory behavior predicts greater parasite diversity in ungulates

description: Long-distance animal movements can increase exposure to diverse parasites,
 but can also reduce infection risk through escape from contaminated
 habitats or culling of infected individuals. These mechanisms have been
 demonstrated within and between populations in single-host/single-parasite
 interactions, but how long-distance movement behaviors shape parasite
 diversity and prevalence across host taxa is largely unknown. Using a
 comparative approach, we analyze the parasite communities of 93 migratory,
 nomadic, and resident ungulate species. We find that migrants have higher
 parasite species richness than residents or nomads, even after considering
 other factors known to influence parasite diversity, such as body size and
 host geographic range area. Further analyses support a novel
 “environmental tracking” hypothesis, whereby migration allows parasites to
 experience environments favorable to transmission year-round. In addition,
 the social aggregation and large group sizes that facilitate migration
 might increase infection risk for migrants. In contrast, we find little
 support for previously-proposed hypotheses, including migratory escape and
 culling, in explaining the relationship between host movement and
 parasitism in mammals at this cross-species scale. Our findings, which
 support mechanistic links between long-distance movement and increased
 parasite richness at the species level, could help predict the effects of
 future environmental change on parasitism in migratory animals.
description: Code_supplementZip file containing R code used to prepare and analyze data as well as all input datasets, including the GMPD
DOI: 10.17632/58bcswpwcx.1
title: A multicriteria model to assessing the environmental risk for municipal solid waste incineration residues

description: The dataset consists of a spreadsheet used to calculate the Cumulative Metal Toxicity Index (CMTI) and Synthetic Risk Indicator (SRI), which together constitute an original model for determining risk assessment for various management methods of municipal solid waste incineration residues.
DOI: 10.5061/dryad.8bm78
title: Data from: Refinement of a theoretical trait space for North American trees via environmental filtering

description: We refer to a theoretical trait space (TTS) as an n-dimensional
 hypervolume (“hypercube”) characterizing the range of values and
 covariations among multiple functional traits, in the absence of explicit
 filtering mechanisms. We previously constructed a 32-dimensional TTS for
 North American trees by fitting the Allometrically Constrained Growth and
 Carbon Allocation (ACGCA) model to USFS Forest Inventory and Analysis
 (FIA) data. Here, we sampled traits from this TTS, representing different
 individual “trees,” and subjected these trees to a series of gap dynamics
 simulations resulting in different annual light levels to explore the
 impact of environmental filtering (light stress) on the trait space.
 Variation in light limitation led to non-random mortality and a refinement
 of the TTS. We investigated potential mechanisms underlying such filtering
 processes by exploring how traits and the environment relate to mortality
 rates at the tree, phenotype (a specific set of trait values), and stand
 (a specific gap scenario) levels. The average light level at the forest
 floor explained 42% of the stand-level mortality, while phenotype- and
 tree-level mortality were best explained by six functional traits,
 especially radiation-use efficiency, maximum tree height, and xylem
 conducting area to sapwood area ratio (ΥX). These six “mortality” traits
 and six traits related to the leaf and wood economics spectra were used to
 construct trait hypercubes represented by trees that died or that survived
 each gap scenario. For trees that survived, the volume of their refined
 trait space decreased linearly with increasing stand-level mortality (up
 to ~50% mortality); the location also shifted, as indicated by non-zero
 distances between the hypercube centroids of surviving trees compared to
 dead trees and the original TTS. Overall, the patterns were consistent
 with empirical studies of functional traits, in terms of which traits
 predict mortality and the direction of the relationships. This work,
 however, also identified potentially important functional traits that are
 not commonly measured in empirical studies, such as ΥX and senescence
 rates of relatively long-lived tissues.
description: parameters_with_phenotype_mortThis file combines the trait data and phenotype level mortality. The vector of traits in columns 1 to 32 in each of the 33,000 rows can be thought of as a phenotype. The last two columns (PAR and m.thetap) represent the light level used when fitting the ACGCA model to FIA data in previous work and m.thetap is the phenotype level mortality (m theta p).stand_mortThis file contains the simulation or stand level mortality. It also has the average light level for each of the 62 gap simulations in this study (PARavg).tree_mortThis file contains tree level mortality (mgp). This file can be used to calculate the mortality data in the other two files.
DOI: 10.17632/knrfnpv99w
title: PMV-PDD for Arabian Gulf Ensembles
DOI: 10.5061/dryad.65gr2
title: Data from: Seed ingestion and germination in rattlesnakes: overlooked agents of rescue and secondary dispersal

description: Seed dispersal is a key evolutionary process and a central theme in the
 population ecology of terrestrial plants. The primary producers of most
 land-based ecosystems are propagated by and maintained through various
 mechanisms of seed dispersal that involve both abiotic and biotic modes of
 transportation. By far the most common biotic seed transport mechanism is
 zoochory, whereby seeds, or fruits containing them, are dispersed through
 the activities of animals. Rodents are one group of mammals that commonly
 prey on seeds (granivores) and play a critical, often destructive, role in
 primary dispersal and the dynamics of plant communities. In North America,
 geomyid, heteromyid and some sciurid rodents have specialized cheek
 pouches for transporting seeds from plant source to larder, where they are
 often eliminated from the pool of plant propagules by consumption. These
 seed-laden rodents are commonly consumed by snakes as they forage, but
 unlike raptors, coyotes, bobcats, and other endothermic predators which
 eat rodents and are known or implicated to be secondary seed dispersers,
 the role of snakes in seed dispersal remains unexplored. Here, using
 museum-preserved specimens, we show that in nature three desert-dwelling
 rattlesnake species consumed heteromyids with seeds in their cheek
 pouches. By examining the entire gut we discovered, furthermore, that
 secondarily ingested seeds can germinate in rattlesnake colons. In terms
 of secondary dispersal, rattlesnakes are best described as diplochorous.
 Because seed rescue and secondary dispersal in snakes has yet to be
 investigated, and because numerous other snake species consume granivorous
 and frugivorous birds and mammals, our observations offer direction for
 further empirical studies of this unusual but potentially important
 channel for seed dispersal.
description: MS Access database Seed
 data from rattlesnake GI tractsRaw data database of
 seeds found in rattlesnake GI tracts. Includes specimen information, prey
 ID, seed counts and ID (where available), and seed
 descriptions.Seed.accdb
DOI: 10.17632/knrfnpv99w.1
title: PMV-PDD for Arabian Gulf Ensembles
DOI: 10.5061/dryad.5rr99
title: Data from: The mosasaur fossil record through the lens of fossil completeness

description: The quality of the fossil record affects our understanding of
 macroevolutionary patterns. Palaeodiversity is filtered through geological
 and human processes; efforts to correct for these biases are part of a
 debate concerning the role of sampling proxies and standardization in
 biodiversity models. We analyse the fossil record of mosasaurs in terms of
 fossil completeness as a measure of fossil quality, using three novel,
 correlating metrics of fossil completeness and 4083 specimens. A new
 qualitative measure of character completeness (QCM) correlates with the
 phylogenetic character completeness metric. Mean completeness by species
 decreases with specimen count; average completeness by substage varies
 significantly. Mean specimen completeness is higher for species‐named
 fossils than those identified to genus and family. We consider the effect
 of tooth‐only specimens. Importantly, we find that completeness of species
 does not correlate with completeness of specimens. Completeness varies by
 palaeogeography: North American specimens show higher completeness than
 those from Eurasia and Gondwana. These metrics can be used to identify
 exceptional preservation; specimen completeness varies significantly by
 both formation and lithology. The Belgian Ciply Formation displays the
 highest completeness; clay lithologies show higher completeness values.
 Neither species diversity nor sea level correlates significantly with
 fossil completeness. A generalized least squares (GLS) analysis using
 multiple variables agrees with this result, but reveals two variables with
 significant predictive value for modelling averaged diversity: sea level,
 and mosasaur and plesiosaur‐bearing formations (the latter is redundant
 with diversity). Mosasaur completeness is not driven by sea level, nor
 does completeness limit the mosasaur diversity signal.
description: Supplementary
 DataSupplementary data. June
 2018.Supplementary
 TablesSupplementary tables.
 June 2018.
DOI: 10.5061/dryad.qp745
title: Data from: Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

description: Under hypoxic conditions, some organisms use an electron transport chain
 consisting of only complex I and II (CII) to generate the proton gradient
 essential for ATP production. In these cases, CII functions as a fumarate
 reductase that accepts electrons from a low electron potential quinol,
 rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction
 in eukaryotes, we investigated the origin and function of rqua, a gene
 encoding an RQ biosynthetic enzyme. Rqua is very patchily distributed
 across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses
 suggest lateral gene transfer (LGT) of rqua from bacteria to eukaryotes
 occurred at least twice and the gene was transferred multiple times
 amongst protists. We demonstrate that RQUA functions in the
 mitochondrion-related organelles of the anaerobic protist Pygsuia and is
 correlated with the presence of RQ. These analyses reveal the role of gene
 transfer in the evolutionary remodeling of mitochondria in adaptation to
 hypoxia.
description: RQUA tree
 datasetsFile - Description ##
 Within MLanalysis ## *iqtree.log logfile from IQTREE analysis
 *IQtreefile.nex IQTREE output tree *seqs.fasta sequences unaligned
 *mafft.fasta sequences aligned with mafft *mafft.bmge_masked.fasta BMGE
 masked alignment ## Within TopologyTests ## *.log IQTREE logfile from site
 likelihood inference *.sitelh site likelihood file from IQTREE
 *_ContrainTrees_BootstrapTrees.tre ML cosntrain trees *_consel.catpv
 output from CONSEL ## FILES ## RQUA_full_datasets/MLanalysis
 rqua.iqtree.log rqua.IQtreefile.nex rqua.mafft.bmge_masked.fasta
 rqua.mafft.fasta rqua.seqs.fasta RQUA_full_datasets/TopologyTests
 RQUA_fulldataset_consel.catpv
 RQUA_fulldataset_ContrainTress_BootstrapTrees.tre
 RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.log
 RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.sitelh
 RQUA_GroupA_datasets/MLanalysis rqua.GroupA.IQtree.log
 rqua.GroupA.IQtree.treefile rqua.GroupA.mafft.bmge_masked.fasta
 rqua.GroupA.mafft.fasta rqua.GroupA.seqs.fasta
 RQUA_GroupA_datasets/TopologyTests RQUA_GroupA_consel.catpv
 RQUA_GroupA_ConstrainTrees.tre
 RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.log
 RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.sitelh
 RQUA_GroupB_datasets/MLanalysis rqua.GroupB.IQtree.log
 rqua.GroupB.IQtree.treefile rqua.GroupB.mafft.bmge_masked.fasta
 rqua.GroupB.mafft.fasta rqua.GroupB.seqs.fasta
 RQUA_GroupB_datasets/TopologyTests RQUA_GroupB_consel.catpv
 RQUA_GroupB_ConstrainTrees.tre
 RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.log
 RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.sitelhRQUA_treeDatasets.zipalphaprotebacteria_datasetsAlignment file and raw tree file for alphaproteobacteria phylogeny. See Figure 2 - figure supplement 2.
DOI: 10.5061/dryad.q2kf0
title: Data from: Breeding sex ratio and population size of loggerhead turtles from Southwestern Florida

description: Species that display temperature-dependent sex determination are at risk
 as a result of increasing global temperatures. For marine turtles, high
 incubation temperatures can skew sex ratios towards females. There are
 concerns that temperature increases may result in highly female-biased
 offspring sex ratios, which would drive a future sex ratio skew. Studying
 the sex ratios of adults in the ocean is logistically very difficult
 because individuals are widely distributed and males are inaccessible
 because they remain in the ocean. Breeding sex ratios (BSR) are sought as
 a functional alternative to study adult sex ratios. One way to examine BSR
 is to determine the number of males that contribute to nests. Our goal was
 to evaluate the BSR for loggerhead turtles (Caretta caretta) nesting along
 the eastern Gulf of Mexico in Florida, from 2013-2015, encompassing three
 nesting seasons. We genotyped 64 nesting females (approximately 28% of all
 turtles nesting at that time) and up to 20 hatchlings from their nests (n=
 989) using 7 polymorphic microsatellite markers. We identified multiple
 paternal contributions in 70% of the nests analyzed and 126 individual
 males. The breeding sex ratio was approximately 1 female for every 2.5
 males. We did not find repeat males in any of our nests. The sex ratio and
 lack of repeating males was surprising because of female-biased primary
 sex ratios. We hypothesize that females mate offshore of their nesting
 beaches as well as en route. We recommend further comparisons of
 subsequent nesting events and of other beaches as it is imperative to
 establish baseline breeding sex ratios to understand how growing
 populations behave before extreme environmental effects are evident.
description: 2013-2015 fsa
 Files.fsa Files for nests
 analyzed on Sanibel Island from 2013-2015Nesting Data
 2013-2015Descriptive data of
 nesting loggerhead females from 2013-2015 on Sanibel Island
 Floridadryad nesting data
 san13-15.xlsx
DOI: 10.5061/dryad.73qg8
title: Data from: Short- and mid-wavelength artificial light influences the flash signals of Aquatica ficta fireflies (Coleoptera: Lampyridae)

description: Urbanization can radically disrupt natural ecosystems through alteration
 of the sensory environment. Habitat disturbances are predicted to favor
 behaviorally flexible species capable of adapting to altered environments.
 When artificial light at night (ALAN) is introduced into urban areas, it
 has the potential to impede reproduction of local firefly populations by
 obscuring their bioluminescent courtship signals. Whether individual
 fireflies can brighten their signals to maintain visibility against an
 illuminated background remains unknown. In this study, we exposed male
 Aquatica ficta fireflies to diffused light of varying wavelength and
 intensity, and recorded their alarm flash signals. When exposed to
 wavelengths at or below 533 nm, males emitted brighter signals with
 decreased frequency. This is the first evidence of individual-level light
 signal plasticity in fireflies. In contrast, long wavelength ambient light
 (≥ 597 nm) did not affect signal morphology, likely because A. ficta
 cannot perceive these wavelengths. These results suggest long wavelength
 lighting is less likely to impact firefly courtship, and its use in place
 of broad spectrum white lighting could augment firefly conservation
 efforts. More generally, this study demonstrates benefits of
 bioluminescent signal plasticity in a "noisy" signaling
 environment, and sheds light on an important yet understudied consequence
 of urbanization.
description: Aquatica_fictaThis .zip contains eight 32 minute recordings of Aquatica ficta alarm flash intensity, each accompanied a key that indicates the condition of the ambient light environment during this time.