cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pzgmsbcns
title: Community composition and species traits and plot positions

description: Biodiversity decline and its cascading effects through trophic
 interactions pose a severe threat to ecosystem service worldwide. Within a
 synthetic conceptual framework for beta-diversity, we proposed a series of
 hypotheses related to multi-trophic community assembly in subtropical
 forests. Our results suggested that, resulting from niche-based bottom-up
 dynamics, producer dissimilarities are predominant in structuring consumer
 dissimilarity, the degree of which highly depends on the trophic
 dependency, the diversity facet and the data quality. More importantly, we
 detected a significant dynamic between niche-based processes (e.g.
 environmental filtering and competitive exclusion) with the increasing
 producer dissimilarity. These findings enrich our mechanistic
 understanding of the ‘Diversity Begets Diversity’ rule and the complexity
 of multi-trophic community assembly, which is fundamental and critical for
 sustainable biodiversity conservation and ecosystem management.
description: Caterpillar sampling was
 conducted in April, June, and September in 2019; spider samples used in
 this work were collected in April, June, and September in 2017. The
 samplings of both caterpillars and spiders were carried out by beating and
 shaking 80 living trees in each plot. A white square sheet (1.5 m × 1.5 m)
 was used to collect all samples dislodged from the tree crown. This
 sampling regime covered all tree species and species richness levels. All
 samples were stored in separate tubes filled with 99.5% ethanol to reduce
 contamination and subsequently stored in a −20 ℃ freezer before DNA
 extractions.
DOI: 10.5061/dryad.rfj6q57c4
title: Leaf traits, plant size and environment data of a common tree species Clausena dunniana in a subtropical broad-leaved forest

description: This dataset contains the leaf traits, plant size and environment
 data of 262 individuals of a widespread species Clausena dunniana in the
 subtropical broad-leaved forests in Maolan National Nature Reserve in the
 karst region of southwestern China. The 262 individuals of C.
 dunniana are distributed at two major topographic habitat types,
 the slope and the hilltop, within the forests of six sites evenly
 distributed in two regions within the Maolan reserve. The
 measured individual plant level leaf traits
 include specific leaf area (SLA), leaf area, leaf dry-matter
 content (LDMC) and leaf thickness. The plant size represents the
 first principal component of plant basal diameter and plant height, and
 the environmental factors include topographic habitat, canopy
 height, and rock-bareness rate.
DOI: 10.5061/dryad.r7sqv9sdc
title: Nitrogen isotope ratios of nitrate, ammonium, and amino acids in sinking particles in the Northwestern North Pacific

description: The database includes sample information and nitrogen isotope measurements
 of nitrate, ammonium, and amino acids in sinking particles in the
 Northwestern North Pacific. The sinking particles were collected in
 sediment traps moored at depths of 200, 500, and 4,810 m at station K2
 (47°N, 160°E; water depth, ~5,200 m). The seawater was sampled with a
 plastic bucket for the surface and Niskin-X sampling bottles for water
 below the surface at stations K2 and KNOT (44°N, 155°E). The model package
 of a 1D nitrogen isotope model includes model source code written in
 Fortran 90, forcing, and initial condition at station K2.
DOI: 10.5061/dryad.n5tb2rbx6
title: Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory

description: To verify the "nearly neutral theory (NNT)," the ratio of
 nonsynonymous to synonymous substitutions (dN/dS) was compared among
 populations of different species. To determine the validity of NNT,
 however, populations that are genetically isolated from each other but
 share the same selection agents and differ in size should be compared.
 Genetically different lineages of obligate asexual Daphnia
 pulex invading Japan from North America are an ideal example as
 they satisfy these prerequisites. Therefore, we analyzed the whole-genome
 sequences of 18 genotypes, including those of the two independently
 invaded D. pulex lineages (JPN1 and JPN2) and compared
 the dN/dS ratio between the lineages. The base
 substitution rate of each genotype demonstrated that the JPN1 lineage
 having a larger distribution range diverged earlier and thus was older
 than the JPN2 lineage. Comparisons of the genotypes within lineages
 revealed that changes in dN/dS occurred after the
 divergence and were larger in the younger lineage, JPN2. These results
 imply that the JPN1 lineage has been more effectively subjected to
 purification selections, while slightly deteriorating mutations are less
 purged in JPN2 with smaller population size. Altogether, the
 lineage-specific difference in the dN/dS ratio for the
 obligate asexual D. pulex was well explained by the NNT.
description: Detailed
 methods are described in the paper.
description: Data set used for Fig. 1, Fig. 2
 and Fig. 3 of the
 paper.
DOI: 10.7291/d1038p
title: Online phylogenetics using parsimony produces slightly better trees and is dramatically more efficient for large SARS-CoV-2 phylogenies than de novo and maximum-likelihood approaches

description: Phylogenetics has been foundational to SARS-CoV-2 research and public
 health policy, assisting in genomic surveillance, contact tracing, and
 assessing emergence and spread of new variants. However, phylogenetic
 analyses of SARS-CoV-2 have often relied on tools designed for de novo
 phylogenetic inference, in which all data are collected before any
 analysis is performed and the phylogeny is inferred once from scratch.
 SARS-CoV-2 datasets do not fit this mould. There are currently over 5
 million sequenced SARS-CoV-2 genomes in public databases, with tens of
 thousands of new genomes added every day. Continuous data collection,
 combined with the public health relevance of SARS-CoV-2, invites an
 "online" approach to phylogenetics, in which new samples are
 added to existing phylogenetic trees every day. The extremely dense
 sampling of SARS-CoV-2 genomes also invites a comparison between
 Likelihood and Parsimony approaches to phylogenetic inference. Maximum
 Likelihood (ML) methods are more accurate when there are multiple changes
 at a single site on a single branch, but this accuracy comes at a large
 computational cost, and the dense sampling of SARS-CoV-2 genomes means
 that these instances will be extremely rare. Therefore, it may be that
 approaches based on Maximum Parsimony (MP) are sufficiently accurate for
 reconstructing phylogenies of SARS-CoV-2, and their simplicity means that
 they can be applied to much larger datasets. Here, we evaluate the
 performance of de novo and online phylogenetic approaches, and ML and MP
 frameworks, for inferring large and dense SARS-CoV-2 phylogenies. Overall,
 we find that online phylogenetics produces similar phylogenetic trees to
 de novo analyses for SARS-CoV-2, and that MP optimizations produce more
 accurate SARS-CoV-2 phylogenies than do ML optimizations. Since MP is
 thousands of times faster than presently available implementations of ML
 and online phylogenetics is faster than de novo, we therefore propose
 that, in the context of comprehensive genomic epidemiology of SARS-CoV-2,
 MP online phylogenetics approaches should be favored.
description: All details for data collection and processing are described
 at https://github.com/bpt26/parsimony. In March 2021, we developed a
 phylogeny consisting of 364,427 SARS-CoV-2 whole genomes, pruned of long
 branches and sequences with multiple ambiguous nucleotides. We assessed
 several phylogenetic inference and optimization methods using this
 dataset, as described in our manuscript. Here we include all necessary
 starting materials for running our analyses.
description: All details for this dataset can be found
 at https://github.com/bpt26/parsimony. The attached protobuf file is the
 outcome of the commands described in subrepository 1.
DOI: 10.5061/dryad.rr4xgxd9h
title: Code and dataset for neural dynamics of causal inference in the macaque frontoparietal circuit

description: Natural perception relies inherently on inferring causal structure in the
 environment. However, the neural mechanisms and functional circuits
 essential for representing and updating the hidden causal structure and
 corresponding sensory representations during multisensory processing are
 unknown. To address this, monkeys were trained to infer the probability of
 a potential common source from visual and proprioceptive signals based on
 their spatial disparity in a virtual reality system. The proprioceptive
 drift reported by monkeys demonstrated that they combined previous
 experience and current multisensory signals to estimate the hidden common
 source and subsequently updated the causal structure and sensory
 representation. Single-unit recordings in premotor and parietal cortices
 revealed that neural activity in the premotor cortex represents the core
 computation of causal inference, characterizing the estimation and update
 of the likelihood of integrating multiple sensory inputs at a
 trial-by-trial level. In response to signals from the premotor cortex,
 neural activity in the parietal cortex also represents the causal
 structure and further dynamically updates the sensory representation to
 maintain consistency with the causal inference structure. Thus, our
 results indicate how the premotor cortex integrates previous experience
 and sensory inputs to infer hidden variables and selectively updates
 sensory representations in the parietal cortex to support behavior. This
 dynamic loop of frontal-parietal interactions in the causal inference
 framework may provide the neural mechanism to answer long-standing
 questions regarding how neural circuits represent hidden structures for
 body awareness and agency.
DOI: 10.5061/dryad.9w0vt4bh5
title: Stronger effect of litter quality than microorganisms on leaf and root litter C and N loss at different decomposition stages following a subtropical land use change

description: Litter decomposition contributes largely to global carbon (C) and nitrogen
 (N) cycling, and it is strongly determined by litter quality and microbial
 community composition in ways that are poorly understood. Here, we
 conducted a 2-year field litter decomposition experiment by collecting
 leaf and root litter of crops (from cropland), shrubs (from shrubland),
 and wood (from woodland) and placing samples for decomposition in woodland
 soil in central China to investigate the effects of litter quality and
 microbial community composition on C and N loss of leaf and root litter of
 three species under different decomposition stages. Our results showed
 that the leaf litter C and N losses of shrubs were significantly higher
 than those of crops and wood, whereas the root litter C and N losses of
 crops were significantly higher than those of shrubs and wood. Generally,
 the leaf litter C and N losses of the three species were higher on average
 than those of fine root litter under the whole decomposition period. For
 the C loss of the three species, litter lignin and phosphorus as well as
 initial litter quality were predominant drivers of root litter
 decomposition, while litter lignin, cellulose, and hemicellulose
 concentrations were dominant for leaf litter decomposition. For N loss,
 litter stoichiometry and litter quality directly governed leaf and root
 litter N loss, and the initial litter quality largely regulated N loss at
 the late decomposition stage. Unexpectedly, the effect of microbial
 community composition on litter C and N loss was relatively weak and only
 exhibited an effect on litter C and N loss during the early stage of
 decomposition. Thus, our results revealed the huge disparity in C and N
 loss of plant species and litter types at different decomposition stages,
 which should be considered jointly when evaluating their roles in
 plant-soil feedbacks under global land use change.
DOI: 10.5061/dryad.8pk0p2npk
title: Environmental-related variation of stoichiometric traits in body and organs of non-native sailfin catfishes Pterygoplichthys spp.

description: Intraspecific variation in stoichiometric traits was thought to be an
 adaptive response to reduce the elemental imbalance between organisms and
 diet in the habitat. Studying the spatial variation of stoichiometric
 traits of non-native species and the factors contributing to the variation
 could help to better understand the invasion mechanism of non-native fish.
 In this study, stoichiometric traits (i.e. carbon [C], phosphorus [P],
 calcium [Ca] and their ratios) variation in the body and organs of
 non-native sailfin catfishes Pterygoplichthys spp. were investigated
 across 13 river sections in the main river basins of south China. The
 relationships between environmental factors and stoichiometric traits were
 analyzed using a general linear model and an information-theoretic
 approach. A manipulated feeding experiment was conducted to investigate
 the impact of food quality on the stoichiometry of sailfin catfishes in a
 greenhouse. Sailfin catfishes exhibited considerable variability in body
 and organ elemental composition. Site identity was the main factor
 contributing to the variation, which could be explained by a combination
 of environmental factors including climate, diet quality, fish species
 richness, and trophic status in the invaded rivers. Water chemistry (i.e.
 total nitrogen and phosphorus, ammonia nitrogen, and soluble reactive
 phosphorus) contributed to the most variation of stoichiometric traits.
 Imbalances of P and Ca between sailfin catfishes and food resources varied
 among sampling sites, reflecting the spatial heterogeneity of nutrient
 limitation. Juvenile sailfin catfishes exhibited stoichiometric
 homeostasis (0&lt;1/H&lt;0.25) for all elemental contents and
 ratios in the feeding experiment. These findings suggested variation in
 stoichiometric traits of sailfin catfishes might be attributed to the
 changes in elemental metabolism to cope with context-specific
 environments. This study provided heuristic knowledge about
 environmental-related variation in stoichiometric traits, which could
 enhance the understanding of the non-native species’ adaptation to
 resource fluctuation in the invaded ecosystems.
DOI: 10.5061/dryad.3xsj3txht
title: KerNet, 3D fluorescence and segmentation datasets of keratin networks from MDCK, HaCaT, and RPE cells

description: Mechanobiology requires precise quantitative spatial information on
 processes taking place in specific 3D microenvironments. Connecting
 microscopical, molecular, biochemical and cell mechanical data with
 defined topologies has turned out to be extremely difficult. Establishing
 such structural and functional 3D maps is particular challenging for the
 cytoskeleton, which consists of long and interwoven filamentous polymers
 coordinating subcellular processes and interactions of cells with their
 environment. Here we present raw data and processed segmented data of
 fluorescence-tagged keratin intermediate filaments from MDCK, HaCaT and
 RPE epithelial cells. The 30 datasets contain unprocessed airyscan
 superresolution 3D image data and numerical network data of the 3D
 arrangement of the keratin intermediate filament cytoskeleton. Information
 is provided on network organization at the subcellular level, including
 mesh arrangement, density and isotropic configuration as well as details
 on filament morphology such as bundling, curvature and orientation. The
 datasets contain data in exchange format for 3d software packages.
 Comparison of the resulting network parameters helps to identify
 similarities and differences of keratin network organization in epithelial
 cell types. The described approach and the presented data are pivotal for
 generating mechanobiological models that can be experimentally tested.
description: Three datasets are
 provided: Confocal airyscan image stacks of
 Madin-Darby Canine Kidney (MDCK) cells stably transfected with a plasmid
 encoding human full-length keratin 8 with an EYFP tag at its
 carboxyterminus. Confocal airyscan image stacks of
 immortalized human HaCaT keratinocyte cell clone B10 expressing
 EYFP-tagged human keratin 5 (HK5-EYFP). Confocal
 airyscan image stacks of retinal pigment epithelium that were dissected
 from homozygous keratin 8-YFP knock-in mice, which synthesize
 fluorescence-tagged keratin 8 from the modified endogenous gene
 locus. <br> The segmentation has been performed
 as described in the corresponding paper.
description: We provide three rar files: MDCK.rar<br>
 HACAT.rar<br> RPE.rar Each files
 contains:<br> -  3D image data of 10 cells<br> -  numerical
 network data from 10 cells<br> -  a pdf file with a description of
 the network data<br> -  corresponding 3D data
DOI: 10.5061/dryad.18931zczq
title: Stegodyphus africanus group feeding performance depending on relatedness

description: Cooperation involving shared-resource systems is prone to ‘the tragedy of
 the commons’, where individuals act in their own self-interest to exploit
 the resource in a manner that is detrimental to the common good of all
 group members. Directing cooperation towards kin provides a solution to
 this problem, and predicts the differential performance depending on
 relatedness of group members. In subsocial spiders, juveniles live in
 transient groups that cooperate in hunting and communal feeding. Prey
 capture is costly in terms of risk of injury and investment of venom and
 digestive enzymes, and therefore presents a situation where individuals
 may attempt to avoid costly interactions and exploit the resource acquired
 by other group members. We tested the prediction that individuals
 differentiate participation and/or investment in cooperative prey capture
 and extra-oral digestion (injection of digestive enzymes into prey prior
 to the initiation of extraction of nutrients) in response to relatedness
 of group members with whom they interact, in the subsocial spider
 Stegodyphus africanus. The performance of groups and interactions over
 prey attack in groups of either related or mixed kin spiderlings were
 determined over a period of four weeks. We show that kin groups attack the
 prey significantly faster, recruit individuals to form feeding groups
 faster, extract prey body mass more efficiently, and experience less
 antagonistic interactions than groups of mixed relatedness, which
 ultimately translates into an elevated growth rate. These results indicate
 that related individuals are more willing to take risks and invest in
 communal digestion when foraging with kin, as predicted by inclusive
 fitness theory as a solution to the tragedy of the commons.
DOI: 10.5061/dryad.zw3r22890
title: Timing of blood sample processing affects the transcriptomic and epigenomic profiles in CD4+ T-cells of atopic subjects

description: Optimal pre-analytical conditions for blood sample processing and
 isolation of selected cell populations for subsequent transcriptomic and
 epigenomic studies are required to obtain robust and reproducible results.
 This pilot study was conducted to investigate the potential effects of
 timing of CD4+ T-cell processing from peripheral blood of atopic and
 non-atopic adults on their transcriptomic and epigenetic profiles. Two
 heparinized blood samples were drawn from each of three atopic and three
 healthy individuals. For each individual, CD4+ T-cells were isolated from
 the first blood sample within 2 hours (immediate) or from the second blood
 sample after 24 hours storage (delayed). RNA sequencing (RNA-Seq) and
 histone H3K27 acetylation chromatin immunoprecipitation sequencing
 (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to
 be differentially expressed in immediately processed CD4+ T-cells from
 atopic versus healthy subjects. These differences disappeared when
 comparing delayed processed cells due to a drastic change in expression
 levels of atopy-related genes in delayed processed CD4+ T-cells from
 atopic donors. This finding was further validated on the epigenomic level
 by examining H3K27 acetylation profiles. In contrast, transcriptomic and
 epigenomic profiles of blood CD4+ T-cells of healthy donors remained
 rather unaffected. Taken together, for successful transcriptomics and
 epigenomics studies, detailed standard operating procedures developed on
 the basis of samples from both healthy and disease conditions are
 implicitly recommended.
DOI: 10.5061/dryad.9ghx3ffjv
title: Grandmaternal age at reproduction affects grandoffspring body condition, reproduction and survival in a wild population of lizards

description: Age at reproduction can influence the survival and future reproduction of
 an individual as well as that of their offspring. Remarkably, it has been
 shown that grandmaternal age at reproduction can also affect the
 characteristics of grandoffspring in humans and in laboratory or
 semi-captive animals. However, currently we do not know whether
 grandmaternal age effects exist in wild populations. We gathered data on
 female age at reproduction, offspring and grandoffspring characteristics
 using a 16-year long-term survey of a natural population of the common
 lizard, Zootoca vivipara. The dataset contains 579 grandoffspring from 135
 litters. Body size at birth was not correlated with grandmaternal age at
 reproduction. However, grandoffspring body condition at birth,
 grandoffspring survival and reproductive performance of granddaughters
 were dependent on grandmaternal age. These relationships were independent
 of maternal age. An age-structured model showed that the global effect of
 grandmaternal age was nonlinear and was largely driven by its effect on
 grandoffspring survival. Fitness was higher for granddaughters produced by
 grandmothers of intermediate ages. The study shows that age can shape
 life-history traits for more than one generation, documenting the
 importance that grandmaternal age can have in wild populations.
description: The data were obtained from a mark-recapture survey of common
 lizards (<em>Zootoca vivipara</em>) conducted each year from
 1989 through 2004 in a natural population at Mont-Lozère (1420 m a.s.l.,
 44°23’03’’N, 3°52’40’’E, Cévennes National Park, southeastern France).
 Pregnant females are captured each year and kept in the laboratory for
 three-four weeks until parturition. At birth, offspring are measured
 (snout-vent length, to the nearest mm), weighed (to the nearest mg), sexed
 and marked by toe-clipping. This protocol allows us to determine the
 maternal lineages, the age at reproduction, litter size, litter success,
 offspring body size and body mass at birth, and offspring sex. Lizards
 that are not born in the laboratory can be aged if they are captured in
 the field as juveniles or subadults, and this allows us to age many
 grandmothers. Offspring are recaptured at the end of the reproductive
 season (in September, <i>i.e.</i> before hibernation) and the
 summer of the next years (in June-July) to estimate their survival.
 Litters do not always result in live offspring, they can contain
 stillborns, unfertilised eggs or abortive embryos. We defined litter size
 as the total litter size, and litter success as the proportion of live
 offspring in a litter.