cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m2h2v
title: Data from: Root elemental composition in Chinese forests: implications for biogeochemical niche differentiation

description: 1. Trait-based community analysis provides a new approach to integrate
 functional ecology with community ecology. However, our understanding of
 the linkages between root chemical traits and community chemical diversity
 and assembly is still in its infancy. 2. Environmental filtering and niche
 differentiation are two opposite driving forces of community assembly
 based on deterministic niche processes. We hypothesize that environmental
 filtering is a strong driver of root chemical assembly at a large spatial
 scale, whereas biogeochemical niche differentiation drives root chemical
 traits divergence among co-occurring species at site scale. 3. We analyzed
 the concentrations of 15 elements in the fine roots of 281 species across
 five forest types of China. Discriminant analysis was used to measure the
 degree of similarity of root chemical traits at the community level and
 biogeochemical niche differentiation at the species level. 4. Root
 chemical traits at the community level showed a systematic shift along
 environmental gradients. The growth rate-related dimension represented by
 root P and Ca was the most important niche dimension associated with
 community root chemical assembly, driven by large-scale environmental
 filters, particularly soils and climate. Biogeochemical niche
 differentiation of co-occurring species could be a consequence of reducing
 nutrient competition, especially the competition for nitrogen. 5. Root
 chemical traits provide a new dimension for assessing the functional niche
 and may help improve our understanding of the underlying mechanisms of
 root chemical assembly from the local to the biome scale.
description: The concentration of 15
 elements in fine roots and the data of community structure
 surveyThe data file contains
 two datasets. 1. The concentration of 15 elements (C, N, K, Ca, Mg, S, Al,
 P, Fe, Mn, Na, Zn, Cu, Ni, and Co) in the fine roots of 281 plant species
 at eight forest sites crossing five forest types along the North–South
 transect in eastern China. 2. Community structure survey of the tree,
 shrub, and herb communities at eight forest sites. Vegetation parameters
 include species number, plant height, diameter at breast height (DBH) for
 all trees with DBH ≥ 2 cm or basal stem diameter for shrubs, and
 aboveground live biomass of each herbaceous species.upload
 data.zip
DOI: 10.5061/dryad.sk805
title: Data from: Diploid males support a two-step mechanism of endosymbiont-induced thelytoky in a parasitoid wasp

description: Background Haplodiploidy, where females develop from diploid, fertilized
 eggs and males from haploid, unfertilized eggs, is abundant in some insect
 lineages. Some species in these lineages reproduce by thelytoky that is
 caused by infection with endosymbionts: infected females lay haploid eggs
 that undergo diploidization and develop into females, while males are very
 rare or absent. It is generally assumed that in thelytokous wasps,
 endosymbionts merely diploidize the unfertilized eggs, which would then
 trigger female development. Results We found that females in the
 parasitoid wasp Asobara japonica infected with thelytoky-inducing
 Wolbachia produce 0.7–1.2 % male offspring. Seven to 39 % of these males
 are diploid, indicating that diploidization and female development can be
 uncoupled in A. japonica. Wolbachia titer in adults was correlated with
 their ploidy and sex: diploids carried much higher Wolbachia titers than
 haploids, and diploid females carried more Wolbachia than diploid males.
 Data from introgression lines indicated that the development of diploid
 individuals into males instead of females is not caused by
 malfunction-mutations in the host genome but that diploid males are most
 likely produced when the endosymbiont fails to activate the female sex
 determination pathway. Our data therefore support a two-step mechanism by
 which endosymbionts induce thelytoky in A. japonica: diploidization of the
 unfertilized egg is followed by feminization, whereby each step correlates
 with a threshold of endosymbiont titer during wasp development.
 Conclusions Our new model of endosymbiont-induced thelytoky overthrows the
 view that certain sex determination mechanisms constrain the evolution of
 endosymbiont-induced thelytoky in hymenopteran insects. Endosymbionts can
 cause parthenogenesis through feminization, even in groups in which
 endosymbiont-diploidized eggs would develop into males following the
 hosts’ sex determination mechanism. In addition, our model broadens our
 understanding of the mechanisms by which endosymbionts induce thelytoky to
 enhance their transmission to the next generation. Importantly, it also
 provides a novel window to study the yet-poorly known haplodiploid sex
 determination mechanisms in haplodiploid insects.
description: Figure2_maleproductionFigure3_mothers_woltiterFigure4_progeny_woltiterFigure5_introgression
DOI: 10.5061/dryad.85s6t
title: Data from: Characterization of the synoptic-scale diversity, biogeography and size distribution of diatoms in the North Pacific

description: The diversity, biogeography, and size distribution of diatoms in the North
 Pacific and underlying mechanisms shaping those patterns have little been
 characterized despite their importance in marine ecosystems. Here, we
 examined the community structure of diatoms in the surface and subsurface
 chlorophyll a maximum (SCM) layers of the North Pacific using light and
 scanning electron microscopy. Diatom carbon biomass in both the subarctic
 and temperate coastal regions was higher than that in the open subtropical
 and tropical waters. Species density was high in the temperate coastal
 region and certain open ocean stations where coastal water could be
 intruded. Diversity was generally higher in the SCM layer than that in the
 surface layer without a clear latitudinal trend. All diatom species in the
 open subtropical waters were observed in the temperate coastal waters,
 suggesting that the coastal regions act as a species bank. Certain
 indigenous species in the subarctic waters were considered as cryophilic
 species. We found that the general patterns of the size spectrum were
 nearly identical among different geographical regions of the North
 Pacific, irrespective of the species composition, environmental
 conditions, and seasonality. Our results provide mechanistic insights
 indicating that the diatom biodiversity in the species bank around the
 coastal region and the following current systems from the coastal to
 oceanic regions could principally determine biodiversity patterns in the
 North Pacific. The species-specific ecophysiological traits of diatoms and
 environmental conditions may further modify the biodiversity patterns and
 size distribution of diatoms.
description: Sugie_Suzuki_LO_doi_10.1002lno.10473
DOI: 10.5061/dryad.8s3682g
title: Data from: Determining the minimum number of protein-protein interactions required to support known protein complexes

description: The prediction of protein complexes from protein-protein interactions
 (PPIs) is a well-studied problem in bioinformatics. However, the currently
 available PPI data is not enough to describe all known protein complexes.
 In this paper, we express the problem of determining the minimum number of
 (additional) required protein-protein interactions as a graph theoretic
 problem under the constraint that each complex constitutes a connected
 component in a PPI network. For this problem, we develop two computational
 methods: one is based on integer linear programming (ILPMinPPI) and the
 other one is based on an existing greedy-type approximation algorithm
 (GreedyMinPPI) originally developed in the context of communication and
 social networks. Since the former method is only applicable to datasets of
 small size, we apply the latter method to a combination of the CYC2008
 protein complex dataset and each of eight PPI datasets (STRING, MINT,
 BioGRID, IntAct, DIP, BIND, WI-PHI, iRefIndex). The results show that the
 minimum number of additional required PPIs ranges from 51 (STRING) to 964
 (BIND), and that even the four best PPI databases, STRING (51), BioGRID
 (67), WI-PHI (93) and iRefIndex (85), do not include enough PPIs to form
 all CYC2008 protein complexes. We also demonstrate that the proposed
 problem framework and our solutions can enhance the prediction accuracy of
 existing PPI prediction methods. ILPMinPPI can be freely downloaded from
 http://sunflower.kuicr.kyoto-u.ac.jp/~nakajima/.
description: ILPMinPPI_data
DOI: 10.5061/dryad.b064t9c5
title: Data from: Low heritabilities, but genetic and maternal correlations between red squirrel behaviours.

description: Consistent individual differences in behaviour, and behavioural
 correlations within and across contexts, are referred to as animal
 personalities. These patterns of variation have been identified in many
 animal taxa and are likely to have important ecological and evolutionary
 consequences. Despite their importance, genetic and environmental sources
 of variation in personalities have rarely been characterized in wild
 populations. We used a Bayesian animal model approach to estimate genetic
 parameters for aggression, activity and docility in North American red
 squirrels (Tamiasciurus hudsonicus). We found support for low
 heritabilities (0.08-0.12), and cohort effects (0.07-0.09), as well as low
 to moderate maternal effects (0.07-0.15) and permanent environmental
 effects (0.08-0.16). Finally, we found evidence of a substantial positive
 genetic correlation (0.68) and maternal effects correlation (0.58) between
 activity and aggression providing evidence of genetically-based
 behavioural correlations in red squirrels. These results provide evidence
 for the presence of heritable variation in red squirrel behaviour, but
 also emphasize the role of other sources of variation, including maternal
 effects, in shaping patterns of variation and covariation in behavioural
 traits.
description: StruggleTestStruggle test scores collected in the field. See ReadMe for more information.OpenField+MISRaw scores from analysis of open field and mirror-image stimulation trials using JWatcher. See ReadMe for more information.pedigreePedigree. See ReadMe for more information.ReadMeReadMe for data.
DOI: 10.5061/dryad.vq2s1
title: Data from: Can plan recommendations improve the coverage decisions of vulnerable populations in health insurance marketplaces?

description: Objective: The Affordable Care Act’s marketplaces present an important
 opportunity for expanding coverage but consumers face enormous challenges
 in navigating through enrollment and re-enrollment. We tested the
 effectiveness of a behaviorally informed policy tool—plan
 recommendations—in improving marketplace decisions. Study Setting: Data
 were gathered from a community sample of 656 lower-income, minority, rural
 residents of Virginia. Study Design: We conducted an incentive-compatible,
 computer-based experiment using a hypothetical marketplace like the one
 consumers face in the federally-facilitated marketplaces, and examined
 their decision quality. Participants were randomly assigned to a control
 condition or three types of plan recommendations: social normative,
 physician, and government. For participants randomized to a plan
 recommendation condition, the plan that maximized expected earnings, and
 minimized total expected annual health care costs, was recommended. Data
 Collection: Primary data were gathered using an online choice experiment
 and questionnaire. Principal Findings: Plan recommendations resulted in a
 21 percentage point increase in the probability of choosing the earnings
 maximizing plan, after controlling for participant characteristics. Two
 conditions, government or providers recommending the lowest cost plan,
 resulted in plan choices that lowered annual costs compared to
 marketplaces where no recommendations were made. Conclusions: As millions
 of adults grapple with choosing plans in marketplaces and whether to
 switch plans during open enrollment, it is time to consider marketplace
 redesigns and leverage insights from the behavioral sciences to facilitate
 consumers’ decisions.
description: plan_reccomendations_PONE_D_15_42499R1_no_demographicsThis is a Stata data file (version 12). The data are labeled. At the request of Dryad and to limit the potential for indirect identification of study participants, demographic variables on age, race/ethnicity, income, marital status, and education are omitted from this data set. However, the estimates of interest for this paper are consistent across model specifications that do and do not include these demographic variables.
DOI: 10.5061/dryad.p9t061vc
title: Data from: Ecological limits on diversification of the Himalayan core Corvoidea

description: Within regions, differences in the number of species among clades must be
 explained by clade age, net diversification rate, or immigration. We
 examine these alternatives by assessing historical causes of the low
 diversity of a bird parvorder in the Himalayas (the core Corvoidea, 57
 species present) relative to its more species rich sister clade. The core
 Corvoidea contain ecologically diverse species spanning a large range of
 body sizes and elevations. Despite this diversity, on the basis of
 ecological, morphological, and phylogenetic information, we infer that the
 best explanation for the low number of species within the core Corvoidea
 is one in which ecology limits diversification. Within the core Corvoidea,
 body size is correlated with elevation; large species are found at high
 elevations, and small species at lower elevations. Cladogenetic events
 leading to ecological differences between species in body size and shape
 mostly occurred millions of years ago, and the rate of evolutionary change
 has declined towards the present. Elevational distributions have been
 evolutionarily more labile, but are also associated with ancient
 cladogenetic events. We suggest the core Corvoidea occupy a restricted
 volume of ecological space in competition with other bird species, and
 this limits in situ diversification and/or immigration.
description: Time calibrated tree
 XMLXML file created using
 BEAUti v1.6.2. to produce the time-calibrated phylogeny presented in
 Figure 1 of the manuscript. The tree contains 85 taxa and 8 fossil or
 biogeographic calibration points. The file can be run in Beast
 v1.6.2.Morphological
 measurements (Table S5)Morphological
 measurements of 2 males specimens of the 57 Himalayan core Corvoidea
 species taken by Jonathan Kennedy at the Field Museum of Natural History
 Chicago.
DOI: 10.5061/dryad.91mk9
title: Data from: Climate oscillation during the Quaternary associated with landscape heterogeneity promoted allopatric lineage divergence of a temperate tree Kalopanax septemlobus (Araliaceae) in East Asia

description: We investigated the biogeographic history of Kalopanax septemlobus, one of
 the most widespread temperate tree species in East Asia, using a combined
 phylogeographic and palaeodistribution modelling approach. Range-wide
 genetic differentiation at nuclear microsatellites (G′ST = 0.709; 2205
 samples genotyped at five loci) and chloroplast DNA (GST = 0.697; 576
 samples sequenced for 2055 bp at three fragments) was high. A major
 phylogeographic break in Central China corresponded with those of other
 temperate species and the spatial delineation of the two temperate forest
 subkingdoms of East Asia, consistent with the forests having been isolated
 within both East and West China for multiple glacial–interglacial cycles.
 Evidence for multiple glacial refugia was found in most of its current
 range in China, South Japan and the southernmost part of the Korean
 Peninsula. In contrast, lineage admixture and absence of private alleles
 and haplotypes in Hokkaido and the northern Korean Peninsula support a
 postglacial origin of northernmost populations. Although
 palaeodistribution modelling predicted suitable climate across a
 land-bridge extending from South Japan to East China during the Last
 Glacial Maximum, the genetic differentiation of regional populations
 indicated a limited role of the exposed sea floor as a dispersal corridor
 at that time. Overall, this study provides evidence that differential
 impacts of Quaternary climate oscillation associated with landscape
 heterogeneity have shaped the genetic structure of a wide-ranging
 temperate tree in East Asia.
description: Kalopanax_nSSR_cpHapNuclear microsatellite genotype and chloroplast DNA haplotype data for Kalopanax septemlobus
DOI: 10.5061/dryad.s1660
title: Data from: Optimal taxonomic groups for biodiversity assessment: a meta-analytic approach

description: A fundamental decision in biodiversity assessment is the selection of one
 or more study taxa, a choice that is often made using qualitative criteria
 such as historical precedent, ease of detection, or available technical or
 taxonomic expertise. A more robust approach would involve selecting taxa
 based on the a priori expectation that they will provide the best possible
 information on unmeasured groups, but data to inform such hypotheses are
 often lacking. Using a global meta-analysis, we quantified the proportion
 of variability that each of 12 taxonomic groups (at the Order level or
 above) explained in the richness or composition of other taxa. We then
 applied optimization to matrices of pairwise congruency to identify the
 best set of complementary surrogate groups. We found that no single taxon
 was an optimal surrogate for both the richness and composition of
 unmeasured taxa if we used simple methods to aggregate congruence data
 between studies. In contrast, statistical methods that accounted for
 well-known drivers of cross-taxon congruence (spatial extent, grain size,
 and latitude) lead to the prioritization of similar surrogates for both
 species richness and composition. Advanced statistical methods were also
 more effective at describing known ecological relationships between taxa
 than simple methods, and show that congruence is typically highest between
 taxonomically and functionally dissimilar taxa. Birds and vascular plants
 were most frequently selected by our algorithm as surrogates for other
 taxonomic groups, but the extent to which any one taxon was the ‘optimal’
 choice of surrogate for other biodiversity was highly context-dependent.
 In the absence of other information – such as in data-poor areas of the
 globe, and under limited budgets for monitoring or assessment – ecologists
 can use our results to assess which taxa are most likely to reflect the
 distribution of the richness or composition of ‘total’ biodiversity.
description: Data on cross-taxon
 congruence from the ecology literatureThe file contains four
 tabs: 'articles' is a list of articles investigated to identify
 suitable data; 'sites' contains information on the spatial
 characteristics of the selected survey locations; 'congruence'
 contains the raw data on cross-taxon congruence extracted from each
 article; and 'taxa' gives taxonomic information for each group
 listed in the dataset.Westgate_etal_2016_Ecography_data.xlsx
DOI: 10.5061/dryad.373f5
title: Data from: Illness beliefs in end stage renal disease and associations with self-care modality choice

description: Background: Interest in self-care haemodialysis (HD) has increased because
 it improves patients’clinical and quality-of-life outcomes. Patients who
 undertake self-management for haemodialysis may hold illness beliefs
 differently to those choosing institutional care at the time of making the
 modality choice or moulded by their illness and dialysis treatment
 experience. Illness perceptions amongst predialysis patients and in those
 undertaking fully-assisted and self-care haemodialysis are being
 investigated in a combined cross-sectional and longitudinal study. Study
 Design: The study data are derived from the BASIC-HHD study, a multicentre
 observational study on factors influencing home haemodialysis uptake. 535
 patients were enrolled into three groups: Predialysis CKD-5 group,
 prevalent ‘in-centre’ HD and self-care HD groups (93% at home). We explore
 illness perceptions in the cross-sectional analyses of the three study
 groups, using the revised Illness Perception Questionnaire (IPQ-R).
 Predialysis patients’ illness beliefs were reassessed prospectively,
 typically between 4 and 12 months after dialysis commencement. Results:
 Illness belief subscales are significantly different between in-centre and
 self-care HD groups. In a step-wise hierarchical regression analysis,
 after adjustment for age, education, marital status, diabetes, dialysis
 vintage, depression, anxiety scores, and IPQ-R subscales, personal control
 (p = 0.01) and illness coherence (p = 0.04) are significantly higher in
 the self-care HD group. In the predialysis group, no significant
 associations were found between illness representations and modality
 choices. In prospectively observed predialysis group, scores for personal
 control, treatment control, timeline cyclical and emotional
 representations reduced significantly after commencing dialysis and
 increased significantly for illness coherence. Conclusions: Illness
 beliefs differ between hospital and self-care haemodialysis patients.
 Patient’s affect and neurocognitive ability may have an important role in
 determining illness beliefs. The impact of modality upon illness
 representations may also be significant and remains to be explored.
description: Illness Perception in
 End Stage Renal disease- EXCEL fileIPQ-R DATA FOR
 DRYAD.xlsx