cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.x69p8czjr
title: Species diversity in a beech windthrow

description: On the basis of long-term surveys of permanent plots and traps we examined
 the communities of saproxylic beetles, fungi, herbs and trees on an
 untreated 22 hectare large beech forest windthrow and asked whether the
 results lend support to the intermediate disturbance hypothesis (IDH). We
 studied species richness and the similarity of community composition.
 Additionally, we grouped species by their frequency trend over time to
 successional model types to examine whether, corresponding to the IDH, the
 diversity of these groups explained peak richness at intermediate
 intervals after the disturbance. In line with the IDH, species richness
 showed a hump-backed temporal course for alpha and gamma diversity. We
 found evidence for a linear succession directly after the disturbance.
 This, however, did not continue, and in all species groups a partial
 recovery of the initial community was observed. In the case of fungi,
 herbs and trees, but not for saproxylic beetles, alpha diversity was
 driven by the diversity of the successional model types. Our results
 underline that the mechanisms driving species richness after disturbances
 are more complex than the IDH suggests, and that these mechanisms vary
 with species group. We assumed that, besides competition, legacy effects,
 facilitation, habitat heterogeneity and random saturation of the species
 pool are important. In case of trees and herbs we found indications for
 strong legacy and competition effects. For fungi and beetles, substrate
 heterogeneity and microclimate were assumed to be important. We concluded
 that disturbances contribute to increasing species richness not only by
 reducing the effectiveness of competitors but also by increasing the
 amount and diversity of resources, as well as their rate of change over
 time. We have archived the data of species occurences over years per
 plot. 
description: The data were collected in the field by different methods per
 species group. Tree and herb species were registered on permanent plots.
 Beetles (Coleptera) were caught in trunk-eclectors. Fungi were registered
 and, in part, collected on permanent plots. The determination of species
 was made in the field in case of trees and herbs, afterwards in case of
 beetles and partly afterwards in case of fungi. Data prcoessing is
 described in detail in the published paper. 
description: Ther are no missing values.
DOI: 10.5061/dryad.95x69p8m5
title: Evolutionary conservation of centriole rotational asymmetry in the human centrosome

description: Centrioles are formed by microtubule triplets in a nine-fold symmetric
 arrangement. In flagellated protists and in animal multiciliated cells,
 accessory structures tethered to specific triplets render the centrioles
 rotationally asymmetric, a property that is key to cytoskeletal and
 cellular organization in these contexts. In contrast, centrioles within
 the centrosome of animal cells display no conspicuous rotational
 asymmetry. Here, we uncover rotationally asymmetric molecular features in
 human centrioles. Using ultrastructure expansion microscopy, we show that
 LRRCC1, the ortholog of a protein originally characterized in flagellate
 green algae, associates preferentially to two consecutive triplets in the
 distal lumen of human centrioles. LRRCC1 partially co-localizes and
 affects the recruitment of another distal component, C2CD3, which also has
 an asymmetric localization pattern in the centriole lumen. Together,
 LRRCC1 and C2CD3 delineate a structure reminiscent of a filamentous
 density observed by electron microscopy in flagellates, termed the
 ‘acorn’. Functionally, the depletion of LRRCC1 in human cells induced
 defects in centriole structure, ciliary assembly and ciliary signaling,
 supporting that LRRCC1 cooperates with C2CD3 to organizing the distal
 region of centrioles. Since a mutation in the LRRCC1 gene has been
 identified in Joubert syndrome patients, this finding is relevant in the
 context of human ciliopathies. Taken together, our results demonstrate
 that rotational asymmetry is an ancient property of centrioles that is
 broadly conserved in human cells. Our work also reveals that
 asymmetrically localized proteins are key for primary ciliogenesis and
 ciliary signaling in human cells.
DOI: 10.5061/dryad.6djh9w11x
title: The evolution and biogeographic history of epiphytic thalloid liverworts

description: Among liverworts, the epiphytic lifestyle is not only present in leafy
 forms but also in thalloid liverworts, which so far has received little
 attention in evolutionary and biogeographical studies. Metzgeria,
 with about 107 species worldwide, is the only genus of thalloid liverworts
 that comprises true epiphytes. In the present study, we provide the first
 comprehensive molecular phylogeny, including estimated divergence times
 and ancestral ranges of this genus. Analyses are based on a plastid marker
 dataset representing about half of the Metzgeria species
 diversity. We could show for the first time with molecular data
 that Austrometzgeria is indeed a member
 of Metzgeria and that the morpho-species M.
 furcata and M. leptoneura are not monophyletic,
 but rather represent geographically well-defined clades. Our analyses
 indicated that Metzgeria started to diversify in the
 Cretaceous in an area encompassing today’s South America and Australasia.
 Thus, Metzgeria is one of the few known epiphytic
 liverwort genera whose biogeographic history was directly shaped by
 Gondwana vicariance. Subsequent dispersal events in the Cenozoic resulted
 in the colonization of Asia, Africa, North America, and Europe and led to
 today’s worldwide distribution of its species. We also provide the first
 reliable stem age estimate for Metzgeria due to the
 inclusion of its sister taxon Vandiemenia in our dating
 analyses. Additionally, this stem age estimate of about 240 million years
 most likely marks the starting point of a transition from a terrestrial to
 an epiphytic lifestyle in thalloid liverworts of the Metzgeriales. We
 assume that the Cretaceous Terrestrial Revolution played a key role in the
 evolution of epiphytic thalloid liverworts similar to that known for leafy
 liverworts.
DOI: 10.5061/dryad.h18931zm5
title: Correlates of substitution rate variation in a robust Procellariiform seabird phylogeny

description: Molecular substitution rates vary among branches and can lead to
 inaccurate reconstructions of evolutionary relationships and obscure the
 true phylogeny of affected clades. Body mass is often assumed to have a
 major influence on substitution rate, though other factors such as
 population size, life history traits, and flight demands are also thought
 to have an influence. Birds of the order Procellariiformes—which
 encompasses petrels, storm-petrels and albatrosses—show a striking
 900-fold difference in body mass between the smallest and largest members,
 divergent life history traits, and substantial heterogeneity in
 mitochondrial substitution rates. Here, we used genome-scale nuclear DNA
 sequence data from 4365 ultraconserved element loci (UCEs) in 51
 procellariiform species to examine whether phylogenetic reconstruction
 using genome-wide datasets is robust to the presence of rate
 heterogeneity, and to identify predictors of substitution rate variation.
 Our results provide a backbone phylogeny for procellariiform seabirds and
 resolves several controversies about the evolutionary history of the
 order, demonstrating that albatrosses are basal, storm-petrels are
 paraphyletic and diving petrels nestled within the Procellariidae. We find
 evidence of rate variation; however, all phylogenetic analyses using both
 concatenation and multispecies coalescent approaches recovered the same
 branching topology, including analyses implementing different clock
 models, and analyses of the most and least clock-like loci. Overall, we
 find that rate heterogeneity is little impacted by body mass and age at
 first breeding, but moderately impacted by longevity and hand-wing index,
 a proxy for wing shape and flight efficiency. Our results indicate that
 substitution rate may be the product of interactions among many,
 potentially taxon-specific, variables.
description: We collected blood and tissue samples in the field or from museum
 loans for 51 procellariiform seabirds and sequenced the DNA extracts
 targeting 5000 ultraconserved elements. We built phylogenies using a
 variety of approaches and explore substitution rate variation among
 lineages. We tested for correlations among substitution rate and body
 mass, life history variables, population size, and hand-wing
 index.
description: Supplementary material for <em>Correlates of Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny</em>. Raw data is deposited in Genbank under accession PRJNA749710 Code to reproduce all analyses can be found here: https://github.com/andreaestandia/procellariiform_backbone This repository contains: UCE contigs Alignments and charsets used for: RAxML IQtree Exabayes ASTRAL BEAST Trees produced raw and rooted Partitioning info Coevol 1.4b input and output files, and files used for plots BEAST XML files Main figures in pdf and png formats Supplementary tables and supplementary material
DOI: 10.15468/dl.fugh8p
title: Occurrence Download

description: A dataset containing 374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Minuartia arctica"
 ]
}

 The dataset includes 374 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002905-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m0cfxpp4h
title: Exotics are more complementary over time in tree biodiversity-ecosystem functioning experiments

description: Background and aims The Biodiversity – Ecosystem Functioning (BEF)
 literature proposes that ecosystem functioning increases with biodiversity
 because of complementarity in resource use among species, associated with
 functional diversity. In this study, we challenge the trait-based ecology
 framework by comparing congeneric exotic (European) and native (North
 American) tree species showing similar resource-use functional trait
 values. The trait-based framework suggests that two functionally
 equivalent species should play similar roles in a community, resulting in
 similar interactions and performances. However, several studies showed
 that when growing in mixtures, exotic species that are functionally
 equivalent to native species benefitted from enemy-release, resulting in a
 reduced apparent competition. We hypothesize that exotic species should be
 more productive than native species because the exotic species benefit
 from reduced apparent competition due to enemy-release rather than from
 possessing more competitive resource-use functional traits. Methods We
 study a diversity experiments, part of the International Diversity
 Experiment Network with Trees (IDENT), composed of two identical sites,
 each with two orthogonal diversity gradients: species richness and
 functional diversity. The functional gradient consists of species
 combinations of equal richness but increasing functional diversity, using
 different combinations of species provenance to assess the relationship
 between productivity, functional diversity and species provenance,
 independently of species richness. We grew a total of 12 species (six
 native, six exotic) in different combinations of one, two and six species
 mixtures. The exotic species were selected based on their functional
 equivalence to their native congeneric species. Key Results Eight years
 after planting, we found that exotic species were more productive than
 native species, but only at high functional diversity. Results indicate
 that exotic species overall benefit from a reduced apparent competition,
 and that exotic-increased productivity at high functional diversity is
 consistent with the enemy release hypothesis. Conclusions After eight
 years, exotic species were more productive overall than their native
 counterparts, but only in the most functionally diverse communities. This
 study represents a first step in understanding the relative importance of
 complementarity in resource-use and apparent competition in a context of
 an exotic tree species invasion.
description: Check related article for details
DOI: 10.5061/dryad.4j0zpc8bv
title: The elephant in the family: Costs and benefits of elder siblings on younger offspring life-history trajectory in a matrilineal mammal

description: 1. Many mammals grow up with siblings, and interactions between them can
 influence offspring phenotype and fitness. Among these interactions,
 sibling competition between different-age offspring should lead to
 reproductive and survival costs on the younger sibling, while sibling
 cooperation should improve younger sibling’s reproductive potential and
 survival. However, little is known about the consequences of sibling
 effects on younger offspring life history trajectory, especially in
 long-lived mammals. 2. We take advantage of a large, multigenerational
 demographic dataset from semi-captive Asian elephants to investigate how
 the presence and sex of elder siblings influence the sex, survival until
 five years old, body condition, reproductive success (i.e. age at first
 reproduction and lifetime reproductive success), and long-term survival of
 subsequent offspring. 3. We find that elder siblings have heterogenous
 effects on subsequent offspring life-history traits depending on their
 presence, their sex, and the sex of the subsequent offspring (named focal
 calf). 4. Overall, the presence of an elder sibling (either sex) strongly
 increased focal calf long-term survival (either sex) compared to sibling
 absence. However, elder sisters had higher impact on the focal sibling
 than elder brothers. Focal females born after a female display higher
 long-term survival, and decreased age at first reproduction when raised
 together with an elder sister rather than a brother. Focal males born
 after a female rather than a male showed lower survival but higher body
 weight when both were raised together. We did not detect any sibling
 effects on the sex of the focal calf sex, survival until five years old
 and lifetime reproductive success. 5. Our results highlight the general
 complexity of sibling effects, but broadly that elder siblings can
 influence the life-history trajectory of subsequent offspring. We also
 stress the importance of considering all life stages when evaluating
 sibling effects on life trajectories. 22-Jul-2021 --
DOI: 10.25338/b81p7b
title: Evaluating the quality of ecoinformatics data derived from commercial agriculture: a repeatability analysis of pest density estimates

description: Each year, consultants and field scouts working in commercial agriculture
 undertake a massive, decentralized data collection effort as they monitor
 insect populations to make real-time pest management decisions. These
 data, if integrated into a database, offer rich opportunities for applying
 big data or ecoinformatics methods in agricultural entomology research.
 However, questions have been raised about whether or not the underlying
 quality of these data is sufficiently high to be a foundation for robust
 research. Here I suggest that repeatability analysis can be used to
 quantify the quality of data collected from commercial field scouting,
 without requiring any additional data gathering by researchers. In this
 context, repeatability quantifies the proportion of total variance across
 all insect density estimates that is explained by differences across
 populations and is thus a measure of the underlying reliability of
 observations. Repeatability was moderately high for cotton fields scouted
 commercially for total Lygus hesperus Knight densities (R = 0.631) and
 further improved by accounting for observer effects (R = 0.697).
 Repeatabilities appeared to be somewhat lower than those computed for a
 comparable, but much smaller, researcher-generated data set. In general,
 the much larger sizes of ecoinformatics data sets are likely to more than
 compensate for modest reductions in measurement precision. Tools for
 evaluating data quality are important for building confidence in the
 growing applications of ecoinformatics methods.  Here I report
 the raw data that support these analyses in two files, one reporting the
 data gathered by the commercial pest control consultant and his summer
 field scouts and the second gathered by a team or university researchers.
description: All the data were gathered using sweep sampling in commercial
 cotton fields. A single sample is gathered by swinging the insect net 50
 times across the top of the plant canopy and then counting the number of
 nymphal and adult <em>Lygus</em> spp. captured.
description: Metadata pages included with each data file give simple
 explanations for each variable.  The number of sweep samples made per
 field varies; thus, there are many NA values for fields that received
 fewer than the maximum number of sweep samples.
DOI: 10.5061/dryad.cc2fqz66b
title: 3D printing lifts the lid on black box instruments

description: Within analytical chemistry, chemical instruments involve numerous
 interconnected parts working cohesively towards a specific functionality.
 However, these highly complex mechanisms cannot be fully depicted with a
 2-dimensional textbook model or image, leading to confusion or
 misconceptions during the learning process. To address this comprehension
 gap, an array of chemical instrument components have been designed and
 fabricated with 3D printing to create a hands-on learning experience. The
 models developed were created in interlocking parts to allow disassembly
 and investigation of the inner workings of each instrument component. This
 work produced a series of teaching aids and dynamic models for common
 instruments including a quadrupole, quadrupole-ion-trap, orbitrap, FTICR
 mass spectrometer; a GC injection port, FID, and ECD detectors; an HPLC
 injector; an ICP torch and nebulizer; a Michaelson interferometer; a basic
 monochromator; and a shatterbox sample preparation device. These models
 were designed to be interactive and hand-held 1:1 scale models of
 commercial instrument components. Using these models, students’ learning
 may be expanded from 2 to 3 dimensions; providing hands-on experience with
 modern laboratory instrumentation impossible with commercial
 instrumentation. Models were used in a small Analytical Chemistry lecture
 (n = 8) which demonstrated positive student reception, especially for
 models with kinematic relations to instrument functionality.
description: 5 Datasets are included: (1) - 3D models of analytical
 instruments. These were generated in either Solidworks or OnShape CAD
 software and are included as *.stl files for cross-system utilization. (2)
 - LabVIEW programs for monochromator and Fourier Transform simulations.
 Source code is included (*.llb), as well as an installer and executable
 versions. (3) - *.mp4 video files of mass spectrometry simulations. (4) -
 Assembly Instructions for provided STL files for 3D printing (Assembly
 Guide.docx). (5) - Student Survey - PDF of student survey results
 demonstrated in the manuscript.
DOI: 10.5061/dryad.2z34tmpn2
title: Bluebunch wheatgrass phenology information

description: To reduce maladaptation in cultivated seed lots, seed transfer zones
 (STZs) have been developed for grasslands and other habitats using
 morphological traits and phenological measurements that only capture the
 first day of events such as flowering and seed ripening. Phenology is
 closely linked to plant fitness and may affect genetic loss during
 harvests of seed raised for ecological restoration. Here, we measured the
 detailed phenologies of 27 populations from six STZs of bluebunch
 wheatgrass (Pseudoroegneria spicata) (Pursh) Á. Löve (Poaceae) raised in a
 common garden to test whether existing STZs created using a combination of
 plant morphology and “first-day” phenological measurements adequately
 capture population-level variation in season-long, detailed phenologies.
 We also used detailed phenologies to test whether genetic losses may occur
 during single-pass harvests of commercial seed. Mixed and random effect
 models revealed differences in detailed reproductive phenology among
 populations within two of six STZs. The number of individual plants within
 an STZ not producing harvestable seed during peak harvest levels indicated
 that 10% –27% of individuals from a seed lot could be excluded from a
 single-pass harvest. Although our findings generally support current STZ
 delineations for P. spicata, they point to the possible precautionary
 importance of sourcing from multiple populations and harvesting with
 multiple passes when resources permit.
description: Methods are described in the manuscript, which is in press.
DOI: 10.5061/dryad.wh70rxwnt
title: Genotype by environment interactions for chronic wasting disease in farmed U.S. white-tailed deer

description: Despite the implementation of enhanced management practices, chronic
 wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus;
 hereafter WTD) continues to expand geographically. Herein, we perform the
 largest genome-wide association analysis (GWAA) to date for CWD (n = 412
 CWD-positive; n = 758 CWD-non-detect) using a custom Affymetrix Axiom®
 single nucleotide polymorphism (SNP) array (n = 121,010 SNPs), and confirm
 that differential susceptibility to CWD is a highly heritable (h2 = 0.611
 ± 0.056) polygenic trait in farmed U.S. WTD, but with greater trait
 complexity than previously appreciated. We also confirm PRNP codon 96
 (G96S) as having the largest effects on risk (P ≤ 3.19E-08; Phenotypic
 Variance Explained ≥ 0.025) across three U.S. regions (Northeast, Midwest,
 South). However, 20 CWD-positive WTD possessing codon 96SS genotypes were
 also observed, including one that was lymph node and obex positive. Beyond
 PRNP, we also detected 23 significant SNPs (P-value ≤ 5E-05) implicating ≥
 24 positional candidate genes; many of which have been directly implicated
 in Parkinson’s, Alzheimer’s, and prion
 diseases. Genotype-by-environment (GxE) interaction GWAA revealed
 a SNP in the lysosomal enzyme gene ARSB as having the most significant
 regional heterogeneity of effects on CWD (P ≤ 3.20E-06); with increasing
 copy number of the minor allele increasing susceptibility to CWD in the
 Northeast and Midwest; but with opposite effects in the South. In
 addition to ARSB, 38 significant GxE SNPs (P-value ≤ 5E-05) were also
 detected, thereby implicating ≥ 36 positional candidate genes; the
 majority of which have also been associated with aspects of Parkinson’s,
 Alzheimer’s, and prion diseases.
description: Additional File (AF) 1-29 are detailed summary results and
 outputs from EMMAX GWAA, EMMAX GxE GWAA, and METAL meta-analysis. Table S1
 and Table S2 are supplementary Tables. See ReadMe File.