cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34tmpg4jr
title: Lianas have more acquisitive traits than trees in a dry but not in a wet forest

description: Lianas are increasing in relative abundance and biomass in many tropical
 forests. We tested the hypothesis that lianas conform to the fast and
 acquisitive end of the continuum of plant strategies, allowing lianas to
 acquire resources faster than trees. We assessed functional traits
 representative of the leaf (LES) and wood economics spectrum (WES),
 including plant hydraulics, in 16 liana and 16 tree species in the canopy
 of two tropical forests at the extremes of the climatic and geological
 gradient across the Isthmus of Panama. For both forests, we observed a
 trade-off between the construction of more productive leaves with rapid
 turnover and expensive leaves with slower turnover. We also found trait
 variation associated with wood and hydraulic traits. These two axes were
 orthogonal, suggesting that trade-offs at the leaf and stem, including
 plant hydraulics, operate independently. For the dry forest, lianas had
 cheaper and more efficient leaves than trees. For the wet forest, lianas
 and trees overlapped in leaf and stem characteristics. Moreover, the
 duration of green foliage highly explained the variation between dry
 forest species, reflecting different adaptations to drought. In the wet
 forest, fast-growing species benefited from a higher return on investments
 of leaf vascular tissues than slow-growing species and they had a higher
 capacity to transport water through the leaf. A higher capacity to
 construct more productive leaves and display leaves with lower costs may
 favour lianas over trees in light interception, photosynthetic rates, and
 growth under high light and nutrient availability in dry forests.
 Synthesis: Lianas in a dry tropical forest had a more acquisitive strategy
 than trees, characterized by more productive leaves and more efficient
 display for light interception. In dry environments, lianas appear to
 benefit from high-light and nutrient-rich soils and thus take advantage of
 higher resource conditions compared to trees. By contrast, in a wet
 tropical forest, lianas and trees overlapped in leaf and stem
 characteristics and lianas were not more acquisitive than trees. In wet
 environments, low light availability and nutrient-poor soils in a context
 of low water limitation may constrain variation in resource acquisition
 strategies between lianas and trees.
description: This dataset was collected throughout the study presented in the
 article: <em>Lianas have more acquisitive traits than trees in a dry
 but not in a wet forest</em>
DOI: 10.7272/q6fx77px
title: CRISPR-Cas system of a prevalent human gut bacterium reveals hyper-targeting against phages in a human virome catalog

description: Bacteriophages are abundant within the human gastrointestinal tract, yet
 their interactions with gut bacteria remain poorly understood,
 particularly with respect to CRISPR-Cas immunity. Here, we show that the
 type I-C CRISPR-Cas system in the prevalent gut
 Actinobacterium Eggerthella lenta is transcribed and
 sufficient for specific targeting of foreign and chromosomal DNA.
 Comparative analyses of E. lenta CRISPR-Cas
 systems across (meta)genomes revealed 2 distinct clades according
 to cas sequence similarity and spacer content. We
 assembled a human virome database (HuVirDB), encompassing 1,831 samples
 enriched for viral DNA, to identify protospacers. This revealed matches
 for a majority of spacers, a marked increase over other databases, and
 uncovered “hyper-targeted” phage sequences containing multiple
 protospacers targeted by
 several E. lenta strains. Finally, we
 determined the positional mismatch tolerance of observed
 spacer-protospacer pairs. This work emphasizes the utility of merging
 computational and experimental approaches for determining the function and
 targets of CRISPR-Cas systems.
description: This dataset is a the result of collecting and assembling human
 metagenomic virome sequencing for the purposes of meta-analysis.
description: All scaffolds are identified by their SampleID with metadata
 available at the associated github
 repository: https://github.com/jbisanz/HuVirDB.
DOI: 10.6078/d1nm6n
title: Phylogeny and biogeography of Acaena (Rosaceae) and its relatives: Evidence of multiple long-distance dispersal events across the globe

description: Acaena Mutis ex L. (Rosaceae) is the most complex and ecologically
 variable genus in the subtribe Sanguisorbinae. Although it has been the
 subject of several taxonomic treatments, the largest phylogenetic analysis
 to date only sampled a small fraction of the total global diversity (five
 to seven out of 45 to 50 species). This study included most of the species
 to elucidate the phylogenetic relationships of Acaena and biogeographic
 patterns in Sanguisorbinae. Phylogenetic analyses of non-coding
 nuclear (ITS region) and chloroplast (trnL-F) DNA sequence markers using
 maximum likelihood and Bayesian analyses suggest that Acaena is a
 paraphyletic group with species of Margyricarpus and Tetraglochin nested
 within it. We identified strong support for eight subclades that are
 geographically or taxonomically structured. Nevertheless, the
 species-level relationships within subclades are still uncertain, which
 may be due to rapid diversification and lack of informative characters in
 the markers used. Sanguisorbinae, a primarily Southern Hemisphere clade,
 exhibits a classic Gondwana disjunct distribution. This current
 distribution is explained primarily by long-distance dispersal events
 (eight in total). Our results suggested that Sanguisorbinae split into
 Cliffortia and Acaena around 13.6 mya. While Cliffortia diversified in
 southern South Africa, Acaena experienced several migration events in the
 Southern Hemisphere. Our estimation of the ancestral range suggested that
 Acaena likely originated in South Africa, followed by migration into South
 America and diversification in the temperate regions of Chile and
 Argentina. From there, the genus migrated to polar and other temperate
 areas such as New Zealand, throughout the Andes, and to tropical areas in
 Central America, reaching as far north as California. Our results show
 that the main sources of propagules for dispersal as well as the greatest
 diversity for the genus are located in Chile and New Zealand. The
 evolutionary relationships of species in Acaena combine a history of rapid
 radiations, long-distance dispersals, and genetic variation within some
 taxa. Further research should be undertaken to clarify the infraspecific
 classification of A. magellanica.
DOI: 10.5061/dryad.dfn2z350w
title: Genome-wide investigation and transcriptional profiling of the oxidosqualene cyclase (OSC) genes in wheat (Triticum aestivum L.)

description: Triterpene scaffolds are cyclized by differential functional genes of the
 oxidosqualene cyclase (OSC) gene family, which are widely present in plant
 species. Thirty-nine OSCs genes were identified from the hexaploid bread
 wheat (Triticum aestivum L.) genome. The gene structure organization and
 the distribution of conserved motifs of OSCs gene family revealed that the
 TaOSC proteins are highly conserved. By phylogenetic analysis, all OSC
 proteins from wheat and other cereal crops were clustered into eleven
 subfamilies (Ⅰ-Ⅺ). Based on the publicly available transcriptional
 profiling, the tissue-specific expression patterns of TaOSC during several
 developmental stages revealed diverged expression patterns, indicating
 that the TaOSC family has undergone subfunctionalization. Furthermore,
 homeolog expression bias was commonly detected in the TaOSC subfamilies,
 such as the expression of Ta5A004900 and Ta5D011800 in the subfamily Ⅱ
 were specifically expressed in the leaf sheath and flag leaf sheath. In
 addition, both of two genes were strongly induced by Pst, indicating that
 the two homolog genes are involved in the resistance to powdery mildew.
 Molecular evolution analysis indicated that the TaOSC family genes were
 undergone purifying selection. So, the powdery mildew response may be very
 conservative and important biological function of the Ta5A004900 and
 Ta5D011800 in wheat. In conclusion, these results can be used to explore
 the diversity of triterpenes and clarify the mechanism of triterpene
 cyclization, and also provide useful information for future studies on the
 function of the TaOSC gene family in bread wheat and other important
 crops.
DOI: 10.5061/dryad.59zw3r26f
title: Aboveground carbon stocks and dynamics in Andean forests

description: This dataset (Andean_AGB.xlsx) has the data employed in the paper
 entitled Old-growth Andean forests as globally important carbon
 sinks and future carbon refuges. The data was compiled as the results of
 the work of several research teams spread out across the Andean region.
 The information available here has data about aboveground carbon stocks
 and dynamics and the main explanatory variables, such as climate and
 symbiotic root associations.
description: The dataset comes from forest permanent plots that were surveyed
 by different research teams across the Andean region. Plot size varied
 from 0.32 to 1.28 ha, with a cumulative sample area of 104.4 ha. In each
 plot, we tagged, mapped, measured, and collected vouchers of all trees and
 palms with stem diameter at breast height (DBH, 1.3 m) ≥ 10 cm. DBH was
 measured 50 cm above buttresses or aerial roots when present (where the
 stem was cylindrical). During the second or subsequent set of censuses,
 DBH growth, recruitment, and mortality were recorded. In cases where the
 recorded DBH growth of the second census was less than -0.1 cm
 y<sup>-1</sup> or greater than 7.5 cm
 y<sup>-1</sup>, the DBH of the second census was
 augmented/reduced in order to match these minimum/maximum values. To
 homogenize and validate species names of palms and trees recorded in each
 country and plot, we submitted the combined list from all plots to the
 Taxonomic Name Resolution Service (TNRS;
 http://tnrs.iplantcollaborative.org/) version 3.0. Any species with an
 unassigned TNRS accepted name or with a taxonomic status of ‘no opinion’,
 ‘illegitimate’, or ‘invalid’ was manually reviewed. Families and genera
 were changed in accordance with the new species names. If a full species
 name was not provided or could not be found, the genus and/or family name
 from the original file was retained.
DOI: 10.5061/dryad.qbzkh18gp
title: BayesW time-to-event analysis posterior outputs and summary statistics

description: Here, we develop a Bayesian approach (BayesW) that provides probabilistic
 inference of the genetic architecture of age-at-onset phenotypes in a
 hybrid-parallel sampling scheme that facilitates Bayesian time-to-event
 large-scale biobank analyses. We show in extensive simulation work that
 BayesW achieves a greater number of discoveries, better model performance
 and improved genomic prediction as compared to other approaches. In the UK
 Biobank, we find many thousands of common genomic regions underlying the
 age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and
 type-2 diabetes (T2D), and for the genetic basis of onset reflecting the
 underlying genetic liability to disease. Age-at-menopause and
 age-at-menarche are also highly polygenic, but with higher variance
 contributed by low-frequency variants. Genomic prediction into the
 Estonian Biobank data shows that BayesW gives higher prediction accuracy
 than other approaches.
description: The data consists of the posterior distributions of running
 BayesW model on five phenotypes in UK Biobank: age-at-menopause,
 age-at-menarche, and age-at-diagnosis of coronary artery disease, high
 blood pressure, or type-2-diabetes. The posterior distributions give the
 effect size estimates and the corresponding effect size mixture
 classification for each of the markers analysed.  In
 addition we provide summary statistics for each of the markers analysed,
 giving posterior means, standard deviations and inclusion
 probabilities.
description: The information included in the ReadMe file.
DOI: 10.5061/dryad.51c59zw7t
title: Analyses on the fungus-farming termite, Macrotermes natalensis

description: Kings and queens of eusocial termites can live for decades, while queens
 sustain a nearly maximal fertility. To investigate the molecular
 mechanisms underlying their long lifespan, we carried out transcriptomics,
 lipidomics and metabolomics in Macrotermes natalensis on sterile
 short-lived workers, long-lived kings and five stages spanning twenty
 years of adult queen maturation. Reproductives share gene expression
 differences from workers in agreement with a reduction of several
 aging-related processes, involving upregulation of DNA damage repair and
 mitochondrial functions. Anti-oxidant gene expression is downregulated,
 while peroxidability of membranes in queens decreases. Against
 expectations, we observed an upregulated gene expression in fat bodies of
 reproductives of several components of the IIS pathway, including an
 insulin-like peptide, Ilp9. This pattern does not lead to deleterious fat
 storage in physogastric queens, while simple sugars dominate in their
 hemolymph and large amounts of resources are allocated towards oogenesis.
 Our findings support the notion that all processes causing aging need to
 be addressed simultaneously in order to prevent it.
DOI: 10.5061/dryad.zpc866t7t
title: Data from: Sexually dimorphic dorsal coloration in a jumping spider: testing a potential case of sex-specific mimicry

description: To avoid predation, many animals mimic behaviors and/or coloration of
 dangerous prey. Here we examine potential sex-specific mimicry in the
 jumping spider Habronattus pyrrithrix. Previous work proposed that males’
 conspicuous dorsal coloration paired with characteristic leg-waving
 behavior (i.e., false antennation) may imperfectly mimic hymenopteran
 insects, affording protection to males during mate-searching and
 courtship. In contrast, less active females are cryptic and display less
 leg-waving. Here we test the hypothesis that sexually dimorphic dorsal
 color patterns in H. pyrrithrix are most effective when paired with
 sex-specific behaviors. We manipulated spider dorsal coloration with
 makeup to model the opposite sex and exposed them to a larger salticid
 predator. We predicted that males painted like females should suffer
 higher predation rates than sham-control males. Likewise, females painted
 like males should suffer higher predation rates than sham-control females.
 Contrary to expectations, spiders with male-like coloration were attacked
 more than those with female-like coloration, regardless of their actual
 sex. Moreover, males were more likely to be captured, and were captured
 sooner, than females (regardless of color pattern). With these unexpected
 negative results, we discuss alternative hypotheses for the functions of
 H. pyrrithrix colors, as well as the evolution of defensive coloration
 generally.
description: All methods are described in the accompanying manuscript.
DOI: 10.5061/dryad.ns1rn8ps7
title: A comprehensive phylogenomic platform for exploring the angiosperm Tree of Life

description: Abstract The tree of life is the fundamental biological roadmap for
 navigating the evolution and properties of life on Earth, and yet remains
 largely unknown. Even angiosperms (flowering plants) are fraught with data
 gaps, despite their critical role in sustaining terrestrial life. Today,
 high-throughput sequencing promises to significantly deepen our
 understanding of evolutionary relationships. Here, we describe a
 comprehensive phylogenomic platform for exploring the angiosperm tree of
 life, comprising a set of open tools and data based on the 353 nuclear
 genes targeted by the universal Angiosperms353 sequence capture probes.
 The primary goals of this article are to (i) document our methods, (ii)
 describe our first data release, and (iii) present a novel open data
 portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim
 to generate novel target sequence capture data for all genera of flowering
 plants, exploiting natural history collections such as herbarium
 specimens, and augment it with mined public data. Our first data release,
 described here, is the most extensive nuclear phylogenomic data set for
 angiosperms to date, comprising 3099 samples validated by DNA barcode and
 phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and
 2333 genera (17$\%$). A “first pass” angiosperm tree of life was inferred
 from the data, which totaled 824,878 sequences, 489,086,049 base pairs,
 and 532,260 alignment columns, for interactive presentation in the Kew
 Tree of Life Explorer. This species tree was generated using methods that
 were rigorous, yet tractable at our scale of operation. Despite
 limitations pertaining to taxon and gene sampling, gene recovery, models
 of sequence evolution and paralogy, the tree strongly supports existing
 taxonomy, while challenging numerous hypothesized relationships among
 orders and placing many genera for the first time. The validated data set,
 species tree and all intermediates are openly accessible via the Kew Tree
 of Life Explorer and will be updated as further data become available.
 This major milestone toward a complete tree of life for all flowering
 plant species opens doors to a highly integrated future for angiosperm
 phylogenomics through the systematic sequencing of standardized nuclear
 markers. Our approach has the potential to serve as a much-needed bridge
 between the growing movement to sequence the genomes of all life on Earth
 and the vast phylogenomic potential of the world’s natural history
 collections. [Angiosperms; Angiosperms353; genomics; herbariomics;
 museomics; nuclear phylogenomics; open access; target sequence capture;
 tree of life.]
description: See Materials and Methods in corresponding paper.
DOI: 10.5061/dryad.sj3tx9646
title: Data from: Phylogenomic subsampling and the search for phylogenetically reliable loci

description: Phylogenomic subsampling is a procedure by which small sets of loci are
 selected from large genome-scale datasets and used for phylogenetic
 inference. This step is often motivated by either computational
 limitations associated with the use of complex inference methods, or as a
 means of testing the robustness of phylogenetic results by discarding loci
 that are deemed potentially misleading. Although many alternative methods
 of phylogenomic subsampling have been proposed, little effort has gone
 into comparing their behavior across different datasets. Here, I calculate
 multiple gene properties for a range of phylogenomic datasets spanning
 animal, fungal and plant clades, uncovering a remarkable predictability in
 their patterns of covariance. I also show how these patterns provide a
 means for ordering loci by both their rate of evolution and their relative
 phylogenetic usefulness. This method of retrieving phylogenetically useful
 loci is found to be among the top performing when compared to alternative
 subsampling protocols. Relatively common approaches such as minimizing
 potential sources of systematic bias or increasing the clock-likeness of
 the data are found to fare worse than selecting loci at random. Likewise,
 the general utility of rate-based subsampling is found to be limited: loci
 evolving at both low and high rates are among the least effective, and
 even those evolving at optimal rates can still widely differ in
 usefulness. This study shows that many common subsampling approaches
 introduce unintended effects in off-target gene properties, and proposes
 an alternative multivariate method that simultaneously optimizes
 phylogenetic signal while controlling for known sources of bias.
DOI: 10.15468/dl.t7rap2
title: Occurrence Download

description: A dataset containing 1334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Desmodium uncinatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1334 records from 166 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002799-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2v6wwpzmn
title: Sirius wheat model

description: Sirius is a process-based crop simulation modeldeveloped in C# for Windows
 computes. Initially developed for wheat, Sirius has been extended to model
 inter-plant competition and other species. Sirius is a well validated
 model and was able to simulate accurately crop growth in a wide range of
 environments, including Europe, USA, New Zealand and Australia, and for
 experiments of climate change, e.g. Free-Air Carbon Dioxide Enrichment
 (FACE) experiments.
DOI: 10.5061/dryad.fn2z34tst
title: Canopy height distributions and estimated above-ground biomass across a tropical rain forest landscape in Costa Rica, 1992-2018

description: This publication presents four related data sets that describe canopy
 height distributions and estimated above-ground biomass across an
 old-growth tropical rain forest landscape at the La Selva Biological
 Station, Costa Rica, from 1992 – 2018.  One data set contains
 measured forest heights that were taken annually from 1999-2018 at 231
 points per plot in 18 0.50 ha forest inventory plots (9 plots in 1999, 18
 thereafter).  The second data set contains data from an annual
 evaluation of the precision (repeatability) of these forest heights
 measurements.  The third data set is raw data on canopy heights
 taken in 1992 over the same landscape on 15 100-m transects sampled every
 2.5 m (Clark et al. 1996).  The fourth data set contains data on
 estimated above-ground biomass for all stems &gt;10 cm diameter in the
 same plots as the canopy heights dataset.  The biomass data were
 taken annually from 1997-2018.  Together these data present the
 most detailed data currently available on decadal trends on estimated
 forest biomass and related canopy structure in old-growth tropical rain
 forest.      
description: There are four data sets in this publication.
 Canopy heights 1999-2018.csv.  Methods for the 1999-2018 canopy
 heights data are described in detail in Kellner, Clark and Hubbell 2009
 and Silva et al 2013.  Briefly, canopy heights were measured annually to
 15 m with an extending survey pole on a 5 x 5 m grid in 18 0.50 ha forest
 inventory plots (9 plots in 1999, 18 thereafter).  Heights &gt;15 were
 classified as high canopy. Measurement precision of
 1999_2018 canopy heights data.csv.  The dataset contains data from an
 annual evaluation of measurement precision in the canopy heights data
 described above.  Every year we assessed the precision of the canopy
 height estimates by remeasuring an average of 123 points after a one- to
 several-day interval. Canopy heights 1992.csv.  The
 1992 height data methods are described in detail in Clark et al 1996. 
 Briefly, canopy height was measured with an optical range finder at 2.5 m
 intervals along 15 100 m long transects in old-growth tropical rain forest
 at the La Selva Biological Station, Costa Rica.
 Estimated Above-Ground Biomass 1997-2018.csv.  Methods for the
 Estimated Above-Ground Biomass (EAGB kg) data are described in detail in
 Clark, Clark and Oberbauer 2013 and Clark et al. 2017 and 2019.  Briefly,
 stem diameters of all stems &gt; 10 cm diameter
 were measured annually from 1997-2018 in 18 0.50 forest inventory plots. 
 Stem diameter was converted to EAGB (kg) via an allometric equation (see
 cited references).
description: There are no missing values and all data can be used as
 presented.