cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f1vhhmgvj
title: Adaptation to viscous Snowball Earth Oceans is a path to complex multicellularity

description: Animals, fungi, and algae with complex multicellular bodies all evolved
 independently from unicellular ancestors. The early history of these major
 eukaryotic multicellular clades, if not their origins, co-occur with an
 extreme phase of global glaciations known as the Snowball Earth. Here, I
 propose that the long-term loss of low viscosity environments due to
 several rounds global glaciation drove the multiple origins of complex
 multicellularity in eukaryotes and the subsequent radiation of complex
 multicellular groups. Under this scenario, life adapts to Snowball Earth
 oceans by evolving large size which acts to compensate for high viscosity
 seawater and maintain fluid flow at sufficient levels. Warm, low viscosity
 seawater returned with the melting of the Snowball glaciers and with it,
 by virtue of large multicellular bodies, new ways of life were unveiled.
description: Body sizes compiled from taxonomic and paleontological
 literature.
DOI: 10.15468/dl.5xscq8
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cordyla haraka",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 140 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002663-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pk0p2ngm6
title: Breeding season length predicts duet coordination and consistency in Neotropical wrens (Troglodytidae)

description: Many animals produce coordinated signals, but few are more striking than
 the elaborate male-female vocal duets produced by some tropical songbirds.
 Yet, little is known about the factors driving the extreme levels of vocal
 coordination between mated pairs in these taxa. We examined evolutionary
 patterns of duet coordination and their potential evolutionary drivers in
 Neotropical wrens (Troglodytidae), a songbird family well-known for highly
 coordinated duets. Across 23 wren species we show that the degree of
 coordination and precision with which pairs combine their songs into duets
 varies by species. This includes some species that alternate their song
 phrases with exceptional coordination to produce rapidly alternating duets
 that are highly consistent across renditions. These highly coordinated,
 consistent duets evolved independently in multiple wren species. Duet
 coordination and consistency are greatest in species with especially long
 breeding seasons, but neither duet coordination nor consistency are
 correlated with clutch size, conspecific abundance, or vegetation density.
 These results suggest that tightly coordinated duets play an important
 role in mediating breeding behaviour, possibly by signalling commitment or
 coalition of the pair to mates and other conspecifics.
description: The "Neotropical Wren selections compiled & renamed
 FINAL - ForDryad.csv" consists of start and end times for all male
 and female notes within duets for 23 Neotropical wren species. These were
 extracted from the bounding boxes surrounding each selected note in Raven
 Sound Analysis Software v1.5.  Start-end measurements were collected for a
 random sample of approximately 10 duets from 1-6 pairs of wrens per
 species. These data can be processed to create coordination scores for
 each song in the dataset using code provided in the supplementary data of
 the associated manuscript. The "Neotropical
 Wren_AllSong&NatHistData_ForDryad.csv" was created from the
 averaged values of the coordination scores for each species and combined
 with natural history data for each each species, including breeding season
 length and clutch size (taken from Handbook of the Birds of the World), an
 estimate of species prevalence (estimated from eBird data), and vegetation
 density (calculated from Enhanced Vegetation Index (EVI) data extracted
 from NASA MODIS satellite (product: MOD12A3 v6)).
DOI: 10.5061/dryad.f1vhhmgvk
title: Supplemental material for: NINDS consensus diagnostic criteria for Traumatic Encephalopathy Syndrome

description: Objective: To develop evidence-informed, expert consensus research
 diagnostic criteria for Traumatic Encephalopathy Syndrome (TES), the
 clinical disorder associated with neuropathologically diagnosed Chronic
 Traumatic Encephalopathy (CTE). Methods: A panel of 20 expert
 clinician-scientists in neurology, neuropsychology, psychiatry,
 neurosurgery, and physical medicine and rehabilitation, from 11 academic
 institutions, participated in a modified Delphi procedure to achieve
 consensus, initiated at the First NINDS Consensus Workshop to Define the
 Diagnostic Criteria for TES, April, 2019. Prior to consensus, panelists
 reviewed evidence from all published cases of CTE with neuropathological
 confirmation and they examined the predictive validity data on clinical
 features in relation to CTE pathology from a large clinicopathological
 study (n = 298). Results: Consensus was achieved in 4 rounds of the Delphi
 procedure. Diagnosis of TES requires: 1) substantial exposure to
 repetitive head impacts (RHI) from contact sports, military service, or
 other causes; 2) core clinical features of cognitive impairment (in
 episodic memory and/or executive functioning) and/or neurobehavioral
 dysregulation; 3) a progressive course; and 4) that the clinical features
 are not fully accounted for by any other neurologic, psychiatric, or
 medical conditions. For those meeting criteria for TES, functional
 dependence is graded on 5 levels ranging from independent to severe
 dementia.  A provisional level of certainty for CTE pathology is
 determined based on specific RHI exposure thresholds, core clinical
 features, functional status, and additional supportive features, including
 delayed onset, psychiatric dysfunction, and motor signs. Conclusions: New
 consensus diagnostic criteria for TES were developed with a primary goal
 of facilitating future CTE research. These criteria will be revised as
 updated clinical and pathological information and in vivo biomarkers
 become available.
DOI: 10.5061/dryad.kkwh70s3k
title: Caught in a bottleneck: Habitat loss for woolly mammoths in central North America and the ice-free corridor during the last deglaciation

description: The dataset is to describe the habitat structure and bioenergetic
 characteristics of woolly mammoths (Mammuthus primigenius) in North
 America during the last deglaciation between 15 and 10 ka. The habitat
 structure includes fractional woody cover (FWC) and net primary
 productivity (NPP) for 20 plant functional types (PFTs). NPP
 is based on the dynamic vegetation model LPJ-GUESS
 (LPJG). FWC is based on LPJ-GUESS and fossil pollen records in
 the Neotoma Paleoecology Database. The bioenergetic characteristics
 of woolly mammoths are the results of Niche Mapper, including
 metabolic rate, forage consumption, freshwater consumption, and other
 bioenergetic traits of individual woolly mammoths. These
 data were conducted at a temporal resolution of 100-year means of
 climate simulations every 1,000 years, from 15 to 10 ka. Simulations were
 run for all of North America except Alaska (10° – 80°N, 140° – 45°W) at
 a spatial resolution of 0.5°x0.5° grid latitude and longitude.
description: Please see the Supporting Information of the related
 article.
description: Please see "ReadMe.txt" in the dataset.
DOI: 10.5061/dryad.z08kprrb6
title: Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees

description: Summarizing individual gene trees to species phylogenies using two-step
 coalescent methods is now a standard strategy in the field of
 phylogenomics. However, practical implementations of summary methods
 suffer from gene tree estimation error, which is caused by various
 biological and analytical factors. Greatly understudied is the choice of
 gene tree inference method and downstream effects on species tree
 estimation for empirical data sets. To better understand the impact of
 this method choice on gene and species tree accuracy, we compare gene
 trees estimated through four widely used programs under different
 model-selection criteria: PhyloBayes, MrBayes, IQ-Tree and RAxML. We study
 their performance in the phylogenomic framework of &gt; 800
 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our
 taxon sampling focuses on the genus Pseudapis, a distinct lineage with
 diverse morphological features, but contentious morphology-based taxonomic
 classifications and no molecular phylogenetic guidance. We approximate
 topological accuracy of gene trees by assessing their ability to recover
 two uncontroversial, monophyletic groups, and compare branch lengths of
 individual trees using the stemminess metric (the relative length of
 internal branches). We further examine different strategies of removing
 uninformative loci and the collapsing of weakly supported nodes into
 polytomies. We then summarize gene trees with ASTRAL and compare resulting
 species phylogenies, including comparisons to concatenation-based
 estimates. Gene trees obtained with the reversible jump model search in
 MrBayes were most concordant on average and all Bayesian methods yielded
 gene trees with better stemminess values. The only gene tree estimation
 approach whose ASTRAL summary trees consistently produced the most likely
 correct topology, however, was IQ-Tree with automated model designation
 (MFP). We discuss these findings and provide practical advice on gene tree
 estimation for summary methods. Lastly, we establish the first
 phylogeny-informed classification for Pseudapis s. l. and map the
 distribution of distinct morphological features of the group.
description: This Dryad Digital Repository contains data associated with the
 research paper "Gene tree shape and estimation error with
 ultraconserved elements: An empirical study
 on <em>Pseudapis</em> bees". Specifically, it contains
 the Trinity-assemblies of the de-novo sequenced UCEs, the extracted UCE
 sequences from the included genomes, and the concatenated matrices of the
 80% completeness data set. We further provide all species trees and all
 853 gene trees inferred with RAxML, IQ-Tree 2 (MFP), IQ-Tree 2 (GTR+G),
 MrBayes (rj), MrBayes (GTR+G) and PhyloBayes/EZ-PB as outlined in the
 original paper.
DOI: 10.5061/dryad.gb5mkkwnt
title: Multicellularity and fossilization of soft bodies

description: The reliability of evolutionary reconstructions based on the fossil record
 critically depends on our knowledge of the factors affecting the
 fossilization of soft-bodied organisms. Despite considerable research
 effort, these factors are still poorly understood. In order to elucidate
 the main prerequisites for the preservation of soft-bodied organisms, we
 conducted long-term (1-5 years) taphonomic experiments with the model
 crustacean Artemia salina buried in five different sediments. The
 subsequent analysis of the carcasses and sediments revealed that, in our
 experimental settings, better preservation was associated with the fast
 deposition of aluminium and silicon on organic tissues. Other elements
 such as calcium, magnesium and iron, which can also accumulate quickly on
 the carcasses, appear to be much less efficient in preventing decay. Next,
 we asked if the carcasses of uni- and multicellular organisms differ in
 their ability to accumulate aluminium ions on their surface. The
 experiments with the flagellate Euglena gracilis and the sponge Spongilla
 lacustris showed that aluminium ions are more readily deposited onto a
 multicellular body. This was further confirmed by the experiments with
 uni- and multicellular stages of the social amoeba Dictyostelium
 discoideum. The results lead us to speculate that the evolution of cell
 adhesion molecules, which provide efficient cell-cell and cell-substrate
 binding, probably can explain the rich fossil record of soft-bodied
 animals, the comparatively poor fossil record of non-skeletal unicellular
 eukaryotes, and the explosive emergence of the Cambrian diversity of soft
 bodied fossils.
description: This dataset includes primary data from taphonomic experiments
 wherein Artemia salina nauplii were buried in different sediments
 (proportions of preservational groups in different sediments, elemental
 composition of the exhumed carcasses and sediment particles, pH in the
 different layers of experimental sediments).
DOI: 10.5061/dryad.mcvdncjzx
title: Association of gray matter atrophy patterns with clinical phenotype and progression in multiple sclerosis

description: Objectives. Grey matter (GM) involvement is clinically relevant in
 multiple sclerosis (MS). Using source-based morphometry (SBM), we
 characterized GM atrophy and its 1-year evolution across different MS
 phenotypes. Methods. Clinical and MRI data were obtained at 8 European
 sites from 170 healthy controls (HCs) and 398 MS patients (34 clinically
 isolated syndromes [CIS], 226 relapsing-remitting [RR], 95 secondary
 progressive [SP] and 43 primary progressive [PP] MS). Fifty-seven HC and
 144 MS underwent 1-year follow-up. Baseline GM loss, atrophy progression
 and correlations with disability and 1-year clinical worsening were
 assessed. Results. SBM identified 26 cerebellar, subcortical, sensory,
 motor and cognitive GM components. GM atrophy was found in MS vs HC in
 almost all components (p=range&lt;0.001-0.04). Compared to HCs, CIS
 patients showed circumscribed subcortical, cerebellar, temporal and
 salience GM atrophy, while RRMS patients exhibited widespread GM atrophy.
 Cerebellar, subcortical, sensorimotor, salience and fronto-parietal GM
 atrophy was found in PPMS patients vs HCs, and SPMS vs RRMS. At 1-year, 21
 (15%) patients had clinically worsened. GM atrophy progressed in MS in
 subcortical, cerebellar, sensorimotor, and fronto-temporo-parietal
 components. Baseline higher disability was associated (R2=0.65) with
 baseline lower normalized brain volume (beta=-0.13, p=0.001), greater
 sensorimotor GM atrophy (beta=-0.12, p=0.002) and longer disease duration
 (beta=0.09, p=0.04). Baseline normalized GM volume (odds ratio=0.98,
 p=0.008) and cerebellar GM atrophy (odds ratio=0.40, p=0.01) independently
 predicted clinical worsening (area-under-the-curve=0.83). Conclusion. GM
 atrophy differed across disease phenotypes and progressed at 1-year in MS.
 In addition to global atrophy measures, sensorimotor and cerebellar GM
 atrophy explained baseline disability and clinical worsening.
DOI: 10.5061/dryad.j9kd51cb1
title: Gene modules lists of soybean in response to Fusarium virguliforme colonization

description: The broad host range of Fusarium virguliforme represents
 a unique comparative system to identify and define differentially-induced
 responses between an asymptomatic monocot host, maize (Zea mays), and a
 symptomatic eudicot host, soybean (Glycine max). Using a temporal,
 comparative transcriptome-based approach, we observed that early gene
 expression profiles of root tissue from infected maize suggest that
 pathogen tolerance coincides with the rapid induction of senescence
 dampening transcriptional regulators,
 including ANACs and Ethylene Responsive
 Factors. In contrast, the expression of senescence-associated processes in
 soybean was coincident with the appearance of disease symptom development,
 suggesting pathogen-induced senescence as a key pathway driving pathogen
 susceptibility in soybean. Based on the analyses described herein, we
 posit that root senescence is a primary contributing factor underlying
 colonization and disease progression in symptomatic versus asymptomatic
 host–fungal interactions. This process also supports the lifestyle and
 virulence of F. virguliforme during biotrophy to
 necrotrophy transitions. Further support for this hypothesis lies in
 comprehensive co-expression and comparative transcriptome analyses, and in
 total, supports the emerging concept of necrotrophy-activated senescence.
 We propose that F. virguliforme conditions an environment within
 symptomatic hosts that favors susceptibility through transcriptomic
 reprogramming, and as described herein, the induction of pathways
 associated with senescence during the necrotrophic stage of fungal
 development. This study represents an example of integrating disciplines –
 from genes to cropping systems – and the complementarity of academic
 expertise.
description: Each column is the module name and the genes are included in the
 module.
DOI: 10.5061/dryad.4f4qrfj9q
title: Slab dehydration in Sumatra: Implications for fast and slow earthquakes and arc magmatism

description: The catastrophic 2004 Sumatra-Andaman Mw9.1 earthquake associated with
 destructive tsunamis has characterized Sumatra as one of the most
 dangerous convergence zones. Nevertheless, the effects of the
 thermohydrous state on the strongly coupled megathrust of the incoming
 plate remain enigmatic. By using a 3-D thermomechanical model to compute
 the temperature variation and the complicated phase transition process of
 the water-bearing descending plate which generates unstable thrust slips,
 we find that Sumatran earthquakes at varying depths are likely under the
 control of the inter- or intraplate hydrothermal regime, which occurs in
 or close to the petrological metamorphism transition area. The slab
 dehydration of the water-rich mid-ocean-ridge basalts (MORB) and the
 ultramafic rocks in the oceanic lithosphere releases a large amount of
 fluid to the continental wedge and further facilitates arc magmatism. The
 fluids are prone to upwelling following the subduction channel along the
 plate interface and thus contribute to the clustering of earthquakes updip
 of the dehydration front beneath offshore Sumatra. Brittle failure and
 dehydration embrittlement at depth, along with the temperature differences
 caused by variant slab geometry, are conjectured to greatly influence the
 occurrence of fast and slow earthquakes in Sumatra.
DOI: 10.15468/dl.tas457
title: Occurrence Download

description: A dataset containing 585 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Dillenia indica"
 ]
}

 The dataset includes 585 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002664-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r435mx
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Dioscorea wallichii"
 ]
}

 The dataset includes 30 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002665-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0cfxpnw0q
title: Georeferenced semi-quantitative data of the jellyfish Rhizostoma pulmo (Cnidaria: Scyphozoa) from 1810 to 2019 in the Mediterranean and Black Seas

description: This dataset is a gathering of historical and contemporaneous records of
 the medusae stage of Rhizostoma pulmo on its distributional range. The
 information was compilated to analyze biogeographical patterns and
 temporal changes of the species population dynamics. This compilation
 includes data available in websites and peer-review papers. All references
 are indicated. Data are individualized by month and year from 1810 to
 2019, totalizing 7373 records. Longitude and latitude data are reported,
 as well as the country and the ecoregion (based on Spalding et al. (2007)
 classification). When the location was detailed (e.g. Bay, Port, Estuary),
 it is also indicated. The presence/absence category is designated, as well
 as the abundance or number of individuals reported in the literature.
 Other extra information (as collector name, sampling method or
 environmental parameters), when reported, are also provided.
description: Two different types of data sources were used: scientific
 literature from peer-review papers and citizen science data. Scientific
 papers were assembled through an exhaustive search on Google Scholar and
 Web of Knowledge. The terms used were: ‘<i>Rhizostoma’</i>,
 ‘<i>Rhizostoma pulmo</i>’, ‘Mediterranean jellyfish’,
 ‘Mediterranean medusae’, ‘Black Sea jellyfish’, ‘Black Sea medusae’, and
 the name of each ecoregion followed by ‘jellyfish’, ‘medusae’ or
 ‘<i>Rhizostoma pulmo</i>’. Only papers where the year of
 record was indicated were included in this study. The compiled data were
 qualitative (presence/absence), quantitative (individuals
 100m<sup>-3</sup>) and semi-quantitative (categories of number
 of individuals).
description: A list of the data sources is found in Appendix 1 (Tables S1, S2)
 of the article Leoni, V.; Bonnet, D.; Ramírez Romero, E.; Molinero, J.C.
 Biogeography and phenology of the jellyfish <em>Rhizostoma pulmo
 </em>(Cnidaria: Scyphozoa) in southern European Seas.
DOI: 10.5061/dryad.zpc866t7b
title: Data from: Silurian (late Llandovery–Wenlock) conodont fauna and biostratigraphy from the Yanbian area of Sichuan province, south-west china

description: Late Llandovery–Wenlock conodonts are still inadequately documented in
 China with knowledge chiefly from the Baizitian section of Yanbian County,
 Sichuan Province, SW China. A collection of over 32000 conodont elements
 was recovered from 38 samples from the Xiabaizitian and Shangbaizitian
 formations at this classical locality. The conodont fauna is dominated by
 cosmopolitan species and can be assigned to 50 species representing 17
 genera. Among these, one new species, Apsidognathus yanbianensis sp. nov.
 is proposed herein. Six conodont zones are recognized in this section,
 including the Pterospathodus eopennatus Zone, Pt. amorphognathoides.
 angulatus Taxon-range Zone of the Pt. amorphognathoides amorphognathoides
 Superzone, Kockelella ranuliformis Zone, Kockelella walliseri Taxon-range
 Zone, and Kockelella patula Taxon-range Zone, in ascending order. These
 zones can be correlated with other conodont zones around the world based
 on the occurrences of the stratigraphically diagnostic species. Moreover,
 the stratigraphical ranges of Pterospathodus enable more understanding
 about the correlation of the Telychian guide taxa. At Baizitian, the
 conodont diversity changes and faunal turnover across the Silurian
 Ireviken Bioevent are here documented for the first time from the South
 China palaeoplate.
description: List of conodonts recorded from the Baizitian section, Sichuan,
 SW China