cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.208b1
title: Data from: Bias in phylogenetic measurements of extinction and a case study of end-Permian tetrapods

description: Extinction risk in the modern world and extinction in the geological past
 are often linked to aspects of life history or other facets of biology
 that are phylogenetically conserved within clades. These links can result
 in phylogenetic clustering of extinction, a measurement comparable across
 different clades and time periods that can be made in the absence of
 detailed trait data. This phylogenetic approach is particularly suitable
 for vertebrate taxa, which often have fragmentary fossil records, but
 robust, cladistically-inferred trees. Here we use simulations to
 investigate the adequacy of measures of phylogenetic clustering of
 extinction when applied to phylogenies of fossil taxa while assuming a
 Brownian motion model of trait evolution. We characterize expected biases
 under a variety of evolutionary and analytical scenarios. Recovery of
 accurate estimates of extinction clustering depends heavily on the
 sampling rate, and results can be highly variable across topologies.
 Clustering is often underestimated at low sampling rates, whereas at high
 sampling rates it is always overestimated. Sampling rate dictates which
 cladogram timescaling method will produce the most accurate results, as
 well as how much of a bias ancestor–descendant pairs introduce. We
 illustrate this approach by applying two phylogenetic metrics of
 extinction clustering (Fritz and Purvis's D and Moran's I) to
 three tetrapod clades across an interval including the Permo-Triassic mass
 extinction event. These groups consistently show phylogenetic clustering
 of extinction, unrelated to change in other quantitative metrics such as
 taxonomic diversity or extinction intensity.
description: ResultsAn R file containing all the results for the analysis of tetrapod data, including different timescaling methods and different length timeslices. Corresponds to plots shown in main manuscript and supplementary figures.Tree SetsR file containing sets of cladograms timescaled with different methods that were used in the analyses of tetrapods.Supplementary dataAge data used to timescale cladograms, sources for cladogram topologies and dates of timeslices.Supplementary Figure 1Example timescaled topologies for each of the three focal clades, sauropsids, synapsids and temnospondyls.Figure S1.pdfSupplementary Figure 2Measurement of D through time on three sets of 100 phylogenies timescaled using three different timescaling algorithms.Figure S2.pdfSupplementary Figure 3Measurement of D and Moran's I through time on a set of 100 phylogenies timescaled using the Hedman method.Figure S3.pdfSupplementary Figure 4Measurement of D through time on a set of 100 phylogenies timescaled using the Hedman method and divided into different time bin lengths.Figure S4.pdfScript to measure DR code that takes as input a set of timescaled phylogenies with root ages and a matrix of time bins for analysis. Calculates D and associated p-values for each tree in each time bin.Simulation scriptsR code used to simulate phylogeny and measure D.
DOI: 10.5061/dryad.h5b45
title: Data from: Adding fossil occupancy trajectories to the assessment of modern extinction risk

description: Besides helping to identify species traits that are commonly linked to
 extinction risk, the fossil record may also be directly relevant for
 assessing the extinction risk of extant species. Standing geographical
 distribution or occupancy is a strong predictor of both recent and past
 extinction risk, but the role of changes in occupancy is less widely
 assessed. Here we demonstrate, based on the Cenozoic fossil record of
 marine species, that both occupancy and its temporal trajectory are
 significant determinants of risk. Based on extinct species we develop a
 model on the additive and interacting effects of occupancy and its
 temporal changes on extinction risk. We use this model to predict
 extinction risk of extant species. The predictions suggest a moderate risk
 for marine species on average. However, some species seem to be on a
 long-term decline and potentially at a latent extinction risk, which is
 not considered in current risk assessments.
description: Cleaned taxonomic
 occurrences of Cenozoic marine invertebratesTable of occurrences of
 Cenozoic marine invertebrate species, which are found in at least two
 consecutive time intervals (bins).Raw_data.xlsx
DOI: 10.5061/dryad.8sj5g
title: Data from: From randomness to traplining: a framework for the study of routine movement behavior

description: Memory allows many animals to benefit from the spatial predictability of
 their environment by revisiting known profitable places. Travel route
 optimization or resource acquisition constraints usually lead to repeated
 sequences of visits, which may have major evolutionary and ecological
 implications. However, the study of this behavior has been impaired by a
 lack of concepts and methodologies. We here formally define routine
 movement behavior, provide an index that quantifies the degree of
 repetitiveness in movement sequences in terms of minimal conditional
 entropy, and design a flexible procedure that detects the specific
 subsequences that are repeated. We demonstrate our framework using
 computer simulations and real-world movement data of black-tailed deer
 (Odocoileus hemionus) introduced into a novel environment. The simulation
 example showed that our methods can suitably reveal the increase in the
 level of routine movement behavior during home range (HR) establishment.
 Black-tailed deer did not show such an increase, suggesting that HR
 establishment occurred very fast. In both examples, our procedure
 determining the subsequences that are repeated provides a precise
 visualization of routine movements. Our approach solves limitations in the
 study of routine movement behavior and thus opens promising perspectives
 for the study of the linkages between cognition, foraging strategies, and
 environments. Although we developed it to study routine movement behavior,
 it can be applied to any type of behavioral sequence and should thus be of
 interest to a broad range of behavioral ecologists.
description: deerGPS locations of four
 black-tailed deer tracked for approximately seven months. Four columns:
 id, date, x, ysimulLocations of six
 individuals simulated using the memory-based movement model described in
 details in Riotte-Lambert et al. (2015). The locations of resource patches
 is provided in "patches.csv". The simulation was run for 105,000
 time steps. Four columns: id, time, x, y.patchesTwo-column matrix giving the coordinates of 400 punctual resource patches. These constitute the environment used for the simulation provided in "simul.csv".
DOI: 10.34810/data2450
title: Partitura i enregistrament [score and recording] Rondó en La Major / A major, de Carles Baguer (1768-1808)

description: &lt;p&gt;[CAT] Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical que estan desenvolupant la UB i el CSIC, juntament amb el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grup per a l’Estudi del Patrimoni Musical (GEPAM), el Grup de Recerca Patrimoni Musical Històric de la Institució Milà i Fontanals d’Investigació en Humanitats del CSIC, l’Arquebisbat de Barcelona, la Catedral de Barcelona, l’Arxiu de l’Església de Santa Maria del Pi i l'Oratori de Sant Felip Neri de Barcelona, s'ha recuperat una peça musical de Carles Baguer (1768-1808) que es troba al manuscrit MS. 1378 del fons musical del CRAI Biblioteca de Fons Antic de la Universitat de Barcelona. Aquest dataset conté dos arxius:
&lt;p&gt;- Transcripció del Rondó en La Major de Carles Baguer del manuscrit Ms. 1378.
&lt;p&gt;- Enregistrament sonor de la peça interpretada per: Manuel Grande-Escosa, amb un piano A. Walter de 1803 (còpia moderna de Paul Poletti).
description: &lt;p&gt;[ENG]The Study and Recovery of Musical Heritage project being developed by the UB and the CSIC, together with the CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, ​​the Grupo de Investigación Patrimonio Musical Histórico de la Institución Milá y Fontanals de Investigación en Humanidades of the CSIC, the Archdiocese of Barcelona, ​​the Barcelona Cathedral, the Arxiu de l’Església de Santa Maria del Pi, and the Oratory of Sant Felip Neri in Barcelona, has recovered musical heritage: a musical piece by Carles Baguer (1768-1808) which is found in the manuscript Ms.1378 of the music collection of theCRAI Biblioteca de Fons Antic de la Universitat de Barcelona. This dataset contains two files:
&lt;p&gt;- Transcription of the Rondo in La Major by Carles Baguer from the manuscript Ms. 1378.
&lt;p&gt;- Sound recording of the piece performed by: Manuel Grande-Escosa, with a piano A. Walter from 1803 (modern copy by Paul Poletti).
DOI: 10.15468/dl.s3d9ss
title: Occurrence Download

description: A dataset containing 2277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Centralisation des observations floristiques dans le cadre du SINP - Observations floristiques - plateforme SINP régionale SILENE PACA, Centralisation des observations floristiques - Observations floristiques issues de la base de données du Conservatoire botanique national alpin, INPN - Données flore des CBN agrégées par la FCBN, 16 - Inventaire général de la flore et de la fonge - GENTIANA - Inventaire de la flore de l'Isère, FloraCAT: Banco de datos de los cormófitos de Cataluña, Observations faune et flore du Parc national des Écrins, Pl@ntNet automatically identified occurrences, Centralisation des observations floristiques - Observations floristiques floutées issues de la base de données flore du Conservatoire botanique national alpin, 16 - Inventaire général de la flore et de la fonge - CBNA - inventaire général de la flore et de la fonge réalisé sur le terrain)",
 "Geometry POLYGON((-1.15743 45.76707,-1.64074 45.31058,-2.21523 43.83789,-2.02464 43.22128,-1.15018 42.6383,0.48664 42.25713,3.04276 42.06654,3.80512 41.68536,4.84774 41.98806,6.98906 42.24591,7.83502 43.63812,7.64385 44.04685,7.12965 44.62038,7.12305 45.43782,7.00439 46.11683,6.79608 46.32979,6.48658 46.30349,6.258 46.20234,6.02536 46.08906,5.92017 46.18009,6.11842 46.30551,6.07796 46.34597,5.83447 46.23874,5.12696 45.76707,3.71193 45.72545,1.70037 45.35088,-1.15743 45.76707))",
 "OccurrenceStatus is Present",
 "TaxonKey is Bromopsis erecta",
 "Year 2016-2026"
 ]
}

 The dataset includes 2277 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001478-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpcwu2
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elatostema goudotianum"
 ]
}

 The dataset includes 155 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001480-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cv03k
title: Data from: The plumage and colouration of an enantiornithine bird from the Early Cretaceous of China

description: Brilliant colour displays and diverse feather morphologies that are often
 sexual ornaments are common throughout much of extant Avialae. Here we
 describe a new basal enantiornithine bird specimen recovered from the
 Early Cretaceous Jiufotang Formation of Liaoning Province in northeastern
 China. We present new information on the plumage of Bohaiornithidae as
 well as the first detailed colour reconstruction of an enantiornithine
 bird. The new specimen retains subadult skeletal characteristics,
 including periosteal pitting of the long bone epiphyses and unfused
 elements, while also preserving plumage evidence consistent with sexual
 maturity at the time of death. Exceptionally-preserved feathers cover the
 body, including elongate crown feathers, body contour feathers,
 asymmetrically-veined wing primaries, an alula and two elongate
 rachis-dominated rectrices that may have been sexual ornaments. The crown,
 neck, and body contour feathers retain elongate melanosome morphologies
 associated with weakly iridescent colouration in extant feathers. We
 provide additional evidence of preserved melanin using Raman spectroscopy;
 a rapid, non-destructive chemical technique. The new specimen provides
 data on skeletal ontogeny in the Bohaiornithidae as well as evidence for
 intraspecific communication functions of plumage.
description: Bohaiornithid_SOMBohaiornithid CTA video of the computed tomography (CT) scan of the new bohaiornithid specimen from the Early Cretaceous Jiufotang Formation, near Lamadong Village, Jianchang County, Liaoning Province, China.Bohaiornithid_CT.avi
DOI: 10.5061/dryad.5217f
title: Data from: Synthesis and characterization of azo-guanidine based alcoholic media naked eye DNA sensor

description: DNA sensing always has an open meadow of curiosity for biotechnologists
 and other researchers. Recently, in this field, we have introduced an
 emerging class of molecules containing azo and guanidine functionalities.
 In this study, we have synthesized three new compounds (UA1, UA6 and UA7)
 for potential application in DNA sensing in alcoholic medium. The
 synthesized materials were characterized by elemental analysis, FTIR,
 UV-visible, 1H NMR and 13C NMR spectroscopies. Their DNA sensing potential
 were investigated by UV-visible spectroscopy. The insight of interaction
 with DNA was further investigated by electrochemical (cyclic voltammetry)
 and hydrodynamic (viscosity) studies. The results showed that compounds
 have moderate DNA binding properties, with the binding constants range
 being 7.2 × 103, 2.4 × 103 and 0.2 × 103 M−1, for UA1, UA6 and UA7,
 respectively. Upon binding with DNA, there was a change in colour (a blue
 shift in the λmax value) which was observable with a naked eye. These
 results indicated the potential of synthesized compounds as DNA sensors
 with detection limit 1.8, 5.8 and 4.0 ng µl−1 for UA1, UA6 and UA7,
 respectively.
description: Ataf Ali - Excell
 DataIt contains all data
 files with description of figures in the file name.
DOI: 10.5061/dryad.g4760
title: Data from: Phylogenomic reconstruction of sportive lemurs (genus Lepilemur) recovered from mitogenomes with inferences for Madagascar biogeography

description: The family Lepilemuridae includes 26 species of sportive lemurs, most of
 which were recently described. The cryptic morphological differences
 confounded taxonomy until recent molecular studies; however, some species’
 boundaries remain uncertain. To better understand the genus Lepilemur, we
 analyzed 35 complete mitochondrial genomes representing all recognized 26
 sportive lemur taxa and estimated divergence dates. With our dataset we
 recovered 25 reciprocally monophyletic lineages, as well as an admixed
 clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using
 modern distribution data, an ancestral area reconstruction and an
 ecological vicariance analysis were performed to trace the history of
 diversification and to test biogeographic hypotheses. We estimated the
 initial split between the eastern and western Lepilemur clades to have
 occurred in the Miocene. Divergence of most species occurred from the
 Pliocene to the Pleistocene. The biogeographic patterns recovered in this
 study were better addressed with a combinatorial approach including
 climate, watersheds, and rivers. Generally, current climate and watershed
 hypotheses performed better for western and eastern clades, while
 speciation of northern clades was not adequately supported using the
 ecological factors incorporated in this study. Thus, multiple mechanisms
 likely contributed to the speciation and distribution patterns in
 Lepilemur.
description: lepitotalm23.phyThe phylip alignment file of complete mitochondrial genome sequences from 36 sportive lemur individuals with 15 outgroup taxa with total alignment of 14755lepitotalm23RAxML_bestTreeThe best tree generated from Lepitotal23.phy by RAxML.lepitotalm23BeastMitogenome BEAST xml file from this publicationlepitotalm23nhmpannotationtreefromBeastThe Bayesian tree with divergence time from lepitotalm23Beast.xml by BEAST packageLepitotalm23BestSchemefromPartitionFinderV1.10The best partition Scheme from PartitionFinderV1.10lepitotalm23MrsBayesThe alignment and setting for Mrbayes bayesian analysesLepitotalm23Mrbayes_consustreeThe consensus tree by Mrbayes
DOI: 10.25824/redu/bu3cyk
title: Conjunto de dados de atributos físico-químicos do solo sob diferentes sistemas de preparo e plantas de cobertura em cultivo de cana-de-açúcar

description: Este conjunto de dados contém os resultados de um experimento de campo conduzido ao longo de três ciclos produtivos de cana-de-açúcar (cana-planta e duas socas, safras 2015/16 a 2017/18) no município de Ibitinga, São Paulo, Brasil. O objetivo foi avaliar o impacto da interação entre sistemas de preparo do solo e espécies de plantas de cobertura na qualidade físico-química de um Argissolo Vermelho distrófico. O experimento foi delineado em blocos casualizados em esquema de faixas (fatorial 3x4), com três repetições. Os tratamentos consistiram na combinação de três sistemas de preparo: (1) Plantio Direto (sem revolvimento), (2) Cultivo Mínimo (subsolagem a 0,40 m) e (3) Preparo Profundo (subsolagem a 0,70 m); com quatro espécies de plantas de cobertura antecessoras ao plantio: (a) Amendoim forrageiro (Arachis hypogaea), (b) Milheto (Pennisetum americanum), (c) Crotalária (Crotalaria juncea) e (d) Sorgo forrageiro (Sorghum bicolor). O dataset inclui dados brutos e processados de atributos do solo, abrangendo: Atributos Físicos: Densidade do solo, macroporosidade, microporosidade, porosidade total, diâmetro médio ponderado de agregados (DMP) e resistência do solo à penetração (RP). Atributos Químicos: pH (CaCl₂), matéria orgânica, fósforo (P), potássio (K), cálcio (Ca), magnésio (Mg), acidez potencial (H+Al), soma de bases (SB), capacidade de troca catiônica (CTC) e saturação por bases (V%). Estoque de Carbono: Calculado para as diferentes camadas do solo. Estes dados subsidiaram a tese de doutorado "Cana-de-açúcar: preparo de solo e plantas de cobertura num Argissolo Vermelho", demonstrando como a interação entre o revolvimento do solo e as espécies de cobertura modula a qualidade edáfica em agroecossistemas tropicais.
DOI: 10.5061/dryad.tq0g0
title: Data from: Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation

description: The green anole (Anolis carolinensis) is a lizard widespread throughout
 the southeastern United States and is a model organism for the study of
 reproductive behavior, physiology, neural biology, and genomics. Previous
 phylogeographic studies of A. carolinensis using mitochondrial DNA and
 small numbers of nuclear loci identified conflicting and poorly supported
 relationships among geographically structured clades; these
 inconsistencies preclude confident use of A. carolinensis evolutionary
 history in association with morphological, physiological, or reproductive
 biology studies among sampling localities and necessitate increased effort
 to resolve evolutionary relationships among natural populations. Here, we
 used anchored hybrid enrichment of hundreds of genetic markers across the
 genome of A. carolinensis and identified five strongly supported
 phylogeographic groups. Using multiple analyses, we produced a fully
 resolved species tree, investigated relative support for each lineage
 across all gene trees, and identified mito-nuclear discordance when
 comparing our results to previous studies. We found fixed differences in
 only one clade—southern Florida restricted to the Everglades region—while
 most polymorphisms were shared between lineages. The southern Florida
 group likely diverged from other populations during the Pliocene, with all
 other diversification during the Pleistocene. Multiple lines of support,
 including phylogenetic relationships, a latitudinal gradient in genetic
 diversity, and relatively more stable long-term population sizes in
 southern phylogeographic groups, indicate that diversification in A.
 carolinensis occurred northward from southern Florida.
description: anolis target capture
 phylogeography dryadDirectory 1: Sequence
 alignments; Directory 2: Species trees, multilocus bootstraps, gene tree
 bootstraps; Directory 3: concatenated RAxML analysis output; Directory 4:
 Treemix output and bootstraps; Directory 5: SVDquartets input and output
 files; Directory 6: Genealogical sorting index output; Directory 7:
 extended Bayesian skyline plots input (xml) and output (txt) files;
 Directory 8: GPhoCS input, control, output, and log
 filesdryad.zip
DOI: 10.5061/dryad.j0j5k
title: Data from: Genomic imprinting, disrupted placental expression, and speciation

description: The importance of regulatory incompatibilities to the early stages of
 speciation remains unclear. Hybrid mammals often show extreme
 parent-of-origin growth effects that are thought to be a consequence of
 disrupted genetic imprinting (parent-specific epigenetic gene silencing)
 during early development. Here we test the long-standing hypothesis that
 abnormal hybrid growth reflects disrupted gene expression due to loss of
 imprinting (LOI) in hybrid placentas, resulting in dosage imbalances
 between paternal growth factors and maternal growth repressors. We
 analyzed placental gene expression in reciprocal dwarf hamster hybrids
 that show extreme parent-of-origin growth effects relative to their
 parental species. In massively enlarged hybrid placentas, we observed both
 extensive transgressive expression of growth-related genes and bi-allelic
 expression of many genes that were paternally silenced in normal sized
 hybrids. However, the apparent widespread disruption of paternal silencing
 was coupled with reduced gene expression levels overall. These patterns
 are contrary to the predictions of the LOI model and indicate that hybrid
 misexpression of dosage sensitive genes is caused by other regulatory
 mechanisms in this system. Collectively, our results support a central
 role for disrupted gene expression and imprinting in the evolution of
 mammalian hybrid inviability, but call into question the generality of the
 widely invoked LOI model.
description: PseudotranscriptomesThis archive contains the pseudotranscriptomes and associated files as well as a brief README document describing what each file is, how it was generated, and what it was used for.Dryad_upload.zip