scholarly journals DateLife: Leveraging databases and analytical tools to reveal the dated Tree of Life

2019 ◽  
Author(s):  
Luna L. Sánchez-Reyes ◽  
Brian C. O’Meara
Keyword(s):  
Science Communication ◽  
Divergence Time ◽  
Analytical Techniques ◽  
Branch Length ◽  
Molecular Data ◽  
Academic Community ◽  
Tree Of Life ◽  
Published Data ◽  
Research Education ◽  
Patristic Distance

abstractThe combination of new analytical techniques, availability of more fossil and molecular data, and better practices in data sharing has resulted in a steady accumulation of chronograms in public and open databases such as TreeBASE, Dryad, and Open Tree of Life for a large quantity and diversity of organisms in the last few decades. However, getting a tree with branch lengths proportional to time remains difficult for many biologists and the non-academic community, despite its importance in many areas of research, education, and science communication. datelife is a service implemented via an R package and a web site (http://www.datelife.org/) for efficient reuse, summary and reanalysis of published data on lineage divergence times. The main workflow starts with at least two taxon names as input, either as tip labels on a tree, or as a simple comma separated character string. A name search is then performed across the chronogram database and positively identified source trees are pruned to maintain queried taxa only and stored as a named list of patristic distance matrices. Source chronogram data can be summarised using branch length summary statistics or variance minimizing approaches to generate a single summary chronogram. Source chronogram data can also be used as calibration points to date a tree containing some or all names from the initial query. If there is no information available for any queried taxa, data can be simulated. All source and summary chronograms can be saved in formats that permit easy reuse and reanalysis. Summary and newly generated trees are potentially useful to evaluate evolutionary hypothesis in different areas of research in biology. How well this trees work for this purpose still needs to be tested. datelife will be useful to increase awereness on the existing variation in expert time of divergence data, and might foster exploration of the effect of alternative divergence time hypothesis on the results of analyses, nurturing a culture of more cautious interpretation of evolutionary results.

scholarly journals Health science communication strategies used by researchers with the public in the digital and social media ecosystem: a systematic scoping review protocol

BMJ Open ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. e019833 ◽  
Author(s):  
Guillaume Fontaine ◽  
Andréane Lavallée ◽  
Marc-André Maheu-Cadotte ◽  
Julien Bouix-Picasso ◽  
Anne Bourbonnais
Keyword(s):  
Social Media ◽  
Scoping Review ◽  
Science Communication ◽  
Grey Literature ◽  
Communication Channels ◽  
Health Science ◽  
Published Data ◽  
The Public ◽  
Review Team ◽  
Media Ecosystem

IntroductionThe optimisation of health science communication (HSC) between researchers and the public is crucial. In the last decade, the rise of the digital and social media ecosystem allowed for the disintermediation of HSC. Disintermediation refers to the public’s direct access to information from researchers about health science-related topics through the digital and social media ecosystem, a process that would otherwise require a human mediator, such as a journalist. Therefore, the primary aim of this scoping review is to describe the nature and the extent of the literature regarding HSC strategies involving disintermediation used by researchers with the public in the digital and social media ecosystem. The secondary aim is to describe the HSC strategies used by researchers, and the communication channels associated with these strategies.Methods and analysisWe will conduct a scoping review based on the Joanna Briggs Institute’s methodology and perform a systematic search of six bibliographical databases (CINAHL, EMBASE, IBSS, PubMed, Sociological Abstracts and Web of Science), four trial registries and relevant sources of grey literature. Relevant journals and reference lists of included records will be hand-searched. Data will be managed using the EndNote software and the Rayyan web application. Two review team members will perform independently the screening process as well as the full-text assessment of included records. Descriptive data will be synthesised in a tabular format. Data regarding the nature and the extent of the literature, the HSC strategies and the associated communication channels will be presented narratively.Ethics and disseminationThis review does not require institutional review board approval as we will use only collected and published data. Results will allow the mapping of the literature about HSC between researchers and the public in the digital and social media ecosystem, and will be published in a peer-reviewed journal.

scholarly journals Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon Passos Cristiano ◽  
Natália Martins Travenzoli ◽  
Denilce Meneses Lopes ◽  
Danon Clemes Cardoso
Keyword(s):  
Evolutionary History ◽  
Chromosomal Rearrangements ◽  
Atlantic Coast ◽  
Ecological Impact ◽  
Divergence Time ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

scholarly journals Identifying diffusion patterns of research articles on Twitter: A case study of online engagement with open access articles

2018 ◽  
Vol 28 (1) ◽  
pp. 2-18 ◽  
Author(s):  
Juan Pablo Alperin ◽  
Charles J Gomez ◽  
Stefanie Haustein
Keyword(s):  
Open Access ◽  
Science Communication ◽  
Research Evaluation ◽  
Academic Community ◽  
Public Understanding ◽  
The Public ◽  
Online Engagement ◽  
Understanding Of Science ◽  
Limited Diffusion

The growing presence of research shared on social media, coupled with the increase in freely available research, invites us to ask whether scientific articles shared on platforms like Twitter diffuse beyond the academic community. We explore a new method for answering this question by identifying 11 articles from two open access biology journals that were shared on Twitter at least 50 times and by analyzing the follower network of users who tweeted each article. We find that diffusion patterns of scientific articles can take very different forms, even when the number of times they are tweeted is similar. Our small case study suggests that most articles are shared within single-connected communities with limited diffusion to the public. The proposed approach and indicators can serve those interested in the public understanding of science, science communication, or research evaluation to identify when research diffuses beyond insular communities.

scholarly journals A molecular map of lung neuroendocrine neoplasms

GigaScience ◽  
2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Aurélie A G Gabriel ◽  
Emilie Mathian ◽  
Lise Mangiante ◽  
Catherine Voegele ◽  
Vincent Cahais ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Large Cell ◽  
Molecular Data ◽  
Gene Expression Omnibus ◽  
Neuroendocrine Neoplasms ◽  
Published Data ◽  
Data Generation ◽  
Data Repositories ◽  
Molecular Map ◽  
Pulmonary Carcinoids

Abstract Background Lung neuroendocrine neoplasms (LNENs) are rare solid cancers, with most genomic studies including a limited number of samples. Recently, generating the first multi-omic dataset for atypical pulmonary carcinoids and the first methylation dataset for large-cell neuroendocrine carcinomas led us to the discovery of clinically relevant molecular groups, as well as a new entity of pulmonary carcinoids (supra-carcinoids). Results To promote the integration of LNENs molecular data, we provide here detailed information on data generation and quality control for whole-genome/exome sequencing, RNA sequencing, and EPIC 850K methylation arrays for a total of 84 patients with LNENs. We integrate the transcriptomic data with other previously published data and generate the first comprehensive molecular map of LNENs using the Uniform Manifold Approximation and Projection (UMAP) dimension reduction technique. We show that this map captures the main biological findings of previous studies and can be used as reference to integrate datasets for which RNA sequencing is available. The generated map can be interactively explored and interrogated on the UCSC TumorMap portal (https://tumormap.ucsc.edu/?p=RCG_lungNENomics/LNEN). The data, source code, and compute environments used to generate and evaluate the map as well as the raw data are available, respectively, in a Nextjournal interactive notebook (https://nextjournal.com/rarecancersgenomics/a-molecular-map-of-lung-neuroendocrine-neoplasms/) and at the EMBL-EBI European Genome-phenome Archive and Gene Expression Omnibus data repositories. Conclusions We provide data and all resources needed to integrate them with future LNENs transcriptomic studies, allowing meaningful conclusions to be drawn that will eventually lead to a better understanding of this rare understudied disease.

Global classification and evolution of brushlegged mayflies (Insecta: Ephemeroptera: Oligoneuriidae): phylogenetic analyses of morphological and molecular data and dated historical biogeography

2019 ◽  
Vol 187 (2) ◽  
pp. 378-412 ◽  
Author(s):  
Fabiana Criste Massariol ◽  
Daniela Maeda Takiya ◽  
Frederico Falcão Salles
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Single Species ◽  
Molecular Data ◽  
Neotropical Region ◽  
Fossil Species ◽  
Divergence Time Estimation ◽  
The Family ◽  
Family Based

AbstractOligoneuriidae is a Pantropical family of Ephemeroptera, with 68 species described in 12 genera. Three subfamilies are recognized: Chromarcyinae, with a single species from East Asia; Colocrurinae, with two fossil species from Brazil; and Oligoneuriinae, with the remaining species distributed in the Neotropical, Nearctic, Afrotropical and Palaearctic regions. Phylogenetic and biogeographical analyses were performed for the family based on 2762 characters [73 morphological and 2689 molecular (COI, 16S, 18S and 28S)]. Four major groups were recovered in all analyses (parsimony, maximum likelihood and Bayesian inference), and they were assigned to tribal level, namely Oligoneuriini, Homoeoneuriini trib. nov., Oligoneuriellini trib. nov. and Elassoneuriini trib. nov. In addition, Yawari and Madeconeuria were elevated to genus level. According to Statistical Dispersal-Vicariance (S-DIVA), Dispersal Extinction Cladogenesis (DEC) and divergence time estimation analyses, Oligoneuriidae originated ~150 Mya in the Gondwanan supercontinent, but was probably restricted to the currently delimited Neotropical region. The initial divergence of Oligoneuriidae involved a range expansion to Oriental and Afrotropical areas, sometime between 150 and 118 Mya. At ~118 Mya, the family started its diversification, reaching the Nearctic through dispersal from the Neotropical region and the Palaearctic and Madagascar from the Afrotropical region.

scholarly journals Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity

2019 ◽  
Vol 20 (11) ◽  
pp. 2782 ◽  
Author(s):  
Maria M. Romeiras ◽  
Ana Rita Pena ◽  
Tiago Menezes ◽  
Raquel Vasconcelos ◽  
Filipa Monteiro ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Meta Analysis ◽  
Divergence Time ◽  
Oceanic Islands ◽  
Published Data ◽  
Cabo Verde ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Macaronesian Islands ◽  
Phylogenetic Resolution

Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.

The Oxford Handbook of Interdisciplinarity

2017 ◽  
Keyword(s):  
Interdisciplinary Research ◽  
Academic Community ◽  
Education Administration ◽  
Public And Private ◽  
Policy Makers ◽  
Research Education ◽  
Multiple Networks ◽  
Current State ◽  
Societal Needs ◽  
International Advisory

The second edition of The Oxford Handbook of Interdisciplinarity constitutes an update and revision of a topic of growing academic and societal importance. Interdisciplinarity continues to be prominent both within and outside academia. Academics, policy makers, and members of public and private sectors seek approaches to help organize and integrate the vast amounts of knowledge being produced today, both within research and at all levels of education. This compendium is distinguished by its breadth of coverage, with chapters written by experts from multiple networks and organizations, on topics ranging across science and technology; social sciences, humanities, and arts; and professions. The volume is edited by respected interdisciplinary scholars and supported by an international advisory board to ensure the highest quality and breadth of coverage. The Oxford Handbook of Interdisciplinarity provides a synoptic overview of the current state of interdisciplinary research, education, administration and management, and problem solving—knowledge that spans the disciplines and interdisciplinary fields while also crossing the boundary between the academic community and society at large. Offering the most broad-based account of inter- and transdisciplinarity to date, its essays bring together many of the globe’s leading thinkers on interdisciplinary research, education, and institutional parameters as well as reflections on how knowledge can be better integrated with societal needs.

Cytogenetic and sequence comparison of adultPhyllodistomum(Digenea: Gorgoderidae) from the three-spined stickleback with larvae from two bivalves

Parasitology ◽  
2004 ◽  
Vol 129 (6) ◽  
pp. 771-778 ◽  
Author(s):  
R. PETKEVIČIŪTĖ ◽  
V. STUNŽĖNAS ◽  
G. STANEVIČIŪTĖ
Keyword(s):  
Developmental Stages ◽  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
Chromosome Morphology ◽  
Published Data ◽  
Larval Stages ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
High Level

Due to the low informative value of available morphological characters, cytogenetic and molecular methods, based on rDNA sequencing, were used to characterize adult and larval stages ofPhyllodistomumspp. Species studied have 18 chromosomes with comparable absolute and relative lengths. Conventional Giemsa staining and karyometric analysis revealed clear differences in chromosome morphology of larvalPhyllodistomumspp. infecting two bivalve host species,Sphaerium corneumandPisidium amnicum. However, karyotypes of adultP. foliumfrom three-spined sticklebacks and larval stages fromS. corneumappear almost identical both with respect to the relative lengths and centromeric indices of the corresponding chromosome pairs. The entire internal transcribed spacer (ITS) region (ITS-1, 5.8S and ITS-2) and the D1-D3 region of 28S gene were sequenced and compared. Again, sufficient differences were observed between larvalPhyllodistomumspp., while adultP. foliumand larvae fromS. corneumshowed a high level of similarity. So, both cytogenetic and molecular data support the suggestion that they represent developmental stages of the same species. The results were compared with published data obtained by cytogenetic and molecular studies on the otherPhyllodistomumspecies. Differences revealed in karyotype and rDNA sequences leads to the conclusion that the cercariaeum ofP. foliumsensu Sinitsin, 1905 could not be regarded as the larva of adultP. foliumfrom three-spined stickleback.

scholarly journals Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

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