Special Issue "Open Science Phyloinformatics: Resources, Methods, and Analyses"

A special issue of Life (ISSN 2075-1729).

Deadline for manuscript submissions: closed (28 February 2018)

Special Issue Editors

Guest Editor
Dr. William H Piel

Yale NUS College, Singapore City, Singapore
Website | E-Mail
Interests: arachnology; phyloinformatics; phylogeny
Guest Editor
Dr. Rutger Vos

Naturalis Biodiversity Center, Endless Forms group, Leiden, Netherlands
Website | E-Mail
Interests: comparative genomics; big data; computational biology; open source; emergent characters; phyloinformatics; comparative analysis

Special Issue Information

Dear Colleagues,

Phylogenetic research, today, is increasingly complex and data-intensive, placing increased demands on effective data sharing, analytical reproducibility, and knowledge synthesis. Large trees, vast datasets, and long multi-step analysis pipelines demand that biologists follow best practices in open access, sharing, and data integration. This Special Issue aims to assemble articles on phyloinformatic resources, tools, and research reports that exemplify best practices supporting open science reproducibility and/or demonstrate inference of broad-scale patterns through the integration of large datasets in phylogenetics.

Dr. William H Piel
Dr. Rutger Vos
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 650 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phyloinformatics
  • phylogenomics
  • phylogenetics
  • open science
  • data integration
  • Assembling the Tree of Life (AToL)

Published Papers (3 papers)

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Research

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Open AccessArticle Bioinformatic Workflows for Generating Complete Plastid Genome Sequences—An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade
Received: 1 May 2018 / Revised: 11 June 2018 / Accepted: 19 June 2018 / Published: 21 June 2018
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Abstract
The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck
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The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content. Full article
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)
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Open AccessArticle Integral Phylogenomic Approach over Ilex L. Species from Southern South America
Received: 9 October 2017 / Revised: 3 November 2017 / Accepted: 16 November 2017 / Published: 22 November 2017
Cited by 1 | PDF Full-text (5324 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature
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The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I. paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses. We selected seven introns and nine IGSs as variable non-coding markers that were used in phylogenomic analyses. Eight extra IGSs were proposed as candidate markers. Southern South American species formed one lineage, except for I. paraguariensis, I. dumosa and I. argentina, which occupied intermediate positions among sampled taxa; Euroasiatic species formed two lineages. Some concordant relationships were retrieved from nuclear sequence data. We also conducted integral analyses, involving a supernetwork of molecular data, and a simultaneous analysis of quantitative and qualitative morphological and phytochemical characters, together with molecular data. The total evidence tree was used to study the evolution of non-molecular data, evidencing fifteen non-ambiguous synapomorphic character states and consolidating the relationships among southern South American species. More South American representatives should be incorporated to elucidate their origin. Full article
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)
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Open AccessTechnical Note phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R
Received: 28 March 2018 / Revised: 26 May 2018 / Accepted: 1 June 2018 / Published: 5 June 2018
PDF Full-text (894 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data
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The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate and test our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: Palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis. Full article
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)
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