Article (Scientific journals)
Pitfalls in supermatrix phylogenomics
Philippe, Hervé; Vienne, Damien M. De; Ranwez, Vincent et al.
2017In European Journal of Taxonomy, 283, p. 1-25
Peer Reviewed verified by ORBi
 

Files


Full Text
Philippe_et_al_2017_EJT_postprint_editor.pdf
Publisher postprint (1.83 MB)
Download

All documents in ORBi are protected by a user license.

Send to



Details



Keywords :
supermatrix; systematic error; data quality; incongruence
Abstract :
[en] In the mid-2000s, molecular phylogenetics turned into phylogenomics, a development that improved the resolution of phylogenetic trees through a dramatic reduction in stochastic error. While some then predicted “the end of incongruence”, it soon appeared that analysing large amounts of sequence data without an adequate model of sequence evolution amplifies systematic error and leads to phylogenetic artefacts. With the increasing flood of (sometimes low-quality) genomic data resulting from the rise of high-throughput sequencing, a new type of error has emerged. Termed here “data errors”, it lumps together several kinds of issues affecting the construction of phylogenomic supermatrices (e.g., sequencing and annotation errors, contaminant sequences). While easy to deal with at a single-gene scale, such errors become very difficult to avoid at the genomic scale, both because hand curating thousands of sequences is prohibitively time-consuming and because the suitable automated bioinformatics tools are still in their infancy. In this paper, we first review the pitfalls affecting the construction of supermatrices and the strategies to limit their adverse effects on phylogenomic inference. Then, after discussing the relative non-issue of missing data in supermatrices, we briefly present the approaches commonly used to reduce systematic error.
Disciplines :
Biochemistry, biophysics & molecular biology
Genetics & genetic processes
Author, co-author :
Philippe, Hervé
Vienne, Damien M. De
Ranwez, Vincent
Roure, Béatrice
Baurain, Denis  ;  Université de Liège > Département des sciences de la vie > Phylogénomique des eucaryotes
Delsuc, Frédéric
Language :
English
Title :
Pitfalls in supermatrix phylogenomics
Publication date :
2017
Journal title :
European Journal of Taxonomy
ISSN :
2118-9773
Publisher :
MNHN, Paris, France
Volume :
283
Pages :
1-25
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 25 February 2017

Statistics


Number of views
564 (17 by ULiège)
Number of downloads
696 (5 by ULiège)

Scopus citations®
 
93
Scopus citations®
without self-citations
84
OpenCitations
 
36

Bibliography


Similar publications



Contact ORBi