Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

• Published in: PLoS biology Vol. 9; no. 3; p. e1000602
• Main Authors: Philippe, Hervé, Brinkmann, Henner, Lavrov, Dennis V., Littlewood, D. Timothy J., Manuel, Michael, Wörheide, Gert, Baurain, Denis
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.03.2011; Public Library of Science (PLoS)
• Subjects: Amino acids; Animals; Base Sequence; Biochemistry, biophysics & molecular biology; Biochemistry, Molecular Biology; Biochimie, biophysique & biologie moléculaire; Biological Evolution; Computational Biology/Comparative Sequence Analysis; Databases, Factual; DNA sequencing; Evolution; Evolutionary Biology/Bioinformatics; Evolutionary Biology/Genomics; Genetic engineering; Genetics & genetic processes; Genetics and Genomics/Bioinformatics; Genomes; Genomics - methods; Génétique & processus génétiques; Life Sciences; Molecular Sequence Data; Nucleotide sequencing; Phylogenetics; Phylogeny; Sciences du vivant; Sequence Alignment; Taxonomy; Technological change; Trees; Zoologie; Zoology; United States; Biological Evolution; Sequence Alignment; Animals; Base Sequence; Genomics; Molecular Sequence Data; Phylogeny; Databases, Factual
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.1000602

According to the phylogenies of Schierwater et al. [...]the existence of horizontal transmission (e.g., hybridization of closely related taxa, organelle acquisition through endosymbiosis and horizontal gene transfer) makes phylogenetic trees only pragmatic approximations, which will probably be replaced by phylogenetic networks in the long term (particularly for unicellular organisms). Model of sequence evolution: A statistical description of the process of substitution in nucleotide or amino acid sequences.\n Consequently, we stress the necessity of reducing its impact. Since taxon and gene sampling is being rapidly improved by the relentless progress in sequencing technology (even if obtaining well preserved and correctly identified specimens remains the limiting factor for several key taxa), full achievement of the ultimate goal of phylogenomics--i.e., accurate resolution of the Tree of Life--will primarily hinge on better procedures for the selection of orthologous and least saturated genes as well as on improved models of sequence evolution.