Academic Journal

Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices.

Bibliographic Details
Title: Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices.
Authors: Laumer CE; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, EBML-EBI South Building, Hinxton CB10 1SD, UK.
Source: Integrative and comparative biology [Integr Comp Biol] 2018 Oct 01; Vol. 58 (4), pp. 623-639.
Publication Type: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't
Language: English
Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101152341 Publication Model: Print Cited Medium: Internet ISSN: 1557-7023 (Electronic) Linking ISSN: 15407063 NLM ISO Abbreviation: Integr Comp Biol Subsets: MEDLINE
Imprint Name(s): Publication: 2006- : Oxford : Oxford University Press
Original Publication: McLean, VA : Society for Integrative and Comparative Biology, c2002-
MeSH Terms: Genome* , Phylogeny*, Genomics/*methods , Invertebrates/*classification , Sequence Analysis, DNA/*methods, Animals ; Invertebrates/genetics
Abstract: Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.
Entry Date(s): Date Created: 20180709 Date Completed: 20190403 Latest Revision: 20200930
Update Code: 20221216
DOI: 10.1093/icb/icy075
PMID: 29982611
Database: MEDLINE