Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?. (19th February 2018)

• Record Type: Journal Article
• Authors: Richards, Emilie J; Brown, Jeremy M; Barley, Anthony J; Chong, Rebecca A; Thomson, Robert C
• Editors: Mueller, Rachel
• Is Part Of: Systematic biology. Volume 67:Number 5(2018:Oct.)
• Page Start: 847
• Page End: 860
• Publication Date: 2018-02-19
• Subjects: Gene tree discordance -- phylogenomics -- posterior prediction -- model adequacy; Biology -- Classification -- Periodicals; Biology -- Periodicals; Biologie -- Classification -- Périodiques; Biologie -- Périodiques; 578.012
• DOI: 10.1093/sysbio/syy013
• Languages: English
• ISSNs: 1063-5157

Abstract

Abstract: The use of large genomic data sets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological vs. methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.