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Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice

Citation

Grievink, LS and Penny, D and Holland, BR, Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice, Genome Biology and Evolution, 5, (4) pp. 681-687. ISSN 1759-6653 (2013) [Refereed Article]


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Licensed under Creative Commons Attribution-Non-Commercial 3.0 Unported (CC BY NC 3.0) http://creativecommons.org/licenses/by-nc/3.0/

DOI: doi:10.1093/gbe/evt032

Abstract

Phylogenetic studies based onmolecular sequence alignments are expected to becomemore accurate as the number of sites in the alignments increases.With the advent of genomic-scale data, where alignments have very large numbers of sites, bootstrap values close to 100%and posterior probabilities close to 1 are the norm, suggesting that the number of sites is now seldom a limiting factor on phylogenetic accuracy. This provokes the question, should we be fussy about the sites we choose to include in a genomic-scale phylogenetic analysis? If some sites contain missing data, ambiguous character states, or gaps, then why not just throw them away before conducting the phylogenetic analysis? Indeed, this is exactly the approach taken in many phylogenetic studies. Here, we present an example where the decision on howto treat sites withmissing data is of equal importance to decisions on taxon sampling and model choice, and we introduce a graphical method for illustrating this.

Item Details

Item Type:Refereed Article
Keywords:maximum likelihood, site likelihood, Mesostigma, missing data, influential sites, taxon sampling
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Mathematical Sciences
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:84544
Year Published:2013
Funding Support:Australian Research Council (FT100100031)
Web of Science® Times Cited:7
Deposited By:Mathematics and Physics
Deposited On:2013-05-17
Last Modified:2017-10-30
Downloads:258 View Download Statistics

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