84544 - Missing data and influential sites.pdf (508.1 kB)
Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice
journal contribution
posted on 2023-05-17, 17:39 authored by Grievink, LS, Penny, D, Barbara HollandBarbara HollandPhylogenetic 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.
Funding
Australian Research Council
History
Publication title
Genome Biology and EvolutionVolume
5Issue
4Pagination
681-687ISSN
1759-6653Department/School
School of Natural SciencesPublisher
Oxford University PressPlace of publication
United KingdomRights statement
Licensed under Creative Commons Attribution-Non-Commercial 3.0 Unported (CC BY NC 3.0) http://creativecommons.org/licenses/by-nc/3.0/Repository Status
- Open