title: Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice.
abstract: Phylogenetic studies based on molecular sequence alignments are expected to become more 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 how to treat sites with missing data is of equal importance to decisions on taxon sampling and model choice, and we introduce a graphical method for illustrating this.
authors.affiliation: The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Israel. liat.sg@mail.huji.ac.il
authors.forename: Liat
authors.initials: L
authors.lastname: Shavit Grievink
authors.forename: David
authors.initials: D
authors.lastname: Penny
authors.forename: Barbara R
authors.initials: BR
authors.lastname: Holland
mesh_terms: D000460:Chlorophyta / Q000145:classification* / Q000235:genetics; D002965:Classification / Q000379:methods*; D030561:Databases, Nucleic Acid; D008957:Models, Genetic; D010802:Phylogeny; D057949:Streptophyta / Q000145:classification* / Q000235:genetics*