title: Heterotachy and tree building: a case study with plastids and eubacteria.
abstract: The nature of heterotachy at the center of recent controversy over the relative performance of tree-building methods is different from the form of heterotachy that has been inferred in empirical studies. The latter have suggested that proportions of variable sites (p(var)) vary among orthologues and among paralogues. However, the strength of this inference, describing what may be one of the most important evolutionary properties of sequence data, has remained weak. Consequently, other models of sequence evolution have been proposed to explain some long-branch attraction (LBA) problems that could be attributed to differences in p(var). For an empirical case with plastid and eubacterial RNA polymerase sequences, we confirm using capture-recapture estimates and simulations that p(var) can differ among orthologues in anciently diverged evolutionary lineages. We find that parsimony and a least squares distance method that implements an overly simple model of sequence evolution are susceptible to LBA induced by this form of heterotachy. Although homogeneous maximum likelihood inference was found to be robust to model misspecification in our specific example, we caution against assuming that it will always be so.
authors.affiliation: The Allan Wilson Centre, Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand. p.j.lockhart@massey.ac.nz
authors.forename: Peter
authors.initials: P
authors.lastname: Lockhart
authors.forename: Phil
authors.initials: P
authors.lastname: Novis
authors.forename: Brook G
authors.initials: BG
authors.lastname: Milligan
authors.forename: Jamie
authors.initials: J
authors.lastname: Riden
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.forename: Tony
authors.initials: T
authors.lastname: Larkum
mesh_terms: D001419:Bacteria / Q000235:genetics; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D018087:Plastids / Q000235:genetics
chemical_list: D012321:DNA-Directed RNA Polymerases