title: The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods.
abstract: Recently developed comparative phylogenetic methods offer a wide spectrum of applications in evolutionary biology, although it is generally accepted that their statistical properties are incompletely known. Here, we examine and compare the statistical power of the ML and Bayesian methods with regard to selection of best-fit models of fruiting-body evolution and hypothesis testing of ancestral states on a real-life data set of a physiological trait (autodigestion) in the family Psathyrellaceae. Our phylogenies are based on the first multigene data set generated for the family. Two different coding regimes (binary and multistate) and two data sets differing in taxon sampling density are examined. The Bayesian method outperformed Maximum Likelihood with regard to statistical power in all analyses. This is particularly evident if the signal in the data is weak, i.e. in cases when the ML approach does not provide support to choose among competing hypotheses. Results based on binary and multistate coding differed only modestly, although it was evident that multistate analyses were less conclusive in all cases. It seems that increased taxon sampling density has favourable effects on inference of ancestral states, while model parameters are influenced to a smaller extent. The model best fitting our data implies that the rate of losses of deliquescence equals zero, although model selection in ML does not provide proper support to reject three of the four candidate models. The results also support the hypothesis that non-deliquescence (lack of autodigestion) has been ancestral in Psathyrellaceae, and that deliquescent fruiting bodies represent the preferred state, having evolved independently several times during evolution.
authors.affiliation: Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary, H-6726 Szeged, Közép Fasor 52, Hungary. cortinarius2000@yahoo.co.uk
authors.forename: László G
authors.initials: LG
authors.lastname: Nagy
authors.forename: Alexander
authors.initials: A
authors.lastname: Urban
authors.forename: Leif
authors.initials: L
authors.lastname: Orstadius
authors.forename: Tamás
authors.initials: T
authors.lastname: Papp
authors.forename: Ellen
authors.initials: E
authors.lastname: Larsson
authors.forename: Csaba
authors.initials: C
authors.lastname: Vágvölgyi
mesh_terms: D000363:Agaricales / Q000235:genetics*; D001499:Bayes Theorem; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D048690:Fruiting Bodies, Fungal / Q000235:genetics*; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal