The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota).Syst Biol. 2008 Feb; 57(1):141-56.SB
Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions. This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apex of the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex has been highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using Bayesian Markov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrial rDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method for assessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather than on likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood on a posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly different depending on the method used; different methods often assign high confidence to different states at a given node. The two fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similar likelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting an improved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in the Lecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is 12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apex types. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny corresponds well with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae, Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.