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- Ekman, Stefan, 1965-, et al.
(författare)
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The Limitations of Ancestral State Reconstruction and the Evolution of the Ascus in the Lecanorales (Lichenized Ascomycota)
- 2008
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Ingår i: Systematic Biology. - London : Taylor & Francis. - 1063-5157 .- 1076-836X. ; 57:1, s. 141-156
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Forskningsöversikt (refereegranskat)abstract
- Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasinglyfrequent. They rely on constancy of character state change rates over trees, a correlation between neutral geneticchange 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 apexof the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex hasbeen highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using BayesianMarkov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrialrDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method forassessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather thanon likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood ona posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly differentdepending on the method used; different methods often assign high confidence to different states at a given node. Thetwo fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similarlikelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting animproved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in theLecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apextypes. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny correspondswell with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae,Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.
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