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Citation for Study 10823

Citation title: "The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods".

Study name: "The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods".

This study is part of submission 10813 (Status: Published).

Citation

Nagy L., Urban A., ?rstadius L., Larsson E., Papp T., & V?gv?lgyi C. 2010. The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods. Molecular Phylogenetics and Evolution, .

Authors

• Nagy L.
• Urban A.
• ?rstadius L.
• Larsson E.
• Papp T.
• V?gv?lgyi C.

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.

Keywords

Basidiomycetes, character evolution, fruiting body, multigene phylogeny, phylogenetic comparative method, reversible-jump MCMC

External links

• DOI: 10.1016/j.ympev.2010.08.022

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10823
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref19173,
  	 author = {L?szl? G.  Nagy and Alexander  Urban and Leif  ?rstadius and Ellen  Larsson and Tam?s  Papp and Csaba  V?gv?lgyi},
  	 title = {The evolution of autodigestion in the mushroom family Psathyrellaceae  (Agaricales) inferred from Maximum Likelihood and Bayesian methods},
  	 year = {2010},
  	 keywords = {Basidiomycetes, character evolution, fruiting body, multigene phylogeny, phylogenetic comparative method, reversible-jump MCMC},
  	 doi = {10.1016/j.ympev.2010.08.022},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 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.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19173
  AU  - Nagy,L?szl? G. 
  AU  - Urban,Alexander 
  AU  - ?rstadius,Leif 
  AU  - Larsson,Ellen 
  AU  - Papp,Tam?s 
  AU  - V?gv?lgyi,Csaba 
  T1  - The evolution of autodigestion in the mushroom family Psathyrellaceae  (Agaricales) inferred from Maximum Likelihood and Bayesian methods
  PY  - 2010
  KW  - Basidiomycetes
  KW  - character evolution
  KW  - fruiting body
  KW  - multigene phylogeny
  KW  - phylogenetic comparative method
  KW  - reversible-jump MCMC
  UR  - http://dx.doi.org/10.1016/j.ympev.2010.08.022
  N2  - 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.
  L3  - 10.1016/j.ympev.2010.08.022
  JF  - Molecular Phylogenetics and Evolution
  VL  - 
  IS  - 
  ER  -