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Citation for Study 292

Citation title: "Integration of morphological and molecular data sets in estimating fungal phylogenies.".

This study was previously identified under the legacy study ID S3x31x98c12c48c42 (Status: Published).

Citation

Lutzoni F., & Vilgalys R. 1995. Integration of morphological and molecular data sets in estimating fungal phylogenies. Canadian Journal of Botany, 73: S649-S659.

Authors

• Lutzoni F.
• Vilgalys R.

Abstract

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history.

Keywords

data sets heterogeneity; homogeneity test; lichen phylogeny; Omphalina; ribosomal DNA

External links

• DOI: 10.1139/b95-307

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S292
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref16498,
  	 author = {Francois M.  Lutzoni and Rytas  Vilgalys},
  	 title = {Integration of morphological and molecular data sets in estimating fungal phylogenies.},
  	 year = {1995},
  	 keywords = {data sets heterogeneity; homogeneity test; lichen phylogeny; Omphalina; ribosomal DNA},
  	 doi = {10.1139/b95-307},
  	 url = {},
  	 pmid = {},
  	 journal = {Canadian Journal of Botany},
  	 volume = {73},
  	 number = {},
  	 pages = {S649--S659},
  	 abstract = {To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical.  Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule.  Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies.  In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined.  One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 16498
  AU  - Lutzoni,Francois M. 
  AU  - Vilgalys,Rytas 
  T1  - Integration of morphological and molecular data sets in estimating fungal phylogenies.
  PY  - 1995
  KW  - data sets heterogeneity; homogeneity test; lichen phylogeny; Omphalina; ribosomal DNA
  UR  - http://dx.doi.org/10.1139/b95-307
  N2  - To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical.  Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule.  Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies.  In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined.  One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history.
  L3  - 10.1139/b95-307
  JF  - Canadian Journal of Botany
  VL  - 73
  IS  - 
  ER  -