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MBE Advance Access published online on January 22, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh052
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted November 4, 2003
© 2004 Society for Molecular Biology and Evolution

Original Articles

Are Combined Analyses Better than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta)

Andrey A. Gontcharov 1*, Birger Marin 1, and Michael Melkonian 1

1 Botanisches Institut, Lehrstuhl I, Universität zu Köln, Gyrhofstr. 15, D-50931 Köln, Germany

* To whom correspondence should be addressed. E-mail: gontcharov{at}ibss.dvo.ru.


  Abstract

Although the combination of different genes in phylogenetic analyses is a promising approach, the methodology is not well established and analyses often suffer from inadequate, non-congruent taxon sampling, long-branch attraction or conflicting evolutionary models of the genes analyzed. Conflicts or congruence between multi-gene and single-gene phylogenies as well as the assumed superiority of the multi-gene approach are often difficult to assess solely because of incongruent taxon sampling. In the present study a data set of 43 nuclear-encoded SSU rDNA and plastid-encoded rbcL gene sequences was generated from the same strains of conjugating green algae (Zygnematophyceae, Streptophyta). Phylogenetic analyses used the genes individually and in combination, either as concatenated sequences or with the log-likelihood summation method. Single-gene analyses, though mostly congruent, revealed some conflicting nodes and showed different patterns of statistical support. Combined analyses confidently resolved the conflicts between the single-gene analyses, enhanced phylogenetic resolution and were better supported by morphological information. Long branch taxa were not the same for the two genes analyzed and thus their effect on phylogenetic resolution was minimized in the combined analyses.

Key Words: Combined analyses, phylogeny, rbcL, SSU rDNA, Streptophyta, Zygnematophyceae


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