Abstract
Correct combination of plastid (cp) and nuclear (nr) DNA data for plant phylogenetic reconstructions is not a new issue, but with an increasing number of nrDNA loci being used, it is of ever greater practical concern. For accurately reconstructing the phylogeny and evolutionary history of plant groups, correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data. We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011. Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets, or did not address in detail possible reasons for incongruence between the two data sets. By reviewing various methods, we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data, which includes four steps: identifying significant incongruence, determining conflicting taxa, providing possible interpretations for incongruence, and reconstructing the phylogeny after treating incongruence. Particular attention is given to explanation of the cause of incongruence. We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.
Highlights
Correct combination of plastid and nuclear DNA data for plant phylogenetic reconstructions is not a new issue, but with an increasing number of nrDNA loci being used, it is of ever greater practical concern
A robust and wellsupported phylogenetic tree is a prerequisite for understanding and explaining many life phenomena, otherwise erroneous conclusions will be generated in an incorrect phylogenetic context
The issue of combining cpDNA and nrDNA data sets is not new, but it is of greater practical concern today, with the vast amount of molecular data available, especially as an increasing number of low-copy nuclear genes are used in plant phylogenetics [13,14,19,20]
Summary
To investigate how empirical studies usually treat incongruence between cpDNA and nrDNA data sets and to explore the possible cause of incongruence between the two, we chose the journal Systematic Botany and examined its published articles. If a paper used both the ILD test and tree-based comparisons, where the ILD test indicated the cpDNA and nrDNA data were significantly incongruent but the tree-based comparisons found that incongruence was weakly supported, we recorded it as “congruent”. Tree-based comparisons identified incongruence in 15 studies, of which the cpDNA and nrDNA data were still combined in seven studies. Ten studies were indicated to be incongruent by using both the ILD test and tree-based comparisons, of which the data were still combined in seven studies.
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