Abstract
The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.
Highlights
Rooting evolutionary trees is usually considered a simple step in phylogenetic construction
The outgroup method is the most widely used in phylogenetic studies but the correct indication of the root position strongly depends on the availability of a proper outgroup (Hendy & Penny, 1989; Wheeler, 1990; Tarrío, Rodríguez-Trelles & Ayala, 2000)
We assumed that the outgroup method yields the correct root position in every tree
Summary
Rooting evolutionary trees is usually considered a simple step in phylogenetic construction. The outgroup method is the most widely used in phylogenetic studies but the correct indication of the root position strongly depends on the availability of a proper outgroup (Hendy & Penny, 1989; Wheeler, 1990; Tarrío, Rodríguez-Trelles & Ayala, 2000). This apparently simple requisite may prove rather limiting when studying viruses (Stavrinides & Guttman, 2004), mostly because of extremely high and diverse. The theoretical basis of MPR relies on the assumption that all OTUs in a given tree should display the same
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