Resolving the phylogenetic position of coelacanth: The closest relative is not always the most appropriate outgroup

Abstract

Determining the phylogenetic relationship of two extant lineages of lobe-finned fish, coelacanths and lungfishes, and tetrapods is important for understanding the origin of tetrapods.We analyzed data sets fromtwo previous studies along with a newly collected data set, eachofwhichhadvaryingnumbers of species andgenes andvarying extentofmissing sites.Wefoundthat inall thedata sets the sister relationship of lungfish and tetrapodswas constructed with the use of cartilaginous fish as the outgroup with a high degree of statistical support. In contrast,when ray-finned fishwere used as the outgroup, which is taxonomically an immediate outgroup of lobe-finned fish and tetrapods, the sister relationship of coelacanth and tetrapods was supported most strongly, although the statistical support wasweaker. Even though it is generally accepted that the closest relative is an appropriate outgroup, our analysis suggested that the large divergence of the ray-finned fish as indicated by their long branch lengths and different amino acid frequencies made them less suitable as an outgroup than cartilaginous fish.