Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species

Abstract

The phylogenetic relationship among the kingdoms Animalia, Plantae, and Fungi remains uncertain, because of lack of solid fossil evidence. In spite of the extensive molecular phylogenetic analyses since the early report, this problem is a longstanding controversy; the proposed phylogenetic relationships differ for different authors, depending on the molecules and methods that they use. To settle this problem, we have accumulated 23 different protein species from the three kingdoms and have inferred the phylogenetic trees by three different methods-the maximum-likelihood method, the neighbor-joining method, and the maximum-parsimony method-for each data set. Although inferred tree topologies differ for different protein species and methods used, both the maximum-likelihood analysis based on the difference (Δl) between the total log-likelihood of a tree and that of the maximum-likelihood tree and bootstrap probability (P) of 23 proteins consisting of 10,051 amino acid sites in total have shown that a tree ((A,F),P), in which Plantae (P) is an outgroup to an Animalia (A)-Fungi (F) clade, is the maximum-likelihood tree; the Δl (=0.0) and P (94%) of ((A,F),P) are significantly larger than those of ((A,P),F) (Δl = -54.4 ± 36.3; and P = 6%) and ((F,P),A) (Δl = -141.1 ± 30.9; and P = 0%). Furthermore, even if sequence data were selected for 14 proteins from which identical tree topologies were inferred among the three methods, the ((A,F),P) tree is significant; Δl = 0.0 and P = 96% for ((A,F),P), Δl = - 53.9 ± 29.6 and P = 4% for ((A,P),F), and Δl = -111.1 ± 25.5 and P = 0% for ((F,P),A). From these results, we conclude that Animalia is more closely related to Fungi than to Plantae.