Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates

Abstract

The colonization of land by tetrapod ancestors is one of the major questions in the evolution of vertebrates. Despite intense molecular phylogenetic research on this problem during the last 15 years, there is, until now, no statistically supported answer to the question of whether coelacanths or lungfish are the closest living relatives of tetrapods. We determined DNA sequences of the nuclear-encoded recombination activating genes (Rag1 and Rag2) from all three major lungfish groups, the Australian Neoceratodis forsteri, the South American Lepidosiren paradoxa and the African lungfish Protopterus dolloi, and the Indonesian coelacanth Latimeria menadoensis. Phylogenetic analyses of both the single gene and the concatenated data sets of RAG1 and RAG2 found that the lungfishes are the closest living relatives of the land vertebrates. These results are supported by high bootstrap values, Bayesian posterior probabilities, and likelihood ratio tests.

Fig. 1.

Phylogenetic tree inferred by using the ML method from 22 species and 689 amino acid positions from the Rag1 gene. To test the robustness of the internal nodes, 2,000 bootstrap replicates each for minimum evolution and MP (TBR, 10 times random addition) were performed. Furthermore, ML estimates were obtained either from tree-puzzle in the form of QP support values or from mrbayes in the form of posterior probabilities (Ba) given in percentage.

Fig. 2.

Phylogenetic tree inferred by using the ML method from 18 species and 389 amino acid positions from the Rag2 gene. The same phylogenetic analyses were done as described in Fig. 1.

Fig. 3.

Phylogenetic tree inferred by using the ML method from 14 species and 1,078 amino acid positions from the concatenated RAG1 and RAG2 data sets. The same phylogenetic analyses were done as described in Fig. 1. Note that (i) the sequence named salamander is a fusion between the RAG1 sequence of Pleurodeles and the RAG2 sequence of Pachytriton and (ii) the outgroup sequence named sharks is a fusion between the RAG1 sequence of Carcharhinus and the RAG2 sequence of Triakis.