One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods.

The only currently unresolved portion of the backbone phylogeny of the vertebrates involves the relationships among coelacanths, lungfishes, and tetrapods. Despite active research on this question over the past three decades, it is still difficult to determine statistically whether lungfishes alone or both lungfishes and coelacanths together are closely related to tetrapods. To resolve this controversy, we assembled a data set comprising 1,290 nuclear genes encoding 690,838 amino acid residues by analyzing available genome and transcriptome data. Phylogenetic analyses of this data set provided overwhelming evidence that the lungfishes are the closest living relatives of the land vertebrates. This result is strongly supported by high bootstrap values from maximum likelihood and maximum parsimony analyses, Bayesian posterior probabilities of CAT model analysis, and topological tests. Additionally, a species tree analysis without data concatenation also strongly supported this result.