Copyright zyxwvutsrqponm 0 1996 by the Genetics Society of America The Complete Nucleotide Sequence of the Mitochondrial Genome of the Lungfish zyxwv (A-otqPterus zyxwvuts dolloi) Supports Its Phylogenetic Position zy as a Close Relative of Land Vertebrates Rafael Zardoya and Axel Meyer Department zyxwvutsrqpon of Ecology and Evolution and Program in Genetics, State University of New York, Stony Brook, New York 11 794-5245 zy Manuscript received June 10, 1995 Accepted for publication January 13, 1996 ABSTRACT The complete DNA sequence (16,646 bp) of the mitochondrial genome of the African lungfish, Protopterusdolloi, was determined. The evolutionary position of lungfish as possibly the closest living relative among fish of land vertebrates made its mitochondrial DNA sequence particularly interesting. Its mitochondrial gene order conforms to the consensus vertebrate gene order. Several sequence motifs and secondary structures likely involved in the regulation of the initiation of replication and transcription of the mitochondrial genome are conserved in the lungfish and are more similarto those of land vertebrates than those of ray-finned fish. A novel feature discovered is that the putative origin of L- strand replication partially overlaps the adjacent tRNAcys. The phylogenetic analyses of genes coding for tRNAs and proteins confirm the intermediate phylogenetic position of lungfish between ray-finned fishes and tetrapods. The complete nucleotide sequence of the African lungfish mitochondrial genome was used to estimate which mitochondrial genes are most appropriate to elucidate deep branch phyloge- nies. Only a combined set of either protein or tRNA mitochondrial genes (but not each gene alone) is able to confidently recover the expected phylogeny among vertebrates that have diverged up to but not over -400 mya. T HE transition from lifeinwater to life on land, -360 mya (BENTON 1990), was one of the most consequential events in the history of vertebrates. It was accompanied by a variety of refined morphological and physiological modifications, e.g., reductions and rear- rangements of the skull bones and modifications of swimming fins into load-bearing limbs (e.g., PANCHEN and SMITHSON 1987). Two groups of lobe-finned fish (Table l), the lungfish and the coelacanth (Latimm’u chalumnae) have bothbeen implicated as the closest living relative of tetrapods (reviewed in MEYER 1995). Lungfish were discovered zyxwvuts > 150 years ago (BISCHOFF 1840) and for several reasons, e.g., they are obligate airbreathers, were initially believed to be amphibians, not fish. In the lower Devonian (-400 mya) lungfish were a speciesrich group that inhabited both marine and freshwater environments (e.g., reviewed in CLOUTIER 1991). However, only a very smallnumber of “relict” species survive today. These are the Australian lungfish, Neoceratodus zyxwvuts forsteri, the South American lung- fish, Lqbidosiren paradoxa, and four species in the genus Protqterus from Africa. These living fossils are of inter- est to evolutionary biology since their morphology, physiology, and biochemistry might be representative of that of the common ancestor of all land vertebrates. Therefore, lungfish have been widely studied by paleon- Corresponding authm: Rafael Zardoya, Department of Ecology and Evolution, State University of New York, Stony Brook, NY 117945245. E-mail: rzardoya@life.bio.sunysb.edu Genetics zyxwvutsrqpon 142 1249-1263 (April, 1996) tologists, comparative morphologists and recently de- velopmental biologists. The other extant group of lobe-finned fish, the coe- lacanths were believed to have gone extinct -80 mya, but in 1938, the only surviving species of this lineage of fishes was discovered off the coast of East Africa. Since its sensational rediscovery, the coelacanth is of- ten depicted in textbooks as the “missing link” be- tweenfish and all land vertebrates i.e., amphibians, reptiles, birds and mammals (ROMER 1966). However, many morphological, paleontological (e.g., reviewed in PATTERSON 1980; ROSEN et al. 1981), andmost mo- lecular (MEYER and WILSON 1990; MEYER and DOLVEN 1992; HEDGES et al. 1993; reviewed in MEYER 1995; but see YOKOBORI et al. 1994) data suggest that lungfish and not the coelacantharemore closely related to tetrapods. Hence, the nucleotide sequence of the lungfish mitochondrial genome is of interest, both in terms of the evolution of the mitochondrial gene or- der in vertebrates and in terms of the phylogeny of land vertebrates. Until now, the complete mitochondrial DNA se- quences of 19 vertebrate species have been reported. Thirteen of them are from mammals, four from fishes, but only one of an amphibian and one of a bird have been determined. Remarkably, the structure and orga- nization of vertebrate mitochondrial genomes is quite conserved and only minor rearrangements have been described for the chicken (DESIARDINS and Mows Downloaded from https://academic.oup.com/genetics/article/142/4/1249/6222037 by guest on 12 September 2021