Lungfish

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.

Abstract: Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ the land and ultimately gave rise to all land vertebrates, including humans1–3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution. A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.

Abstract: The origin of tetrapods is a major outstanding issue in vertebrate phylogeny. Each of the three possible principal hypotheses (coelacanth, lungfish, or neither being the sister group of tetrapods) has found support in different sets of data. In an attempt to resolve the controversy, sequences of 44 nuclear genes encoding amino acid residues at 10,404 positions were obtained and analyzed. However, this large set of sequences did not support conclusively one of the three hypotheses. Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy.

Abstract: The vomeronasal (VN) (Jacobson's) organs are paired chemosensory organs located in the vertebrate nose. They generally are formed only in tetrapods (Negus, 1958). Accessory olfactory bulbs and nerves that may innervate rudimentary VN organs have been described in the African lungfish Protopterus (Rudebeck, 1944) and the paddle fish Polyodon (Story, 1964). True VN organs are not normally formed in recent fishes, and in birds, aquatic reptiles, aquatic mammals, and higher primates (including man) the VN organs are vestigial or lost (Parsons, 1967, 1970). The VN organs are normally sensory pockets of rather uniform morphology. They are situated in the palate, and each organ may be connected with the mouth cavity and the nasal cavity by a nasopalatine duct (Fig. 1). In some species the organs are connected with either the mouth cavity by means of a palatine duct, or with the nasal cavity by a nasal duct. Comparative studies on anurans, reptiles, and mammals show a rather uniform histology-cytology (Graziadei, 197 1). The phylogenetic history of VN organs is obscure (Negus, 1958; Moulton and Beidler, 1967; Parsons, 1971). I briefly discussed these organs in connection with studies on the ontogeny and evolution of the olfactory organs and other structures of the nose in lower vertebrates, like lungfish and urodeles (Bertmar, 1969). Recent studies on reindeer (Bertmar, 1975, 1980) make it possible to present a theory on the evolution of the VN organs from fish to mammals. The theory is based on my earlier studies on fishes (Bertmar, 1965, 1969, 1972) and tetrapods (Bertmar, 1966, 1975, 1980), but also on literature studies on other vertebrates (Bertmar, 1969, 1980, for references). It is mainly based on comparisons of the position, gross and fine structure, and the ontogeny of the organs. These criteria are therefore not repeated each time an evolutionary line is presented in the following discussion. Finally, only the main types of VN organs are discussed, and variations in different groups are usually excluded.