Complete Mitochondrial Genome Sequences of the South American and the Australian Lungfish: Testing of the Phylogenetic Performance of Mitochondrial Data Sets for Phylogenetic Problems in Tetrapod Relationships

We determined the complete nucleotide sequences (16403 and 16572 base pairs, respectively) of the mitochondrial genomes of the South American lungfish, Lepidosiren paradoxa, and the Australian lungfish, Neoceratodus forsteri (Sarcopterygii, Dipnoi). The mitochondrial DNA sequences were established in an effort to resolve the debated evolutionary positions of the lungfish and the coelacanth relative to land vertebrates. Previous molecular phylogenetic studies based on complete mtDNA sequences, including only the African lungfish, Protopterus dolloi, sequence were able to strongly reject the traditional textbook hypothesis that coelacanths are the closest relatives of land vertebrates. However, these studies were unable to statistically significantly distinguish between the two remaining scenarios: lungfish as the closest relatives to land vertebrates and lungfish and coelacanths jointly as their sister group (Cao et al. 1998; Zardoya et al. 1998; Zardoya and Meyer 1997a). Lungfish, coelacanths, and the fish ancestors of the tetrapod lineage all originated within a short time window of about 20 million years, back in the early Devonian (about 380 to 400 million years ago). This short divergence time makes the determination of the phylogenetic relationships among these three lineages difficult. In this study, we attempted to break the long evolutionary branch of lungfish, in an effort to better resolve the phylogenetic relationships among the three extant sarcopterygian lineages. The gene order of the mitochondrial genomes of the South American and Australian lungfish conforms to the consensus gene order among gnathostome vertebrates. The phylogenetic analyses of the complete set of mitochondrial proteins (without ND6) suggest that the lungfish are the closest relatives of the tetrapods, although the support in favor of this scenario is not statistically significant. The two other smaller data sets (tRNA and rRNA genes) give inconsistent results depending on the different reconstruction methods applied and cannot significantly rule out any of the three alternative hypotheses. Nuclear protein-coding genes, which might be better phylogenetic markers for this question, support the lungfish–tetrapod sister-group relationship (Brinkmann et al. 2004).This article contains online supplementary material.Reviewing Editor: Dr. Rafael Zardoya     

A new assemblage of Cenozoic lungfishes (Dipnoi: Lepidosirenidae) from the late Oligocene Nsungwe Formation,Rukwa Rift Basin,southwestern Tanzania

Lungfish (Dipnoi) date back to the Devonian, and some fossil taxa as well as extant African lungfishes are known for their ability to aestivate, tolerating low-oxygen environments associated with seasonal drying. Extant lungfishes are separated into two families: Lepidosirenidae (Protopterus in Africa and Lepidosiren in South America) and Neoceratodontidae (Neocerotadus in Australia). African lungfishes were more geographically and phylogenetically diverse on the continent in the past than they are today, with only 5% of extinct taxa recorded from the sub-Saharan fossil record. Given the sparse record of Lepidosirenidae fossils from continental Africa, any new materials are important for understanding diversification of the clade. Here we describe new lungfish fossils cautiously referable to Protopterus annectens and Protopterus aethiopicus, which are strongly supported sister taxa based on the molecular phylogeny. Specimens were collected from the late Oligocene Nsungwe Formation in the Rukwa Rift Basin (RRB) of southwestern Tanzania. The late Oligocene Nsungwe Formation represents a sequence of continental rift-fill deposits of the Songwe sub-basin of the RRB and is subdivided into the lower Utengule and upper Songwe members. Recovery of such material from the Paleogene of Africa below the equator addresses a sizable gap in the lungfish fossil record. It also expands the Nsungwe Formation fauna that includes invertebrates, alestid fishes, ptychadenid anurans, snakes, and several clades of mammals, deepening paleoecological insights into the late Oligocene record of the continental African interior. At present, P. aethiopicus and P. dolloi have an extensive modern eastern African distribution associated with the rift lakes and a region where extant members of P. annectens are not presently known. Fossil specimens described herein document presence of the clade during Paleogene volcanic activity in the western branch of the Eastern African Rift System.     

Hearing in the African lungfish (Protopterus annectens): pre-adaptation to pressure hearing in tetrapods?

Lungfishes are the closest living relatives of the tetrapods, and the ear of recent lungfishes resembles the tetrapod ear more than the ear of ray-finned fishes and is therefore of interest for understanding the evolution of hearing in the early tetrapods. The water-to-land transition resulted in major changes in the tetrapod ear associated with the detection of air-borne sound pressure, as evidenced by the late and independent origins of tympanic ears in all of the major tetrapod groups. To investigate lungfish pressure and vibration detection, we measured the sensitivity and frequency responses of five West African lungfish (Protopterus annectens) using brainstem potentials evoked by calibrated sound and vibration stimuli in air and water. We find that the lungfish ear has good low-frequency vibration sensitivity, like recent amphibians, but poor sensitivity to air-borne sound. The skull shows measurable vibrations above 100 Hz when stimulated by air-borne sound, but the ear is apparently insensitive at these frequencies, suggesting that the lungfish ear is neither adapted nor pre-adapted for aerial hearing. Thus, if the lungfish ear is a model of the ear of early tetrapods, their auditory sensitivity was limited to very low frequencies on land, mostly mediated by substrate-borne vibrations.     

Pulmonary oxygen diffusing capacity of the South American lungfish Lepidosiren paradoxa: physiological values by the Bohr method

Lungfish (Dipnoi) may represent the sister group to all land vertebrates and are therefore important for reconstructing the conquest of land by tetrapods. We determined venous and arterial blood gases, pulmonary O(2) uptake, and the form of the hemoglobin-O(2) dissociation curves in the South American lungfish Lepidosiren paradoxa. Measurements were performed at 25 degrees and 35 degrees C. Based on this information, we calculated its pulmonary O(2) diffusing capacity (D(L)O(2)), using the Bohr integration procedure. D(L)O(2) increased with temperature to reach about 0.04 mL stpd kg(-1) min(-1) mmHg(-1) at 35 degrees C. This value represents about 40% of the morphometric diffusing capacity and is similar to physiological values in some amphibians and reptiles.     

Lungfish Axial Muscle Function and the Vertebrate Water to Land Transition

The role of axial form and function during the vertebrate water to land transition is poorly understood, in part because patterns of axial movement lack morphological correlates. The few studies available from elongate, semi-aquatic vertebrates suggest that moving on land may be powered simply from modifications of generalized swimming axial motor patterns and kinematics. Lungfish are an ideal group to study the role of axial function in terrestrial locomotion as they are the sister taxon to tetrapods and regularly move on land. Here we use electromyography and high-speed video to test whether lungfish moving on land use axial muscles similar to undulatory swimming or demonstrate novelty. We compared terrestrial lungfish data to data from lungfish swimming in different viscosities as well as to salamander locomotion. The terrestrial locomotion of lungfish involved substantial activity in the trunk muscles but almost no tail activity. Unlike other elongate vertebrates, lungfish moved on land with a standing wave pattern of axial muscle activity that closely resembled the pattern observed in terrestrially locomoting salamanders. The similarity in axial motor pattern in salamanders and lungfish suggests that some aspects of neuromuscular control for the axial movements involved in terrestrial locomotion were present before derived appendicular structures.     

True enamel covering in teeth of the Australian lungfish Neoceratodus forsteri

Lungfish are a unique order of sarcopterygian fish cleidographically positioned between tetrapods and fish. An uninterrupted 400-million-year-old fossil record has documented lungfish skeletal elements to remain virtually unchanged since the Early Devonian. In the current study we investigated the enamel layer of lungfish teeth in order to determine whether there was evidence for higher vertebrate "true" enamel in the Australian lungfish. Juvenile lungfish from the Brisbane River were processed for light and electron microscopy and analyzed for parameters indicative of true enamel formation. Using anti-amelogenin primary antibodies for immunodetection and Western blots, enamel protein epitopes were detected in developing lungfish teeth. Using transmission electron microscopy and electron diffraction analysis, long and parallel-oriented hydroxyapatite crystals were observed in lungfish outer tooth coverings. Our findings indicate that Australian lungfish teeth are covered by a layer of true enamel. Based on the lungfish fossil record we conclude that features of true enamel formation may be as old as 400 million years. Based on taxonomic classification we confirm that true enamel is found not only in tetrapods but also in the sarcopterygian clade of the Gnathostomata.     

A fibrous membrane suspends the multifocal lens in the eyes of lampreys and African lungfishes

The sharpness and thus information content of the retinal image in the eye depends on the optical quality of the lens and its accurate positioning in the eye. Multifocal lenses create well‐focused color images and are present in the eyes of all vertebrate groups studied to date (mammals, reptiles including birds, amphibians, and ray‐finned fishes) and occur even in lampreys, i.e., the most basal vertebrates with well‐developed eyes. Results from photoretinoscopy obtained in this study indicate that the Dipnoi (lungfishes), i.e., the closest piscine relatives to tetrapods, also possess multifocal lenses. Suspension of the lens is complex and sophisticated in teleosts (bony fishes) and tetrapods. We studied lens suspension using light and electron microscopy in one species of lamprey (Lampetra fluviatilis) and two species of African lungfish (Protopterus aethiopicus aethiopicus and Protopterus annectens annectens). A fibrous and highly transparent membrane suspends the lens in both of these phylogenetically widely separated vertebrate groups. The membrane attaches to the lens approximately along the lens equator, from where it extends to the ora retinalis. The material forming the membrane is similar in ultrastructure to microfibrils in the zonule fibers of tetrapods. The membrane, possibly in conjunction with the cornea, iris, and vitreous body, seems suitable for keeping the lens in the correct position for well‐focused imaging. Suspension of the lens by a multitude of zonule fibers in tetrapods may have evolved from a suspensory membrane similar to that in extant African lungfishes, a structure that seems to have appeared first in the lamprey‐like ancestors of allextant vertebrates. J. Morphol. 271:980–989, 2010. © 2010 Wiley‐Liss, Inc.     

THE NASAL APPARATUS IN DIPNOI, WITH SPECIAL REFERENCE TO PROTOPTERUS

An investigation is made of the homology of the nasal apparatus of the Dipnoi, in order to determine whether the posterior naris is homologous with the choana of tetrapods or with the posterior external naris of fishes. The ontogeny of the nasal capsule of Protopterus is described in detail. The nervous and venous systems of tho snout region of Protopterus are also duscrbed. It is found that whereas the pattern of the nervous and vascular systems is very similar in all Dipnoi, the structuro of the nasal capsule in the Lepidosiren-Protopterus stock differs greatly from that of the Neoceratodus stock. the homology of the various components of the depnoan nasal coasule is revised and it is shown that there are no evidences of a direct relationship of the Dipnoi with the tetrapods. It is further concluded that the posterior naris of Dipnoi is homologous with the posterior external naris of fishes.     

Relationship between cerebro-spinal fluid pH and pulmonary ventilation of the South American lungfish, Lepidosiren paradoxa (Fitz.)

The respiratory control in land vertebrates (Tetrapoda) is mainly linked to regulation of acid-base status, which involves peripheral and central chemoreceptors. The lungfish (Dipnoi) might constitute the sister group of all land vertebrates (Tetrapoda) and possess a combination of real lungs and reduced gills. In this context, we evaluated the possible presence of central respiratory chemoreceptors in the South American Lungfish, Lepidosiren paradoxa. Pulmonary ventilation and respiratory frequency increased significantly with reductions of CSF pH by means of mock CSF solutions. This suggests that Lepidosiren possess central acid-base receptors.     

Lungfish albumin is more similar to tetrapod than to teleost albumins: purification and characterisation of albumin from the Australian lungfish, Neoceratodus forsteri

Lobe-finned fish, particularly lungfish, are thought of as the closest extant relatives to tetrapods. Albumin, the major vertebrate plasma protein, has been well studied in tetrapods, but there exists no comparative study of the presence and characteristics of albumin in lobe-finned fish versus other vertebrates. There is a controversy over the presence of albumin in fish, although it is present in salmonids and lamprey. The presence of albumin in lungfish has also recently been documented. We identified albumin in plasma of the Australian lungfish, Neoceratodus forsteri, using a combination of agarose gel electrophoresis, [(14)C]palmitic acid binding and SDS-PAGE. Lungfish albumin was purified using DEAE-ion exchange chromatography, and has a mass of 67 kDa, is present at approximately 8 g/L in plasma and like other fish albumins, does not bind nickel. However, like tetrapod albumins, it is not glycosylated. N-terminal and internal peptide sequencing generated 101 amino acids of sequence, which showed a high degree of identity with tetrapod albumins. Despite the similarity in sequence but congruent with the evolutionary distances separating them, lungfish albumin did not cross-react with anti-chicken or anti-tuatara A albumin antisera. Lungfish albumin has characteristics more akin with tetrapod albumin and less like those of other fish.     

Evolution of tissue-specific keratins as deduced from novel cDNA sequences of the lungfish Protopterus aethiopicus

Lungfishes are possibly the closest extant relatives of the land vertebrates (tetrapods). We report here the cDNA and predicted amino acid sequences of 13 different keratins (ten type I and three type II) of the lungfish Protopterus aethiopicus. These keratins include the orthologs of human K8 and K18. The lungfish keratins were also identified in tissue extracts using two-dimensional polyacrylamide gel electrophoresis, keratin blot binding assays and immunoblotting. The identified keratin spots were analyzed by peptide mass fingerprinting which assigned seven sequences (inclusively Protopterus K8 and K18) to their respective protein spot. The peptide mass fingerprints also revealed the fact that the major epidermal type I and type II keratins of this lungfish have not yet been sequenced. Nevertheless, phylogenetic trees constructed from multiple sequence alignments of keratins from lungfish and distantly related vertebrates such as lamprey, shark, trout, frog, and human reveal new insights into the evolution of K8 and K18, and unravel a variety of independent keratin radiation events.     

Bile salts of the lungfishes Lepidosiren, Neoceratodus and Protopterus and those of the coelacanth Latimeria chalumnae Smith.

1. Bile salts of the coelacanth Latimeria chalumnae Smith (five specimens) and of the three living genera of lungfish (Dipnoi) were examined as completely as possible and compared. 2. The small 'bile acid' fractions include no more than traces of well-known C27 or C24 acids (free or conjugated) and the functioning bile salts must be regarded as alcohol sulphates. 3. Comparison of the alcohols suggest that (a) Latimeria stands biochemically outside the animal group which includes the Dipnoi, (b) Protopterus and Lepidosiren are more closely related to one another than either is to Neoceratodus, (c) all four primitive osteiychtheans have some amphibian affinities, (d) there are affinities between Latimeria and Dipnoi and ostariophysan families (especially Cyprinidae and Catostomidae) and (e) there are biochemical links between Dipnoi and lampreys.     

Structural and biochemical characterization of the lungfish (Lepidosiren paradoxa) liver basic fatty acid binding protein

Only one fatty acid-binding protein (FABP) from the liver of the lungfish (Lepidosiren paradoxa) was isolated and characterized. The sequence comparison of lungfish FABP with that of the known members of the liver FABP (L-FABP) and liver basic FABP (Lb-FABP) subfamilies indicates that it is more closely related to chicken, iguana, frog, axolotl, catfish, and shark Lb-FABPs than to mammalian and axolotl L-FABPs. Lungfish liver expression of this single Lb-FABP contrasts with the other fish studied so far which coexpress an Lb-FABP with heart-adipocyte and/or intestinal FABP types. The lungfish liver FABP expression pattern resembles that of tetrapods, which only expresses liver type FABPs. Lungfish Lb-FABP is one of the two FABPs reported to have a disulfide bridge. The molecular modeling of lungfish Lb-FABP predicts that nine of the conserved residues of Lb-FABPs are oriented toward the binding cavity, thus suggesting they are related to the protein binding characteristics.     

Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data

The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.     

Translocation of marbled African lungfish,Protopterus aethiopicus (Telostei: Protopteridae), and its fishery in Lake Baringo,Kenya

The translocation of the marbled African lungfish Protopterus aethiopicus into Lake Baringo created a new fishery for the local community, who capture them primarily in a bottom-set long line fishery. Its introduction, development and current fishery status in the lake are documented. Annual catch data were obtained from the District Fisheries Office, while catch and effort data of the long line fishery were recorded at one active fish-landing site between February and October 2001. Lungfish comprise a significant component of commercial landings, sometimes exceeding catches of the Baringo tilapia Oreochromis niloticus baringoensis as the most landed species by weight. Daily catch rates and effort varied considerably, ranging from 5.51–15.18kg day^?1 and from 50–590 baited hooks day^?1, respectively. Daily catch per fisher ranged from 0–35.72kg, while the overall mean catch per unit effort (CPUE) was only 0.003kg per hook-hour. This study provides the only baseline CPUE data for a lungfish long line fishery that the authors are aware of, for comparison with future studies in this or other lakes where lungfish are similarly exploited. Recommendations for improved management and the maintenance of a viable lungfish long line fishery in Lake Baringo are presented.     

Development of the Snout of the Australian Lungfish Neoceratodus forsteri (Krefft, 1870), with Special Reference to Cranial Nerves

Abstract The anatomy and embryology of the dipnoan snout and olfactory organ play a major role in the discussion about the phylogenetic position of Dipnoi and the question of ancestry of Tetrapoda. This is primarily due to the fact that an internal nostril is regarded as an important preadaptive organ of the ancestors of tetrapods. Two conflicting scenarios of phylogenetic change were proposed in favour of different hypotheses of relationship. One emphasizes the similarities between Dipnoi and Chondrichthyes concerning this complex of characters. The other supports the idea of a close relationship of Dipnoi and Tetrapoda and a common origin of a ‘choana’ from the posterior external nostril of fishes. Accordingly, there is need for a detailed embryological and anatomical study which could help to clarify homologies and the basis of character evaluation. This, in the first place, concentrates on Neoceratodus forsteri. A plate reconstruction of the larval head provides many new insights which are important for comparison with the lepidosirenid lungfishes Protopterus and Lepidosiren and with other vertebrate taxa. The value of the peripheral nervous system as a topographical reference is critically reviewed. The results support the hypothesis that lungfish form a ‘primitive’ teleostomate group, closely adjoining Chondrichthyes in many characteristics of the snout formation. The relations between cranial nerves in the snout and the developing nasal sac, however, do not support the conclusion that the recent selachian condition is the exceptional ancestral character state of the lungfish snout. Dipnoi lack a ‘choana’, but nevertheless a closer relationship to tetrapods is not excluded. A vestigial and transitory naso-buccal connection in larvae of Neoceratodus might indicate such common ancestry, but has a completely different functional significance among fishes. It is shared with several plagiostomes and is, therefore, probably not useful as a synapomorphy of Dipnoi and Tetrapoda.