Relationship among coelacanths,lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences

To clarify the relationship among coelacanths, lungfishes, and tetrapods, the amino acid sequences deduced from the nucleotide sequences of mitochondrial cytochrome oxidase subunit I (COI) genes were compared. The phylogenetic tree of these animals, including the coelacanth Latimeria chalumnae and the lungfish Lepidosiren paradoxa, was inferred by several methods. These analyses consistently indicate a coelacanth/lungfish clade, to which little attention has been paid by previous authors with the exception of some morphologists. Overall evidence of other mitochondrial genes reported previously and the results of this study equally support the coelacanth/lungfish and lungfish/tetrapod clades, ruling out the coelacanth/tetrapod clade.Correspondence to: K. Watanabe 0592     

Habitat and population size of the coelacanth Latimeria chalumnae at Grand Comoro

Synopsis In 1987 and 1989 coelacanths were observed for the first time in their natural habitat with the help of submersibles. Coelacanths were found between 150–253 m depth, their preferential depth seems to be around 200 m; the water temperature ranged between 16.5–22.8° C. During the day coelacanths aggregate in small non-aggressive groups in sheltered lava-caves. Caves might be a limiting factor for distribution. At night they leave the caves for hunting by drifting singly along the steep lava slopes. They migrate between different caves located within a large home range covering more than 8 km coastline. Coelacanths are site-attached, some for a period of at least 2 years. Our own observations and earlier catch records show that only the west coast of Grand Comoro is a suitable coelacanth habitat with more structural complexity and prey fish abundance than other coastlines of the island. From our survey we estimated a total coelacanth population off Grand Comoro to be 150–210 individuals; a saturated population would be 370–510 individuals. This small relict population seems to be stable. International protection of coelacanths against commercial interests is needed     

The ecology and conservation of the coelacanth Latimeria chalumnae

Synopsis Studies on the ecology of the living coelacanth, Latimeria chalumnae, are reviewed and assessed. Early predictions on the life history of the coelacanth have proved to be accurate but recent findings have improved our understanding of its habitat and feeding preferences, diel activity patterns and social behaviour. A history of coelacanth conservation reveals that there has been a sustained concern for the survival of this species which has eventually culminated in several effective conservation actions in recent years. The coelacanth is threatened by a number of socio-economic and biological factors, but international action directed at managing the fishery in the Comoros should ensure that the species survives. Recent observations on living coelacanths in their natural environment have greatly improved our knowledge of the behaviour and relative abundance of adults. Important priorities for future research include studies on the distribution and abundance of juveniles and breeding adults, both off the Comoros and elsewhere. The coelacanth is a highly specialised, precocial fish which occupies a unique place in biology. Co-ordinated international efforts should continue to be made to understand and conserve this remarkable fish.     

Coelacanths: a human responsibility

The living coelacanth Latimeria chalumnae has a unique position in world biodiversity which raises important questions about conservation and ethics. Some relevant details of coelacanth biology are summarized, including those obtained by direct observation from submersibles. The importance of the coelacanth for evolutionary theory and palaeontology is shown to be paralleled in cultural, literary and artistic areas of human heritage. Threats to the Comoran coelacanths from artisanal fishing are described and conservation measures discussed in relation to local customs and economies as well as the promotion of tourism to spread a new awareness and concern for coelacanths worldwide.     

An inventory of all known specimens of the coelacanth Latimeria chalumnae,with comments on trends in the catches

Synopsis A list is presented of all known specimens of the coelacanth Latimeria chalumnae based on a survey of the literature and of museum, aquarium and university holdings. Details are given of the date, place, time and depth of capture, the name and age of the fisherman, the length, weight and sex of the fish, the first literature record, the method of preservation and the present location of specimens, if known. A new number is assigned to each specimen. At least 172 coelacanths are known to have been caught since 1938. The first coelacanth was caught off South Africa but all properly documented, subsequent specimens have been caught off the islands of Grand Comoro and Anjouan in the Comoros. An appeal is made to the Comoran authorities for each specimen that is caught to be made available for scientific study. Museum authorities are also encouraged to allow their specimens to be X-rayed or dissected so that vital information can be obtained on fecundity, foetal nutrition and dietary preferences. It is essential for the coelacanth conservation effort that this inventory is maintained by the Coelacanth Conservation Council.     

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Coelacanths are known as "living fossils" because their morphology has changed very little from that in the fossil record. To elucidate why coelacanths have evolved so slowly is thus of primary importance in evolutionary biology. In the present study, we determined the entire sequence of the HOX cluster of the Tanzanian coelacanth (Latimeria chalumnae) and compared it with that of the Indonesian coelacanth (L. menadoensis), which was available in the literature. The most intriguing result was the extremely small genetic divergence between the two coelacanths. The synonymous divergence of the HOX coding region between the two coelacanths was estimated to be 0.07%, which is ~11-fold smaller than that of human-chimp. When we applied the estimated divergence time of the two coelacanths of 6 million years ago (MYA) and 30 MYA, which were proposed in independent mitochondrial DNA analyses, the synonymous substitution rate of the coelacanth HOX cluster was estimated to be ~11-fold and 56-fold smaller than that of human-chimp, respectively. Thus, the present study implies that the reduction of the nucleotide substitution rate in coelacanth HOX genes may account for the conservation of coelacanth morphology during evolution.     

Early Growth Stages in Coelacanth Fishes

ALL known specimens of the Recent coelacanth fish, Latimeria, are large specimens (mostly more than 100 cm total length) and only one female with eggs has been recorded^1,2. Consequently, the ontogeny and the early growth stages of the Recent coelacanth are unknown. In the fossil record, one specimen of Holophagus (= Undina) from the Upper Jurassic of Solnhofen, southern Germany, has been recorded with two young coelacanths inside³. Watson has argued from this finding that the coelacanths are viviparous but it seems more reasonable to interpret this fossil specimen as a cannibal that had just swallowed two young of its own kind. This interpretation is favoured by the position of the two specimens and by the discovery of other fossil coelacanths containing large specimens of other kinds of fishes in their stomachs⁴.     

Population divergence in East African coelacanths

The coelacanth, Latimeria chalumnae, occurs at the Eastern coast of Africa from South Africa up to Kenya. It is often referred to as a living fossil mainly because of its nearly unchanged morphology since the Middle Devonian. As it is a close relative to the last common ancestor of fish and tetrapods, molecular studies mostly focussed on their phylogenetic relationships. We now present a population genetic study based on 71 adults from the whole known range of the species. Despite an overall low genetic diversity, there is evidence for divergence of local populations. We assume that originally the coelacanths at the East African Coast derived from the Comoros population, but have since then diversified into additional independent populations: one in South Africa and another in Tanzania. Unexpectedly, we find a split of the Comoran coelacanths into two sympatric subpopulations. Despite its undeniably slow evolutionary rate, the coelacanth still diversifies and is therefore able to adapt to new environmental conditions.     

The demography of the coelacanth Latimeria chalumnae

Synopsis The very sparse data that are available on the abundance, population structure and biology of the coelacanth Latimeria chalumnae off Grand Comoro are summarised, and some simple numerical analyses are carried out to explore certain aspects of the population dynamics, particularly the age-profile of the population. The object has not been to provide estimates of key demographic parameters, such as mortality rates, but to propose various scenarios that are useful for comparison with real data as they become available. The analysis also makes it possible to reach some preliminary conclusions that are relevant to the management of the coelacanth population. For instance, it appears that the catch rate of coelacanths by artisanal fishermen may have a negligible effect on coelacanth survivorship, and it is more likely that population size and structure are determined by natural mortality rates and birth rates. It is suggested that predation is the main cause of natural mortality and that the main predators of coelacanths are likely to be large sharks. Interference with the traditional patterns of the Comoran artisanal fishery may threaten the coelacanth. Several important gaps in our knowledge of coelacanth demography are identified.     

Probable evolution of the coelacanth's reproductive style: lecithotrophy and orally feeding embryos in cichlid fishes and in Latimeria chalumnae

Synopsis The living coelacanth is a livebearer. Yolk seems to be the main source of nutrients and of oxygen to the embryo (fetus). Long before birth, young may also possibly feed orally on histotrophe secretion and egg debris. This type of reproduction evolved, as in most other fishes, from oviparity. The Carboniferous coelacanth Rhabdoderma exiguum had eggs of much lesser yolk volume and may represent an earlier form of oviparity with hiding, guarding or brooding type of parental care. The Jurassic coelacanth Holophagus (Undina) and the Cretaceous Axelrodichthys appear to have already evolved the internal-bearing style. Much of this evolutionary sequence is similar to that in cichlids. Ancestral cichlids are substrate tenders and nesters, with small eggs, little yolk and a feeding larva with indirect development. Mouthbrooding cichlids evolved a few, large eggs with denser yolk, direct development and, ultimately, orally feeding embryos while yolk is still in ample supply. Mixed feeding from yolk and orally ingested food in cichlids and in coelacanths is shown to be an enhanced mode of food delivery to the embryos over that from each source separately, in order to produce directly a better developed or larger young at the time of release, i.e. independence. Increase in egg size is regarded as an environmentally induced, altered pattern of yolk synthesis and an initial component of the epigenetic mechanism leading towards greater specialization. Carotenoids are incorporated within the yolk to assist the oxidative metabolism of the developing embryo.     

Interspecies Insertion Polymorphism Analysis Reveals Recent Activity of Transposable Elements in Extant Coelacanths

Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.     

Predicting suitable environments and potential occurrences for coelacanths (Latimeria spp.)

Extant coelacanths (Latimeria chalumnae) were first discovered in the western Indian Ocean in 1938; in 1998, a second species of coelacanth, Latimeria menadoensis, was discovered off the north coast of Sulawesi, Indonesia, expanding the known distribution of the genus across the Indian Ocean Basin. This study uses ecological niche modeling techniques to estimate dimensions of realized niches of coelacanths and generate hypotheses for additional sites where they might be found. Coelacanth occurrence information was integrated with environmental and oceanographic data using the Genetic Algorithm for Rule-set Production (GARP) and a maximum entropy algorithm (Maxent). Resulting models were visualized as maps of relative suitability of sites for coelacanths throughout the Indian Ocean, as well as scatterplots of ecological variables. Our findings suggest that the range of coelacanths could extend beyond their presently known distribution and suggests alternative mechanisms for currently observed distributions. Further investigation into these hypotheses could aid in forming a more complete picture of the distributions and populations of members of genus Latimeria, which in turn could aid in developing conservation strategies, particularly in the case of L. menadoensis.     

Some 20th century fish discoveries

Of the approximately 1.5 million species described to date, about 48 170 (3.2%) are vertebrates. Of these 24 618 (51%) are fishes. Amazingly, 41% of fishes are found in fresh water which makes up a negligible percentage of the water on earth. The sea accounts for 97% of all water on the planet and contains 58% of the fish species, mostly from shallow, warm-coastal areas. The families Cichlidae, Cyprinidae, Characidae, Loricariidae, and Cyprinodontidae constitute about half of all the recently described new freshwater fish species named in the period 1978–1993. The Gobiidae and Serranidae are the marine families with the largest number of recently described new species. The most new freshwater teleost names came from South America (39%), Africa (32%) and Asia (17%). New fish species continue to be described at the rate of roughly 130–160 each year. An estimated 13 775 new fish names have been proposed in this century, representing about 56% of all currently known fish species. Three species are discussed in detail to represent remarkable examples of 20th century fish discoveries: the coelacanth Latimeria chalumnae, the salamanderfish Lepidogalaxias salamandroides of Western Australia, and the megamouth shark Megachasma pelagios. This revised version was published online in July 2006 with corrections to the Cover Date.     

A newly recognized fossil coelacanth highlights the early morphological diversification of the clade

Previously considered an actinopterygian or an osteichthyan incertae sedis, the Devonian (Givetian-Frasnian) Holopterygius nudus is reinterpreted as a coelacanth. This genus is among the oldest coelacanths known from articulated remains, but its eel-like morphology marks a considerable departure from the conventional coelacanth body plan. A cladistic analysis places Holopterygius as the sister taxon of the Carboniferous (Serpukhovian) genus Allenypterus. Despite the specialized morphology of these genera, they occupy a surprisingly basal position in coelacanth phylogeny; only Diplocercides and Miguashaia are further removed from the crown. A morphometric analysis reveals that coelacanths were anatomically disparate early in their history. Conflicts between this result and those of previous studies challenge the adequacy of systematic character sets for describing historical patterns of morphological variety. Coelacanths have long had an iconic place in the study of vertebrate evolution for their apparent anatomical conservatism over geological time, but Holopterygius provides clear evidence for rapid morphological evolution early in the history of this clade.     

Why coelacanths are not ‘living fossils’

A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a ‘living fossil’ that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra‐specific molecular diversity does not imply low mutation rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra‐species levels of molecular diversity, inter‐species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as ‘living fossil’, ‘basal lineage’, or ‘primitive extant species’ do not make sense from a tree‐thinking perspective. Editor's suggested further reading in BioEssays Tree thinking for all biology: the problem with reading phylogenies as ladders of progress Abstract     

Evaluation of natural food for planktivorous fish in Lakes Phewa, Begnas, and Rupa in Pokhara Valley, Nepal

Six floating 4-m³ cages stocked with 40 silver carp per cage (three cages) and 40 bighead carp per cage (three cages) were placed in each of the three subtropical Lakes Phewa, Begnas, and Rupa. The fish were cultured, without supplying artificial feed, from August 1994 to December 1995. Fish growth was positively correlated with water temperature, and a slight loss in weight occurred in January when water temperature fell below 16°C in all the lakes. Fish growth was better in Lake Phewa than in Lakes Begnas and Rupa, where food might not have been sufficient or of a quality to sustain fish growth. The fish fed on mostly indigestible phytoplankton, Microcystis aeruginosa in Lake Begnas and on Tabellaria fenestrata and Microcystis aeruginosa in Lake Rupa, which can lead to poor fish growth. The maximum growth rate of silver carp (5.8 g day⁻¹) and bighead carp (4.7 g day⁻¹) occurred in Lake Phewa when Ceratium hirundinella and Peridinium spp. were abundant from August through October. The food particles found in the gut were mostly similar in silver and bighead carp, though Cladocerans (Bosmina longirostris) were observed sparsely in the gut contents of bighead carp only. Received: May 21, 1999 / Accepted: September 28, 1999     

Bibliography of the living coelacanth Latimeria chalumnae,with comments on publication trends

Synopsis A list of published references on the coelacanth Latimeria chalumnae is provided. All known publications in the scientific literature are included as well as popular articles and press reports that are considered to provide new information or interpretations. Marked trends are noticeable in the literature as different disciplines have been applied to research on the coelacanth over the past five decades. The bibliography lists a total of 823 publications including 490 papers in journals, 37 books, 3 theses, 45 chapters in books, 166 popular articles, 22 reports and 60 newspaper articles. Studies on taxonomy and morphology initially dominated the literature followed by reports on research in the fields of physiology, behaviour, breeding biology, ecology and conservation as frozen and eventually live specimens became available for study. The literature on the living coelacanth is predominantly in English, French, Japanese and German but references in 12 other languages were also traced. The dominant authors in the first decades of coelacanth research were the French scientists J. Millot and J. Anthony and the South African describer of the first and second coelacanths, J.L.B. Smith. In subsequent years French, British, American, South African, Japanese, Canadian and German authors, among others, have made significant contributions.     

The histological structure of the calcified lung of the fossil coelacanth Axelrodichthys araripensis (Actinistia: Mawsoniidae)

Abstract: The palaeohistological study of the calcified internal organ of Axelrodichthys araripensis Maisey, 1986, a coelacanthiform from the Lower Cretaceous of Brazil (Crato (Aptian) and Santana (Albian) formations of the Araripe Basin), shows that the walls of this organ consist of osseous blades of variable thickness separated from each other by the matrix. This indicates that, in the living individuals, the walls were reinforced by ossified plates, probably separated by conjunctive tissue. This calcified sheath present in Axelrodichthys, as well as in other fossil coelacanths, lies in ventral position relative to the gut and its single anterior opening is located under the opercle, suggesting a direct connection with the pharynx or the oesophagus. The calcified organ of Axelrodichthys, like that of other fossil coelacanths, is here regarded as an ‘ossified lung’ and compared with the ‘fatty lung’ of the extant coelacanth Latimeria. The reinforcement of the pulmonary walls by the overlying osseous blades could be interpreted as a means of adapting volumetric changes in the manner of bellows, a necessary function for ventilation in pulmonary respiration. Other functional hypotheses such as hydrostatic and/or acoustic functions are also discussed.     

Fossil juvenile coelacanths from the Devonian of South Africa shed light on the order of character acquisition in actinistians

A new coelacanth genus from the Famennian (Upper Devonian) of South Africa is described, principally from presumed juveniles. S erenichthys kowiensis gen. et sp. nov. uniquely shares with Diplocercides a ventral expansion of the elbow‐like lachrymojugal, as well as a symmetrical diphycercal tail supported by expanded neural and haemal spines and radials. Serenichthys is distinguished from Diplocercides by a number of derived characters, including possession of longer anterior parietals, a more crescent‐shaped postorbital with a more anteriorly positioned infraorbital canal, and a far smaller squamosal, which is well separated from the skull roof. By contrast, Serenichthys appears to lacks a second dorsal fin lobe, a derived feature present in Diplocercides. Most specimens of Serenichthys are between 3 and 6 cm in length. They have large eyes, and dermal bones of the skull ornamented with long wavy ridges, similar to the dermal ornament of other Devonian coelacanths such as Gavinia. Larger isolated operculae also collected from the Waterloo Farm locality and attributed to Serenichthys indicate that with growth the ridges on the dermal bones transformed into elongate tubercles, reminiscent of those of Diplocercides and Carboniferous taxa. Phylogenetic analysis resolves Serenichthys as the sister group of Holopterygius and all known post‐Devonian coelacanths. The clade including the unusual leaf‐shaped coelacanths, the Devonian Holopterygius and Carboniferous Allenypterus, branches from the coelacanth lineage immediately crownward of Serenichthys. The presence of abundant juveniles within an estuarine setting strongly parallels the discovery of similarly sized juveniles of Rhabdoderma exiguus together with eggs and yolk‐sack larvae in the Upper Carboniferous Mazon Creek biota. It is therefore argued that Serenichthys, like Rhabdoderma, was using the sheltered estuarine environment as a nursery. © 2015 The Linnean Society of London     

Impacts of two biomanipulation fishes stocked in a large pen on the plankton abundance and water quality during a period of phytoplankton seasonal succession

Silver and bighead carp were stocked in a large pen to control the nuisance cyanobacterial blooms in Meiliang Bay of Lake Taihu. Plankton abundance and water quality were investigated about once a week from 9 May to 7 July in 2005. Biomass of both total crustacean zooplankton and cladocerans was significantly suppressed by the predation of pen-cultured fishes. There was a significant negative correlation between the N:P weight ratio and phytoplankton biomass. The size-selective predation by the two carps had no effect on the biomass of green alga Ulothrix sp. It may be attributed to the low fish stocking density (less than 40 g m⁻³) before June. When Microcystis dominated in the water of fish pen, the pen-cultured carps effectively suppressed the biomass of Microcystis, as indicated by the significant decline of chlorophyll a in the >38 μm fractions of the fish pen. Based on the results of our experiment and previous other studies, we conclude that silver and bighead carp are two efficient biomanipulation tools to control cyanobacterial (Microcystis) blooms in the tropical/subtropical eutrophic waters. Moreover, we should maintain an enough stocking density for an effective control of phytoplankton biomass.