Latimeria Menadoensis Research Articles

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 6million years ago (MYA) and 30MYA, 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.

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.

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.

Mitochondrial genomic divergence in coelacanths (Latimeria): slow rate of evolution or recent speciation?

Dating the divergence between the two known living species of coelacanths has remained a difficult issue because of the very ancient origin of this lineage of fish, which is more closely related to tetrapods than to other fishes. We sequenced the complete mitochondrial genome of a recently captured individual of the Indonesian coelacanth in order to solve this issue. Using an approach based on loglinear models, we studied the molecular divergence between the two species of coelacanths and three other pairs of species, one that has diverged recently (Pan) and two that have diverged more distantly in the past. The loglinear models showed that the divergence between the two species of coelacanths is not significantly different from the two species of Pan. A detailed gene by gene analysis of the patterns of nucleotide and amino acid substitutions between these two pairs of species further supports the similarity of these divergences. On the other hand, a molecular dating analysis suggested a much older origin of the two coelacanth species (between 20 and 30 million years ago). We discuss the potential reasons for this discrepancy. The analysis of new individuals of the Indonesian coelacanth will certainly help to solve this issue.

Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths.

The Pdx1 or Ipf1 gene encodes an important homeodomain-containing protein with key roles in pancreas development and function. Mutations in human PDX1 are implicated in developmental defects and disease of the pancreas. Extensive research, including genome sequencing, has indicated that Pdx1 is the only member of its gene family in mammals, birds, amphibians, and ray-finned fish, and with the exception of teleost fish, this gene forms part of the ParaHox gene cluster along with Gsx1 and Cdx2. The ParaHox cluster, however, is a remnant of a 4-fold genome duplication; the three other ParaHox paralogues lack a Pdx-like gene in all vertebrate genomes examined to date. We have used bacterial artificial chromosome cloning and synteny analysis to show that the ancestor of living jawed vertebrates in fact had more ParaHox genes, including two Pdx genes (Pdx1 and Pdx2). Surprisingly, the two Pdx genes have been retained in parallel in two quite distantly related lineages, the cartilaginous fish (sharks, skates, and chimeras) and the Indonesian coelacanth, Latimeria menadoensis. The Pdx2 gene has been lost independently in ray-finned fish and in tetrapods.

Isolation of a Latimeria menadoensis heat shock protein 70 (Lmhsp70) that has all the features of an inducible gene and encodes a functional molecular chaperone

Molecular chaperones facilitate the correct folding of other proteins, and heat shock proteins form one of the major classes of molecular chaperones. Heat shock protein 70 (Hsp70) has been extensively studied, and shown to be critically important for cellular protein homeostasis in almost all prokaryotic and eukaryotic systems studied to date. Since there have been very limited studies conducted on coelacanth chaperones, the main objective of this study was to genetically and biochemically characterize a coelacanth Hsp70. We have successfully isolated an Indonesian coelacanth (L. menadoensis) hsp70 gene, Lmhsp70, and found that it contained an intronless coding region and a potential upstream regulatory region. Lmhsp70 encoded a typical Hsp70 based on conserved structural and functional features, and the predicted upstream regulatory region was found to contain six potential promoter elements, and three potential heat shock elements (HSEs). The intronless nature of the coding region and the presence of HSEs suggested that Lmhsp70 was stress-inducible. Phylogenetic analyses provided further evidence that Lmhsp70 was probably inducible, and that it branched as a clade intermediate between bony fish and tetrapods. Recombinant LmHsp70 was successfully overproduced, purified and found to be functional using ATPase activity assays. Taken together, these data provide evidence for the first time that the coelacanth encodes a functional molecular chaperone system.

Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus

BackgroundThe mammalian neurohypophysial hormones, vasopressin and oxytocin are involved in osmoregulation and uterine smooth muscle contraction respectively. All jawed vertebrates contain at least one homolog each of vasopressin and oxytocin whereas jawless vertebrates contain a single neurohypophysial hormone called vasotocin. The vasopressin homolog in non-mammalian vertebrates is vasotocin; and the oxytocin homolog is mesotocin in non-eutherian tetrapods, mesotocin and [Phe2]mesotocin in lungfishes, and isotocin in ray-finned fishes. The genes encoding vasopressin and oxytocin genes are closely linked in the human and rodent genomes in a tail-to-tail orientation. In contrast, their pufferfish homologs (vasotocin and isotocin) are located on the same strand of DNA with isotocin gene located upstream of vasotocin gene separated by five genes, suggesting that this locus has experienced rearrangements in either mammalian or ray-finned fish lineage, or in both lineages. The coelacanths occupy a unique phylogenetic position close to the divergence of the mammalian and ray-finned fish lineages.ResultsWe have sequenced a coelacanth (Latimeria menadoensis) BAC clone encompassing the neurohypophysial hormone genes and investigated the evolutionary history of the vertebrate neurohypophysial hormone gene locus within a comparative genomics framework. The coelacanth contains vasotocin and mesotocin genes like non-mammalian tetrapods. The coelacanth genes are present on the same strand of DNA with no intervening genes, with the vasotocin gene located upstream of the mesotocin gene. Nucleotide sequences of the second exons of the two genes are under purifying selection implying a regulatory function. We have also analyzed the neurohypophysial hormone gene locus in the genomes of opossum, chicken and Xenopus tropicalis. The opossum contains two tandem copies of vasopressin and mesotocin genes. The vasotocin and mesotocin genes in chicken and Xenopus, and the vasopressin and mesotocin genes in opossum are linked tail-to-head similar to their orthologs in coelacanth and unlike their homologs in human and rodents.ConclusionOur results indicate that the neurohypophysial hormone gene locus has experienced independent rearrangements in both placental mammals and teleost fishes. The coelacanth genome appears to be more stable than mammalian and teleost fish genomes. As such, it serves as a valuable outgroup for studying the evolution of mammalian and teleost fish genomes.

Can the comparative study of the morphology and histology of the scales of Latimeria menadoensis and L. chalumnae (Sarcopterygii: Actinistia, Coelacanthidae) bring new insight on the taxonomy and the biogeography of recent coelacanthids?

Abstract SEM (Scanning electron microscopy) and photonic microscopy (ground sections) studies confirm that the scales of the coelacanth Latimeria menadoensis have strong morphological and histological similarities with the scales of L. chalumnae . They are both elasmoid scales, the external layer of which is made of radial ridges that are overlaid, on the posterior field, by odontodes. The odontodes of L. menadoensis are made of the typical mineralized tissues described for teeth of the coelacanth and their width is similar to that of L. chalumnae odontodes. Globular corpuscles are found in the isopedine contact with the external layer. Their mineralization seems to be inotropic as in the Mandl's corpuscles of teleost elasmoid scales. Scale organisation in L. menadoensis does not show any characteristics that may support significantly, in the absence of additional evidence, two different species in the extant coelacanths.

‘King of the Sea’: The Prince of Wales and the Stuart Monarchy, 1648–1649

AbstractFrom their outset, the prince of Wales played a politically and symbolically significant part in the English civil wars. But from mid‐1646, with Charles I in the hands of his enemies, primary responsibility for the military and diplomatic aspirations of the House of Stuart devolved almost entirely upon the king's eldest son. Indeed, this essential fact was central to the king's own strategic thinking because he had persuaded himself that his opponents must seek an accommodation with him as long as his successor was at large. The threat posed by the prince became violent reality in 1648 when he commissioned a string of mutinies and rebellions across England and Wales and briefly reasserted royal dominion of the seas. Although his martial and maritime escapades came to nothing, they nevertheless gave the prince his first opportunity to wield the instruments of sovereign power in the exercise of an authority independent of his father's. The second civil war also sharpened the contrast between the prince's freedom of action and the king's hapless captivity. The fortunes of the Stuart monarchy had hit rock bottom, but in the eyes of at least some royalists, an obvious solution had also begun to suggest itself.

Cloning and sequence analysis of the neuropeptide Y receptors Y5 and Y6 in the coelacanth Latimeria chalumnae

Two coelacanth species, Latimeria chalumnae and Latimeria menadoensis, the recently discovered second species, have a key evolutionary position at the divergence of bony fishes and tetrapods. Together with lungfishes, they are the only living species separating the species-rich tetrapods from the other major group of vertebrates, the ray-finned fishes. The coelacanth is therefore of great importance for comparisons of gene families that differ between these two groups, such as the neuropeptide Y (NPY) receptor family. In this work we have sequenced the full-length genes for two NPY receptors in Latimeria chalumnae. Phylogenetic analysis indicated that the two sequences are orthologs of the mammalian Y5 and Y6 receptors. The Y5 gene has been implicated in appetite stimulation in mammals but is absent from teleost fishes. The presence of the Y5 receptor in Latimeria together with phylogenetic analysis shows that Y5 existed before the separation of bony fishes and tetrapods. The Latimeria receptor has about 62 % identity to tetrapod Y5 sequences and contains the extended third intracellular loop with several highly conserved motifs that may be involved in signal transduction. The Latimeria Y6 receptor has about 60% identity to tetrapod Y6 sequences. The functional role of Y6 is unclear as the gene is seemingly functional in some mammals but is non-functional in others. The Y6 receptor is also missing in teleost fishes. Our results confirm an early vertebrate origin for all NPY receptor subtypes presently found in mammals followed by differential gene loss in the different classes of vertebrates.

A distal enhancer and an ultraconserved exon are derived from a novel retroposon

Hundreds of highly conserved distal cis-regulatory elements have been characterized so far in vertebrate genomes. Many thousands more are predicted on the basis of comparative genomics. However, in stark contrast to the genes that they regulate, in invertebrates virtually none of these regions can be traced by using sequence similarity, leaving their evolutionary origins obscure. Here we show that a class of conserved, primarily non-coding regions in tetrapods originated from a previously unknown short interspersed repetitive element (SINE) retroposon family that was active in the Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in the Silurian period at least 410 million years ago (ref. 4), and seems to be recently active in the 'living fossil' Indonesian coelacanth, Latimeria menadoensis. Using a mouse enhancer assay we show that one copy, 0.5 million bases from the neuro-developmental gene ISL1, is an enhancer that recapitulates multiple aspects of Isl1 expression patterns. Several other copies represent new, possibly regulatory, alternatively spliced exons in the middle of pre-existing Sarcopterygian genes. One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE, contains a 31-amino-acid-residue alternatively spliced exon of the messenger RNA processing gene PCBP2 (ref. 6). These add to a growing list of examples in which relics of transposable elements have acquired a function that serves their host, a process termed 'exaptation', and provide an origin for at least some of the many highly conserved vertebrate-specific genomic sequences.

The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths

We determined the whole mitochondrial genome sequence for Indonesian coelacanth Latimeria menadoensis. The genome content and organization were identical to that of typical vertebrates including Comoran coelacanth, Latimeria chalumnae. The overall nucleotide differences between the two species (excluding the control region) was 4.28%. The divergence time between the two species was estimated using whole mitochondrial genome data from the two coelacanths and 26 actinopterygians that represent major actinopterygian lineages plus an outgroup. Partitioned Bayesian analyses were conducted with the two data sets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding ND6 gene) and concatenated nucleotide sequences from 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The molecular clock analysis was also conducted with the concatenated amino acid sequences from the 12 protein-coding genes after removing faster or more slowly evolving sequences. Using the sarcopterygian–actinopterygian split as a calibration point (450 Mya), divergence time estimation between L. menadoensis and L. chalumnae fell in the range of 40–30 Mya, which is much older than those of the previous studies (<6.3 Mya). Assuming that the most recent ancestor of Latimeria was distributed continuously along the deep coasts of Africa through Eurasia, our estimate is in agreement with the hypothesis that the collision of India with Eurasia (50 Mya) and the subsequent siltation caused by the formation of major rivers resulted in a coelacanth habitat disjunction that allowed populations on either side of India to diverge.

Coelacanth genome sequence reveals the evolutionary history of vertebrate genes

The coelacanth is one of the nearest living relatives of tetrapods. However, a teleost species such as zebrafish or Fugu is typically used as the outgroup in current tetrapod comparative sequence analyses. Such studies are complicated by the fact that teleost genomes have undergone a whole-genome duplication event, as well as individual gene-duplication events. Here, we demonstrate the value of coelacanth genome sequence by complete sequencing and analysis of the protocadherin gene cluster of the Indonesian coelacanth, Latimeria menadoensis. We found that coelacanth has 49 protocadherin cluster genes organized in the same three ordered subclusters, alpha, beta, and gamma, as the 54 protocadherin cluster genes in human. In contrast, whole-genome and tandem duplications have generated two zebrafish protocadherin clusters comprised of at least 97 genes. Additionally, zebrafish protocadherins are far more prone to homogenizing gene conversion events than coelacanth protocadherins, suggesting that recombination- and duplication-driven plasticity may be a feature of teleost genomes. Our results indicate that coelacanth provides the ideal outgroup sequence against which tetrapod genomes can be measured. We therefore present L. menadoensis as a candidate for whole-genome sequencing.

Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensis.

The Hox genes encode transcription factors that play a key role in specifying body plans of metazoans. They are organized into clusters that contain up to 13 paralogue group members. The complex morphology of vertebrates has been attributed to the duplication of Hox clusters during vertebrate evolution. In contrast to the single Hox cluster in the amphioxus (Branchiostoma floridae), an invertebrate-chordate, mammals have four clusters containing 39 Hox genes. Ray-finned fishes (Actinopterygii) such as zebrafish and fugu possess more than four Hox clusters. The coelacanth occupies a basal phylogenetic position among lobe-finned fishes (Sarcopterygii), which gave rise to the tetrapod lineage. The lobe fins of sarcopterygians are considered to be the evolutionary precursors of tetrapod limbs. Thus, the characterization of Hox genes in the coelacanth should provide insights into the origin of tetrapod limbs. We have cloned the complete second exon of 33 Hox genes from the Indonesian coelacanth, Latimeria menadoensis, by extensive PCR survey and genome walking. Phylogenetic analysis shows that 32 of these genes have orthologs in the four mammalian HOX clusters, including three genes (HoxA6, D1, and D8) that are absent in ray-finned fishes. The remaining coelacanth gene is an ortholog of hoxc1 found in zebrafish but absent in mammals. Our results suggest that coelacanths have four Hox clusters bearing a gene complement more similar to mammals than to ray-finned fishes, but with an additional gene, HoxC1, which has been lost during the evolution of mammals from lobe-finned fishes.

Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments

We have PCR amplified and sequenced the rhodopsin (RH1) and evolutionarily closely related RH2 genes of the Indonesian coelacanth, now referred to as Latimeria menadoensis. When the RH1 and RH2 coding sequences are constructed, expressed in cultured cells, and reconstituted with 11-cis-retinal, the resulting visual pigments have wavelengths of maximal absorption (λmax) of 485 and 479 nm, respectively. These λmax values are identical to those of the African coelacanth, Latimeria chalumnae, showing that the Indonesian coelacanths also detect a narrow range of color. Statistical analyses show that the adaptation of the coelacanths toward the deep-sea started as early as 200 million years ago.

Biogeography of the Indonesian coelacanths.

Living coelacanths (Latimeria chalumnae) are normally found only in the western Indian Ocean, where they inhabit submarine caves in the Comores Islands1. Two specimens have since been caught off the island of Manado Tua, north Sulawesi, Indonesia, some 10,000 kilometres away2. We sought to determine the ecological and geographic distribution of Indonesian coelacanth populations with a view to drawing up conservation measures for this extremely rare fish2,3. During our explorations, we discovered two living Indonesian coelacanths 360 km southwest of Manado Tua.

Two living species of coelacanths?

During the period of September 1997 through July 1998, two coelacanth fishes were captured off Manado Tua Island, Sulawesi, Indonesia. These specimens were caught almost 10,000 km from the only other known population of living coelacanths, Latimeria chalumnae, near the Comores. The Indonesian fish was described recently as a new species, Latimeria menadoensis, based on morphological differentiation and DNA sequence divergence in fragments of the cytochrome b and 12S rRNA genes. We have obtained the sequence of 4,823 bp of mitochondrial DNA from the same specimen, including the entire genes for cytochrome b, 12S rRNA, 16S rRNA, four tRNAs, and the control region. The sequence is 4.1% different from the published sequence of an animal captured from the Comores, indicating substantial divergence between the Indonesian and Comorean populations. Nine morphological and meristic differences are purported to distinguish L. menadoensis and L. chalumnae, based on comparison of a single specimen of L. menadoensis to a description of five individuals of L. chalumnae from the Comores. A survey of the literature provided data on 4 of the characters used to distinguish L. menadoensis from L. chalumnae from an additional 16 African coelacanths; for all 4 characters, the Indonesian sample was within the range of variation reported for the African specimens. Nonetheless, L. chalumnae and L. menadoensis appear to be separate species based on divergence of mitochondrial DNA.

Indonesian ‘king of the sea’ discovered

On 30 July 1998, an Indonesian population of coelacanth was discovered. It is apparently the same species as the well-known coelacanth from the Comoran archipelago in the Indian Ocean, Latimeria chalumnae Smith.

Review: The Coast Guard under Sail: The U.S. Revenue Cutter Service, 1789-1865, by Irving H. King and Guardians of the Sea: History of the United States Coast Guard, 1915 to the Present, by Robert Erwin Johnson

Book Review| January 01 1991 Review: The Coast Guard under Sail: The U.S. Revenue Cutter Service, 1789-1865, by Irving H. King and Guardians of the Sea: History of the United States Coast Guard, 1915 to the Present, by Robert Erwin Johnson The Coast Guard under Sail: The U.S. Revenue Cutter Service, 1789-1865Irving H. KingGuardians of the Sea: History of the United States Coast Guard, 1915 to the PresentRobert Erwin Johnson John M. Waters John M. Waters Search for other works by this author on: This Site PubMed Google Scholar The Public Historian (1991) 13 (1): 87–88. https://doi.org/10.2307/3378167 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation John M. Waters; Review: The Coast Guard under Sail: The U.S. Revenue Cutter Service, 1789-1865, by Irving H. King and Guardians of the Sea: History of the United States Coast Guard, 1915 to the Present, by Robert Erwin Johnson. The Public Historian 1 January 1991; 13 (1): 87–88. doi: https://doi.org/10.2307/3378167 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Public Historian Search This content is only available via PDF. Copyright 1991 Regents of the University of California Article PDF first page preview Close Modal You do not currently have access to this content.

The Dragon King of the Sea

The Dragon King of the Sea