Coelacanth, the case of the missing link

The coelacanth genome is about the same size as the human genome. It is, however, evolving more slowly than the lungfish or the tetrapods, indicating that the latter are more closely related to early land animals than are coelacanths, writes Laasya Samhita.

The term “missing link” is often used in the popular press, and equally often deplored by biologists as a rather glamorous over simplification. It refers to an organism with features intermediate between two existing classes of living organisms, and is thought of as a bridge between them during the course of evolution. In fact, the existence of organisms with features of two different classes of animals is both exciting and important to our understanding of organic evolution, but rarely has it been reduced to the level of a single animal. Rather, several animals with features transitional between two currently existing classes of animals have been discovered from the study of fossils found all over the world. Sometimes, these represented paths that explored a novel form which did not evolve further into anything else, what is referred to as an “evolutionary dead end”. In other cases, some features have evolved many times over evolutionary time (for instance the ability to fly, instinctively linked with birds by a layperson, has evolved many times, among insects, birds and mammals as well) and so cannot be used as sole evidence to speak of “the” missing link. Fossil evidence shows that several intermediate species were not as successful in establishing themselves as the two species “flanking” them and went extinct.

Over the years palaeontologists have discovered several interesting and amazing creatures as fossils. Perhaps among the most popular examples is the flying dinosaur, the archaeopteryx, with the feathered wings of a bird but carrying a tail and teeth like those of dinosaurs. It was hailed as the oldest bird and the possible link between reptiles and birds.

Another fascinating organism that has been hailed as a missing link is the coelacanth. Interest in the coelacanth has recently resurfaced as its genome sequence was worked out and made public just two months ago. The coelacanth is special among all those fossils hailed as “missing links” because it suddenly emerged as a live specimen off the coast of East Africa in 1938. Samantha Weinberg in her book “A fish caught in time” describes the events leading up to and following its discovery. In 1839, the Swiss scientist Louis Agassiz described the fossil of an unusual fish tail found in the north of England. He named it Coelacanthus granulatus, because the fin rays were hollow (Coelacanthus is Greek for hollow spine) and the scales appeared to be decorated with tubercles (granulatus). After this, several Coelacanth-like fossils were discovered all over the world, from China to Brazil to Madagascar. The oldest fossil dated back to about 400 million years (the Devonian period), while the most recent was about 70 million years old (the Cretaceous period). It was generally assumed that the creatures had become extinct around 70 million years ago along with the dinosaurs.

It was known that sometime in the end of the Devonian period, a species of freshwater fish evolved limb like structures and moved on to “conquer” land. There were three main candidates for such “Ichthyostega” or “walking fish”: the lungfish, the rhipidistian and the coelacanth. But poring over fossils, it was hard to determine which was the best bet, as the search was both for limb-like structures as well as the ability to breathe on land, that is the presence of lung like structures.

Studies comparing lungfish and coelacanths tended to support the lungfish as closer than the coelacanths to the first vertebrate on land. However, because similarities between genes are believed to be clues to relatedness between groups of animals, the Coelacanth genome sequence was eagerly awaited. Lungfish genomes contain about 100 billion base pairs of DNA. The Coelacanth genome is about the same size as the human genome — about 3 billion base pairs. The complete sequence of the African coelacanth was worked out two months ago and the study published in the journal Nature. The study compared sequences of genes involved in limb development as well as regulation of genes involved in building a body plan compatible with life on land. It also compared several gene sets across lungfish, tetrapods and coelacanths.

The result of this comparison showed that indeed the lungfish are more closely related to early land animals than are coelacanths. In order to assess the rate at which the coelacanth genome has evolved, the authors calculated a “substitution rate” which estimates how frequently the coelacanth genome has undergone mutations over evolutionary time. The conclusion was that the coelacanth genome has been evolving at a significantly slower rate than the genes of lungfish and tetrapods. In fact, the authors suggest that the strange prehistoric appearance of the current day coelacanth is because of the slow rate of evolution of its genome. This is a somewhat surprising result, because in other aspects, the coelacanth genome appears to be similar to its lungfish or tetrapod counterparts. Critics argue that because all genomes contain regions that change more frequently than others, the choice of gene sets that have been compared could have biased the findings. Without knowledge of how the coelacanth genome is regulated, it is not easy to determine which genes should be compared with which between lungfish and tetrapods. However, it does appear clear that coelacanths are not the immediate ancestors of the first land vertebrates.