An international team of researchers from institutions such as Broad Institute at MIT/Harvard, the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape (UWC) and Rhodes University (RU) has decoded the genome of a creature whose evolutionary history is both enigmatic and illuminating: the African coelacanth. A sea-cave dwelling, five-foot long fish with limb-like fins, the coelacanth was once thought to be extinct. A living coelacanth was discovered off the African coast in 1938, and since then, questions about these ancient-looking fish – popularly known as “living fossils” – have loomed large. Coelacanths today closely resemble the fossilised skeletons of their more than 300-million-year-old ancestors. Its genome confirms what many researchers had long suspected: genes in coelacanths are evolving more slowly than in other organisms.
“We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at,” said Jessica Alföldi, a research scientist at the Broad Institute and co-first author of a paper on the coelacanth genome, which appears in Nature this week. “This is the first time that we’ve had a big enough gene set to really see that.”
Researchers hypothesise that this slow rate of change may be because coelacanths simply have not needed to change: they live primarily off of the Eastern African coast (a second coelacanth species lives off the coast of Indonesia), at ocean depths where relatively little has changed over the millennia.
Because of their resemblance to fossils dating back millions of years, coelacanths today are often referred to as “living fossils” – a term coined by Charles Darwin. But the coelacanth is not a relic of the past brought back to life: it is a species that has survived, reproduced, but changed very little in appearance for millions of years. “It’s not a living fossil; it’s a living organism,” said Alföldi. “It doesn’t live in a time bubble; it lives in our world, which is why it’s so fascinating to find out that its genes are evolving more slowly than ours.”
The coelacanth genome has also allowed scientists to test other long-debated questions. For example, coelacanths possess some features that look oddly similar to those seen only in animals that dwell on land, including “lobed” fins, which resemble the limbs of four-legged land animals (known as tetrapods). Another odd-looking group of fish known as lungfish possesses lobed fins too. It is likely that one of the ancestral lobed-finned fish species gave rise to the first four-legged amphibious creatures to climb out of the water and up on to land, but until now, researchers could not determine which of the two is the more likely candidate.
In addition to sequencing the full genome – nearly 3 billion “letters” of DNA – from the coelacanth, the researchers also looked at RNA content from coelacanth (both the African and Indonesian species) and from the lungfish. This information allowed them to compare genes in use in the brain, kidneys, liver, spleen and gut of lungfish with gene sets from coelacanth and 20 other vertebrate species. Their results suggested that tetrapods are more closely related to lungfish than to the coelacanth.
However, the coelacanth is still a critical organism to study in order to understand what is often called the water-to-land transition. Lungfish may be more closely related to land animals, but at 100 billion letters in length, the lungfish genome is simply too unwieldy for scientists to sequence, assemble, and analyze. The coelacanth’s more modest-sized genome (comparable in length to our own) is yielding valuable clues about the genetic changes that may have allowed tetrapods to flourish on land.
By looking at what genes were lost when vertebrates came on land as well as what regulatory elements – parts of the genome that govern where, when, and to what degree genes are active – were gained, the researchers made several unusual discoveries:
- Sense of smell. The team found that many regulatory changes influenced genes involved in smell perception and detecting airborne odors. They hypothesise that as creatures moved from sea to land, they needed new means of detecting chemicals in the environment around them.
- Immunity. The researchers found a significant number of immune-related regulatory changes when they compared the coelacanth genome to the genomes of animals on land. They hypothesised that these changes may be part of a response to new pathogens encountered on land.
- Evolutionary development. Researchers found several key genetic regions that may have been “evolutionarily recruited” to form tetrapod innovations such as limbs, fingers and toes, and the mammalian placenta. One of these regions, known as HoxD, harbors a particular sequence that is shared across coelacanths and tetrapods. It is likely that this sequence from the coelacanth was co-opted by tetrapods to help form hands and feet.
- Urea cycle. Fish get rid of nitrogen by excreting ammonia into the water, but humans and other land animals quickly convert ammonia into less toxic urea using the urea cycle. Researchers found that the most important gene involved in this cycle has been modified in tetrapods.
Sequencing the full coelacanth genome was uniquely challenging for many reasons. Coelacanths are endangered animals, meaning that samples available for research are almost nonexistent. This meant that each sample obtained was precious: researchers would have one shot at sequencing the collected genetic material, according to Alföldi. But the difficulties in obtaining a sample and the challenges of sequencing it also knit the community together.
South African lead researcher Professor Alan Christoffels started working on a coelacanth project 10 years ago in Singapore when he was part of a team that analysed the developmental genes (HOX genes) of the coelacanth. At that time there was no completely sequenced genome sequence. About a year ago, Christoffels was invited to participate in the genomic analysis of the Coelacanth genome together with his team from UWC’s South African Bioinformatics Institute (SANBI). The team included three postdocs – namely Drs Hesse, Panji and Picone – as well as software programmer Peter van Heusden, and SANBI staff members Dr Junaid Gamieldien and Mario Jonas.
“Each of the international teams focused on one aspect of the evolution of this species. We identified what is called “gene expansions” in this ancient organism and found that some of these multiple copies of the same gene are peculiar to coelacanth. This phenomenon usually indicates new adaptations in the context of an organism’s functions. More specifically we identified a class of olfactory genes whose function fits a model for vertebrate adaptation,” says Christoffels
Researchers from 40 institutions across 12 countries contributed to this work. Many funding agencies around the world provided support, from South Africa these included the South African Institute for Aquatic Biodiversity (SAIAB) African Coelacanth Ecosystem Programme (ACEP) funded by the South African National Department of Science and Technology, which supported the collection of samples from coelacanths found off Sodwana Bay on the East coast of South Africa, Rhodes University (RU), and the National Human Genome Research Institute, which supported the Broad Institute’s contributions including genome sequencing.
About the Coelacanth:
In 1938, a South African museum curator discovered an unusual fish among the catch of a local trawler. This fish was curiously similar to fossils from the Cretaceous period and was soon identified as a modern coelacanth – named by Prof JLB Smith, who identified it, as Latimeria chalumnae after the curator, Marjori Courtnay-Latimer who had discovered it. A second species, the Indonesian coelacanth (Latimeria menadoensis), was discovered in 1998. The coelacanth is a member of the ancient group of lobe-finned fishes, all of which were thought to have been extinct since the Late Cretaceous period, seventy million years ago. Both known species of coelacanth are threatened (the West Indian Ocean/Indonesian coelacanth is critically endangered), making this the most endangered order of animals in the world.
About SANBI:
The South African National Bioinformatics Institute within the University of the Western Cape (not to be confused with the similarly named South African Biodiversity Institute) is a Medical Research Council Unit for bioinformatics capacity development with the mission to conduct cutting edge bioinformatics and computational biology research relevant to South African, African and global populations.
For more information about SANBI’s involvement in the project mentioned above, please contact Professor Alan Christoffels at alan@sanbi.ac.za or via telephone at 021 959 2969. For more general information about SANBI, you can visit the SANBI website at www.sanbi.ac.za or contact the SANBI offices at (021) 959 3645 or via email at info@sanbi.ac.za.