An international consortium of experts led by Prof Chris Amemiya from the Benaroya Research Institute at Virginia Mason and the University of Washington has decoded the genome of the African coelacanth, Latimeria chalumnae.
The African coelacanth, Latimeria chalumnae (Hans Fricke / Max-Planck Institute)
A sea-cave dwelling, five-foot long fish with limb-like fins, the coelacanth was once known only from fossils and was thought to have gone extinct about 65 million years ago.
The first living coelacanth was discovered off the African coast in 1938, and since then, questions about these ancient-looking fish have loomed large.
Coelacanths today closely resemble the fossilized 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. This is the first time that we’ve had a big enough gene set to really see that,” said Dr Jessica Alföldi from the Broad Institute, co-author of a paper published in Nature.
Researchers hypothesize 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.’ 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.
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.
In addition to sequencing the full genome 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 its genome remains inscrutable: 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 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 hypothesize 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 hypothesized 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.
The scientists said: “the coelacanth genome may hold other clues for researchers investigating the evolution of tetrapods.”
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Bibliographic information: Chris T. Amemiya et al. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496, pp. 311–316; doi:10.1038/nature12027
