Coelacanth genome sequenced

April 19, 2013 • 4:08 pm

by Greg Mayer

Coelacanths are one of the three surviving groups of sarcopterygian (lobe-finned) fishes, and along with lungfish, one of the two groups that have remained fish in the vernacular sense (we tetrapods, the third surviving group, have of course become legged). The coelacanths also have a tremendous back story: known in the fossil record from the Devonian (over 350 mya) till the end of the Mesozoic Era (about 65 mya) but not afterward, it came as a great shock when one popped up in South Africa in 1938.

Latimeria chalumnae, the coelacanth (model)
Latimeria chalumnae, the coelacanth (model). Notice lobed fins.

Marjorie Courtenay-Latimer, curator of the local museum, got it at the fishing wharf in East London, Cape Province, where a fishing captain had put it aside for her as an unusual specimen. The discovery of a living specimen of a fish long thought extinct, and one related to tetrapods to boot, was a worldwide sensation. Others eventually turned up at various points in the western Indian Ocean, and in 1998 a population was discovered in Indonesia at the opposite end of the Indian Ocean.

Yesterday, a group led by Chris Amemiya (and including friend-of-this-site Neil Shubin) published the genome sequence of the coelacanth in the journal Nature. It is open access, and remarkably long and detailed given Nature‘s cramped editorial style. To me, two things stand out after a quick look. First, the coelacanth is the next closest relative to the tetrapods, after the lungfish. This is what was expected, but the paper provides much stronger support for this, using a  large data set (251 judiciously chosen genes). Note that, in an especially nice touch, Homo sapiens is represented in the figure by Miss Courtenay-Latimer herself.

Phylogenetic tree using coelacanth genomic data (Fig. 1 from Amemiya etal. 2013).
Phylogenetic tree using coelacanth genomic data (Fig. 1 from Amemiya etal. 2013).

Second, although, slightly more distantly related genealogically to tetrapods than lungfish, the slowly evolving coelacanths provide better comparisons for inferring events in early tetrapod genomic evolution than do the highly genomically derived lungfish. As Ammemiya et al. put it,

The vertebrate land transition is one of the most important steps in our evolutionary history. We conclude that the closest living fish to the tetrapod ancestor is the lungfish, not the coelacanth. However, the coelacanth is critical to our understanding of this transition, as the lungfish have intractable genome sizes (estimated at 50–100Gb)47. Here we have examined vertebrate adaptation to land through coelacanth whole-genome analysis, and have shown the potential of focused analysis of specific gene families involved in this process. Further study of these changes between tetrapods and the coelacanth may provide important insights into how a complex organism like a vertebrate can markedly change its way of life.

This is a bit reminiscent to the situation in studies of vertebrate origins: it now seems clear that sea squirts (urochordates) are closer genealogically to vertebrates than lancelets (cephalochordates), yet lancelets provide better comparative material for investigating early vertebrate evolution than do the highly derived sea squirts.


Amemiya, C., et al. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311-316. (pdf)

Holland, P. 2006 My sister is a sea squirt? Heredity 96:424–425. (pdf)