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DNA of “living fossil” decoded

April 17, 2013
Courtesy of the Broad Institute of MIT
and World Science staff

Re­search­ers have de­cod­ed the ge­nome of a fish of­ten seen as the most fa­mous “liv­ing fos­sil”: the Af­ri­can coe­la­canth.

A five-foot (1.5 me­ter) long sea-cave dwell­er with limb-like fins, the fish was once thought to be ex­tinct, un­til a liv­ing one turned up off the Af­ri­can coast in 1938. Since then, ques­tions about the primitive-looking crea­ture—thought to be a rel­a­tive of the first land-walking, four-legged an­i­mals—have loomed large.

An Af­ri­can coe­la­canth (L. chalum­nae), pho­tographed us­ing a Re­mote­ly Op­er­ated Ve­hi­cle off the coast of Tan­ga, Tan­za­nia. (Cred­it: Aq­ua­ma­rine Fu­ku­shi­ma )


Coela­canths closely re­sem­ble the fos­sil­ized skele­tons of their more than 300-million-year-old an­ces­tors. Their ge­nome con­firms what many had sus­pected: the genes are evolv­ing slow­ly, the sci­en­tists said.

They’re “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 of the Mas­sa­chu­setts In­stit­tute of Tech­nol­o­gy and a col­la­bo­ra­tor in the work. “This is the first time that we’ve had a big enough gene set to really see that.”

The find­ings ap­pear in the re­search jour­nal Na­ture this week.

Re­search­ers spec­u­late that the change may be so slow be­cause coe­la­canths haven’t needed to change. They live mainly off of the East­ern Af­ri­can coast—a sec­ond coe­la­canth spe­cies lives off the coast of In­done­si­a—at depths where not much has changed over the mil­len­nia.

“There are still a few places on Earth where or­gan­isms don’t have to change, and this is one of them,” said Ker­stin Lindblad-Toh, the pa­per’s sen­ior au­thor and sci­en­tif­ic di­rec­tor of the ver­te­brate ge­nome bi­ol­o­gy group at the Broad In­sti­tute.

Coela­canths are of­ten called “liv­ing fos­sils,” a term coined by Charles Dar­win.

The de­cod­ed ge­nome has al­so let sci­en­tists test oth­er long­stand­ing ques­tions, the re­search­ers said. For ex­am­ple, coe­la­canths have some fea­tures that look oddly si­m­i­lar to those seen only in land-dwelling an­i­mals, in­clud­ing “lobed” fins, which re­sem­ble the limbs of four-leg­ged land an­i­mals, called tet­ra­pods. 

Anoth­er odd-looking group of fish known as lung­fish has lobed fins too. It’s con­sid­ered likely that one of the an­ces­tral lobe-finned fish spe­cies gave rise to the first four-leg­ged crea­tures to climb on to land, but un­til now, re­search­ers could­n’t fig­ure out which of the two fish types is more closely re­lat­ed. 

The find­ings sug­gest the an­swer is lung­fish, the in­ves­ti­ga­tors said.

But the coe­la­canth is still a key or­gan­ism to study in or­der to un­der­stand what is of­ten called the water-to-land tran­si­tion, the re­search­ers said. Lung­fish may be more closely re­lat­ed to land an­i­mals, but its ge­nome is too long for sci­en­tists to an­a­lyze in prac­ti­cal terms. The coe­la­canth’s smaller ge­nome, com­pa­ra­ble in length to our own, is yield­ing clues about the changes that may have al­lowed tet­ra­pods to flour­ish on land, the in­ves­ti­ga­tors said.

Besides se­quenc­ing the full coe­la­canth ge­nome, nearly three bil­lion “let­ters” of DNA, the re­search­ers checked RNA con­tent from coe­la­canth—both Af­ri­can and In­done­sian—and lung­fish. RNA is a chem­i­cal cous­in of DNA al­so used as part of the body’s ge­net­ic sys­tem.

By check­ing which 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 said they made some un­usu­al find­ings. For in­stance, they iden­ti­fied sev­er­al re­gions of the ge­nome that may have been ev­o­lu­tion­arily “re­cruit­ed” to form tet­ra­pod in­nova­t­ions such as limbs, fin­gers and toes, and the pla­cen­ta. One of these re­gions, known as HoxD, har­bors a se­quence shared across coe­la­canths and tet­ra­pods and seems to have been co-opted by tet­ra­pods to help form hands and feet, they added.

“This is just the be­gin­ning of many anal­y­ses on what the coe­la­canth can teach us about the emer­gence of land ver­te­brates, in­clud­ing hu­mans,” said Chris Amemiya of the Uni­vers­ity of Wash­ing­ton, one of the col­la­bo­ra­tors in the work.

Se­quenc­ing the full coe­la­canth ge­nome was an ar­du­ous task for many rea­sons, the group added. Coela­canths are an en­dan­gered spe­cies, so sam­ples 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.

“The in­terna­t­ional na­ture of the work, its ev­o­lu­tion­ary val­ue and his­to­ry, and the fact that it was a tech­nic­ally chal­leng­ing proj­ect really brought peo­ple to­geth­er,” said Lindblad-Toh.


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Researchers have decoded the genome of a fish often seen as the most famous “living fossil”: the African coelacanth, thought to be a relative of the first land-walking animals. A five-foot (1.5 meter) long sea-cave dweller with limb-like fins, the fish was once thought to be extinct, until a living one turned up off the African coast in 1938. Since then, questions about the primitive-looking creature have loomed large. Coelacanths closely resemble the fossilized skeletons of their more than 300-million-year-old ancestors. Their genome confirms what many had suspected: the genes are evolving slowly, the scientists said. They’re “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 of the Massachusetts Instittute of Technology and a collaborator in the work. “This is the first time that we’ve had a big enough gene set to really see that.” The findings appear in the research journal Nature this week. Researchers speculate that the change may be so slow because coelacanths haven’t needed to change. They live mainly off of the Eastern African coast—a second coelacanth species lives off the coast of Indonesia—at depths where not much has changed over the millennia. “There are still a few places on Earth where organisms don’t have to change, and this is one of them,” said Kerstin Lindblad-Toh, the paper’s senior author and scientific director of the vertebrate genome biology group at the Broad Institute. Coelacanths are often called “living fossils,” a term coined by Charles Darwin. The decoded genome has also let scientists test other longstanding questions, the researchers said. For example, coelacanths have some features that look oddly similar to those seen only in land-dwelling animals, including “lobed” fins, which resemble the limbs of four-legged land animals, called tetrapods. Another odd-looking group of fish known as lungfish has lobed fins too. It’s considered likely that one of the ancestral lobe-finned fish species gave rise to the first four-legged creatures to climb on to land, but until now, researchers couldn’t figure out which of the two fish types is more closely related. The findings suggest the answer is lungfish, the investigators said. But the coelacanth is still a key organism to study in order to understand what is often called the water-to-land transition, the researchers said. Lungfish may be more closely related to land animals, but its genome is too long for scientists to analyze in practical terms. The coelacanth’s smaller genome, comparable in length to our own, is yielding clues about the changes that may have allowed tetrapods to flourish on land, the investigators said. In addition to sequencing the full coelacanth genome, nearly three billion “letters” of DNA, the researchers also checked RNA content from coelacanth—both African and Indonesian—and lungfish. RNA is a chemical cousin of DNA also used as part of the body’s genetic system. By checking which 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 said they made some unusual findings. For instance, they identified several regions of the genome that may have been evolutionarily “recruited” to form tetrapod innovations such as limbs, fingers and toes, and the placenta. One of these regions, known as HoxD, harbors a sequence shared across coelacanths and tetrapods and seems to have been co-opted by tetrapods to help form hands and feet, they added. “This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans,” said Chris Amemiya of the University of Washington, one of the collaborators in the work. Sequencing the full coelacanth genome was an arduous task for many reasons, the group added. Coelacanths are an endangered species, so samples 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. “The international nature of the work, its evolutionary value and history, and the fact that it was a technically challenging project really brought people together,” said Lindblad-Toh.