Daily Archives: April 18, 2013

The fish known as a living fossil for its close resemblance to ancient predecessors had its genome sequenced by scientists who say it offers clues to how animal ancestors crawled out of the sea.

African coelacanth, discovered alive in 1938 after having been presumed extinct for 70 million years, was found to have genes that reveal how land animals hands, feet, immune systems and other body features may have evolved, according to a report in the journal Nature.

The coelacanth can grow to two meters (six feet) and live as many as 60 years in the wild, according to National Geographic. Their front fins are fleshy, resembling the limbs of four-legged land animals. The gene sequencing enabled researchers to see changes between water and air, to the sense of smell, the immune system, and the bodys ability to eliminate waste.

People had these romantic views of the coelacanth, that it was a fish lost in time or something like that, said Jessica Alfoldi, a research scientist at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, and a study author. We found that actually, the vast majority of the genome isnt slow-evolving.

The genes, or the minority of the genome that codes proteins, havent changed much, the report found. Thats because the deep-sea caves where the coelacanth live likely dont have many predators or much competition for resources, Alfoldi said.

Evolution acts strongly on genes when they need to change, Alfoldi said. Thats why we dont look like fish anymore.

The group did an analysis of which genes and regulatory DNA were lost, gained or altered. They found changes to regulatory DNA, which influenced genes involved in smell, suggesting a change from underwater smelling to detecting airborne odors. Also, a large number of immune system regulatory DNA changed, possibly as a response to the different types of pathogens found on land.

Several genetic regions may have been used to form limbs, fingers, toes, and, in mammals, the placenta. Of note is a region called HOXD, which is shared between coelacanths and four-legged land animals. This sequence is probably what altered to allow for hands and feet, the researchers said.

Waste elimination changed when the ancestors of landlubbers first crawled out of the sea. Protein is broken into sugars and nitrogen; fish get rid of the nitrogen by excreting ammonia into the water. Humans and other land animals convert the ammonia to urea in the liver; urea and water together are known as urine. One of the key genes in this cycle was modified in land animals, when compared to the fish.

The research was supported by grants from the National Human Genome Research Institution.

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Living-Fossil Fish’s Genome Gives Clues of Landlubbers

Public release date: 17-Apr-2013 [ | E-mail | Share ]

Contact: Kay Branz kbranz@benaroyaresearch.org 206-342-6903 Immune Tolerance Network

An historic fish, with an intriguing past, now has had its genome sequenced, providing a wealth of information on the genetic changes that accompanied the adaptation from an aquatic environment to land. A team of international researchers led by Chris Amemiya, PhD, Director of Molecular Genetics at the Benaroya Research Institute at Virginia Mason (BRI) and Professor of Biology at the University of Washington, will publish "The African coelacanth genome provides insights into tetrapod evolution" April 18 as the cover article in Nature. The coelacanth genome was sequenced by the Genome Center at the Broad Institute of MIT and Harvard, and analyzed by an international consortium of experts.

Sequencing the coelacanth genome has been a long-sought goal and a major logistical milestone, says Dr. Amemiya. He and scientists throughout the world have campaigned for sequencing of the fish for over a decade. "Analysis of changes in the genome during vertebrate adaptation to land has implicated key genes that may have been involved in evolutionary transitions," he says. These include those regulating immunity, nitrogen excretion and the development of fins, tail, ear, eye, and brain as well as those involved in sensing of odorants. The coelacanth genome will serve as a blueprint for better understanding tetrapod evolution.

"This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans, and, combined with modern empirical approaches, can lend insights into the mechanisms that have contributed to major evolutionary innovations," says Dr. Amemiya.

The coelacanth is critical to study because it is one of only two living lobe-finned fish groups that represent deep and evolutionarily informative lineages with respect to the land vertebrates. The other is the lungfish, which has an enormous genome that currently makes it impractical to sequence. The lobe-finned fishes are genealogically placed in-between the ray-finned fishes (such as goldfish and guppies) and the tetrapods the first four-limbed vertebrates and their descendants, including living and extinct amphibians, reptiles, birds and mammals. A lobe-finned ancestor(s) underwent genomic changes that accompanied the transition of life in an aquatic environment to life on land. The coelacanth is undeniably a fish, however, phylogenetic analyses show that its genes are more like those of tetrapods than of ray-finned fishes. Additionally, coelacanth genes evolve at a considerably slower rate than those of tetrapods, a fact that is coincident with its apparently slow rate of morphological change.

"For evolutionary biologists the coelacanth is an iconic animal, as familiar as Darwin's finches on the Galapagos," says Toby Bradshaw, PhD, Professor and Chair, Department of Biology, University of Washington. "This paper by Chris and colleagues gives us our first comprehensive look at the coelacanth's place in our evolutionary history, and provides fascinating insights into the specific vertebrate genes involved in the critical transition from water to land it seems that both loss and gain of gene function were required. I find the proposed gain-of-function changes in gene regulation for limb development particularly compelling, supported by experimental evidence that the lobed fins of the coelacanth really are akin to prototypical legs. Making legs from fins is a wonderful example of Francois Jacob's observation that 'evolution is a tinkerer, not an engineer.'" Adds Gerald Nepom, MD, PhD, Director of the Benaroya Research Institute, "This work represents a major accomplishment by a large and talented group of investigators, opening a new book of knowledge about adaptation that is now available to all scientists who want to better understand our complex genetic origins."

Genome sequencing is a laboratory and computational process that determines the complete DNA sequence of an organism's genome. Deciphering the genetic makeup of the coelacanth provides valuable clues for biologists studying the evolution of vertebrates. It was an international sensation when a living specimen of the coelacanth was first discovered in l938 as this lineage of fish was thought to have gone extinct 70 million years ago. The living coelacanth has many anatomical similarities with its fossil relatives and seems to have undergone seemingly little morphological change since the Devonian period approximately 360 million years ago. It still possesses what many would consider to be a prehistoric appearance, and, as for many similar species that do not show much change over long evolutionary periods, is often dubbed a "living fossil." The relationship of the slow rate of evolution of its genes and its morphological appearance remains unknown and largely speculative. Today, coelacanths are on the endangered species list and biological tissues can only be obtained from expired animals that have been caught accidentally by fishermen.

In addition to this landmark genome paper in Nature, several companion papers are being edited by Drs. Amemiya and Axel Meyer for publication in a special open access coelacanth genome issue of the Journal of Experimental Zoology (Molecular and Developmental Evolution).

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Genome sequencing of the living coelacanth sheds light on the evolution of land vertebrate

Apr. 17, 2013 An historic fish, with an intriguing past, now has had its genome sequenced, providing a wealth of information on the genetic changes that accompanied the adaptation from an aquatic environment to land. A team of international researchers led by Chris Amemiya, PhD, Director of Molecular Genetics at the Benaroya Research Institute at Virginia Mason (BRI) and Professor of Biology at the University of Washington, will publish "The African coelacanth genome provides insights into tetrapod evolution" April 18 as the cover article in Nature.

The coelacanth genome was sequenced by the Genome Center at the Broad Institute of MIT and Harvard, and analyzed by an international consortium of experts.

Sequencing the coelacanth genome has been a long-sought goal and a major logistical milestone, says Dr. Amemiya. He and scientists throughout the world have campaigned for sequencing of the fish for over a decade. "Analysis of changes in the genome during vertebrate adaptation to land has implicated key genes that may have been involved in evolutionary transitions," he says. These include those regulating immunity, nitrogen excretion and the development of fins, tail, ear, eye, and brain as well as those involved in sensing of odorants. The coelacanth genome will serve as a blueprint for better understanding tetrapod evolution.

"This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans, and, combined with modern empirical approaches, can lend insights into the mechanisms that have contributed to major evolutionary innovations," says Dr. Amemiya.

The coelacanth is critical to study because it is one of only two living lobe-finned fish groups that represent deep and evolutionarily informative lineages with respect to the land vertebrates. The other is the lungfish, which has an enormous genome that currently makes it impractical to sequence. The lobe-finned fishes are genealogically placed in-between the ray-finned fishes (such as goldfish and guppies) and the tetrapods the first four-limbed vertebrates and their descendants, including living and extinct amphibians, reptiles, birds and mammals. A lobe-finned ancestor(s) underwent genomic changes that accompanied the transition of life in an aquatic environment to life on land. The coelacanth is undeniably a fish, however, phylogenetic analyses show that its genes are more like those of tetrapods than of ray-finned fishes. Additionally, coelacanth genes evolve at a considerably slower rate than those of tetrapods, a fact that is coincident with its apparently slow rate of morphological change.

"For evolutionary biologists the coelacanth is an iconic animal, as familiar as Darwin's finches on the Galapagos," says Toby Bradshaw, PhD, Professor and Chair, Department of Biology, University of Washington. "This paper by Chris and colleagues gives us our first comprehensive look at the coelacanth's place in our evolutionary history, and provides fascinating insights into the specific vertebrate genes involved in the critical transition from water to land it seems that both loss and gain of gene function were required. I find the proposed gain-of-function changes in gene regulation for limb development particularly compelling, supported by experimental evidence that the lobed fins of the coelacanth really are akin to prototypical legs. Making legs from fins is a wonderful example of Francois Jacob's observation that 'evolution is a tinkerer, not an engineer.'" Adds Gerald Nepom, MD, PhD, Director of the Benaroya Research Institute, "This work represents a major accomplishment by a large and talented group of investigators, opening a new book of knowledge about adaptation that is now available to all scientists who want to better understand our complex genetic origins."

Genome sequencing is a laboratory and computational process that determines the complete DNA sequence of an organism's genome. Deciphering the genetic makeup of the coelacanth provides valuable clues for biologists studying the evolution of vertebrates. It was an international sensation when a living specimen of the coelacanth was first discovered in l938 as this lineage of fish was thought to have gone extinct 70 million years ago. The living coelacanth has many anatomical similarities with its fossil relatives and seems to have undergone seemingly little morphological change since the Devonian period approximately 360 million years ago. It still possesses what many would consider to be a prehistoric appearance, and, as for many similar species that do not show much change over long evolutionary periods, is often dubbed a "living fossil." The relationship of the slow rate of evolution of its genes and its morphological appearance remains unknown and largely speculative. Today, coelacanths are on the endangered species list and biological tissues can only be obtained from expired animals that have been caught accidentally by fishermen.

In addition to this landmark genome paper in Nature, several companion papers are being edited by Drs. Amemiya and Axel Meyer for publication in a special open access coelacanth genome issue of the Journal of Experimental Zoology (Molecular and Developmental Evolution).

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Read the original:
Coelacanth genome informs land vertebrate evolution

Credit: Chip Clark/Smithsonian Institution

CAMBRIDGE, Mass., April 17 (UPI) -- The genome of the African coelacanth, a creature whose evolutionary history is enigmatic, sheds light on the evolution of land vertebrates, researchers say.

The genome of the coelacanth, a fish once believed extinct until live examples began to be caught in the 20th century, is providing a wealth of information on the genetic changes that accompanied the adaptation from an aquatic environment to land, scientists said.

Because of their resemblance to fossils dating back millions of years, coelacanths are sometimes dubbed "living fossils," a tag researchers say is inappropriate.

"It's not a living fossil; it's a living organism," research scientist Jessica Alfoldi of the Broad Institute in Cambridge, Mass., said. "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."

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.

The coelacanth genome can serve as a blueprint for better understanding tetrapod evolution, the researchers said.

"This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans, and, combined with modern empirical approaches, can lend insights into the mechanisms that have contributed to major evolutionary innovations," study co-author Chris Amemiya, a biologists at the University of Washington, said.

Read more:
Genome of unique fish species may give clues to vertebrate evolution