Category Archives: Genome

Washington, April 18 (ANI): Genome sequencing of a historic fish has provided a wealth of information on the genetic changes that accompanied the adaptation from an aquatic environment to land.

The African 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, said 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, who led team.

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 said.

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," asserted 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.

"For evolutionary biologists the coelacanth is an iconic animal, as familiar as Darwin's finches on the Galapagos," said Toby Bradshaw, PhD, Professor and Chair, Department of Biology, University of Washington.

The study will be published as the cover article in Nature. (ANI)

The rest is here:
Fish genome offers insights into evolution of land vertebrate

VICTORIA, British Columbia--(BUSINESS WIRE)--

Bruker and the University of Victoria-Genome British Columbia Proteomics Centre (UVic GBC Proteomics Centre) have announced a collaborative effort for the development and validation of high-throughput assays for determining hemoglobin variants and diabetes risk, using Brukers MALDI Biotyper platform for clinical mass spectrometry, and based on intellectual property developed at the UVic GBC Proteomics Centre.

Diabetes: The liquid chromatography, immunoassay and electrophoresis-based methods which are currently used to screen and monitor for blood disorders are expensive, laborious and time-consuming. In 2009, the Expert Committee of the International Diabetes Foundation recommended the use of the hemoglobin-based A1c (hbA1c) test as the method of choice for diagnosing and monitoring diabetes. In contrast to previous assays, it is expected that the new MALDI (Matrix-Assisted Laser Desorption Ionization) TOF-MS (time-of-flight mass spectrometry) based test for hbA1c and genetic hemoglobin variants designed for use on the MALDI Biotyper platform will provide advantages with regards to specificity, accuracy, speed of analysis and cost per analysis. These performance and cost advantages, coupled with the ease of use and speed of a MALDI-TOF assay, are anticipated to result in higher patient screening rates, which is especially important in the case of diabetes where early detection of at-risk subjects can lead to the prevention of disease onset. Complications of undiagnosed or poorly controlled diabetes include cardiovascular disease, chronic renal failure, retinal damage which can lead to blindness, several kinds of nerve damage, and micro-vascular damage.

Hemoglobin Variants: Some well-known genetic hemoglobin variants are responsible for diseases such as sickle-cell anemia, C disease, and a separate class of diseases known as thalassemias. Diabetes is also reflected in the blood by an increase in the level of glycated hemoglobin, which is measured in the hbA1c test. In general, individuals with inherited blood disorders are physiologically vulnerable and are at higher risk of infection, stroke, heart failure, liver and acute chest syndrome. Late diagnosis of diseases such as sickle-cell anemia can result in delay of treatment and irreversible damage to major organs, including increased risk of stroke or kidney damage.

The MALDI Biotyper platform is already in widespread clinical use with over 800 systems installed globally. Applications include clinical routine microbial identification, environmental and pharmaceutical analysis, taxonomical research, food and consumer product safety and quality control, as well as marine microbiology. The MALDI Biotyper is available in a research-use-only version, as well as in an IVD-CE version according to EU directive EC/98/79 in various European countries, and as a Class 1 Medical Device to clinical microbiology sites in Canada. In the United States of America the MALDI Biotyper is available for research use only, not for use in diagnostic procedures.

Dr. Gary Kruppa, Vice President for Business Development at Bruker Daltonics, stated: The MALDI Biotyper is a versatile, robust, benchtop system that is well suited for use in clinical laboratories as evidenced by its large installed base. We are very pleased to be working with the world-class team of researchers at the UVic GBC Proteomics Centre on the development and validation of high throughput iMALDI tests to further broaden the clinical applications of the MALDI Biotyper platform.

Professor Christoph Borchers, Director of the GBC UVic Proteomics Centre, commented: The collaboration with Bruker is an excellent match. We believe that further development of our MALDI and immunoMALDI (iMALDI) technology will lead to commercialization of MALDI-TOF based tests for a number of important diseases. Developing and validating these tests in collaboration with Bruker gives us a partner ready to deploy such tests on the clinically accepted MALDI Biotyper platform, which will reduce our time to market.

About Bruker Corporation

Bruker Corporation (BRKR) is a leading provider of high-performance scientific instruments and solutions for molecular and materials research, as well as for industrial, diagnostics and applied analysis. For more information, please visit http://www.bruker.com.

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Bruker and the Genome British Columbia Proteomics Centre at the University of Victoria Announce Collaboration on ...

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

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

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

Workers at the National Museum of Kenya show a coelacanth caught by Kenyan fishermen in 2001.

Workers at the National Museum of Kenya show a coelacanth caught by Kenyan fishermen in 2001.

Scientists have unraveled the genome of the coelacanth, a rare and primitive fish once thought to be extinct, shedding light on how closely it's related to the first creatures to emerge from the sea.

The coelacanth, a fish that can reach up to 5 feet long and lives in deep ocean caves, had only been seen in fossils and was thought to have gone extinct some 70 million years ago. That was until 1938, when fishermen from the Comoros islands off the coast of Africa captured one in a net. A second coelacanth species was discovered off the Indonesian island of Sulewesi in 1997.

The coelacanth's genome shows "that the lungfish, and not the coelacanth, is the closest living relative to the tetrapods," according to an abstract of a study published in the journal Nature.

"The lungfish-coelacanth question has gone back and forth over the years; the lungfish answer is not new, but this is a much better, bigger data set so it does tip the balance a bit," researcher John Hutchinson, professor of evolutionary biomechanics from the Royal Veterinary College, told the BBC.

According to National Geographic:

"The most striking feature of this 'living fossil' is its paired lobe fins that extend away from its body like legs and move in an alternating pattern, like a trotting horse. Other unique characteristics include a hinged joint in the skull which allows the fish to widen its mouth for large prey; an oil-filled tube, called a notochord, which serves as a backbone; thick scales common only to extinct fish, and an electrosensory rostral organ in its snout likely used to detect prey."

The analysis of the genome also shows that the coelacanth's genes evolved very slowly, an apparent confirmation of what paleontologists have long believed that the fish has changed little in the past 400 million years.

"If you think about it, this might be correlated to the fact that the coelacanth lives in a rather extreme and stable environment," Professor Kerstin Lindblad-Toh, from the University of Uppsala in Sweden and the Broad Institute of MIT and Harvard, told the BBC.

Read the original here:
Scientists Sequence Genome Of 'Living Fossil' Fish

An international team of researchers join forces to decode the genome of the once-thought-to-be-extinct African coelacanth

Singapore, Apr 18, 2013 - (ACN Newswire) - An enigmatic prehistoric fish has brought scientists at A*STAR's Institute of Molecular and Cell Biology (IMCB) together with researchers from all over the world to crack its genomic code. Findings from the study are providing new insights into the evolutionary history of the African coelacanth (Figure 1)(1) and possible clues as to how aquatic creatures transitioned to life on land.

Coelacanths resemble the fossilised skeletons of their ancestors from more than 300-million years ago (Figure 2). By sequencing its genome and comparing it to genes of other vertebrate species, the researchers have uncovered valuable information on genetic changes that may have helped aquatic animals to transition from water to land, and adapt to life on land. Their findings include many genes and regulatory elements that were gained and genes that were lost when vertebrates came on land. The research findings were published in the 18 April online issue of the prestigious journal, Nature.

The most interesting feature of the coelacanth is its fleshy fins, which resemble the limbs of land animals (Figure 3). The team has found several important regions of the genome used in the formation of limbs, which suggest that land animals (tetrapods) adopted these sequences from coelacanths to help them form limbs. The researchers also found that there are many regulatory changes that influence genes involved in the perception of smell, as creatures that transitioned to land needed new means of detecting chemicals in their environment.

While sequencing the genome of the coelacanth provides some answers, more information on how some vertebrates adapted to land while others remained in the water can be discerned from future research of coelacanth's physiological systems such as the immune system, respiratory system, and reproductive system.

Prof. Byrappa Venkatesh, Research Director IMCB, whose group was involved in the project said, "The coelacanth with its distinctive fleshy fins represents an intermediary phase in the evolution of land animals from aquatic fishes. By comparing the genomes of coelacanth, human and other vertebrates our group has been able to discover gene regulatory elements that played a key role in the development of our limbs and fingers as well as our ability to detect air-borne odorants. Mutations in these elements can potentially lead to genetic diseases."

Prof Hong Wan Jin, Executive Director IMCB, said, "This is the same IMCB group that sequenced the puffer fish genome in 2002 soon after the completion of the human genome and they are truly a pioneer in the field of comparative genomics. I am pleased to note that they are now part of yet another major international collaboration in genomics and are continuing to make significant contributions to our understanding of the structure, function and evolution of the human genome."

Press document (with Figures): http://www.a-star.edu.sg/?TabId=828&articleType=ArticleView&articleId=1803

(1) A deep-sea cave dwelling, five-foot long fish with limb-like fins

Notes for Editor:

Read more from the original source:
A*STAR Scientists Decipher Genome Code of a Living Fossil

17 April 2013 Last updated at 13:54 ET By Rebecca Morelle Science reporter, BBC World Service

The genetic secrets of a "living fossil" have been revealed by scientists.

Researchers sequenced the genome of the coelacanth: a deep-sea fish that closely resembles its ancestors, which lived at least 300 million years ago.

The study found that some of the animal's genes evolved very slowly, giving it its primitive appearance.

The work also shed light on how the fish was related to the first land-based animals.

The coelacanth has four large, fleshy fins, which some scientists believe could have been the predecessors of limbs.

It had been suggested that this fish was closely related to early tetrapods - the first creatures to drag themselves out of the ocean, giving rise to life on land.

But the study, published in the journal Nature, suggested that another fish called the lungfish, which also has four limbs, had more genes in common with land-based animals.

Slow to change

The coelacanth can reach up to 2m-long and is found lurking in caves deep beneath the waves.

See more here:
Genome of 'living fossil' sequenced

Aquamarine Fukushima

An African coelacanth, photographed using a Remotely Operated Vehicle off the coast of Tanga, Tanzania.

By John Roach, Contributing Writer, NBC News

The genome of the coelacanth, an ancient-looking lobed-finned fish, has been sequenced and is already providing insight to the evolutionary changes that allowed the first four-limbed animals, called tetrapods, to crawl out of the water and on to land.

The sequence and preliminary analysis, reported Thursday in the journal Natureby a team spanning 40 research institutions and 12 countries,is a "massive piece of work," Xiaobo Xu, a paleontologist at Kean University who was not involved in the effort, told NBC News in an email.

"The paper really provides rare and valuable genomic data for offering heavy-weight opinions on issues bearing on the fish (to) tetrapod transition," he said.

It also settles a debate that has long raged amongst evolutionary biologists: what fish is the closest relative of tetrapods: the coelacanth or the equally odd-looking lobed-finned lungfish. The winner, according to analysis of the newly-published genome, is the lungfish.

"We think we have definitively shown it now," Jessica Alfldi, a research scientist at the Broad Institute of MIT and Harvard and co-first author of the paper, told NBC News. "They are very close, which is why it took so much data to figure it out."

Slow evolving genes Scientists thought coelacanths went extinct about 70 million years ago, during the Late Cretaceous period. That changed when a fish trawler off the South African coast delivered a fresh-caught coelacanth to a local natural history museum in 1938, proving that the fish are alive and well.

The coelacanths' odd, ancient-looking looks raised eyebrows and earned it the nickname "living fossil" much to the chagrin of evolutionary biologists, noted Alfldi. ("It makes people think there was no evolution," she explained.)

Read more:
Genome of ancient-looking fish gives clues to first limbed landlubbers