- Reservoir of mutations enabled cichlid fish to adapt to varied environments; results shed light on mechanisms of vertebrate evolution.
- The study, led by Director of Science at The Genome Analysis Centre (TGAC) Federica Di Palma examines the molecular basis of adaption and evolution in vertebrates by sequencing the genomes of African cichlid fish species
The new study, published in Nature, was a collaboration between scientists at The Genome Analysis Centre, the Broad Institute, Eawag Swiss Federal Institute for Aquatic Sciences and Georgia Institute of Technology.
The cichlid fish species as a model system gives us valuable insight into human biology and disease. Federica Di Palma said: “By learning how natural populations, such as fishes, adapt and evolve under selective pressures, we can learn how these pressures affect humans in terms of health and disease.”
The African cichlid fishes are some of the most phenotypically diverse groups of organisms on the planet, with over 2,000 known species. Some lakes are home to hundreds of distinct species that evolved from a common ancestral species that left its ancient river habitat to colonize lakes. Like Darwin’s finches, the cichlids are a dramatic example of adaptive radiation, the process by which multiple species ‘radiate’ from an ancestral species through adaptation.
“Our study reveals a spectrum of methods that nature uses to allow organisms to adapt to different environments,” said senior author Kerstin Lindblad-Toh, Scientific Director of Vertebrate Genome Biology at the Broad Institute: “These mechanisms are likely to be at work in humans and other vertebrates, and by focusing on the remarkably diverse cichlid fishes we were able to study this process on a broad scale for the first time.”
The researchers examined the cichlid genome as a model system to determine how the fish diversify broadly in a relatively short time. The researchers sequenced the DNA and RNA from ten tissues of five distinct lineages of African cichlids and found many interesting features. For example, compared to an ancestral lineage the East African cichlid genomes possess an excess of gene duplications; alterations in regulatory, non-protein-coding elements in the genome; accelerated evolution of protein-coding elements, especially in genes for pigmentation; and other distinct features that affect gene expression.
“It’s not one big change in the genome of this fish, but lots of different molecular mechanisms used to achieve this amazing adaptation and speciation,” said Federica.
Ole Seehausen, senior author and Head of Fish Ecology and Evolution at Eawag Aquatic Research, said: “African cichlid fish stand out amongst fish by their incredible richness of species that evolved without geographical isolation and that now coexist within individual lakes. We were puzzled about how their genomic blueprint could accommodate all the different forms and functions.
“We learned that the radiation ancestors had an opportunity to amass genomic variation of many different kinds. At the time this was probably rather useless genomic variation, but has now become incredibly beneficial millions of years later when the opportunity for major adaptive radiations arose, changing the way we think about evolutionary processes.”
This work was funded in part by the National Human Genome Research Institute (NHGRI), the Swiss National Science Foundation, the German Science Foundation, Biomedical Research Council of A*STAR, Singapore, the European Research Council, and the Wellcome Trust. TGAC is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
The paper, titled: “The genomic substrate for adaptive radiation in African cichlid fish” is published in Nature.
The Genome Analysis Centre (TGAC) is a world-class research institute focusing on the development of genomics and computational biology. TGAC is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) – £7.4M in 2013/14 – as well as support from other research funders. TGAC is one of eight institutes that receive strategic funding from BBSRC. TGAC operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
TGAC offers state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a Training programme through courses and workshops, and an Outreach programme targeting schools, teachers and the general public through dialogue and science communication activities. ww.tgac.ac.uk
About the Broad Institute of Harvard and MIT
The Eli and Edythe L. Broad Institute of Harvard and MIT was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.
Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to www.broadinstitute.org
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, and with an annual budget of around £467M (2012-2013), we support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
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