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African Cichlid Fish Study Reveals Diverse Molecular Mechanisms Underlying Evolution

13 October 2014

In an effort to understand the molecular basis of adaptation in vertebrates, BBSRC-funded researchers have sequenced the genomes and transcriptomes of five species of the African cichlid fish and uncovered a variety of features that enable the fish to thrive in new habitats and ecological niches.

In addition to helping explain the complex genomic mechanisms that give rise to incredible diversity among cichlid fishes, the findings from these 'natural mutants' shed new light on the molecular process of evolution in all vertebrate 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.

October 2014

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