Reservoir of mutations enabled cichlid fish to adapt to varied environments; results shed light on mechanisms of vertebrate evolution.
In an effort to understand the molecular basis of adaptation in vertebrates, researchers sequenced the genomes and transcriptomes of five species of the African cichlid fish. The researchers uncovered a variety of features in the cichlid genome that enabled the fishes to thrive in new habitats and ecological niches within the Great Lakes of East Africa. 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 research paper, done in collaboration with scientists at the Broad Institute, Eawag Swiss Federal Institute for Aquatic Sciences and Georgia Institute of Technology, in addition to international scientists in the cichlid research community, appears in the September, advance online edition of Nature.
Using the cichlid fish species as a model system gives us valuable insight into human biology and disease. Federica Di Palma, last author of the Nature study, previously Assistant Director of Vertebrate Sequencing and Analysis at the Broad, said: “This study shows how important it is to fund underpinning biology research in non-conventional model organisms. 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 the lake. 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 also 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 wanted to examine the cichlid genome as a model system and determine what allowed these fishes to diversify broadly in a relatively short time. The researchers sequenced the DNA and RNA – the genome and transcriptomes (all the messenger RNA) from ten tissues – of five distinct lineages of African cichlids. The sequenced species include the Nile tilapia, representing the ancestral lineage, and four East African species: a species that inhabits a river near Lake Tanganyika; a species from Lake Tanganyika that appeared 10-20 million years ago; a cichlid species from Lake Malawi that appeared less than 5 million years ago; and a very recent species from Lake Victoria that radiated less than 15,000 to 100,000 years ago.
After analysing the data, the researchers found a surprising number of genomic elements at play. Compared to the 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, such as insertions of transposable elements and regulation by novel microRNAs.
“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. Some changes in the genome appear to have accumulated before the species left the rivers to colonize lakes and radiated into hundreds of species. This suggests that the cichlids were once in a period of reduced constraint. During this time, the fishes accumulated diversity through genetic mutations, and the relaxed constraint – in which all individuals thrived, not just the fittest – allowed genetic variation to accumulate. As the fish later inhabited new environmental niches within the lakes, new species could form quickly through selection. In this way, a reservoir of mutations – and resultant phenotypes – represented a ‘genomic toolkit’ that allowed quick adaptation.
More work remains to fully dissect the mechanisms and may involve the sequencing of many more cichlid species. This effort could help explain how similar forms or traits evolved in parallel in different lakes, converging on the same morphology through distinct lineages.
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.
The paper, titled: “The genomic substrate for adaptive radiation in African cichlid fish” is published in Nature.
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.
Image: A young Neolamprologus brichardi, one of East African cichlid fish species sequenced
About TGAC
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. www.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 http://www.broadinstitute.org.
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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.
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