Genetic rewiring behind spectacular evolutionary explosion in East Africa

January 19, 2021

Genetic rewiring could have driven an evolutionary explosion in the shapes, sizes and adaptations of cichlid fish, in East Africa's answer to Darwin's Galapagos finches.

Published in BMC Genome Biology, an Earlham Institute (EI) study, with collaborators at the University of East Anglia (UEA) and Wisconsin Institute for Discovery, shows that 'genetic rewiring' at non-coding regions - rather than mutations to protein-coding regions of genes - may play an important role in how cichlid fish are able to rapidly adapt to fill a staggeringly wide range of environmental niches in the East African Rift lakes.

The results could help future studies to improve breeding of economically important cichlid species such as tilapia - a staple in aquaculture.

Darwin's famous finches are one of the most well-known examples of evolution by natural selection, and specifically adaptive radiation. The birds he observed on the Galapagos archipelago had differences in their beaks that could be matched to fit their specific feeding habits - whether they ate big or small seeds, insects, or even used tools to find food.

Amazingly, in the 2-3 million years it took 14 species of finch to evolve on the Galapagos Islands, around 1,000 species of cichlid evolved in Lake Malawi alone.

"In the Great Lakes of East Africa, and within the last few million years, a few ancestral lineages of cichlid fish have independently radiated and given rise to well over 2,000 species - and we're still finding new ones," says first author Dr Tarang Mehta, a postdoctoral scientist in EI's Haerty Group.

"They occupy a really large diversity of freshwater ecological niches in lakes, rivers and even swamps: this includes sandy substrates, mud, rocks, and vegetated bottoms. As a result, they are all adapted to different dietary habits and niches in these areas."

By looking at gene expression across different cichlid tissues in five representative species from East African rivers and the Great Rift Lakes, the team discovered an evolutionary rewiring of several important genes linked to the adaptability seen in cichlids. The effect which was particularly prominent in the vision of fish species.

"We found out that the most rewired genes are associated with the visual system," explains Dr Mehta. "Essentially, if you look at the different species of fish we used in the study, you could see major differences in the regulation network around opsin genes they use for vision depending on where they live and what they eat.

"For example, the Lake Malawi rock-dwelling species, M. zebra, feeds on UV-absorbing phytoplankton algae. That generally requires increased expression of a particular opsin, SWS1, which helps with sensitivity to UV light. That may well explain why it has a more complex regulatory network around SWS1 compared with the Lake Tanganyika benthivore, N. brichardi, which does not share the same diet or habitat."

Armed with some genes of interest, the team confirmed the mechanisms behind these gene regulatory differences in the lab. Looking at the fine scale, they identified small changes in the DNA sequence of regulatory regions at the start of genes important for trait differences between species, including the visual system.

Rather than the gene itself being modified, it was the regions of DNA known as binding sites that are targeted by transcription factors - the proteins which determine whether a gene is turned on or turned off. In this way, the different species of fish can be said to have had their visual system 'rewired' for different functions.

Taking this further, the team was able to show that these changes could be commonly associated throughout cichlid fish in Lake Malawi, with diet and ecology-dependent rewiring showing that changes in transcription factor binding could be key to fine-tuning visual sensitivity.

Depending on the trait, cichlids appear to utilise an array of genetic mechanisms to generate phenotypic novelty however, the 'tinkering' of regulatory systems appears more widespread in cichlid fish than previously discovered. This evolutionary plasticity could well explain the explosion of species in such a small area over a relatively short time.

"It's a proof of concept," says Dr Mehta. "As more data comes out, we'll be able to look at this in depth in representative clades from each of the different radiations, not just in Lake Malawi but also Lake Tanganyika, Lake Victoria and even in some of the cichlids in South America."

Professor Federica Di Palma, Professorial Fellow of Biodiversity at UEA, said: "We have released an impressive amount of expression data which will further aid studies into the adaptive radiation of cichlids for the future. We are now deciphering the complexity of these cis-regulatory regions by using genome-wide CRISPR screens.

"The wider impact of our regulatory gene network approach will also help inform evolution of agriculturally important traits for tilapia such as growth rate and tolerance to different local water conditions, as well as for general aquaculture and fisheries."
You can access the paper, here:

Earlham Institute

Related Science Articles from Brightsurf:

75 science societies urge the education department to base Title IX sexual harassment regulations on evidence and science
The American Educational Research Association (AERA) and the American Association for the Advancement of Science (AAAS) today led 75 scientific societies in submitting comments on the US Department of Education's proposed changes to Title IX regulations.

Science/Science Careers' survey ranks top biotech, biopharma, and pharma employers
The Science and Science Careers' 2018 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Science in the palm of your hand: How citizen science transforms passive learners
Citizen science projects can engage even children who previously were not interested in science.

Applied science may yield more translational research publications than basic science
While translational research can happen at any stage of the research process, a recent investigation of behavioral and social science research awards granted by the NIH between 2008 and 2014 revealed that applied science yielded a higher volume of translational research publications than basic science, according to a study published May 9, 2018 in the open-access journal PLOS ONE by Xueying Han from the Science and Technology Policy Institute, USA, and colleagues.

Prominent academics, including Salk's Thomas Albright, call for more science in forensic science
Six scientists who recently served on the National Commission on Forensic Science are calling on the scientific community at large to advocate for increased research and financial support of forensic science as well as the introduction of empirical testing requirements to ensure the validity of outcomes.

World Science Forum 2017 Jordan issues Science for Peace Declaration
On behalf of the coordinating organizations responsible for delivering the World Science Forum Jordan, the concluding Science for Peace Declaration issued at the Dead Sea represents a global call for action to science and society to build a future that promises greater equality, security and opportunity for all, and in which science plays an increasingly prominent role as an enabler of fair and sustainable development.

PETA science group promotes animal-free science at society of toxicology conference
The PETA International Science Consortium Ltd. is presenting two posters on animal-free methods for testing inhalation toxicity at the 56th annual Society of Toxicology (SOT) meeting March 12 to 16, 2017, in Baltimore, Maryland.

Citizen Science in the Digital Age: Rhetoric, Science and Public Engagement
James Wynn's timely investigation highlights scientific studies grounded in publicly gathered data and probes the rhetoric these studies employ.

Science/Science Careers' survey ranks top biotech, pharma, and biopharma employers
The Science and Science Careers' 2016 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Three natural science professors win TJ Park Science Fellowship
Professor Jung-Min Kee (Department of Chemistry, UNIST), Professor Kyudong Choi (Department of Mathematical Sciences, UNIST), and Professor Kwanpyo Kim (Department of Physics, UNIST) are the recipients of the Cheong-Am (TJ Park) Science Fellowship of the year 2016.

Read More: Science News and Science Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to