How "supergenes" in fish help to develop new species

Cichlids from Lake Malawi in East Africa provide a fascinating clue to understanding how the diversity of life on Earth evolved. In this single lake, over 800 different species of cichlids have evolved from a common ancestor. This development took place in a fraction of the time that separates humans from chimpanzees. It is also remarkable that this formation of so many species took place without physical barriers. The fish lived in one and the same body of water during the process, without the cichlids being locally separated.

Astonishingly many species, astonishingly fast
Some of these cichlids became large predatory fish during this evolution, others adapted to eat algae, dig through sand or feed on plankton. Each species found its own ecological niche. How did this happen so quickly?
In the study, lead authors Hannes Svardal from the University of Antwerp and Moritz Blumer from the University of Cambridge, together with an international research team, analysed the genetic material of the cichlids. Astrid Böhne from the Leibniz Institute for the Analysis of Biodiversity Change in Bonn analysed possible sex chromosomes together with other researchers.

During their investigations, the researchers noticed a special feature in the genes: "We discovered that in some species, large parts of the DNA on five chromosomes are inverted - a type of mutation known as chromosome inversion," says Hannes Svardal. Astrid Böhne emphasises that an astonishing number of cichlid species in Malawi have undergone an inversion of genomic regions: "These inversions play a major role in the success of the cichlid species in Lake Malawi. We were able to show that the inversions in the Malawi cichlids were passed on via gene flow between species, which in turn formed new species explosively. These are adapted in a variety of ways to different ecological conditions in the lake and have changed their bodies accordingly."

Keeping species separate
Normally, when animals reproduce, the DNA is reshuffled in a process called "recombination" - the genetic material of both parents is combined. However, when a chromosome is flipped, the mixing in that region is blocked. This means that certain gene combinations can be passed on unchanged, generation after generation. These preserved gene blocks are sometimes referred to as "supergenes".
In Malawian cichlids, these supergenes appear to play several important roles. Although cichlid species can still interbreed, the reversed DNA helps to separate the species. It prevents their genes from mixing too much. This is particularly useful in parts of the lake where the fish live side by side - such as in open sandy areas where there is no physical separation between habitats.

Key factor in evolution
Interestingly, the genes in these supergenes often control traits that are crucial for survival and reproduction - such as vision, hearing and behaviour. Fish that live up to 200 metres deep in a lake, for example, need different visual abilities than fish near the surface. The supergenes help to maintain these special adaptations. Lead author Moritz Blumer, PhD student at the University of Cambridge, emphasises: "We have found cases where hybridisation events, i.e. mating between species, have enabled the transfer of entire inversions. This means that certain ecological adaptations have been transferred."

What can we learn from cichlids about other species?
Co-first author Valentina Burskaia from the University of Antwerp emphasises another fascinating detail: the researchers found that "in some cases, these inverted regions now function as sex chromosomes and help determine whether a fish becomes male or female. Since sex chromosomes can influence how new species form, this raises exciting new questions about how evolution works."
Although the current study focuses on cichlids, chromosome reversals also occur in many other animals, including humans. They are increasingly recognised as a key factor in evolution and biodiversity.

The Science publication thus provides important insights into the process of speciation, which researchers have been studying for a long time. Insights into how supergenes arise and spread bring us closer to answering one of the biggest questions in science: how life on Earth has become so rich and diverse.

Original publication
Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation, Science, www.science.org/doi/10.1126/science.adr9961