4 min readHere’s what you’ll learn when you read this story:
- In Lake Malawi, Africa, fish known as cichlids have been evolving astonishingly fast—the lake hosts at least 800 species of them.
- Researchers who sequenced the genomes of these fish found that inverted groups of genes enabled rapid and efficient evolution, and prevented detrimental genes from being passed on.
- Some cichlid species have been able to adapt to deeper parts of the lake, which is reflected in “supergenes” that include inversions that help them adapt.
Some creatures are frozen in evolutionary time—they look about the same today as they did before the first dinosaurs hatched. Then, there are cichlids—a family of fish that seems to have pressed the fast-forward button on their genetic VCR to find a scene in their evolution that would otherwise not have played out for hundreds of thousands, or maybe millions, of years.
How organisms like these can evolve and diversify so unbelievably fast has long remained a mystery. The phenomenon is known as adaptive radiation—one lineage descends from a single ancestor and diversifies rapidly so that the new lineages evolve detailed adaptations to the features of their environment. Adaptive radiation is thought to be at least part of the reason why the Cambrian explosion was such an abrupt eruption of life. In addition, hybridization can reintroduce older genetic variants into populations and recombine them in ways that allow organisms to seize advantages in their circumstances and surroundings.
During recombination, mutations form new alleles (alternative forms of a gene that appear in the same location of a chromosome), potentially boosting chances of survival. Recombination, however, can also be detrimental—both to an organism surviving and to the emergence of more species, if it breaks apart existing adaptive combinations of genes. So, evolution has found another way. Through a process called chromosomal inversion, a segment of DNA will break, flip, and reattach so that genes end up in reverse order (gene clusters that are created by inversion are often referred to as supergenes). When beneficial groups of traits remain intact like this, it allows for more efficient evolution. And that’s exactly what happened in cichlids.
Near the southeast edge of Africa is Lake Malawi, an expanse of strikingly turquoise water shimmering with fish (some local businesses are even named after the cichlids). It’s there that a common cichlid ancestor gave rise to over 800 species in an astoundingly short span of time—some morphed into predators, and others fed on algae or plankton. When researcher Hannes Svardal and his research team investigated what could have caused such extreme diversification, they sequenced the genomes of over 1,300 cichlids and found evidence of introgression (the reintroduction of genes through repeated interbreeding) and chromosomal inversion in multiple species.
“We show that five large inversions segregate across and within many species and groups in the Lake Malawi radiation,” the team said in a study recently published in Science. “By suppressing recombination, large chromosomal inversions can cause affected genomic regions to show evolutionary histories consistently distinct from the rest of the genome.”
Previous studies had found that three large subradiations of cichlids exist in Lake Malawi. Rhampochromis, a genus whose species tend to live in midwater, and Diplotaxodon, whose species prefer the depths, made up one group. Another includes utaka, which live in semi-open water, along with species that prefer either the shallow or deep regions of the lake bottom. Mbuna, which are mostly rock dwellers, make up the last radiation. Svardal used the genome of Astatotilapia calliptera (also known as the eastern happy or eastern river bream) as a reference since this species is the closest to the original cichlid lineage that newer species evolved from. Its sequin-like scales flash a rainbow of colors in sunlight.
Supergenes contain genes that make survival possible. By studying cichlid species living in deeper parts of the lake, they found these species had evolved sensory and physiological adaptations that made it possible to live at those depths. Inversions in individual fish caused higher levels of expression in genes associated with tissues related to the nervous system, including touch and vision. Genes that were related to the vascular system and promoted survival under higher pressures and lower oxygen levels were also expressed more. Further genomic analysis suggested that there could even be additional gene variants from inversions, which might have not been immediately obvious because they are either smaller or present in fewer species.
“Inversions in the Malawi cichlid adaptive radiation show supergene-like signs of adaptive evolution and repeated introgression associated with speciation,” Svardal said. “Together with [introgression], this provides a substrate for rich evolutionary dynamics.”
