Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid radiation
Moritz Blumer, Valentina Burskaia, I. V. Artyushin, Jaysmita Saha, Julia Camacho-Garcia, Francisco Campuzano Jiménez, Alexander Hooft van Huysduynen, Joel Elkin, Bettina Fischer, Natalie Van Houtte, Chenxi Zhou, Sophie Gresham, Milan Malinsky, Tyler Linderoth, Wilson Sawasawa, Grégoire Vernaz, Iliana Bista, Aaron Hickey, Marek Kučka, Sandra Louzada, Richard Zatha, Fengtang Yang, Bosco Rusuwa, M. Emília Santos, Yingguang Frank Chan, Domino A. Joyce, Astrid Böhne, Eric A. Miska, Maxon Ngochera, George F. Turner, Richard Durbin, Hannes Svardal
Abstract
Chromosomal inversions can contribute to adaptive speciation by linking coadapted alleles. By querying 1375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon through admixture, whereas the others established early in the deep benthic clade. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage, and a notable excess of protein changing substitutions points toward selection on neurosensory, physiological, and reproductive genes. These results indicate that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system.