Mapping the genomic basis of trophic level adaptation in Lake Malawi cichlid fishes
Authors: Aldo Carmona Baez 1,2,3; Kaitlin Coyle 2,3,4; Melissa Lamm 1,3,5; Emily Moore 2,3,6; Natalie Roberts 1,3,7; Ethan Dickson 1,3,8; Katara Griffith 1,3,9; Gargi Damle 1,3,10; Erin Peterson 1,2,3,4; Patrick Ciccotto 3,11; Maddy Arena 1,3; Reaghan Julke 1,3; David Reif 1,2,3; Reade Roberts 1,2,3
Affiliations: 1) Genetics and Genomics Academy, North Carolina State University; 2) Graduate Program in Genetics, North Carolina State University; 3) Department of Biological Sciences, North Carolina State University; 4) Q2 Solutions. Durham, NC; 5) Novogene, Research Triangle Park; 6) Division of Biological Sciences, University of Montana; 7) Prestage Department of Poultry Science, North Carolina State University; 8) RNA Biology Laboratory, National Cancer Institute; 9) Genetics, Bioinformatics, and Computational Biology, Virginia Tech University; 10) BiNGS Core, Mount Sinai Icahn School of Medicine; 11) Warren Wilson College
Keywords: Comparative genomics & genome evolution
Trophic specialization is key to the phenotypic and species diversity observed across life. Despite its importance, very few studies have explored the genetic basis of trophic level itself as a complex trait. In this study, we used recently diverged Malawi cichlid species as a model to identify candidate genes involved in trophic level differences with a forward genetics approach. We performed pairwise Fst scans among carnivore, omnivore, and herbivore species. These comparative genomics scans detected numerous regions of divergence by trophic level, including genes previously implicated in trophic adaptations in cichlids and other species. We then compared the results of the Fst scans with the recombination patterns identified in two hybrid crosses of four genera representing three different trophic levels.
Our results suggest that regions of the genome identified in the Fst scans are located in the vicinity of putative structural variants identified via recombination patterns in the hybrid crosses. These analyses point out the potential impact that genomic structural rearrangements have had in the evolution of trophic level evolution in the Malawi cichlid radiation.