Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Abstract

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

New insights into the evolutionary dynamic and lineage divergence of gasdermin E in metazoa

“…Fish of various groups account for more than half of all vertebrate species and have been used widely as important models to study evolutionary transitions from invertebrate to vertebrate (Bi et al, 2021;Vernaz et al, 2021). In our study, only the most primitive forms of GSDM, GSDME and GSDMF, were found in fish.…”

Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids

“…This potential link between the evolution of three-node motifs as part of GRNs associated with cichlid adaptive traits requires further experimental verification. This is beyond that described for cis -regulatory sites previously ( Mehta et al 2021 ), as well as support based on large-scale genotyping ( Malinsky et al 2018 ; McGee et al 2020 ; Ronco et al 2021 ) and transcriptome evolution ( El Taher et al 2021 ); epigenetic divergence ( Kratochwil and Meyer 2014 ; Vernaz et al 2021 ); transgenesis assays ( Brawand et al 2014 ; Santos et al 2014 ); population studies and CRISPR mutant assays ( Kratochwil et al 2018 ); and transcriptomic/ cis- regulatory assays ( Hofmann et al 2009 ; O’Quin et al 2010 ; Nandamuri et al 2018 ; Sandkam et al 2020 ) of cichlid species.…”

Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations

“…Despite the fact that studies on epigenetic variation in natural animal populations are scarce when they are compared to plant studies, some discernible patterns have emerged after we have reviewed them. As result of our review, regardless of whether we focused on crustaceans, mollusks, fish, reptiles, birds, or mammals, the DNA methylation variation was larger than the genetic variation was among and/or within wild animal populations [ 53 , 56 , 64 , 65 , 66 , 67 , 68 ]. For example, Smith et al studied the DNA methylation variation in fish ( Etheostoma olmstedi ) using the MSAP technique.…”

“…Vernaz et al found a substantial methylome divergence between six Lake Malawi cichlid species that show extensive phenotypic diversity despite having them extremely low DNA sequence divergence. These DMRs were enriched in transposons and were associated with the transcription changes of ecologically relevant genes that are related to energy expenditure and lipid metabolism in the cichlid’s liver [ 68 ].…”