Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish

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  • Grégoire Vernaz
    University of Cambridge
  • Alan G. Hudson
    University of Hawaiʻi, Honolulu
  • M. Emília Santos
    University of Cambridge
  • Bettina Fischer
    University of Cambridge
  • Madeleine Carruthers
    University of Bristol
  • Asilatu H. Shechonge
    Tanzania Fisheries Research Institute (TAFIRI)
  • Nestory P. Gabagambi
    Tanzania Fisheries Research Institute (TAFIRI)
  • Alexandra M. Tyers
    Max Planck Institute for Biology of Ageing
  • Benjamin P. Ngatunga
    Tanzania Fisheries Research Institute (TAFIRI)
  • Milan Malinsky
    University of Bern
  • Richard Durbin
    University of Cambridge
  • George F. Turner
  • Martin J. Genner
    University of Bristol
  • Eric A. Miska
    University of Cambridge
Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.
Original languageEnglish
Pages (from-to)1940-1951
Number of pages12
JournalNature Ecology and Evolution
Volume6
Issue number12
Early online date20 Oct 2022
DOIs
Publication statusPublished - Dec 2022

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