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Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish

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Santos, M Emília 
Fischer, Bettina 
Carruthers, Madeleine  ORCID logo


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 focusses on two lake ecomorphs that diverged ~1,000 years ago, as well as a population in the nearby river from which they separated ~10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterised by different morphologies, depth preferences and diet. We report extensive genome-wide methylome divergence between the two lake ecomorphs, as well as 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, haemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common garden experiment, we found that global methylation profiles are often rapidly remodelled across generations, but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to early stages of vertebrate speciation.


Funder: Wellcome Trust (Wellcome); doi:

Funder: Cancer Research UK (CRUK); doi:

Funder: EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions); doi:

Funder: NERC

Funder: Leverhulme Trust; doi:


Animals, Lakes, Biological Evolution, Cichlids, Ecosystem, Epigenesis, Genetic

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Nature Ecology and Evolution

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Nature Research
Wellcome Trust (104640/Z/14/Z)
Wellcome Trust (219475/Z/19/Z)
Cancer Research UK (A27826)
Wellcome Trust (092096/Z/10/Z)
Wellcome Trust (203144/Z/16/Z)
Cancer Research UK (C6946/A24843)
Natural Environment Research Council (NE/R01504X/1)
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