Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
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In: Nature Ecology and Evolution, Vol. 6, No. 12, 12.2022, p. 1940-1951.
Research output: Contribution to journal › Article › peer-review
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T1 - Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish
AU - Vernaz, Grégoire
AU - Hudson, Alan G.
AU - Santos, M. Emília
AU - Fischer, Bettina
AU - Carruthers, Madeleine
AU - Shechonge, Asilatu H.
AU - Gabagambi, Nestory P.
AU - Tyers, Alexandra M.
AU - Ngatunga, Benjamin P.
AU - Malinsky, Milan
AU - Durbin, Richard
AU - Turner, George F.
AU - Genner, Martin J.
AU - Miska, Eric A.
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
U2 - 10.1038/s41559-022-01894-w
DO - 10.1038/s41559-022-01894-w
M3 - Article
VL - 6
SP - 1940
EP - 1951
JO - Nature Ecology and Evolution
JF - Nature Ecology and Evolution
SN - 2397-334X
IS - 12
ER -