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

Research output: Contribution to journalArticlepeer-review

Standard Standard

Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. / Vernaz, Grégoire; Hudson, Alan G.; Santos, M. Emília et al.
In: Nature Ecology and Evolution, Vol. 6, No. 12, 12.2022, p. 1940-1951.

Research output: Contribution to journalArticlepeer-review

HarvardHarvard

Vernaz, G, Hudson, AG, Santos, ME, Fischer, B, Carruthers, M, Shechonge, AH, Gabagambi, NP, Tyers, AM, Ngatunga, BP, Malinsky, M, Durbin, R, Turner, GF, Genner, MJ & Miska, EA 2022, 'Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish', Nature Ecology and Evolution, vol. 6, no. 12, pp. 1940-1951. https://doi.org/10.1038/s41559-022-01894-w

APA

Vernaz, G., Hudson, A. G., Santos, M. E., Fischer, B., Carruthers, M., Shechonge, A. H., Gabagambi, N. P., Tyers, A. M., Ngatunga, B. P., Malinsky, M., Durbin, R., Turner, G. F., Genner, M. J., & Miska, E. A. (2022). Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. Nature Ecology and Evolution, 6(12), 1940-1951. https://doi.org/10.1038/s41559-022-01894-w

CBE

Vernaz G, Hudson AG, Santos ME, Fischer B, Carruthers M, Shechonge AH, Gabagambi NP, Tyers AM, Ngatunga BP, Malinsky M, et al. 2022. Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. Nature Ecology and Evolution. 6(12):1940-1951. https://doi.org/10.1038/s41559-022-01894-w

MLA

VancouverVancouver

Vernaz G, Hudson AG, Santos ME, Fischer B, Carruthers M, Shechonge AH et al. Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. Nature Ecology and Evolution. 2022 Dec;6(12):1940-1951. Epub 2022 Oct 20. doi: 10.1038/s41559-022-01894-w

Author

Vernaz, Grégoire ; Hudson, Alan G. ; Santos, M. Emília et al. / Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. In: Nature Ecology and Evolution. 2022 ; Vol. 6, No. 12. pp. 1940-1951.

RIS

TY - JOUR

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 -