Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
Challis, Richard J
Tyers, Alexandra M
Ngatunga, Benjamin P
Genner, Martin J
Turner, George F
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Malinsky, M., Challis, R. J., Tyers, A. M., Schiffels, S., Terau, Y., Ngatunga, B. P., Miska, E., et al. (2015). Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake. Science, 350 1493-1498. https://doi.org/10.1126/science.aac9927
The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here, we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700m diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet and trophic morphology. With whole genome sequences of 146 fish, we identify 98 clearly demarcated genomic ‘islands’ of high differentiation and demonstrate association of genotypes across these islands to divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight vision associated genes), hormone signaling and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.
The work was funded by Royal Society-Leverhulme Trust Africa Awards AA100023 and AA130107 (M.J.G., B.P.N. and G.F.T.), a Wellcome Trust PhD studentship grant 097677/Z/11/Z (M.M.), Wellcome Trust grant WT098051 (S.S. and R.D.), Wellcome Trust and Cancer Research UK core support and a Wellcome Trust Senior Investigator Award (E.A.M.), a Leverhulme Trust Research Fellowship RF-2014-686 (M.J.G.), a University of Bristol Research Committee award (M.G.), a Bangor University Anniversary PhD studentship (to A.M.T.) and a Fisheries Society of the British Isles award (G.F.T.). Raw sequencing reads are in the SRA nucleotide archive: RAD sequencing (BioProject: PRJNA286304; accessions SAMN03768857 to SAMN03768912) and whole genome sequencing (BioProject PRJEB1254: sample accessions listed in Table S16). The RAD based phylogeny and alignments have been deposited in TreeBase (TB2:S18241). Whole genome variant calls in the VCF format, phylogenetic trees, and primer sequences for Sequenom genotyping are available from the Dryad Digital Repository (http://dx.doi.org/10.5061/dryad.770mc). RD declares his interests as a founder and non-executive director of Congenica Ltd., that he owns stock in Illumina from previous consulting, and is a scientific advisory board member of Dovetail Inc. We thank R. Schley for generating pharyngeal jaw data; S. Mzighani, J. Kihedu and staff of the Tanzanian Fisheries Research Institute for logistical support; A. Smith, H. Sungani, A. Shechonge, P. Parsons, J. Swanstrom, G. Cooke and J. Bridle for contributions to sampling and aquarium maintenance, the Sanger Institute sequencing core for DNA sequencing and Dr. H. Imai (Kyoto University) for the use of spectrometer in his laboratory.
Wellcome Trust (097677/Z/11/Z)
Wellcome Trust (092096/Z/10/Z)
External DOI: https://doi.org/10.1126/science.aac9927
This record's URL: https://www.repository.cam.ac.uk/handle/1810/252609