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Origins of shared genetic variation in African cichlids

Loh, Yong-Hwee E. and Bezault, Etienne and Muenzel, Frauke M. and Roberts, Reade B. and Swofford, Ross and Barluenga, Marta and Kidd, Celeste E. and Howe, Aimee E. and Di Palma, Federica and Lindblad-Toh, Kerstin and Hey, Jody and Seehausen, Ole and Salzburger, Walter and Kocher, Thomas D. and Streelman, J. Todd. (2012) Origins of shared genetic variation in African cichlids. Molecular biology and evolution, Vol. 30, no. 4. pp. 906-917.

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Official URL: http://edoc.unibas.ch/dok/A6070366

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Abstract

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of about 200 genic and non-genic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ~160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic vs. non-genic SNPs, as well as for SNPs at putative CpG vs. non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for about 8% of loci, with contributions from both genic and non-genic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.
Faculties and Departments:05 Faculty of Science > Departement Umweltwissenschaften > Zoologie > Evolutionary Biology (Salzburger)
UniBasel Contributors:Salzburger, Walter
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:Oxford University Press
ISSN:0737-4038
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:21 Jun 2013 12:29
Deposited On:21 Jun 2013 12:27

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