Abstract
BackgroundEast African lake cichlids are one of the most impressive examples of an adaptive radiation. Independently in Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. Whereas most analyses in cichlids focused on nucleotide substitutions across species to investigate the genetic bases of this explosive radiation, to date, no study has investigated the contribution of structural variants (SVs) in the evolution of adaptive traits across the three Great Lakes of East Africa.ResultsHere, we annotate and characterize the repertoires and evolutionary potential of different SV classes (deletion, duplication, inversion, insertions and translocations) in four cichlid species: Haplochromis burtoni, Metriaclima zebra, Neolamprologus brichardi and Pundamilia nyererei. We investigate the patterns of gain and loss evolution for each SV type, enabling the identification of lineage specific events. Both deletions and inversions show a significant overlap with SINE elements, while inversions additionally show a limited, but significant association with DNA transposons. Inverted regions are enriched for genes regulating behaviour, or involved in skeletal and visual system development. We also find that duplicated regions show enrichment for genes associated with “antigen processing and presentation” and other immune related categories. Our pipeline and results were further tested by PCR validation of selected deletions and inversions, which confirmed respectively 7 out of 10 and 6 out of 9 events.ConclusionsAltogether, we provide the first comprehensive overview of rearrangement evolution in East African cichlids, and some important insights into their likely contribution to adaptation.
Highlights
East African lake cichlids are one of the most impressive examples of an adaptive radiation
Our initial predictions showed a bias towards small (< 1 kb) deletions (240229). This number might be inflated as a result of our Structural Variant (SV) detection pipeline, where deletions are identified using read pairs mapped in a concordant way
We found enrichment for “neuron development” (GO:0048666) associated with events in the Haplochromine lineage
Summary
East African lake cichlids are one of the most impressive examples of an adaptive radiation. In Lake Victoria, Tanganyika, and Malawi, several hundreds of species arose within the last 10 million to 100,000 years. African cichlids represent one of the best examples of rapid adaptive radiation [1,2,3,4]. The adaptation to different ecological niches in Lakes Malawi, Tanganyika and Victoria has given rise to several hundreds of species in a period of just a few million years [5,6,7]. A great example of adaptation is represented by the evolution of the cichlid visual system, involving eight different opsin genes [19,20,21].
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