PT  - JOURNAL ARTICLE
AU  - Karen L. Carleton
AU  - Matt Conte
AU  - Milan Malinsky
AU  - Sri Pratima Nandamuri
AU  - Ben Sandkam
AU  - Joana I Meier
AU  - Salome Mwaiko
AU  - Ole Seehausen
AU  - Thomas D Kocher
TI  - Movement of transposable elements contributes to cichlid diversity
AID  - 10.1101/2020.02.26.961987
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.02.26.961987
4099  - http://biorxiv.org/content/early/2020/02/26/2020.02.26.961987.short
4100  - http://biorxiv.org/content/early/2020/02/26/2020.02.26.961987.full
AB  - African cichlid fishes are a prime model for studying the mechanisms of speciation. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for variation in cichlid phenotypes. Cichlids have some of the largest known shifts in vertebrate visual sensitivity. These shifts arise mainly from the differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi (LM) cichlids, we have thus far identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or of the opsin gene itself. Here we show that these indels are caused by the movement of transposable elements (TEs). These precise indels are not found outside of LM, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. A similar indel has arisen independently outside of LM at one locus, suggesting that some locations are primed for TE insertion and the resulting indels. Increased TE mobility may be associated with interspecific hybridization, which disrupt mechanisms of TE suppression. Overall, our study suggests that TEs may contribute to key regulatory changes, and may facilitate rapid phenotypic change and possibly speciation in African cichlids.