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Movement of transposable elements contributes to cichlid diversity

View ORCID ProfileKaren L. Carleton, View ORCID ProfileMatt Conte, View ORCID ProfileMilan Malinsky, View ORCID ProfileSri Pratima Nandamuri, View ORCID ProfileBen Sandkam, View ORCID ProfileJoana I Meier, View ORCID ProfileSalome Mwaiko, View ORCID ProfileOle Seehausen, View ORCID ProfileThomas D Kocher
doi: https://doi.org/10.1101/2020.02.26.961987
Karen L. Carleton
1Department of Biology, University of Maryland, College Park MD 20742 USA
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  • For correspondence: kcarleto@umd.edu
Matt Conte
1Department of Biology, University of Maryland, College Park MD 20742 USA
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Milan Malinsky
2Wellcome Sanger Institute, Cambridge, UK
3Zoological Institute, University of Basel, Basel, Switzerland
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Sri Pratima Nandamuri
1Department of Biology, University of Maryland, College Park MD 20742 USA
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Ben Sandkam
1Department of Biology, University of Maryland, College Park MD 20742 USA
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Joana I Meier
4Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
5Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
6Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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Salome Mwaiko
4Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
5Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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Ole Seehausen
4Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
5Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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Thomas D Kocher
1Department of Biology, University of Maryland, College Park MD 20742 USA
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Abstract

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.

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Posted February 26, 2020.
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Movement of transposable elements contributes to cichlid diversity
Karen L. Carleton, Matt Conte, Milan Malinsky, Sri Pratima Nandamuri, Ben Sandkam, Joana I Meier, Salome Mwaiko, Ole Seehausen, Thomas D Kocher
bioRxiv 2020.02.26.961987; doi: https://doi.org/10.1101/2020.02.26.961987
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Movement of transposable elements contributes to cichlid diversity
Karen L. Carleton, Matt Conte, Milan Malinsky, Sri Pratima Nandamuri, Ben Sandkam, Joana I Meier, Salome Mwaiko, Ole Seehausen, Thomas D Kocher
bioRxiv 2020.02.26.961987; doi: https://doi.org/10.1101/2020.02.26.961987

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