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Genomic consequences of domestication of the Siamese fighting fish

Young Mi Kwon, View ORCID ProfileNathan Vranken, Carla Hoge, Madison R Lichak, Kerel X Francis, Julia Camacho-Garcia, View ORCID ProfileIliana Bista, View ORCID ProfileJonathan Wood, View ORCID ProfileShane McCarthy, View ORCID ProfileWilliam Chow, Heok Hui Tan, View ORCID ProfileKerstin Howe, View ORCID ProfileSepalika Bandara, View ORCID ProfileJohannes von Lintig, Lukas Rüber, Richard Durbin, Hannes Svardal, Andres Bendesky
doi: https://doi.org/10.1101/2021.04.29.442030
Young Mi Kwon
1Zuckerman Mind Brain Behavior Institute, Columbia University; NY, USA
2Department of Ecology Evolution and Environmental Biology, Columbia University; NY, USA
3Department of Biological Sciences, Columbia University; NY, USA
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Nathan Vranken
4Department of Biology, University of Antwerp; 2020 Antwerp, Belgium
5Department of Biology, KU Leuven; 3000 Leuven, Belgium
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  • ORCID record for Nathan Vranken
Carla Hoge
1Zuckerman Mind Brain Behavior Institute, Columbia University; NY, USA
3Department of Biological Sciences, Columbia University; NY, USA
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Madison R Lichak
1Zuckerman Mind Brain Behavior Institute, Columbia University; NY, USA
2Department of Ecology Evolution and Environmental Biology, Columbia University; NY, USA
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Kerel X Francis
1Zuckerman Mind Brain Behavior Institute, Columbia University; NY, USA
2Department of Ecology Evolution and Environmental Biology, Columbia University; NY, USA
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Julia Camacho-Garcia
4Department of Biology, University of Antwerp; 2020 Antwerp, Belgium
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Iliana Bista
7Wellcome Sanger Institute; Cambridge, UK
8Department of Genetics, University of Cambridge; Cambridge, UK
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  • ORCID record for Iliana Bista
Jonathan Wood
7Wellcome Sanger Institute; Cambridge, UK
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  • ORCID record for Jonathan Wood
Shane McCarthy
7Wellcome Sanger Institute; Cambridge, UK
8Department of Genetics, University of Cambridge; Cambridge, UK
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  • ORCID record for Shane McCarthy
William Chow
7Wellcome Sanger Institute; Cambridge, UK
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Heok Hui Tan
9Lee Kong Chian Natural History Museum, National University of Singapore; Singapore
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Kerstin Howe
7Wellcome Sanger Institute; Cambridge, UK
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  • ORCID record for Kerstin Howe
Sepalika Bandara
10Department of Pharmacology, Case Western Reserve University; OH, USA
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  • ORCID record for Sepalika Bandara
Johannes von Lintig
10Department of Pharmacology, Case Western Reserve University; OH, USA
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Lukas Rüber
11Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern; Bern 3012, Switzerland
12Naturhistorisches Museum Bern; Bern 3005, Switzerland
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Richard Durbin
7Wellcome Sanger Institute; Cambridge, UK
8Department of Genetics, University of Cambridge; Cambridge, UK
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  • For correspondence: a.bendesky@columbia.edu hannes.svardal@uantwerpen.be rd109@cam.ac.uk
Hannes Svardal
4Department of Biology, University of Antwerp; 2020 Antwerp, Belgium
6Naturalis Biodiversity Center; 2333 Leiden, The Netherlands
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  • For correspondence: a.bendesky@columbia.edu hannes.svardal@uantwerpen.be rd109@cam.ac.uk
Andres Bendesky
1Zuckerman Mind Brain Behavior Institute, Columbia University; NY, USA
2Department of Ecology Evolution and Environmental Biology, Columbia University; NY, USA
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  • For correspondence: a.bendesky@columbia.edu hannes.svardal@uantwerpen.be rd109@cam.ac.uk
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Abstract

Siamese fighting fish, commonly known as betta, are among the world’s most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced multiple individuals across five species within the B. splendens species complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from other Betta species and have also introgressed into wild populations of those species. We identify dmrt1 as the main sex determination gene in ornamental betta but not in wild B. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics.

One-Sentence Summary Genomic analyses reveal betta fish were domesticated more than 1,000 years ago and the genes that changed in the process.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 30, 2021.
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Genomic consequences of domestication of the Siamese fighting fish
Young Mi Kwon, Nathan Vranken, Carla Hoge, Madison R Lichak, Kerel X Francis, Julia Camacho-Garcia, Iliana Bista, Jonathan Wood, Shane McCarthy, William Chow, Heok Hui Tan, Kerstin Howe, Sepalika Bandara, Johannes von Lintig, Lukas Rüber, Richard Durbin, Hannes Svardal, Andres Bendesky
bioRxiv 2021.04.29.442030; doi: https://doi.org/10.1101/2021.04.29.442030
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Genomic consequences of domestication of the Siamese fighting fish
Young Mi Kwon, Nathan Vranken, Carla Hoge, Madison R Lichak, Kerel X Francis, Julia Camacho-Garcia, Iliana Bista, Jonathan Wood, Shane McCarthy, William Chow, Heok Hui Tan, Kerstin Howe, Sepalika Bandara, Johannes von Lintig, Lukas Rüber, Richard Durbin, Hannes Svardal, Andres Bendesky
bioRxiv 2021.04.29.442030; doi: https://doi.org/10.1101/2021.04.29.442030

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