DOI: 10.1101/496034Dec 13, 2018Paper

Evolution of regulatory networks controlling adaptive traits in cichlids

BioRxiv : the Preprint Server for Biology
Tarang K MehtaFederica Di-Palma


Seminal studies in vertebrate protein evolution concluded that gene regulatory changes likely drive anatomical innovations. Even in the unparalleled East African cichlid fish radiation, we demonstrate cis-regulatory divergence as a contributor to phenotypic diversity. To further investigate this mechanism, we extended the Arboretum algorithm, initially designed for yeast adaptation to study the evolution of regulatory expression divergence in complex vertebrate species. For the first time, we reconstruct tissue-specific gene regulatory networks underpinning evolutionary adaptations from multiple vertebrate species in a phylogeny. Our framework consists of identifying ancestral reconstructed and extant species gene co-expression modules and integrating their associated regulators to investigate gene regulatory network evolution contributing to traits of phenotypic diversity in the East African cichlids. Along the phylogeny, we identify tissue-specific co-expression patterns across six tissues of five cichlids species that were predicted to be regulated by divergent suites of regulators. We report striking cases of rapid network rewiring for adaptive trait genes, such as the visual system. In regulatory regions of visual opsin ge...Continue Reading

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Biological Evolution
Gene Expression
Single Nucleotide Polymorphism
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