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Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes

Carruthers, Madeleine; Edgley, Duncan E; Saxon, Andrew D; Gabagambi, Nestory P; Shechonge, Asilatu; Miska, Eric A; Durbin, Richard; ... Genner, Martin J; + view all (2022) Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes. Molecular Biology and Evolution 10.1093/molbev/msac251. (In press). Green open access

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Abstract

Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow littoral and deep benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory-variants are important targets of selection driving ecologically-relevant divergence in gene expression during adaptive diversification.

Type: Article
Title: Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/molbev/msac251
Publisher version: https://doi.org/10.1093/molbev/msac251
Language: English
Additional information: Copyright © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10160275
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