RT Journal Article
SR Electronic
T1 Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.01.07.475335
DO 10.1101/2022.01.07.475335
A1 Madeleine Carruthers
A1 Duncan E. Edgley
A1 Andrew D. Saxon
A1 Nestory P. Gabagambi
A1 Asilatu Shechonge
A1 Eric A. Miska
A1 Richard Durbin
A1 Jon R. Bridle
A1 George F. Turner
A1 Martin J. Genner
YR 2022
UL http://biorxiv.org/content/early/2022/01/08/2022.01.07.475335.abstract
AB Rapid ecological speciation along depth gradients has taken place independently and repeatedly in freshwater fishes. While the extent of genomic divergence between ecomorphs is often well understood, the molecular mechanisms facilitating such rapid diversification are typically unclear. In Lake Masoko, an East 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 from jaw tissue, we explore two major regulatory transcriptional mechanisms, expression and splicing QTL variants and examine their contribution to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 4.2% were regulated by cis-regulatory expression QTLs, and 6.4% were regulated by cis-regulatory splicing QTLs. There were also strong signals of divergent selection of differentially expressed genes that showed divergent regulation from expression, splicing or both QTL variants, including genes associated with major jaw plasticity and adaptation networks, adaptive immune system response, and oxidoreductase processes. These results suggest that transcriptome plasticity and modification have important roles during early-stage ecological speciation and demonstrate the role of regulatory-variants as important targets of selection driving ecologically-relevant divergence in gene expression that is associated with adaptive diversification.Competing Interest StatementThe authors have declared no competing interest.