Regulation of gene expression is thought to play a major role in adaptation but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.
Data has been deposited to the Sequence Read Archive under the accession PRJNA530695. All scripts used in data analysis are available at https://github.com/jpverta/verta_jones_elife_2019.git
Predominance of cis-regulatory changes in parallel expression divergence of sticklebacksNCBI Sequence Read Archive, PRJNA530695.
- Felicity C Jones
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Animal experimentation: All of the animals were housed at an approved animal facility and handled according to Baden-Württemberg State approved protocols at the Max Planck Institute for Developmental Biology, Tübingen, Germany (license numbers 35/9185.82-5 and 35/9185.40).
- Juliette de Meaux, University of Cologne, Germany
© 2019, Verta & Jones
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.