Genomics of Adaptation and Speciation

Felicity Jones

FJones Fig2.headshot crop 200 240 dpi
  • PhD studies at the Institute of Evolutionary Biology, University of Edinburgh, 2000-05
  • Postdoctoral training in the Department of Developmental Biology, Stanford University, 2007-2012
  • Max Planck Research Group Leader at the FML since 2012

Research Interest

The Jones group studies how variation in genome function in natural populations facilitates adaptation to different environments and the evolution of new species. We combine diverse functional genomic and population genomic techniques to study adaptive divergence in epigenomics and gene regulation, recombination, and adaptation from standing genetic variation. Our work leverages divergent natural populations and their hybrid zones in a powerful evolutionary model system: threespine stickleback fish. Compared to traditional model organisms, sticklebacks provide a powerful system to understand genome function in the context of natural populations and the environment.

We have a research project available for PhD candidates interested in studying chromatin variaition and gene regulation in the context of the environment. Using chromatin profiling (ATACseq), ChIPseq of histone modifications, and transgenic reporter assays in marine and freshwater sticklebacks, we have identified with high genomic resolution thousands of divergent regulatory marks that differ between these marine and freshwater ecotypes (StickleCODE). We aim to understand how chromatin state changes under different environmental conditions, influencing gene expression levels, and adaptation to different environmental conditions.

 

 

  • FJones Image3
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Epigenomic marks and chromatin accessibiltiy are predictive of functional regulatory elements. Here we show an H3K27ac mark predictive of active enhancers that differs between marine and freshwater sticklebacks. The mark is present in the liver of freshwater sticklebacks but absent in marine stickleback livers. Transgenic reporter assays confirm the underlying 500bp sequence of freshwater fish contains an active enhancer that drives GFP expression in the developing liver.

Available PhD Projects

Project1: Characterize how chromatin state changes under different environmental conditions and relate this to changes in gene expression (ATACseq)

Project 2: Characterize the 3D genome and study chromosome conformational interactions between regulatory elements and the promoters they control (HiC/3C/CaptureC)

Project 3: Use forward genetic mapping to identify the molecular basis of marine and freshwater divergence in chromatin state (ATACseq, DNAseq)

Selected Reading

1) Jones FC, Grabherr MG, Chan YF, Russell P et al. (2012b) The genomic basis of adaptive evolution in threespine sticklebacks.  Nature 484, 55-61.

2) Chan YF, Marks ME, Jones FC, Villarreal Jr G et al. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 327, 302-305.

3) O'Brown NM, Summers BR, Jones FC, Brady SD, Kingsley DM (2015) A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA. eLife 10.7554/eLife.05290