Molecular Genetics of Adaptation and Speciation

Felicity Jones

FelicityJonesNov2012-06 crop2
  • 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

What are the genomic changes and molecular mechanisms underlying adaptation and speciation in natural populations? How does the genome evolve? The threespine stickleback fish is an excellent vertebrate model for these questions: a recent adaptive radiation has resulted in a diversity of phenotypes, divergent ecotypes and species pairs. With high quality genomic, genetic, transgenic and molecular toolkits, and the ease of study of embryonic and adult phenotypes in fish lab, sticklebacks enable us to bridge molecular and developmental biology, genomics, and evolutionary ecology. We exploit natural evolutionary replicates to functionally dissect the molecular mechanisms and evolutionary processes underlying adaptive traits and the evolution of new species.

Whole genome analysis of parallel divergent stickleback ecotypes has resulted in one of the highest resolution maps of adaptive loci in vertebrates (Jones et al Nature, 2012). The majority of adaptive loci are intergenic (non-coding) and in regions of low recombination, suggesting that regulatory elements and the genomic recombination landscape are important in shaping the genomic basis of adaptation and speciation.

Our current research involves:

  • Comparative epigenomics of diverging species (eg ChIPseq, ATACseq, HiC to functionally annotate and understand how the 3D genome contributes to adaptive phenotypes)
  • Meiotic recombination hot and cold spots (eg using new 3rd generation sequencing technology 10X chromium linked-reads) to study recombination hot spots and build de novo diploid genome assemblies in diverging species;
  • Comparative transcriptomics and RNAseq allele specific expression of diverging ecotypes to identify cis-regulated cis- and trans-variation in gene expression.
  • Functional genomic dissection to demonstrate phenotypic affect of adaptive mutations (eg transgenic enhancer assays, and genome editing);
  • Population genomics and field studies of natural populations and contact zones between diverging species in order to understand evolutionary processes and selective pressures acting across the genome during speciation.


Techniques we employ range from bioinformatics & population genomics to DNA & RNAseq, ChIPseq & Capture C, transgenic enhancer assays and Crispr/Cas9 genome editing, and manipulation of environmental conditions in our state-of-the-art fish facility. Our ultimate aim is to understand the molecular mechanisms and evolutionary processes influencing divergent adaptation, hybrid inferiority and the evolution of new species.

  • FCJones
    click to enlarge

Whole genome sequencing suggests regulatory mutations and recombination suppression are important in adaptive divergence of stickleback marine and freshwater ecotypes.

  • FCJones
    click to enlarge

Genetic techniques including transgenic reporter assays and genome editing allow functional testing of adaptive mutations. Above, green fluorescent protein expressed in the developing heart of a threespine stickleback embryo.

Available PhD Projects

We are looking for a bioinformatician interested in functional genomics and meiotic recombination to join our team.

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.