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 is the molecular basis of adaptive trait variation? How do new species evolve? The threespine stickleback fish is an excellent organism in which to address such questions in vertebrates: diverse naturally occurring populations with rapidly evolving adaptive phenotypes, over 250 sequenced genomes, plus a suite of powerful genetic and transgenic tools. 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 mutations in regulatory sequence and the recombination landscape are important in adaptive evolution. These results show that, adaptation to new freshwater environments often involves the use of pre-existing ‘standing’ genetic variation that is present at low frequencies in the marine population.

Our current research involves:

  • population genomics to identify adaptive mutations and study factors affecting the source and availability of adaptive genetic variation;
  • new third generation sequencing technology (10X chromium) to build de novo diploid genome assemblies and study variation in recombination across diverging species and its genetic basis;
  • molecular techniques in the wetlab to functionally dissect the phenotypic affect of adaptive mutations;
  • and field studies of natural populations and contact zones between diverging species in order to understand selective pressures acting across the genome in naturally diverging species.


Techniques we employ range from bioinformatics & population genetics 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

Unfortunately we have no new projects available to IMPRS this year. 

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.