Genomics 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

How does the genome function? What mutations underlie adaptation and speciation? Whole genome analysis of parallel divergent stickleback species has resulted in one of the highest resolution maps of adaptive loci in vertebrates (Jones et al Nature, 2012) and shown that adaptive loci are intergenic (non-coding) and in regions of low recombination. 

We research:

  • Regulation of Gene Expression to identify cis- and trans- regulatory elements underlying adaptation using transcriptomics (RNAseq and allele-specific expression)
  • Comparative Regulomics and Epigenetics to functionally annotate and understand how the 3D genome contributes to adaptive phenotypes. We do this using using ATACseq chromatin profiling, ChIPseq of epigenetic marks, and functional transgenic tests of adaptive mutations.
  • Recombination in Adaptive Divergence to understand how the genomic recombination landscape influences individual fitness.  We are using new linked-read genome sequencing technology, ChIPseq, pedigree sequencing, and studies of hybrids and recombinants in natural populations to build de novo diploid genome assemblies in diverging species, study recombination hot- and cold-spots, and how recombination influences individual fitness during adaptive divergence.
  • Population Genomics to study molecular signatures of natural selection in wild populations (selective sweeps) and Genetic Mapping (QTL and GWAS) to identify mutations controlling adaptive traits.
  • Standing Genetic Variation in 10000 genomes to quantify the frequency and linkage among pre-existing adaptive alleles and how this constrains the rate of adaptation in natural populations.



  • 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
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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 people with experience in genomics, bioinformatics, and/or evolution to join our team to work on:

1. how open chromatin and regulatory elements change under different environmental conditions
2. the fitness of recombinants in natural populations and hybrid zone.

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) Verta J-P, Jones FC (2018) Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. (In Review)

3) Dreau A, Venu V, Gaspar L, Jones FC (2018) Genome-wide recombination map construction from single individuals using linked-read sequencing. (Submitted)