Molecular Mechanisms of Adaptive Divergence and Speciation

What mutations underlie adaptation and speciation?
How does the genome function?

We are researching:

1) Regulation of Adaptive Gene Expression Divergence
Molecular basis of adaptive divergence in gene expression using transcriptomics (RNAseq, allele-specific expression)

2) Comparative Regulomics and Epigenetics
Regulatory elements underlying adaptive evolution using ATACseq chromatin profiling, ChIPseq of epigenetic marks, functional tests of adaptive mutations using genetic and transgenic techniques such as enhancer assays, genome editing

3) Recombination in Adaptive Divergence
How the genomic recombination landscape (recombination hot- and coldspots) evolve during adaptive divergence using ChIPseq, linked-read sequencing of gametes, and pedigree sequencing

4) Genetic mapping of adaptive traits
Forward genetic mapping the molecular basis of divergence in adaptive traits using QTL mapping and GWAS in natural populations

5) Population Genomics and Diploid Genome Assemblies
Diploid de novo genome assemblies, population genomics and molecular signatures of natural selection in wild populations (selective sweeps) to identify the loci underlying adaptive divergence of stickleback species pairs (marine-freshwater ecotypes, benthic-limnetic ecotypes).

6) Standing Genetic Variation in Adaptation
How the availability of pre-existing adaptive alleles (standing genetic variation) and association among adaptive alleles across the genome promote and constrain adaptation in natural populations.


Whole genome sequencing of 21 marine and freshwater populations around the world revealed high resolution signals of marine-freshwater adaptive divergence - candidate genes for contributing to reproductive isolation

Stickleback - a powerful model organism for evolutionary genomics

We leverage natural evolutionary replicates to functionally dissect the molecular mechanisms & evolutionary processes that give rise to adaptive traits and biodiversity. 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 putatively regulatory) and in regions of low recombination. This suggests the mutations in regulatory sequence and the recombination landscape are important in adaptive evolution. How do these mutations affect gene expression, phenotypes and fitness? How do recombination ’hot’ & ’cold’ spots vary across the genome? What are the factors that constrain and promote the availability of adaptive genetic variation in naturally evolving populations?

Example of Tol2 transgenic gain-of-function assay: Cardio myosin light chain promoter drives expression of green fluorescent protein in the developing heart of a three spine stickleback. The threespine stickleback has undergone an adaptive radiation in the last 10,000-20,000 generations resulting in a diversity of forms including parallel reproductively isolated species-pairs. These provide valuable biological replicates of the evolutionary process


Our research is funded by the Max Planck Society, a European Research Council Consolidator Grant, the Deutsche Forschungsgemeinschaft, an Alexander von Humboldt Foundation Postdoctoral Fellowship to Dr Saad Arif and an Human Frontier Science Program Fellowship to Dr Enni Harjunmaa.


Selected Publications

1.    Jones FC*, Grabherr MG*, Chan YF*, Russell P*, Mauceli E, Zody MC, Pirun M, Johnson J, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady, SD, Zhang H, Pollen AA, Howes T, Amemiya C, Broad Whole Genome Sequencing Platform and Whole Genome Assembly Team, Lander ES, DiPalma F, Lindblad-Toh K, and Kingsley DM.  (2012)  The genomic basis of adaptive evolution in threespine sticklebacks.  Nature 484:55-61.

2.    Jones FC, Chan YF, Schmutz J., Brady SD, Southwick A, Myers RM, Schluter D, & Kingsley DM.  (2012)  A genome-wide genotyping array reveals patterns of global and species-pair divergence in threespine stickleback.  Current Biology 22, 794-800.

3.    Chan YF, Marks ME, Jones FC, Villarreal G Jr, Shapiro MD, Brady SD, Southwick AM, Absher, DM, Grimwood J, Schmutz J, Myers RM, Petrov D, Jonsson B, Schluter D, Bell MA & Kingsley DM.  (2010)  Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.  Science 327 (5963): 302-305.

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

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

see full publication list here