Molecular Mechanisms of Adaptation and Speciation

How does the genome facilitate adaptation and speciation in new environments?
We study genome function in the context of the wild using threespine stickleback fish.

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 gene regulation, epigenomics, 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.

What We Investigate

Regulation of Gene Expression

The genomic basis of adaptation involves mostly non-coding, regulatory mutations. How do these mutations contribute to adaptation? We study the regulation of gene expression using RNAseq, allele-specific expression, CaptureC and functional transgenic assays.

Chromatin and the Environment

The epigenome regulates gene expression allowing cells with the same DNA to achieve different functions. How do epigenome differences contribute to divergent adaptation in natural populations? We use chromatin and histone profiling to study and map the genetic basis of adaptive epigenome variation.

Recombination in Adaptive Evolution

Meiotic recombination shuffles the genome and impacts the rate of adaptation. We use linked-read gamete sequencing, ChIPseq and nuclear family sequencing, to study the molecular basis of variation in meiotic double-strand breaks and crossover hot- and cold-spots in diverging stickleback species.

Adaptation from Standing Genetic Variation

Rapid adaptation to new environments often involves natural selection on pre-existing mutations. What facilitates and constrains the availability of this adaptive genetic variation? We study this by combining population genetic theory with empirical studies of rare alleles in thousands of genomes.

Future Plans

Our long term goals are to have mechanistic insight into the genome function in the wild.  We aim to understand at a molecular level how the genome interacts with the environment to influence phenotype and adaptation.  This genomic understanding provides important insight that will help us identify factors and processes that may facilitate and constrain the evolution of biodiversity.

Selected Publications

Verta J-P, Jones FC (2019) Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. eLife 2019;8:e43785. PDF

Dreau A, Venu V, Gaspar L, Jones FC (2018) Genome-wide recombination map construction from single individuals using linked-read sequencing. Nature Communications 10:4309-4320. PDF

Indjeian VB, Kingman, G, Jones FC, Guenther C, Grimwood J, Schmutz J, Myers RM, Kingsley DM (2015) Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins. Cell 164, 45-56. PDF

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. PDF

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. PDF