Adaptation

Most species find themselves in a wide range of environments, such as plants occupying a latitudinal gradient or microbes living within the leaves of alternative host plants. An understanding of the genetic basis of adaptation will reveal the extent to which the genetic architecture of adaptive alleles is shared across environments, as well as point to those traits that allow organisms to persist in these environments. To what extent is adaptation driven by novel versus ancestral and widespread genes? We are interested in local adaptation of both Arabidopsis thaliana and the generalist microbes that associate with it (and other hosts). The unparalleled genetic resources available in A. thaliana, including the ability to rapidly map the genetic basis of ecologically important traits and test the functional importance of particular alleles, makes this plant an eminently suitable model for such botanical work. Bacterial pathogens, with their relatively small and easily manipulatable genomes, are equally powerful systems. A determination of adaptive alleles allows exploration of the evolutionary genetics of adaptation and the potential for adaptive responses to a changing environment.

Ongoing Projects

Local Adaptation and the Accessory Genome

> Local adaptation and the accessory genome

Pseudomonas syringae contains >2,500 ‘core’ genes that are widespread and likely encode vital functions. An even larger number of genes are found in a small percentage of strains; these constitute the ‘accessory’ genome. What is the function of the accessory genome, and to what extent do these genes underlie local adaptation? We are using comparative genomics and saturation mutagenesis of P. syringae strains from a variety of hosts to explore these questions.

Local adaptation of A. thaliana in Sweden

Populations of A. thaliana in the north and south of Sweden are both genetically differentiated and occupy ecologically distinct habitat types. Using 200 fully sequenced accessions that together constitute a Swedish GWAS mapping population, we are performing large field experiments across years to determine the loci associated with plant fitness across sites, the phenotypic traits associated with fitness differences, and the history of alleles responsible for local adaptation.

Selected publications:

Frachon, L., Libourel, C., Villoutreix, R., Carrère, S., Glorieux, C., Huard-Chauveau, C., Navascués, M., Gay, L., Vitalis, R., Baron, E., Amsellem, L., Bouchez, O., Vidal, M., Le Corre, V., Rob, D., Bergelson, J. and F. Roux(2017) Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nature Ecology & Evolution, 1 (10): 1551. https://doi.org/10.1038/s41559-017-0297-1
A resurrection experiment in six micro-habitats with an A. thaliana population revealed rapid phenotypic evolution across only eight generations.  Although evolutionary change was consistent at the level of the phenotype, the genetic bases were distinct in the different micro-habitats. Adaptive evolutionary change was largely driven by rare QTL’s with intermediate degrees of pleiotropy under strong selection.

Bodenhausen, N., Horton, M. W. and J. Bergelson (2013)  Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE, 8 (2). https://doi.org/10.1371/journal.pone.0056329
This study provides the first characterization of the microbiome of A. thaliana using non-culture based methods. Although there is substantial overlap in the membership of the root and shoot communities, as well as the epiphytic and endophytic communities, we observed differences in community structure. We also found overlap between culture-based and non-culture based characterizations, with the most common OTU’s corresponding to taxa that were  previously cultured.

Hancock, A. M., Brachi, B., Faure, N., Horton, M. W., Jarymowycz, L. B., Sperone, F. G., Toomajian, C., Roux, F. and J.Bergelson (2011) Adaptation to climate across the Arabidopsis thaliana genome. Science, 334 (6052): 8386. https://doi.org/10.1126/science.1209244
A genome scan of A. thaliana accessions collected from across its range effectively identifies alleles associated with adaption to climate and enables prediction of the relative fitness of accessions in a novel climate. Results provide a set of candidates for dissecting the molecular bases of climatic adaptation and provide insights about the prevalence of selective sweeps, which has implications for predicting rates of adaptation.

University of Chicago, Dept. of Ecology & Evolution