Assistant Professor of Organismic & Evolutionary Biology
Office: Biolabs 1105, 16 Divinity Avenue
Lab Website: http://www.oeb.harvard.edu/faculty/bomblies/
The overarching interest of the lab is to understand the molecular mechanisms of evolutionary adaptation, but we see this broadly to include both adaptation to the internal environment (e.g. adaptive evolution in response to genome change) and the external environment (e.g. habitat adaptation). Most of our work focuses on Arabidopsis arenosa. This lovely relative of A. thaliana is an obligate outcrosser, tetraploid through most of its range, and widely distributed in Europe.There are two main areas we are interested in pursuing with this species:
(1) Adaptation to whole genome duplication. Arabidopsis arenosa is autotetraploid through most of its central European range (that is, it has duplicated its entire genome, but the duplication was within the species and did not involve hybridization). The tetraploids are outcrossing and fertile. From artificially double diploids, we know that the diploid genome is not already competent to sustain stable meiosis in the polyploid state, yet the polyploids show cytologically diploid-like behavior (this was figured out with our collaborator James Higgins in Chris Franklin's group at the University of Birmingham in the UK). This suggests that the established tetraploid has adapted to its polyploid genome state. How did this happen, what processes were modified and how? We are using a combination of genomics, transcriptomics, molecular genetics and cytology to address how meiosis and other key cellular processes may have stabilized in tetraploid evolution. We are also beginning to analyze the molecular evolution of meiosis-related genes in diploid and tetraploid A. arenosa. Our first study on this topic, a genome scan for signatures of selection in the autotetraploid A. arenosa genome, is already complete and in press at PLoS Genetics. Now we are pursuing follow-up work.
(2) Biogeography and Habitat adaptation. Arabidopsis arenosa autotetraploids have adapted to a wide range of habitats, ranging from the apparently ancestral shaded limestone outcrop habitat to silicaceous outcrops, serpentine, railways, acid bogs, beaches, and heavy metal contaminated mine tailings. We are using RADseq markers and low pass sequencing of population pools to study the evolutionary history of diploid and tetraploid A. arenosa populations and how these colonized their present range and habitats. We have also found that tetraploid populations found in distinct habitats (railways versus outcrops) show striking differences in flowering time, vernalization responsiveness, perenniality and plant architecture. Within the scope of an NSF-funded study, we are beginning to use a combination of genetic mapping, transcriptome analyses and phenotyping to better characterize these differences both molecularly and phenotypically. We have begun to map flowering time and plant architecture traits in segregating F2 populations (we are focusing at least initially on the contrast of shaded outcrops versus exposed drought-prone railways). We are also beginning studies of the potential role of epigenetic regulation in natural variation for flowering and vernalization responsiveness.
(3) Gene network evolution. One striking observation from our genome scan is that signatures of selection are often seen in genes whose products are known to interact. These are also often connected in networks to additional genes that are differentiated between populations. This suggests that these genes may be adaptating to the genome rather than to habitat. We are currently exploring this with a large population resequencing study and follow-up experiments to test functional modules of related genes.
Current group members:
Ben Hunter – Postdoc. Flowering time in A. arenosa. Molecular genetics of hybrid necrosis and temperature responses in A. thaliana.
Kevin Wright - Postdoc. Flowering time and meiotic adaptation in A. arenosa.
Brian Arnold – PhD student . Population genetics and genomics of A. arenosa.
Pierre Baduel – PhD student . Flowering time adaptation in A. arenosa.
JulieVu - Undergraduate research assistant. Flowering in A. arenosa.
Katherine Xue - Undergraduate senior thesis student. Evolution and function of the meiosis gene ASYNAPSIS1.
Maria Surinova - visiting PhD student from the Czech Republic. Population genomics and gene network evolution in A. arenosa.
Masooma Naseer Cheema - Visiting scientist from Pakistant. microRNA targeting of defense genes.
Dina Benayad - High school student. Working with Kevin Wright.
Arnold, B.*, Corbett-Detig, R. B.*, Hartl, D. and Bomblies, K. (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, In Press. * = contributed equally.
Hollister, J., Arnold, B., Svedin, E., Xue, K., Dilkes, B. and Bomblies, K. (2012) Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genetics, 8(12): e1003093.
Hunter, B.*, Wright, K*., and Bomblies, K.New approaches to studying natural variation andwhat they can teach us. Curr Op in Plant Biology, 16 (1) 85-91.* equal contribution.
Arnold, B., Bomblies, K. and Wakeley, J. (2012) Extending coalescent theory to autotetraploids. Genetics. Vol 192, pp. 195-204.
Hunter, B., Hollister, J. D. and Bomblies, K. (2012) Epigenetic inheritance: What news for evolution? Current Biology. Dispatch article. Vol 22, pp. R54-R56.
Hunter, B. and Bomblies, K. (2010) The genetics of speciation in the Arabidopsis genus. Invited review. In: The Arabidopsis Book. American Society of Plant Biologists. Ames, IA
Bomblies, K. (2010). Doomed lovers: mechanisms of isolation and incompatibility in plant speciation. Invited review. Annual review of Plant Biology 61, pp. 109-124.
Bomblies, K. (2010) Evolution: Redundancy as an opportunity for innovation. Dispatch article. Current Biology. 20, pp. R320-R322.
Bomblies, K. (2009). Too much of a good thing? Hybrid necrosis as a by-product of plant immune system diversification. Invited review. Botany 87, pp. 1013-1022.
General Audience Publications
Bomblies, K. Plant Immunity in a changing world. Essay contribution to “Future Science – 19 essays from the Cutting Edge” edited by Max Brockmann (2011).
Bomblies, K. The stunning diversity of plants. 10 Questions Interview. Seed magazine. February 22, 2010.