Tom Ellis

Post-doctoral researcher interested in the intersection of quantitative genetics, data analysis and lunch.

Flower colour in a snapdragon hybrid zone

Natural hybrid zones occur where partially diverged populations come into contact and interbreed. This means that new combinations of genes from each population which are continuously being combined in new hybrids, and tested by natural selection. This makes them fascinating ‘evolutionary laboratories’ for observing natural selection in real time.

During my PhD with Nick Barton at IST Austria, I studied a hybrid zone of the snapdragon Antirrhinum majus in the Pyrenees mountains. Parental types have either yellow or magenta flowers, with hybrids showing a spectrum of white, pink and orange flowers.

  1. By mapping changes in flower colour onto the species tree of Antirrhinum and its relatives I found that evolutinary has tended to favour transitions to flowers with a single magenta or yellow pigment, and away from unpigmented (white) or double-pigmented flowers.
  2. I carried out a large-scale pollination assay of wild plants over three years to try to identify whether colour preferences by bumblebee pollinators could contribute to selection on flower colour.
  3. I developed a novel method, FAPS, for jointly inferring parental and sibling relationships from SNP data which was two orders of magnitude faster than the state of the art, and allows the user to fully account for uncertainty in the pedigree.
  4. I extended FAPS to incorporate additional covariates, and used that to jointly infer the pedigree and the distribution of pollen disersal distances.

Local adaptation in Arabidopsis thaliana

Local adaptation is the process by which populations respond to the selection pressures in their local environment over time. Among the best ways to investigate this is to use reciprocal transplant experiments, where individuals from two or more locations are reared in common gardens at each site. As a postdoc with Jon Ågren at Uppsala university in Sweden I was involved in setting up and analysising large scale reciprocal transplants using ecotypes of Arabidopsis thaliana originating in Sweden and Italy to examine the prevalent selection pressures at each site, which aspects of plant phenotype they act on, and to identify the regions of the genomes that respond to that selection. A particular strength of this project is that experiments have been carried out for more than a decade, which means we can investigate how consistent these effects are between years, and try and identify selection events which occur only rarely but have major impacts on survival and fecundity.

Methylation variation in Arabidopsis thaliana

Nucleotides, especially cytosines, can be methylated by adding a methyl group (CH~3~). Ecotypes of Arabidopsis thaliana from across Europe show remarkable variation in cytosine methylation, and this variation is correlated with climate of origin and transposable element load, but the meaning of this variation is not clear. My current work focusses is part of a broader effort to understand the biology of these observations. In particular, my projects focus on growing plants under field conditions. This is in contrast to most previous work which has investigated methylation variation in controlled growth chambers, which can never capture the full range of environmental cues that might affect the regulation of methylation marks.

Scientific publications

  • Ellis, T. J., Nizhynska V., Pisupati R., Mollá-Morales A., Nordborg M., (2024), Bisulphite sequencing in the presence of cytosine-conversion errors, bioRxiv 2024.09.16.613193
  • Dahan-Meir T., Ellis, T. J., Mafessoni, F., Sela, H., Rudich O., Manisterski J., Avivi-Ragolsky N., Raz A., Feldman M., Anikster Y, Nordborg M., Levy AA, (2024), 36-year study reveals the effects of microhabitats on a wild wheat population. Molecular Ecology, e17512. PDF.
  • Ellis, T. J., & Ågren, J. (2024). Adaptation to soil type contributes little to local adaptation in an Italian and a Swedish population of Arabidopsis thaliana growing on contrasting soils. Biology Letters. Open access.
  • Clauw, P., Ellis, T. J. (joint first author), Liu, H. J., & Sasaki, E. (2024). Beyond the standard GWAS-a guide for plant biologists. Plant And Cell Physiology, pcae079. PDF
  • Ellis, T. J., Field D. L., Barton, N. H. (2024), Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone. bioRxiv: 2024.01.05.574354
  • Lee, G., Sanderson, B. J., Ellis, T. J., Dilkes, B. P., McKay, J. K., Ågren, J., & Oakley, C. G. (2024). A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation. Proceedings of the National Academy of Sciences, 121(6), e2317461121.
  • Butković A., Ellis, T. J. (joint first author), González, R., Jaegle, B., Nordborg, M., Elena S. F., (2024), Genetic basis of Arabidopsis thaliana responses to infection by naïve and adapted isolates of turnip mosaic virus, eLife 2023;12:RP89749. DOI: (https://doi.org/10.7554/eLife.89749) PDF
  • Durán, P., Ellis, T. J. (joint first author), Thiergart, T. , Ågren, J. & Hacquard, S.,(2022) Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations. New Phytologist, 236: 608–621. PDF
  • Ellis, T. J., Postma, F. M., Oakley, C. G., & Ågren, J. (2021). Life‐history trade‐offs and the genetic basis of fitness in Arabidopsis thaliana. Molecular Ecology, 30(12), 2846-2858. PDF
  • Thiergart, T., Durán, P., Ellis, T., Vannier, N., Garrido-Oter, R., Kemen, E., Roux F., Ågren J., Schulze-Lefert, P. & Hacquard, S. (2020). Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature ecology & evolution, 4(1), 122-131. PDF
  • Ellis, T. J., Field, D. L., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular ecology resources, 18(5), 988-999. PDF
  • Ellis, T. J., & Field, D. L. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of botany, 117(7), 1133-1140. PDF
  • Streinzer, M., Ellis, T, Paulus, H. F., & Spaethe, J. (2010). Visual discrimination between two sexually deceptive Ophrys species by a bee pollinator. Arthropod-Plant Interactions, 4(3), 141-148. PDF