PhD thesis: the population genomics of herbicide resistance adaptation

Adaptation is a fundamental process in evolutionary biology. In many cases, the ability of a species to adapt determines their formation, their success, and their persistence.  My research focuses on disentangling the genomics of adaptation to herbicide resistance in Brassicaceae and common waterhemp, Amaranthus tuberculatus – pretty much looking how superweeds have come to be so super! Specifically, I’m interested in learning more about questions like:

  1. What is the rate of adaptation in natural populations and how much does this vary across species?
  2. How does ploidy and mating system influence key population genetic parameters limiting the rate of adaptation? (see figure below)
  3. What are the genomic and demographic consequences of strong selection?
  4. To what extent is the genetics of resistance adaptation across the range convergent, and how much does this depend on parallel standing genetic variation versus new mutation?

Figure 1 (Flowchart)

Weed-Herbicide systems provide a great system for studying the genetics of adaptation; in addition to the evolutionary forces that all natural populations experience (gene flow, genetic drift, mutation), the recurrent application of herbicides provides strong and predictable selection pressure against weed populations. I use comparative, lab and field-based approaches to address these question.


In the summer of 2016, I went out to Alberta & Saskatchewan with Corlett Wood (pictured below). We collected 12 species in the Brassicaceae family, with a particular interest in the selfing diploid, Stinkweed (Thlaspi arvense), the diploid outcrosser, Wild mustard (Sinapis arvensis), and the tetraploid diploid, Shepherds purse (Capsella bursa-pastoris). By studying the comparative genomics of herbicide resistance in these species, I can contrast how the rate and mode of adaptation vary between species that differ in mating system and ploidy.

Amaranthus tuberculatus

This September, I drove out to Ridgetown campus, University of Guelph to meet with collaborator Peter Sikkema and do some collections of Amaranthus tuberculatus var. rudis (Common Waterhemp). The population genetics gods blessed me with the opportunity to conform to all their assumptions – yay for dioecious annuals! With cross resistance to multiple herbicides, including widespread glyphosate resistance, common waterhemp has traditionally been a huge issue for crop loss in the midwestern United States. However, seed dispersal likely via agricultural machinery has facilitated the spread of common Waterhemp across much of United States, making its way into Ontario in 2002. A subspecies native to Ontario, Amaranthus tuberculcatus var. tuberculatus occurs in naturalized environments alongside bodies of water, in contrast to the ruderal disturbed environemnt in which we find the US native waterhemp. We are interested to see whether the colonization of Ontario by the US native var. rudis may have been accompanied by introgression with our var. tuberculatus, and how that relates to levels of glyphosate resistance. Glyphosate resistance in a few Amaranthus species is conferred by target gene (EPSPS) amplification, a somewhat novel mode of resistance, of which we know little about the mechanism (possibly facilitated by TE’s?) and the distribution of gene copy number (across individuals and even across the genome!). Here are some pictures from my trip to Ridgetown and the surrounding area: