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 patterns left behind on the genome by the process of adaptation to herbicide resistance in mustard family, Brassicaceae and common waterhemp, Amaranthus tuberculatus—pretty much getting a glimpse into how superweeds have become so super! Specifically, I’m interested in addressing:

  1. The extent to which adaptation occurs via de novo mutation or standing genetic variation;
  2. Whether mutations are arising independently across populations or are spreading through gene flow;
  3. What key population and species-level factors influence the rate and nature of evolution.

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 genomic, lab and field-based approaches to address these question.

Brassicaceae

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, and 10 other species in the Brassicaceae, I can contrast how the rate and mode of adaptation vary between species that differ in mating system and ploidy.

In particular to this system, I’m interested in estimating the extent that resistance adaptation occurs from new mutation versus standing variation, and the role of gene flow in the spread of adaptive alleles. Moreover, how these processes differ across species!

 

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). 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, more recently, southwestern Ontario. Anndd the population genetics gods blessed me with the opportunity to conform to all their assumptions – yay for dioecious annuals!

Resistance to glyphosate mostly occurs via non-target site, polygenic mechanisms, as well as a novel form of herbicide resistance, target gene amplification.  I’m interested in characterizing the number of origins and signals of selection from what may be a much rarer class of mutation compared to the more common genetic bases of resistance. I’m also looking to get a better understanding of the genetic basis of non-target site resistance through a genome-wide association study of naturally occurring resistant individuals.

This is system also provides a really unique opportunity to investigate provide insight into the importance of ancestral standing genetic variation for polygenic traits such as non-target site resistance (NTSR), and evolutionary forces that may maintain them. In addition to the agriculturally-problematic weed, Amaranthus tuberculatus var. rudis, there is another subspecies native to Ontario, Amaranthus tuberculcatus var. tuberculatus, that occurs only in pristine non-agricultural environments along side bodies of water. These two very closely related species that occur in distinct environments and importantly differ in their exposure to herbicide can thus allow me to test whether there is genetic variation for NTSR before the onset of selection. This may be the case as genes responsible for conferring NTSR may have robust roles in detoxification to other environmental variables. 

Here are some pictures of Amaranthus from my trip to Ridgetown and the surrounding area – see if you can spot the two varieties!

 

 

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