Research

Overview

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 contemporary agricultural environments in the Brassicaceae and common waterhemp, Amaranthus tuberculatus. 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.

2015-09-07-17-26-27
the contemporary agricultural landscape

Contemporary adaptation in Amaranthus tuberculatus

Harboring cross-resistance to up to five herbicides and including glyphosate, the invasion of common waterhemp in agricultural environments is becoming increasingly problematic for crop loss. With the weedy-agricultural waterhemp variety (Amaranthus tuberculatus var. rudis) having a range historically limited to the midwestern United States, first reports of waterhemp occurring in agricultural fields in Ontario, Canada underlines the need to better understand processes mediating the spread of resistant, weedy species.

To this end, I am currently working to identify the demographic origins of agricultural populations (have Ontario agricultural populations arisen via translocation of a midwestern type, or via de novo agricultural adaptation) and the genetic origins of resistance (what is the role of independent vs shared origins of resistance adaptation across populations and regions) – Keep your eyes out for a forthcoming paper!

Furthermore, with two subspecies historically occurring in allopatry and in distinct selective environments, I will be coupling extensive contemporary sampling across the range and ancient herbarium samples to identify genomic underpinnings of contemporary agricultural adaptation, the extent to which the subspecies are locally adapted, and the evolutionary dynamics governing gene flow between subspecies across environments and time.

Here are some pictures of Amaranthus from my trip 2017 trip to Ridgetown, Ontario and the surrounding area where the two subspecies now occur in sympatry – see if you can spot them both!

 


Comparative population genomics of adaptation in Brassicaeceae

Looking across 12 species in the Brassicaceae family collected from common agricultural fields in the Prairies, Canada, I plan on taking a novel approach to investigate the population genomic signals of adaptation and genome structure across species. Here I will be investigating the proportion of the genome under positive vs. purifying selection within species, and how repeatable these genomic regions under selection are across species and populations from the same environments. I will also test the extent to which the strength of selection influences the prevalence of hard vs. soft selective sweeps – how does the degree of mutation limited-adaptation vary across the genome compared to at focal resistance loci under strong selection?

By studying the comparative genomics of selection and herbicide resistance in 12 species in the Brassicaceae, 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), I can contrast how the rate and mode of adaptation vary between species that differ in key life history characteristics—mating system and ploidy.

 

 

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