Polygenic adaptation in domesticated crops

Many of the traits that we care about are quantitative, which means that variation in these traits is controlled by a large number of genes. Adaptation in quantitative traits often occurs through polygenic adaptation: small shifts in the allele frequencies of many loci that are not detectable through standard selection scans. Polygenic adaptation may be especially common in domestication, where a number of quantitative traits have been under selection, both consciously and unconsciously. I am developing and applying methods for identifying polygenic adaptation in publicly available genomic datasets in crops, allowing me to detect specific traits that show evidence of polygenic adaptation in space, across the landscape of domesticated crops and in time, throughout crop breeding. I am particularly interested in figuring out how population structure (variable relatedness between individuals) will affect methods for detecting polygenic adaptation

Maintenance of variation within populations

What evolutionary processes maintain phenotypic variation within populations? How much of this variation is adaptive and how much is the result of a balance between mutation and purifying selection?

I am characterozomg genetic and phenotypic variation within a natural population of Capsella grandiflora. I conducted a genome-wide association mapping study which will attempt to connect genetic sequence, gene expression levels, and physical traits. My goals bas been not only to find the genetic variants that affect phenotypic variation, but also to describe how selection acts on these variants. To do this, I use gene expression as a model phenotype and have focussed on local genetic variants that affect expression of single genes and variants that affect the correlated expression of a large number of genes.

Population genomics of Capsella grandiflora

What role does selection play in shaping genomic variation? I collaborated with Robert Williamson to explore this in a sample of 13 C. grandiflora individuals collected from across the species range. In particular, I examined whether positive selection has significantly contributed to divergence between C. grandiflora and its close relatives by looking for reduced diversity around replacement substitutions, as would be expected if selective sweeps have been common. I also tested for variation in the strength of selection between genes with different expression levels. You can read more about this work here . We also collaborated with Ramesh Arunkumar to measure selection on pollen-expressed genes and this work is described here.

My research systems

Capsella grandiflora is a small weedy annual native to northern Greece and Albania. It’s an obligate outcrosser and a member of the Brassicaceae family. It often gets mistaken for Arabidopsis, but, unlike Arabidopsis, it has heart-shaped fruit and somewhat larger flowers.

The population I have focussed on on is located on a trail head near the Greek town of Monodendri.

Population ESP

Maize (Zea mays subsp. mays) is not only delicious but a great genetic model for thinking about adaptation during domestication and breeding. Maize is currently grown at a staggering scale over 96 million acres in the US alone but is also grown world-wide in a range of habitats.

Corn