experimental evolution with yeast

The SGRP is a set of Saccharomyces cerevisiae strains collected from locations around the world that represents the natural variation present in this species in the wild.  

 

By using SGRP populations in long-term selection experiments, we simulate ecologically relevant scenarios in the lab.  

 

These experiments allow us to test hypotheses about:

  • physiological consequences of adaptation to stress

  • the origins and fates of adaptive alleles

  • the repeatability of evolution

  • advantages of recombination and outcrossing

  • the evolution of aging

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photo: molly burke

experimental evolution with Drosophila

While we work with yeast, we collaborate with like-minded labs doing selection experiments with other organisms.  We are involved in ongoing projects with Drosophila populations selected for physiological and fitness traits.  

We use phenotype and genome data from these populations to investigate evolution in real time, and to assess the limits of what we can learn from these experiments.

Here we see Molly thinking hard about flies (photo cred: Steve Zylius)

genetics and evolution of aging

Genome-wide association studies (GWAS) present a promising method for identifying genetic variants relevant for human healthspan and age-related disease. But longevity GWAS in humans face a number of challenges, principally the absence of large and well-controlled case panels.  

Carrying out longevity GWAS in laboratory experiments with model organisms can circumvent some of these challenges.  Our goal is to better understand the genetics underlying longevity in multiple sexual species.

This figure shows a region of candidate SNPs on chromosome 2L associated with extreme longevity in Drosophila melangaster.

(published in 2014 in Genome Biology and Evolution)

using "synthetic recombinant" populations to study the genetic basis of complex traits

Classic approaches to dissecting the genetic basis of complex phenotypes - QTL mapping and genome-wide association studies - have significant limitations.  In traditional QTL mapping, QTL are typically mapped to broad intervals containing many genes. Genome-wide association mapping takes advantage of historical recombination in natural populations and therefore has the potential for very high resolution. Unfortunately, this approach requires very large sample sizes and high-density SNP maps, and even so is prone to false-positives.

 

"Synthetic recombinant" populations can bridge many of the gaps left by these traditional approaches, and they have become an important tool for basic genetics research. Notable experimental systems include the Drosophila Synthetic Reference Population (DSPR), the Arabidopsis Multiparent Advanced Generation Inter-Cross (MAGIC) population, and the Collaborative Cross in mice.

The Burke lab works with a number of synthetic recombinant yeast populations, and we occasionally work with the DSPR.