Evolutionary Population Genomics, Development, and Ecology
Our lab has long used the microcrustacean Daphnia as a model system for understanding the evolutionary links between genomics, cell / developmental biology, and ecology. Many aspects of the biology of this organism make it an optimal platform for connecting diverse areas of biology. Daphnia are found globally in most lakes and ponds. They reproduce both clonally and sexually, so genotypes can be maintained indefinitely in the lab, while controlled crosses can also be made. Moreover, the sexual resting eggs of Daphnia are preserved viably in the sediments of lakes, so lake cores can yield a “living fossil” record as the resting eggs are hatched and maintained in the lab.
We have sequenced > 2000 genomes for the pond-dwelling D. pulex and for the closely related lake dweller D. pulicaria, and are using this information to decipher the genetic mechanisms driving the differences among the two, including a two-fold difference in life span, and reverse reactions to photoperiods.
The complete genome sequences for 20 other species are providing a broad overview of diversification at a broader level.
To determine the degree to which populations experience fluctuating selection over time, one population is being studied on an annual basis, with a series of ten years of population-genomic data having now been obtained.
An atlas of gene expression for the full transcriptome is being developed across developmental stages and tissues, including at the single-cell level. In addition, we are currently trying to get Crispr-Cas9 working more efficiently, so we can perform genetic transformations.
We have discovered a novel, widespread variant that prevents carriers from producing male offspring, and are now attempting to identify the molecular mechanisms underlying such suppression.