Our research aims to understand the genetic, developmental, and population-level processes by which new phenotypes evolve. Molecular mechanisms by which gene expression is regulated and evolves are of particular interest.

Evolution of an adaptive phenotype
Drosophila novamexicana lives in the southwestern US and has evolved yellow pigmentation in the 380,000 years since it split from D. americana. D. americana lives east of the Rocky mountains and has a brown body color. Pigmentation varies among populations of D. americana, with flies captured from the western edge of the species range (e.g. Montana, Nebraska) having lighter pigmentation than flies captured from more eastern populations. There is no evidence of population structure between eastern and western populations of D. americana, suggesting that the difference in pigmentation is maintained by selection for adaptive phenotypes best suited to their local environment. The ecological factor driving selection is unknown, although UV protection, thermotolerance, and desiccation resistance have all been proposed.

Long-term goals of this project are to (1) identify the genetic mechanisms underlying pigmentation differences within and between species, (2) determine how these changes impact the development of body color, and (3) characterize the relationship between alleles underlying polymorphism and divergence of pigmentation.

To accomplish these goals, we are investigating the following specific questions:

1. Which genes contribute to pigmentation differences within and between species?
2. Does the variation in these genes affect regulation or protein function?
3. Which nucleotide substitutions are responsible for the phenotypic effects?
4. Do the same genes, alleles and (ultimately) nucleotides underlie pigmentation differences within and between species? If so, do the alleles predate speciation?

The evolution of gene regulation
Changes in gene expression are an important source of biodiversity. However, the molecular mechanisms by which gene expression changes on a genomic scale remain largely unknown.

Mutations affecting gene expression can be located within the affected gene itself (in cis ) or in another gene that affects its expression (in trans ). Using an allele specific assay, we've found that many of the expression differences between species are caused by cis -acting variants. In contrast, trans -regulatory variants are primarily responsible for the expression difference between strains of the same species. These data suggests that selection may alter the relative frequency of cis- and trans -acting variants over time. We investigate this hypothesis by elucidating basic properties of regulatory mutations and comparing the frequency of cis - and trans - changes between species separated for different amounts of time.   In addition to testing the specific hypothesis presented, these studies also aim to provide a more complete understanding of regulatory evolution in general.

Our current work focuses on answering the following questions:

1. What is the frequency of new regulatory mutations?
2. Does the structure of regulatory networks shape the production of regulatory variation?
3. Do new cis - and trans -regulation regulatory mutations have different properties?
4. Do different genes have a different propensity for cis - and trans -regulatory changes?
5. Does the relative contribution of cis and trans mutations change over time?