Adaptive Evolution of Gene Expression and Alternative Splicing

University Of Wisconsin-Madison, Madison WI

Investigators

Abstract

A single gene often encodes numerous proteins by assembling different components from the original DNA sequence. These proteins have different functions. Thus, the number and type of proteins produced from a gene, i.e., gene regulation, are important aspects of how an organism functions. The investigators will look across the whole genome in natural populations of the fruit fly that have adapted to different temperature environments. By comparing gene regulation among these populations, they will learn how gene regulation changes as organisms adapt to their environment. The project will provide an unusually complete view of the causes, mechanisms, and consequences of the evolution of gene regulation. It will also inform how insects adapt to novel environments. Thus, they will also learn about the factors that limit the geographic ranges of insects that are agricultural pests or disease vectors. Broader impacts of this project include extensive training of young scientists, including members of underrepresented groups in science. The project will also strengthen scientific connections between U.S. researchers and their counterparts in Africa. Finally, the team will improve the quality of scientific reference material available to the public online. The fruit fly Drosophila melanogaster originated from warm regions of Africa; this research focuses on three parallel instances of adaptation to colder climates. The project includes the collection of RNA sequence data from three pairs of warm- and cold-adapted populations that encompass these three climate transitions. By applying a population genetic framework to this data set, population differences in gene expression and alternative splicing that were most likely driven by local adaptation can be identified. Crosses between warm- and cold-adapted populations will allow these changes to be classified as either cis-encoded at the affected gene, or trans-encoded by another gene. For cis-encoded cases of adaptive expression or splicing evolution, patterns of genetic variation can illuminate key details of natural selection's mode of action. Researchers will use existing population genomic data to test whether selection favored new mutations or standing genetic variation. The project also entails the genetic mapping of cold tolerance differences for each population pair. The combination of mapping results, population genomic analysis of existing data, and the above RNA sequencing results will identify notable candidate genes for local adaptation via cis-acting changes in gene regulation. Probing the interface between genetic adaptation and the thermal environment will test whether gene regulatory changes alter or maintain ancestral regulation, and whether such changes result in gene regulatory networks that are less buffered against perturbation. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.