The Begun Lab

      at UC Davis

     Drosophila Evolutionary Genetics
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Begun Lab Research

      We are interested in understanding the population genetic mechanisms responsible for patterning genomic variation across the genome within and between species. The vast majority of our work uses Drosophila as a model system. Our work spans a wide range of evolutionary genomics approaches, including: 1) using population genetics data from particular classes of genes (i.e., sex-related genes, immunity genes) to make inferences about evolutionary mechanisms, 2) using population genetics data from different classes of nucleotide sites throughout the genome to reveal heterogenous forces acting across these classes, 3) using genetic analysis of particular phenotypes to understand the molecular basis of phenotypic variation, 4) using gene expression data to develop sets of candidate genes for phenotypes we are interested in studying.


Origin and evolution of "novel" Drosophila genes

      We use a combination of molecular and computational approaches to identify newly evolved genes in Drosophila. Recent work includes analysis of an Adh-derived retrogene in the obscura group and a comparative analysis of recently evolved Adh-derived fly genes (Corbin Jones). We have also been characterizing male expressed genes that are present in only a subset of melanogaster group species. Our long term goal is a population genetic investigation of the origin and spread of novel genes and functional characterization in different species of the melanogaster subgroup of Drosophila

Drosophila Population Genomics

      The availability of population genetics data on a genomic scale will transform the way we do science. We are involved in two Drosophila population genomics efforts. First, we have been working on creating a population genetic dataset based on light shotgun sequences from six D. simulans strains and one high quality D. yakuba genome from reads produced by the Washington University Genome Center. The second project (led by Langley) proposes sequencing 7 Mb of DNA from each of 50 D. melanogaster strains using Affymetrix chip-based resequencing. We hope to eventually completely sequence the unique, euchromatic portion of each of the 50 lines and then determine the sequence of roughly 1000 strains of D. melanogaster. You can read more about these two projects at

Genetics of adaptation in D. melanogaster

      D. melanogaster shows clinal variation along latitudinal transects on multiple continents for several phenotypes, allozyme variants, SNPs, and chromosome inversions. Previous investigation suggested that many such clines are due to spatially varying selection, but the genomic extent of such selection is unknown. We mapped differentiation throughout the genome by hybridizing DNA from temperate and subtropical populations to Affymetrix tiling arrays. The resulting portrait of differentiation implicated many interesting new functions in genotype-by-environment interactions including chorion proteins, proteins regulating meiotic recombination and segregation, gustatory and olfactory receptors, and proteins affecting synaptic function and behavior. Our long term goal is to understand the mechanisms by which natural selection maintains genetic variation in these populations.