Genomics on a phylogeny: Evolution of genes and genomes in the genus Drosophila

Authors: CLARK, ANDREW - CORNELL UNIV; EISEN, MICHAEL - LAWRENCE BRKLY NAT LAB; SMITH, DOUGLAS - AGENCOURT BIOSCI CORP; BERGMAN, CASEY - UNIV MANCHESTER; GELBART, WILLIAM - MIT; OLIVER, BRIAN - NIH; MARKOW, THERESE - UNIV ARIZONA; KAUFMAN, THOMAS - INDIANA UNIV; KELLIS, MANOLIS - MIT; Evans, Jay

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/1/2007
Publication Date: 10/21/2007
Citation: Clark, A.G., Eisen, M.B., Smith, D.R., Bergman, C.M., Gelbart, W., Oliver, B., Markow, T.A., Kaufman, T.C., Kellis, M., Evans, J.D. 2007. Genomics on a phylogeny: Evolution of genes and genomes in the genus Drosophila. Nature. 450(7167):203-218.

Interpretive Summary: Insects are among the most important animals for agriculture, whether as beneficials or pests. This genome project, involving a comparison of 12 fly species, gives insights into important traits found across the insects, from bees to moths and beetles. These comparisons are already speeding the rate at which new processes involving disease resistance, behavior, and development are discovered. The analysis of immune function in this paper, for example, points toward changes in the immune system within flies that have a large impact on how one interprets immune genes in honey bees. This resource will be used widely by scientists to better determine how to increase or decrease the populations of insects critical for agriculture.

Technical Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of inferences in evolutionary genomics. The genomes of 12 Drosophila species, nine of which are presented here for the first time (sechellia, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence can be used to gain insight into evolutionary processes on a genomic scale. These genome sequences augment the remarkable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyze fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology, and evolution. Comparative genomic data allow many internal checks on data quality, producing higher confidence in robust results than single genome analyses can provide. Despite the remarkable similarities among these Drosophila species, we identified many lineage-specific changes in protein-coding genes, noncoding RNA genes, and cis-regulatory regions that deviate from strict neutrality and may prove to underlie differences in ecology and behaviour of these diverse species.