Quantification of ortholog losses in insects and vertebrates

Stefan Wyder¹^,2 , Evgenia V Kriventseva³^,2 , Reinhard Schröder⁴ , Tatsuhiko Kadowaki⁵ and Evgeny M Zdobnov¹^,2^,6

¹Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland

²Swiss Institute of Bioinformatics, rue Michel-Servet, 1211 Geneva, Switzerland

³Department of Structural Biology and Bioinformatics, University of Geneva Medical School, rue Michel-Servet, 1211 Geneva, Switzerland

⁴Interf. Institut für Zellbiologie, Abt. Genetik der Tiere, Universität Tübingen, 72076 Tübingen, Germany

⁵Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan

⁶Imperial College London, South Kensington Campus, London SW7 2AZ, UK

author email corresponding author email

Genome Biology 2007, 8:R242doi:10.1186/gb-2007-8-11-r242


Published:	16 November 2007

Subject areas: Evolution, Genome studies

Abstract

Background

The increasing number of sequenced insect and vertebrate genomes of variable divergence enables refined comparative analyses to quantify the major modes of animal genome evolution and allows tracing of gene genealogy (orthology) and pinpointing of gene extinctions (losses), which can reveal lineage-specific traits.

Results

To consistently quantify losses of orthologous groups of genes, we compared the gene repertoires of five vertebrates and five insects, including honeybee and Tribolium beetle, that represent insect orders outside the previously sequenced Diptera. We found hundreds of lost Urbilateria genes in each of the lineages and assessed their phylogenetic origin. The rate of losses correlates well with the species' rates of molecular evolution and radiation times, without distinction between insects and vertebrates, indicating their stochastic nature. Remarkably, this extends to the universal single-copy orthologs, losses of dozens of which have been tolerated in each species. Nevertheless, the propensity for loss differs substantially among genes, where roughly 20% of the orthologs have an 8-fold higher chance of becoming extinct. Extrapolation of our data also suggests that the Urbilateria genome contained more than 7,000 genes.

Conclusion

Our results indicate that the seemingly higher number of observed gene losses in insects can be explained by their two- to three-fold higher evolutionary rate. Despite the profound effect of many losses on cellular machinery, overall, they seem to be guided by neutral evolution.