Multiple large-scale gene and genome duplications during the evolution of hexapods

Abstract

Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs.Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage-balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth.

Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera

“…In total, 14 (∼30%) of the Drosophila lineagespecific expanded developmental gene families covered here have been previously identified as such (Supplementary Data File 6). Also the taxonomic distribution of recently identified whole genome duplication events in the insect tree of life is consistent with our findings (Li et al, 2018).…”

“…Besides Diptera, this includes Lepidoptera, Coleoptera, and Hymenoptera. Recent analyses suggest that, in contrast to the angiosperms, whole genome duplications occurred during only one of these massive diversifications of insect clades, i.e., in the Lepidoptera (Li et al, 2018). Our pilot comparison of DGD numbers detected an exceptional role of localized tandem gene duplication in the Diptera (Figure 6).…”