Multiple Large-Scale Gene and Genome Duplications During the Evolution of Hexapods
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Multiple large-scale gene and genome duplications during the evolution of hexapods Zheng Lia,1, George P. Tileyb,c,1, Sally R. Galuskaa, Chris R. Reardona, Thomas I. Kiddera, Rebecca J. Rundella,d, and Michael S. Barkera,2 aDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; bDepartment of Biology, University of Florida, Gainesville, FL 32611; cDepartment of Biology, Duke University, Durham, NC 27708; and dDepartment of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210 Edited by Michael Freeling, University of California, Berkeley, CA, and approved March 12, 2018 (received for review June 14, 2017) Polyploidy or whole genome duplication (WGD) is a major contrib- than 800,000 described hexapod species (25) are known polyploids utor to genome evolution and diversity. Although polyploidy is (17, 20). However, until recently there were limited data available recognized as an important component of plant evolution, it is to search for evidence of paleopolyploidy among the hexapods generally considered to play a relatively minor role in animal and other animal clades. Thus, the contributions of polyploidy to evolution. Ancient polyploidy is found in the ancestry of some animal evolution and the differences with plant evolution have animals, especially fishes, but there is little evidence for ancient remained unclear. WGDs in other metazoan lineages. Here we use recently published To search for evidence of WGDs among the hexapods, we transcriptomes and genomes from more than 150 species across the leveraged recently released genomic data for the insects (26). insect phylogeny to investigate whether ancient WGDs occurred Combined with additional datasets from public databases, we assembled 128 transcriptomes and 27 genomes with at least one during the evolution of Hexapoda, the most diverse clade of animals. representative from each order of Hexapoda (SI Appendix and Using gene age distributions and phylogenomics, we found evidence Dataset S1). We selected data from chelicerates, myriapods, for 18 ancient WGDs and six other large-scale bursts of gene and crustaceans as outgroups. Ancient WGDs were initially identi- duplication during insect evolution. These bursts of gene duplication fied in the distributions of gene ages (Ks plots) produced by occurred in the history of lineages such as the Lepidoptera, Trichop- DupPipe (27, 28). We also used the MultitAxon Paleopolyploidy tera, and Odonata. To further corroborate the nature of these Search (MAPS) algorithm (8) to infer WGDs or other large- duplications, we evaluated the pattern of gene retention from scale genome duplications that are shared among descendant putative WGDs observed in the gene age distributions. We found taxa. MAPS uses multispecies gene trees to infer the phyloge- a relatively strong signal of convergent gene retention across netic placement of significant bursts of ancient gene duplication many of the putative insect WGDs. Considering the phylogenetic based on comparison with simulated gene trees with and without breadth and depth of the insect phylogeny, this observation is WGDs. Simulations were conducted with GenPhyloData (29) consistent with polyploidy as we expect dosage balance to drive with background gene birth and death rates estimated from the parallel retention of genes. Together with recent research on WGDgc (30) for each MAPS analysis (Datasets S3 and S4). plant evolution, our hexapod results suggest that genome dupli- Analyses of synteny within the Bombyx mori genome (31) pro- cations contributed to the evolution of two of the most diverse vided additional evidence that significant duplications inferred lineages of eukaryotes on Earth. by our MAPS analyses may result from large-scale genome du- plication events. We also compared the synonymous divergence insects | genomics | polyploidy | genome duplication | hexapods of putative WGD paralogs with the orthologous divergence enome duplication has long been considered a major force Significance Gof genome evolution and a generator of diversity. Evidence of paleopolyploidy is found in the genomes of many eukaryotes, Polyploidy or whole genome duplication (WGD) is considered a such as yeasts, teleost fishes, and plants (1–4). Polyploid speciation major force in plant evolution, but less important in animals. is perhaps most important among plants where nearly one-third of The most diverse group of animals, the insects, are thought to contemporary vascular plant species have recently duplicated ge- have evolved without ever experiencing a WGD. Our analyses nomes (5, 6). All extant seed plants have also experienced at least of diverse genomic data found evidence for 18 ancient WGDs one ancient whole genome duplication (WGD) (7, 8), and many and at least six other bursts of gene duplication during the flowering plants have undergone multiple rounds of paleo- evolution of insects. Further, we found that the functional EVOLUTION polyploidy (2, 3, 9). The creation of new genes (10, 11), higher patterns of gene retention and loss in these insect genomes are turnover of genome content (12, 13), and increased rates of consistent with the signatures of WGDs. The expanding col- adaptation (14) following polyploidy have likely contributed to lection of genomic data for insects will provide many oppor- the diversification of flowering plants (12, 15). tunities to further evaluate the evidence for WGDs and In contrast to plants, polyploid speciation among animals is understand the impact of polyploidy on insect evolution. generally regarded as exceptional (16, 17). The most well-known polyploidization events in animals are two rounds of ancient Author contributions: Z.L., G.P.T., R.J.R., and M.S.B. designed research; Z.L., G.P.T., S.R.G., C.R.R., T.I.K., and M.S.B. performed research; Z.L., G.P.T., S.R.G., C.R.R., and T.I.K. contrib- WGD (the 2R hypothesis) that occurred in the ancestry of all uted new reagents/analytic tools; Z.L., G.P.T., S.R.G., C.R.R., T.I.K., and M.S.B. analyzed vertebrates (18, 19). However, most known cases of polyploidy in data; and Z.L., G.P.T., R.J.R., and M.S.B. wrote the paper. animals are found among parthenogenetic and hermaphroditic The authors declare no conflict of interest. groups (17, 20). If paleopolyploidy is indeed fundamental to the This article is a PNAS Direct Submission. evolution of animal life across deep time, as it is in plants, we would expect to find WGDs throughout the most species-rich Published under the PNAS license. animal lineages: molluscs and arthropods. Little is known about 1Z.L. and G.P.T. contributed equally to this work. ancient WGD among invertebrates, but there is growing evidence 2To whom correspondence should be addressed. Email: [email protected]. for paleopolyploidy in molluscs (21) and chelicerates (22–24). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. There is no evidence of paleopolyploidy among Hexapoda, the 1073/pnas.1710791115/-/DCSupplemental. most diverse lineage of animals on Earth. Only 0.01% of the more Published online April 19, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1710791115 PNAS | May 1, 2018 | vol. 115 | no. 18 | 4713–4718 Downloaded by guest on September 23, 2021 among lineages to place inferred genome duplications in phylo- Overall, our analyses of gene age distributions found evidence genetic context. Potential ancient WGDs detected in our gene age for 18 independent paleopolyploidizations in the ancestry of distributions were further corroborated by analyses of biased gene 14 orders of hexapods (Fig. 2 and SI Appendix, Fig. S7). We retention across 20 hexapod genomes. observed evidence for ancient WGDs in diverse lineages of hexapods, including springtails, beetles, ants, lice, flies, thrips, Results moths, termites, sawflies, caddisflies, stoneflies, and mayflies. Inference of WGDs from Gene Age Distributions. Our phylogenomic Some of these WGDs were of relatively modest synonymous analyses revealed evidence for WGDs in the ancestry of many divergence and may be correlated with the origins of families or insects. Peaks of gene duplication consistent with WGDs were clades of genera, such as the inferred paleopolyploidization in observed in the gene age distributions of 20 hexapod species Trichocera saltator (Fig. 1D). However, many of these putative (Fig. 1 and SI Appendix, Figs. S1–S4 and Table S1). Each of the WGDs appear to have occurred early in the evolution of dif- inferred WGDs was identified as a significant peak using SiZer ferent hexapod orders with relatively high synonymous di- vergence among paralogs. For example, applying the Drosophila and mixture model analyses (SI Appendix, Fig. S1 and Table S1 × −9 and Dataset S2). Fifteen of these appear as phylogenetically synonymous substitution rate of 5.8 10 substitutions/synonymous independent WGDs because the sampled sister lineages lack site/year (32) to thrips, we estimated that the thrips duplication occurred ∼155 MYA based on the median paralog divergence evidence of the duplications (Fig. 2 and SI Appendix, Figs. S1– of the WGD. However, if thrips have a slower rate of evolution S4). In two cases, multiple sister lineages contained evidence for than Drosophila, then this WGD would be older. paleopolyploidy in their Ks plots. All sampled species of Thy- sanoptera contained evidence of at least one peak consistent Phylogenomic Inference and Simulation of Ancient Large-Scale with paleopolyploidy in their Ks plots (Fig. 1C and SI Appendix, – Genome Duplications. Given the depth of the phylogeny, there Fig. S2 I K). Analyses of orthologous divergence among these may be many WGDs or other large-scale genome duplications in taxa indicated that the putative WGD peaks are older than the the ancestry of hexapods that do not appear in Ks plots due to divergence of these lineages, and we currently infer a single, saturation of substitutions. We conducted 33 MAPS (8) analyses shared WGD in the ancestry of Thysanoptera.