The unifying theme of my research is to make a contribution to unravel the Insect Tree of Life as this could provide essential insights into the evolution of global biodiversity, evolutionary processes and key innovations. The importance of insects not only for medical or agricultural issues but also the need to achieve a deep understanding of insect evolution and phylogeny in general has become obvious in the past.
Focusing on the gap of information for several insect orders and to address fundamental questions in evolutionary biology, I closely collaborate with international scientists in the 1KITE project (http://www.1kite.org/) to infer a robust phylogenetic backbone tree of insects using more than 1,000 newly generated insect transcriptomes. Nowadays one of the major challenges in phylogenomic studies is not the generation of the data but their analyses and interpretation. This has become one of my research interests and it involves the evaluation of how ortholog prediction, missing data, and taxon and gene sampling contribute to the underlying data quality and consequently the resolution of a certain phylogenetic question. Previous results on this topic have clearly demonstrated that the phylogenomic data matrices harbour a high amount of conflicting phylogenetic signal, which needs to be carefully evaluated; e.g. for some splits within insect evolution the taxon sampling and the function of the genes have a huge impact on the inferred relationships. To address mechanistic problems relevant to phylogenetic reconstruction new workflows will be set including already developed tools as well as various new bioinformatic tools. Some key publications are:
Wipfler B, Letsch H, Frandsen PB, ..., Simon S (2019). Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects, Proceedings of the National Academy of Sciences Jan 2019, 201817794; https://doi.org/10.1073/pnas.1817794116
Evangelista DA, Wipfler B, Béthoux O, ..., Simon S (2019). An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea),Proceedings of the Royal Society B: Biological Sciences, https://doi.org/10.1098/rspb.2018.2076
Simon S, Blanke A and K Meusemann (2018). Reanalyzing the Palaeoptera problem - the origin of insect flight remains obscure, Arthropod Structure and Development, May 29. pii: S1467-8039(18)30055-0. https://doi.org/10.1016/j.asd.2018.05.002
Comparative transcriptomics of early insect development (PhD project Wouter Makkinje)
The new sequencing technologies have massively increased the amount of data available for comparative transcriptomics which can be used to infer insect relationships but also to study the transcriptional signatures and dynamics of developmental processes. However, transcriptomic data across developmental stages are mainly available for derived holometabolous insects, especially drosophilid dipteran species. Therefore, several key insect lineages should be established as non-model system for developmental research and to study in depth the evolution of insect embryogenesis. The new development-dependent transcriptomic information of non-model organisms will help to further study in detail an essential large scale developmental paradigm in developmental biology the molecular signatures of embryonic developmental constraints.
Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G and R DeSalle (2017). Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans, Scientific Reports, Oct 19;7(1):13547. https://doi.org/10.1038/s41598-017-13176-8.
Insect Pest Evolution (PhD project Thijmen Breeschoten)
The majority of insect orders include pest species that impact the productivity of crop plants and/or have deleterious effects on human health, and the annual cost of managing these pests steadily increases. Insect herbivores and their host plants interact in a complex manner, and insect herbivores have evolved a multitude of physiological strategies to adapt to plants containing toxic compounds: (including, but not limited to, enzymatic detoxification, excretion, and sequestration). Using comparative phylogenomic approaches, much has been learned about the evolution and mechanisms of plant defenses, but by comparison there is a dearth of robust comparative phylogenomic contrasts of insect pests and their evolution. To understand the evolution of insect pest species and factors that contribute to their success, an interdisciplinary approach will be conducted in order to gain insights on the origin and evolution of pest-genes in Lepidoptera.