Plastid phylogenomics of water lilies, with a focus on partitioning strategies and the development of bioinformatic tools

• Applicant: Michael Gruenstaeudl, Ph.D.
• Subject Area: Evolution and Systematics of Plants and Fungi
• Term: from 2018 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 418670221

The water lilies and relatives form a clade of aquatic, rhizomatous herbs that represents one of the earliest diverging lineages of flowering plants. Recently, the first plastid phylogenomic investigation of this clade indicated that the water lilies were paraphyletic in their current circumscription. Moreover, it indicated that the inferred relationships were dependent on the specific data partitioning scheme employed. In phylogenomic analysis, the application of optimal data partitions as well as best-fitting nucleotide substitution models for these partitions is a critical aspect. Current software tools for the identification of optimal partitioning schemes and best-fitting nucleotide substitution models are not fully standardized regarding data format and analysis algorithm. As a consequence, different software tools identify different partition sets and substitution models as optimal for the current plastid genome dataset of the water lilies. It is currently unknown if these differences lead to significantly different tree topologies upon phylogeny inference or if they are the consequence of a limited taxon sampling. The proposed research project aims to generate a plastid genome dataset that includes more than half of all described species of water lilies and relatives. Based on such a broad taxon sampling, the project aims to evaluate the evolutionary history of the water lilies and the impact of different data partition schemes on their phylogeny inference. Moreover, the proposed investigation aims to assess the impact of software choice on the inference of optimal data partition schemes and nucleotide substitution models. To facilitate this assessment, a novel software script was developed in preparation of this proposal which automates and standardizes the application of different software tools for partition-finding and model-testing. Based on the application of this software script, the monophyly of the water lilies is re-evaluated in the context of different data partition schemes. Upon completion of this project, the scientific community will have a better understanding of (a) the monophyly of the water lilies in their current circumscription, (b) the sensitivity of phylogenetic tree inference to data partitioning of complete plastid genome sequences, and (c) the effect of software choice during inferences of optimal data partitions and best-fitting nucleotide substitution models. The results of the proposed project are far-reaching and may affect our interpretation of early angiosperm evolution as a whole.

• DFG Programme: Research Grants
• International Connection: USA
• Cooperation Partners: Professor Dr. Robert K. Jansen; John H. Wiersema, Ph.D.