TaxonOMICS of Australian Chenopods: a multifaceted study to resolve one of Australia’s most challenging plant families

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Our project focuses on universal molecular and bioinformatics methods for a simplified exploration and description of biodiversity. So far, we have developed a modified RADseq approach for the phylogenetic analysis of rapidly and recently radiated species complexes. This allows, in addition to widely used SNP based approaches, the application of two-step coalescent-based summary methods for species tree inference. We overcame several hurdles of classical RAD data by sequencing libraries with several thousand loci of 300-600 bp length. Furthermore, we developed a comprehensive target group specific data analysis approach to ensure an accurate assembly process, complemented by comparative phylogenetic analyses. This approach has not only been tested successfully for our study group, the Australian Camphorosmeae, but also worked for a broad variety of plant lineages in our lab. The molecular approach is accompanied by the development of an image classification tool to facilitate identification of taxa in the field. So far, we performed a promising pilot study to test the performance of different neural network architectures using the morphologically diverse Australian Camphorosmeae as a trial group. Together with our international collaboration network of phylogenetics, bioinformatics and taxonomy experts we are now set to tackle even more diversity of the Australian Chenopodiaceae during the second SPP Taxon-Omics round. We will extend our study group to the species-rich and cryptic genera Atriplex and Tecticornia, covering nearly 80% of Australian chenopods. In addition to the varying needs of our study groups, we will also extend the spectrum of molecular approaches for species delimitation. Our modified llddRADseq approach will be further refined by incorporating the capturing principle of hyRAD (Suchan et al. 2017) for lineage delimitation in Atriplex and the Camphorosmeae. Extending the RAD based methods, we will utilize a Hyb-Seq approach specially designed for Australian Angiosperm lineages to unravel the species complexes of the enigmatic Tecticornia. Both approaches will then be suitable for phylogenomics of degraded DNA samples aiming at the comprehensive biodiversity resources stored at museums. Besides further refinements for the Camphorosmeae, our image classification approach will be extended for a pilot study in Atriplex using specimen and field imagery. This image-based resource will be implemented alongside already available online keys including detailed descriptions and imagery. However, these keys must first be taxonomically updated based on our phylogenetic species delimitation approaches. In combination, the molecular and bioinformatics approaches will not only reveal the complex evolutionary histories of our study groups and unravel challenging species complexes within, but also serve as a sustainable resource for the next generation of taxonomists targeting the stunning diversity of life in Australia.