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

我们的项目侧重于通用的分子和生物信息学方法，以简化生物多样性的探索和描述。到目前为止，我们已经开发了一种改进的RADseq方法，用于快速和最近辐射的物种复合体的系统发育分析。这允许，除了广泛使用的SNP为基础的方法，两步聚结为基础的总结方法的物种树推理的应用。我们通过测序具有300-600 bp长度的几千个基因座的文库克服了经典RAD数据的几个障碍。此外，我们开发了一种全面的目标群体特定数据分析方法，以确保准确的组装过程，并辅以比较系统发育分析。这种方法不仅在我们的研究小组--澳大利亚樟亚科（Australian Camphorosmeae）中成功地进行了测试，而且在我们实验室的各种植物谱系中也有效。分子的方法是伴随着图像分类工具的发展，以方便在该领域的分类群的识别。到目前为止，我们进行了一个有前途的试点研究，以测试不同的神经网络架构的性能，使用形态多样的澳大利亚樟作为试验组。与我们的生物遗传学，生物信息学和分类学专家的国际合作网络一起，我们现在将在第二轮SPP Taxon-Omics中解决澳大利亚藜科的更多多样性。我们将把我们的研究小组扩展到物种丰富和隐藏的Atriplex和Tecticornia属，覆盖近80%的澳大利亚藜类动物。除了我们的研究小组的不同需求，我们还将扩大物种界定的分子方法的范围。我们的改良llddRADseq方法将通过纳入hyRAD的捕获原理（苏坎等人，2017）进一步完善，用于滨藜和樟亚科的谱系划分。扩展RAD为基础的方法，我们将利用专为澳大利亚被子植物谱系的Hyb-Seq方法来解开神秘的Tecticornia的物种复合体。这两种方法将适用于降解的DNA样品的生物基因组学，旨在全面的生物多样性资源储存在博物馆。除了进一步完善的Camphorosmeae，我们的图像分类方法将被扩展为一个试点研究Atriplex使用标本和现场图像。这个基于图像的资源将与现有的在线密钥一起实施，包括详细的描述和图像。然而，这些关键字必须首先进行分类更新的基础上，我们的系统发育物种划界方法。结合起来，分子和生物信息学方法不仅将揭示我们研究群体的复杂进化历史，并解开其中具有挑战性的物种复合体，而且还将成为下一代分类学家的可持续资源，目标是澳大利亚惊人的生命多样性。

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.