Setting-up a methodological pipeline for species delimitation and species network reconstruction in polyploid complexes

杂交，全基因组复制（同源多倍体），以及两者的结合（异源多倍体）是显花植物进化和物种形成的重要过程。在二倍体和多倍体水平的基因流，多倍体物种的多个形成，往往在相互的亲子关系，和年轻的年龄的多倍体物种辐射占多倍体复合体的分类是一个基于DNA的，系统发育的物种划界方法的最终挑战。此外，多倍体复合体的进化历史的重建仍然受到阻碍，缺乏明确的方法重建网状（种）系统。我们目前的项目提案旨在开发，建立和评估一个方法管道，允许快速发现和界定进化的重要单位（物种），并使用基因组，形态和地理分布数据（包括气候生态位）重建多倍体复合体中的物种树和网络。我们的方法将在银合欢的多倍体复合体中举例说明。（牛眼菊;菊科），其包括约43个物种，倍性水平在2x和22 x之间。多物种结合物种界定（MSCSD）和物种网络重建的分子数据将由两种下一代测序（NGS）方法提供：（a）通过Illumina测序的GBS/RADseq信息，用于群体遗传分析，特别是用于检测分类群之间的实际杂交，和（B）用于物种网络重建的单拷贝核标记的PacBio单分子测序和物种定界假说的测试。我们提出的项目的核心包将处理创建新的生物信息学工具，用于在多倍体水平上应用物种定界和物种树重建方法。除了验证我们提出的工作流程与其他组的SPP在植物中的多倍体复合体的工作，与物种划界的概念和我们的方法在其他生物群体的适用性的方法和哲学问题的一般性讨论的设想。

Hybridisation, whole-genome duplication (autopolyploidy), and the combination of both (allopolyploidy) are paramount processes in the evolution of and species formation in flowering plants. Gene flow at the diploid and polyploid level, multiple formation of polyploid species, often under reciprocal parentage, and the young age of polyploid species radiations account for the taxonomy of polyploid complexes being the ultimate challenge for a DNA-based, phylogenetic species delimitation approach. Additionally, reconstructions of the evolutionary history of polyploid complexes are still hampered by the lack of explicit methods for the reconstruction of reticulate (species) phylogenies. Our present project proposal aims at the development, establishment, and evaluation of a methodological pipeline allowing the fast discovery and delimitation of evolutionary significant units (species) and the reconstruction of species trees and networks in polyploid complexes using genomic, morphological, and geographic distribution data (including climatic niches). Our approach will be exemplified in the polyploid complex of Leucanthemum Mill. (ox-eye daisy; Compositae), which comprises around 43 species with ploidy levels between 2x and 22x. Molecular data for the multi-species coalescent species delimitation (MSCSD) and species network reconstructions will be provided by two next-generation sequencing (NGS) methods: (a) GBS/RADseq information via Illumina sequencing for population genetic analyses, especially for the detection of actual hybridisation among taxa, and (b) PacBio single-molecule sequencing of single-copy nuclear markers for species network reconstructions and the testing of species delimitation hypothesis. The core package of our proposed project will deal with the creation of novel bioinformatic tools for the application of species delimitation and species tree reconstruction methods at polyploid levels. Besides validation of our proposed work-flow with other groups of the SPP working in polyploid complexes in plants, a general discussion of methodological and philosophical issues connected with species delimitation concepts and applicability of our approach in other organism groups is envisaged.