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

建立多倍体复合体物种界定和物种网络重建的方法流程

• 批准号: 350440084
• 负责人: Professor Dr. Christoph Oberprieler
• 金额: --
• 依托单位: Botanischer Garten und Botanisches Museum (BGBM)
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2017
• 资助国家: 德国
• 起止时间: 2016-12-31 至 2021-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/350440084?language=en
• 关键词: Setting; up; methodological; pipeline; species

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.

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)是开花植物进化和物种形成的重要过程。二倍体和多倍体水平上的基因流动，多倍体物种的多重形成(通常是在相互亲子关系下)，以及多倍体物种辐射的年轻，解释了多倍体复合体的分类是基于DNA的系统发育物种划分方法的终极挑战。此外，由于缺乏重建网状(物种)系统发育的明确方法，多倍体复合体进化历史的重建仍然受到阻碍。我们目前的项目建议旨在开发、建立和评估一种方法管道，允许快速发现和划定进化重要单位(物种)，并利用基因组、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。我们的方法将在白花莲的多倍体复合体中得到例证。(牛眼雏菊；菊科)，由大约43个物种组成，倍性水平在2x到22x之间。用于多物种联合物种定界和物种网络重建的分子数据将由两种下一代测序方法提供：(A)通过Illumina测序获得GBS/RADseq信息，用于种群遗传分析，特别是用于检测类群之间的实际杂交；(B)用于物种网络重建和物种定界假说检验的单拷贝核标记的PacBio单分子测序。我们拟议项目的核心内容将涉及创建新的生物信息学工具，以便在多倍体水平上应用物种划界和物种树重建方法。除了验证我们与SPP其他小组在植物多倍体复合体中工作的工作流程外，还设想对与物种划界概念和我们的方法在其他有机体小组中的适用性有关的方法学和哲学问题进行一般性讨论。