Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France.
Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
Methods Mol Biol. 2024;2744:313-334. doi: 10.1007/978-1-0716-3581-0_20.
DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).
DNA 条形码在探索未描述的生物多样性方面发挥着重要作用，并且越来越多地用于在物种水平上划定谱系（见 Miralles 等人的第 4 章）。尽管已经开发了几种方法和程序来从单基因座 DNA 序列（如 DNA 条形码）数据集执行物种划定，但其中大多数最初并未作为用户友好的 GUI 驱动可执行文件提供。尽管它们存在差异，但这些工具大多具有相同的目标，即推断潜在地代表不同物种的子集的新分区。最近，这些工具中的几个已经实现了建议的通用物种分区交换格式 (SPART)，为开发完全致力于综合和比较物种划定的可互操作数字环境铺平了道路。在本章中，我们提供了两种生物信息学工具的详细使用协议，一种用于单基因座分子物种划定 (ASAP)，另一种用于统计比较任何种类的物种划定分析产生的物种分区 (LIMES)。
