Kratochwil Claudius F, Kautt Andreas F, Rometsch Sina J, Meyer Axel
Zoology and Evolutionary Biology Department of Biology University of Konstanz Konstanz Germany.
Present address: Institute of Biotechnology HiLIFE University of Helsinki Helsinki Finland.
Ecol Evol. 2022 Mar 23;12(3):e8751. doi: 10.1002/ece3.8751. eCollection 2022 Mar.
High-throughput DNA sequencing technologies make it possible now to sequence entire genomes relatively easily. Complete genomic information obtained by whole-genome resequencing (WGS) can aid in identifying and delineating species even if they are extremely young, cryptic, or morphologically difficult to discern and closely related. Yet, for taxonomic or conservation biology purposes, WGS can remain cost-prohibitive, too time-consuming, and often constitute a "data overkill." Rapid and reliable identification of species (and populations) that is also cost-effective is made possible by species-specific markers that can be discovered by WGS. Based on WGS data, we designed a PCR restriction fragment length polymorphism (PCR-RFLP) assay for 19 Neotropical Midas cichlid populations ( cf. ), that includes all 13 described species of this species complex. Our work illustrates that identification of species and populations (i.e., fish from different lakes) can be greatly improved by designing genetic markers using available "high resolution" genomic information. Yet, our work also shows that even in the best-case scenario, when whole-genome resequencing information is available, unequivocal assignments remain challenging when species or populations diverged very recently, or gene flow persists. In summary, we provide a comprehensive workflow on how to design RFPL markers based on genome resequencing data, how to test and evaluate their reliability, and discuss the benefits and pitfalls of our approach.
高通量DNA测序技术使得如今相对轻松地对整个基因组进行测序成为可能。通过全基因组重测序（WGS）获得的完整基因组信息有助于识别和界定物种，即使它们极其年轻、隐秘、形态上难以区分或亲缘关系密切。然而，出于分类学或保护生物学目的，全基因组重测序可能成本过高、耗时过长，且往往构成“数据过剩”。通过全基因组重测序发现的物种特异性标记使得快速、可靠且具有成本效益的物种（和种群）识别成为可能。基于全基因组重测序数据，我们为19个新热带米达斯丽鱼种群（参见）设计了一种聚合酶链反应-限制性片段长度多态性（PCR-RFLP）分析方法，该种群包括该物种复合体中所有已描述的13个物种。我们的工作表明，利用现有的“高分辨率”基因组信息设计遗传标记可以大大改善物种和种群（即来自不同湖泊的鱼类）的识别。然而，我们的工作还表明，即使在最佳情况下，即有全基因组重测序信息可用时，当物种或种群分化非常近或基因流持续存在时，明确的分类仍然具有挑战性。总之，我们提供了一个全面的工作流程，介绍如何基于基因组重测序数据设计限制性片段长度多态性标记，如何测试和评估其可靠性，并讨论我们方法的优点和不足。
