Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing rate. The high number of species that have yet to be described have generated extreme crisis to the taxonomist. Therefore, more than in any other era, effective ways to discover and delimitate species are needed. This paper reviews the historically foremost approaches used to delimit species in Ascomycota, the most speciose phylum of Fungi. These include morphological, biological, and phylogenetic species concepts. We argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and disadvantages. Recently the rate of species discovery has increased because of the advancement of phylogenetic approaches. However, traditional phylogenetic methods with few gene regions lack species-level resolution, and do not allow unambiguous conclusions. We detail the processes that affect gene tree heterogeneity, which acts as barriers to delimiting species boundaries in classical low-rank phylogenies. So far, limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal species. In addition to reviewing concepts and methodologies used to delimit species, we present a case study. We applied different species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus Phyllosticta (Dothideomycetes, Botryosphaeriales). Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single species. These problems can be resolved by using multiple loci and coalescence-based methods. Further, we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.

人类活动造成的干扰造成的生物多样性丧失意味着物种正在以越来越快的速度消失。尚未描述的大量物种给分类学家带来了极大的危机。因此，比任何其他时代都更需要发现和界定物种的有效方法。本文回顾了历史上用于在子囊菌门中划定物种的最重要方法，子囊菌门是最特殊的真菌门。这些包括形态学、生物学和系统发育物种概念。我们认为划定物种边界的单一属性具有各种缺陷，每个物种概念都有其自身的优点和缺点。最近，由于系统发育方法的进步，物种发现的速度有所增加。然而，传统的基因区域很少的系统发育方法缺乏物种水平的分辨率，并且不允许得出明确的结论。我们详细介绍了影响基因树异质性的过程，这是在经典的低等级系统发育中划定物种边界的障碍。到目前为止，对基于 DNA 的方法学在真菌物种之间建立有充分支持的边界的认识有限。除了回顾用于划定物种的概念和方法外，我们还提供了一个案例研究。我们应用了不同的物种划分方法来了解植物病原和隐性属中的物种边界 它充当了在经典低阶系统发育中划定物种边界的障碍。到目前为止，对基于 DNA 的方法学在真菌物种之间建立有充分支持的边界的认识有限。除了回顾用于划定物种的概念和方法外，我们还提供了一个案例研究。我们应用了不同的物种划分方法来了解植物病原和隐性属中的物种边界 它充当了在经典低阶系统发育中划定物种边界的障碍。到目前为止，对基于 DNA 的方法学在真菌物种之间建立有充分支持的边界的认识有限。除了回顾用于划定物种的概念和方法外，我们还提供了一个案例研究。我们应用了不同的物种划分方法来了解植物病原和隐性属中的物种边界Phyllosticta（Dothideomycetes，Botryosphaeriales）。几种基于 DNA 的方法过度分裂分类群，而在某些方法中，几个分类群落入一个物种。这些问题可以通过使用多个位点和基于聚结的方法来解决。此外，我们讨论了对理解子囊菌内物种边界至关重要的综合方法，并为物种划界的理想和实用方法提供了几个例子。