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系列的分类学:物种减少及关于种内变异性的经验教训。

Taxonomy of series : species reduction and lessons learned about intraspecific variability.

作者信息

Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson R A, Visagie C M, Yilmaz N, Gené J, Cano J, Chen A J, Nováková A, Yaguchi T, Kolařík M, Hubka V

机构信息

Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.

Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.

出版信息

Stud Mycol. 2022 Dec;102:53-93. doi: 10.3114/sim.2022.102.02. Epub 2022 Nov 16.

Abstract

series members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin () genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (, , , , ). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series to four species, namely , and , and the remaining species are synonymized with either or . The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between and . Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied species complexes and other fungal genera. Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of series : species reduction and lessons learned about intraspecific variability. : 53-93. doi: 10.3114/sim.2022.102.02.

摘要

该系列成员存在于广泛的环境和基质中,如室内环境、食物、临床材料、土壤、洞穴、海洋或高盐生态系统。该系列的分类学经历了多次重新排列,包括物种数量的急剧减少,以及在过去十年中恢复到17个物种。然而,即使使用DNA测序或基质辅助激光解吸电离飞行时间质谱法,在某些分离株中鉴定到物种水平也是有问题的或不可能的,这表明物种界限的定义存在问题。为了修订物种界限,我们收集了一个包含518个菌株的大型数据集。从中,根据钙调蛋白()基因型、基质和地理位置,共选择了213个菌株进行最终分析。该数据集用于基于五个基因座(、、、、)的系统发育分析。除了经典的系统发育方法外,我们还使用了基于多物种合并(MSC)模型的方法,包括一种多位点方法(STACEY)和五种单基因座方法(GMYC、bGMYC、PTP、bPTP、ABGD)。几乎所有的物种界定方法都提出了一个宽泛的物种概念,只有四个物种得到了一致支持。我们还证明,目前应用的物种概念是不可持续的,因为单基因系统发育之间存在不一致,导致使用不同基因区域时会得出不同的物种鉴定结果。形态学和生理学数据表明,总体上缺乏良好的、具有分类学信息的特征,这些特征可用于鉴定如此大量的现有物种。这些特征在物种间的变异性较低,或者种内变异性显著超过种间变异性。基于上述结果,我们将该系列减少到四个物种,即、和,其余物种与或同义。提供了四个被接受物种的修订描述。它们都可以通过本研究中使用的五个基因中的任何一个进行鉴定。尽管物种数量大幅减少,但基于表型特征的鉴定仍然具有挑战性,因为表型特征的变异很大,且在物种间重叠,尤其是和之间。与17个狭义定义的物种类似,这四个广义定义的物种没有特定的生态习性,分布在世界各地。我们预计,采用类似方法并进行广泛采样,可能会导致其他广泛研究的物种复合体和其他真菌属中隐性物种数量出现类似减少。斯克莱纳尔·F、格拉斯内罗娃·K、尤尔耶维奇·Ž、胡布拉肯·J、萨姆森·R·A、维萨吉·C·M、伊尔马兹·N、热内·J、卡诺·J、陈·A·J、诺瓦科娃·A、矢口·T、科拉里奇·M、胡布卡·V(2022年)。系列的分类学:物种减少及关于种内变异性的经验教训。《》:53 - 93。doi: 10.3114/sim.2022.102.02

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/72c4/9903908/c58df7035e92/sim-2022-102-2-g001.jpg

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