Liu Yajuan J, Hodson Matthew C, Hall Benjamin D
Departments of Biology and Genome Sciences, University of Washington, Seattle, WA 98195, USA.
BMC Evol Biol. 2006 Sep 29;6:74. doi: 10.1186/1471-2148-6-74.
At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion.
Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups.
In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.
目前，尽管子囊菌门和担子菌门这两个主要真菌门类已被明确划分，但关于真菌界的系统发育结构尚无广泛接受的共识观点。对于低等真菌，即接合菌门和壶菌门，已经提出了各种不同的观点。微孢子虫可能是也可能不是真菌；球囊霉目（泡囊 - 丛枝菌根真菌）可能是也可能不构成第五个真菌门类，并且鞭毛的丧失在真菌进化过程中可能发生过一次或多次。所有这些问题都可以通过分子系统发育分析来解决，这种分析能为主要分支提供有力的统计支持。迄今为止，基于分子特征的真菌系统发育研究都未满足这一标准。
利用RNA聚合酶II的第二大亚基（RPB2）和最大亚基（RPB1）基因的翻译氨基酸序列，我们推断出了一个真菌系统发育树，该树主要由得到充分支持的单系门类组成。我们的主要结果，每个结果都有显著的统计支持，如下：（1）微孢子虫是真菌界的姐妹类群，不是接合菌门的成员；也就是说，微孢子虫和真菌起源于一个共同祖先。（2）壶菌门是唯一具有带鞭毛发育阶段的真菌门类，是并系的，且是基部谱系。（3）基于毛菌纲、接合菌纲和球囊霉目的样本，接合菌门是单系的。（4）接合菌门、担子菌门和子囊菌门形成一个与壶菌门分开的单系类群。（5）担子菌门和子囊菌门是单系姐妹类群。
总体而言，本文强调了低等真菌（接合菌门和壶菌门）的进化地位和意义。我们的结果表明，鞭毛的丧失在真菌进化早期仅发生过一次；因此，与植物和动物不同，大多数真菌没有鞭毛。我们从基因序列推断出的系统发育树是第一个与广泛接受的基于形态学的真菌分类相一致的系统发育树。我们发现，与其他地方发表的内容相反，四个形态学定义的门类（子囊菌门、担子菌门、接合菌门和壶菌门）并不相互重叠。微孢子虫不包含在真菌界内；相反，它们是真菌的姐妹类群。我们的研究证明了来自大型、进化缓慢的基因的蛋白质序列在推导跨越长进化距离的分辨率高且支持度高的系统发育树方面的适用性。
