A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits
A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits
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DOI：
10.1016/j.ympev.2013.01.014
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发表时间：
2013-05-01
影响因子：
4.1
通讯作者：
Pfister, Donald H.
中科院分区：
文献类型：
--
作者：
Hansen, Karen;Perry, Brian A.;Pfister, Donald H.
焦丝菌科是盘菌纲中最大、最具异质性的一科。它在形态和生态上具有高度多样性，包括腐殖、外生菌根、苔藓共生和寄生物种，存在于广泛的生境中（土壤、烧焦的土地、瓦砾、木材、粪便和活的苔藓植物、植物和地衣内部）。为了评估单系的Pyronemataceae，并提供一个系统发育假说的组，我们编制了一个四基因数据集，包括一个核核糖体和三个蛋白质编码基因的132个不同的盘菌纲物种（4437个核苷酸，所有标记的80%的总142个分类群）。这是迄今为止最全面的Pyronemataceae和Pezizomycetes的分子系统学。在该项目期间产生了394个新序列，每个基因的编号如下：RPB 1（124），RPB 2（99），EF-1 alpha（120）和LSU rDNA（51）。该数据集包括来自40属的93种独特的Pyronemataceae，和来自25属的34种，代表了该纲的另外12个科。简约性，最大似然和贝叶斯分析表明，Pyronemataceae是并系的，由于在家庭内的Ascodesmidaceae和Glaziellaceae嵌套。目前该科有四个谱系，Boubovia，Geopyxis，Pseudombrophila和Pulvinula谱系，与Ascodesmidaceae和Glaziellaceae形成一个单系群。我们主张排除这四个谱系，以承认一个单系的Pyronemataceae。粪菌属（Coprotus）属于盘菌纲（Pezizomycetes），与Boubovia形成一个强有力的单系群。在Pyronemataceae中鉴定了10个强有力的谱系。其中，Pyropyxis和Otidea谱系被确定为Pyronemataceae的其余部分的连续姐妹谱系。高度退化的（gymnohymenial）Monascella被证明属于盘菌纲（Pezizomycetes），并首次被认为与闭囊属的Warcupia密切相关，作为主要是apothecial Otidea的姐妹群。没有一个谱系的pyronemataceous类群在这里确定对应于以前的家庭或亚科分类。使用贝叶斯方法进行的祖先特征状态重建（ASR）支持盘菌纲和火丝菌科的祖先是栖息在土壤中且污染的。外生真菌在盘菌纲的A、B和C谱系中都出现过，并被认为在Pyronemataceae中独立进化了7 - 8次。而专性苔藓共生的生活方式只出现了两次。共生或寄生的Pyronemataceae没有发生向自由生活的、污秽的生活方式的逆转。专业化的各种基板（如燃烧地面和粪便）的建议已经发生了几次，主要是saprobic血统。虽然类胡萝卜素在盘菌纲中至少出现了四次，但盘菌纲是焦丝菌科的祖先。str.，除了Pyropyxis和Otidea谱系，最有可能产生类胡萝卜素，然后在一些分支中丢失（并可能再次获得）。在盘菌纲最深的节中以及在Pyronemataceae的祖先中发现了很高概率的外毛。真毛仅限于Pyronemataceae s的核心组。str.，但也发现于毛孢属（Ascodesmidaceae）、假毛孢属（Pseudombrophila）谱系和绒膜菌科（Chorioactidaceae）、肉壶菌科（Sarcoscyphaceae）和肉壶菌科（Sarcosomataceae）的分支中。焦丝科植物真毛的增加和减少数量。字符串，但仍不确定。在二进制编码（存在或不存在）下的子囊孢子滴注的ASR表明，该特征是快速进化的，易于转移。O 2013 Elsevier Inc. All rights reserved.
Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly diverse, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1 alpha (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodesmidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s. L, whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades ( and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s. str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts. O 2013 Elsevier Inc. All rights reserved.