Origin and diversity of mushrooms in Eastern Canada and phylogenomics of selected groups

了解生物多样性的起源和分布是生物学的基础。我的研究计划的长期目标是在全球范围内调查伞菌纲（担子菌门，真菌）的物种丰富度和进化关系，特别是在伞菌目。后者包括大部分形成蘑菇的真菌，由全世界描述的约10，000种组成，尽管可能存在更多。有几个问题影响了我们对全球和地方真菌多样性和物种分布的估计，特别是：（1）缺乏全面的区域或国家植物群，（2）缺乏现代分类学处理（专著）的大多数群体，（3）存在许多形态相似（神秘）的物种。为了解决这三个问题，我建议在未来五年内开展以下工作：（1）根据文献、植物标本和其他收集数据的历史记录，结合> 1，从安大略和魁北克收集了近10年来的000份有据可查的标本，并在我的实验室用ITS和LSU序列进行了DNA条形码化。这将产生第一个现实的评估蘑菇多样性在加拿大东部，也在许多情况下，允许在系统发育方面的分类修订。后一项工作非常适合本科生的多个小项目。(2)准备鹅膏菌属凯撒利亚组和阴道菌亚科组以及灵芝属的世界专论，这将有助于推断属于这些组的加拿大东部物种的起源和分类。每一组包含大约120个已知物种，其中许多已经在我的拥有或随时可以从各种来源（除了来自非洲的材料）。初步数据表明，5个基因（ITS，EF 1-alpha，LSU，RPB 1和RPB 2）的组合不能完全解决系统发育关系。(3)北美杰克逊鹅膏菌种复合体的群体基因组研究和隐蔽种的检测。这一食用外生菌根真菌种群被认为由4-5个种组成，但种的划分尚不清楚。这个群体的成员广泛分布在美国南部和沿着阿巴拉契亚山脉。在加拿大，A.在魁北克南部的几个地方已经报道了杰克逊氏菌，最近才在安大略南部发现。我建议比较至少60个集合的全基因组序列，这些集合代表了该物种群的整个地理和生态范围的种群。到目前为止，我们已经完成并注释了两个菌株的基因组（一个来自安大略，一个来自墨西哥）;此外，正在从头收集新鲜材料。这项研究应该解决这个物种复杂的物种识别和阐明蘑菇的物种形成过程。

Understanding the origin and distribution of biological diversity is fundamental to biology. The long-term goals of my research program are to investigate species richness and evolutionary relationships in the Agaricomycetes (Basidiomycota, Fungi) in a global scale, more particularly in the Agaricales. The latter includes the bulk of mushroom-forming fungi, and consists of about 10,000 species described worldwide, although many more probably exist. Several problems affect our estimates of fungal diversity and species distribution both globally and locally, particularly: (1) the scarcity of comprehensive regional or national flora, (2) the lack of modern taxonomic treatment (monographs) for most groups, and (3) the existence of many morphologically similar (cryptic) species. To help fix each of these three problems I propose to conduct the following work in the next five years: (1) Completion of a compendium of eastern Canada mushrooms based on historical records from the literature, herbaria, and other collection data, in combination with > 1,000 well-documented collections from Ontario and Quebec that were made in the last ten years and DNA-barcoded in my lab with both ITS and LSU sequences. This will produce a first realistic assessment of mushroom diversity in eastern Canada, and also, in many cases, permit taxonomic revisions in a phylogenetic context. This latter work is very well suited for multiple small projects for undergraduate students. (2) Preparation of world monographs for Amanita sections Caesarea and Vaginateae and for the genus Ganoderma in a phylogenomic framework; this will permit to infer the origin(s) and taxonomy of the eastern Canadian species belonging to these groups. Each group contains about 120 known species, many of which being either already in my possession or readily available from various sources (except material from Africa). Preliminary data indicates that a combination of 5 genes (ITS, EF1-alpha, LSU, RPB1 and RPB2) does not fully resolve phylogenetic relationships. (3) Population genomic studies and detection of cryptic species within the Amanita jacksonii species complex in North America. This species group of edible, ectomycorrhizal fungi is thought to consist of 4-5 species, but species delimitation is unclear. Members of this group are widespread in the southern U.S. and along the Appalaches. In Canada, A. jacksonii has been reported from few localities in southern Quebec, and has only been discovered recently in southern Ontario. I propose to compare whole genome sequences of at least 60 collections reprsentative of populations across the whole geographic and ecological range of this species group. To date, we have completed and annotated the genomes of two strains (one from Ontario, and one from Mexico); also, de novo collecting of fresh material is underway. This study should resolve species recognition within this species complex and shed light into speciation processes in mushrooms.