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An evolutionary view of the taxonomy and ecology of Inocybe (Agaricales) with new perspectives gleaned from GenBank metadata

By Martin Ryberg


Inocybe (Inocybaceae) is one of the most speciose genera among the gilled mushrooms (Agaricales) but large parts of its taxonomy and evolutionary history remain poorly explored. The present thesis shows that the traditional infrageneric classification of Inocybe does not fully reflect evolutionary relationships and that the two most commonly used taxonomic characters, spore shape and presence of a cortina, have not evolved in such a way as to define unique monophyletic groups. The section Rimosae, in its traditional circumscription, is divided into two separate clades by the present analyses, and Rimosae s.str. does not group with the subgenus Inosperma - where it is commonly placed - but forms a separate clade more closely related to the subgenus Inocybe. Also the sections of the subgenus Inocybe, the largest of the subgenera, should in general be interpreted in a strict sense if they are to reflect monophyletic groups. Such a view-point would leave many species with an uncertain placement. On the species level it is shown that many of the traditionally accepted taxa are insufficiently characterized in terms of circumscription and morphological variation. This thesis also explores metadata associated with DNA sequences from molecular ecological studies. These sequences represent a large part of the fungal internal transcribed spacer (ITS) sequences in GenBank that are relatively well annotated regarding ecological and geographical data. They are, however, seldom used as sources of such information. One reason is that they typically lack precise taxonomic annotation and therefore are hard to search in a systematic context. To facilitate the exploration of such sequences, the software suite emerencia ( was developed and is presented as a component of this thesis. The emerencia software was employed to explore the distribution and ecology of Inocybe and was found to have the capacity to significantly expand on our knowledge of the world-wide distribution of the genus and of the ecology of its individual species. This new information was compiled together with information from other sources to explore whether host preference and three characters coding for preference for particular soil conditions are correlated to the phylogeny. This was done using ancestral state reconstruction methods. The results show that while soil moisture preference is not, host preference, preference for calcareous soils, and preference in soil nutritional status are indeed correlated to the phylogeny. This indicates that a well formulated taxonomy that is reflective of phylogenetic relationships can have predictive values for these ecological traits

Topics: Inocybe, Inocybaceae, emerencia, GenBank, Insufficiently identified sequences (IIS)
Year: 2009
DOI identifier: 10.1186/1471-2148-8-50
OAI identifier:

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