title: What can comparative genomics tell us about species concepts in the genus Aspergillus?
abstract: Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.
authors.affiliation: Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, U.S.A.
authors.forename: A
authors.initials: A
authors.lastname: Rokas
authors.forename: G
authors.initials: G
authors.lastname: Payne
authors.forename: N D
authors.initials: ND
authors.lastname: Fedorova
authors.forename: S E
authors.initials: SE
authors.lastname: Baker
authors.forename: M
authors.initials: M
authors.lastname: Machida
authors.forename: J
authors.initials: J
authors.lastname: Yu
authors.forename: D Ryan
authors.initials: DR
authors.lastname: Georgianna
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Dean
authors.forename: Deepak
authors.initials: D
authors.lastname: Bhatnagar
authors.forename: T E
authors.initials: TE
authors.lastname: Cleveland
authors.forename: J R
authors.initials: JR
authors.lastname: Wortman
authors.forename: R
authors.initials: R
authors.lastname: Maiti
authors.forename: V
authors.initials: V
authors.lastname: Joardar
authors.forename: P
authors.initials: P
authors.lastname: Amedeo
authors.forename: D W
authors.initials: DW
authors.lastname: Denning
authors.forename: W C
authors.initials: WC
authors.lastname: Nierman