DOI: 10.5061/dryad.38889
title: Data from: Unravelling species boundaries in the Aspergillus viridinutans complex (section Fumigati): opportunistic human and animal pathogens capable of interspecific hybridization

description: Although Aspergillus fumigatus is the major agent of invasive
 aspergillosis, an increasing number of infections are caused by its
 cryptic species, especially A. lentulus and the A. viridinutans species
 complex (AVSC). Their identification is clinically relevant because of
 antifungal drug resistance and refractory infections. Species boundaries
 in the AVSC are unresolved since most species have uniform morphology and
 produce interspecific hybrids in vitro. Clinical and environmental strains
 from six continents (n = 110) were characterized by DNA se- quencing of
 four to six loci. Biological compatibilities were tested within and
 between major phylogenetic clades, and ascospore morphology was
 characterised. Species delimitation methods based on the multispecies
 coalescent model (MSC) supported recognition of ten species including one
 new species. Four species are confirmed op- portunistic pathogens; A.
 udagawae followed by A. felis and A. pseudoviridinutans are known from
 opportunistic human infections, while A. felis followed by A. udagawae and
 A. wyomingensis are agents of feline sino-orbital aspergillosis. Recently
 described human-pathogenic species A. parafelis and A. pseudofelis are
 synonymized with A. felis and an epitype is designated for A. udagawae.
 Intraspecific mating assay showed that only minor part of the
 heterothallic species can readily generate sexual morph in vitro.
 Interspecific mating assay revealed that five different species
 combinations were biologically compatible. Hybrid ascospores had atypical
 surface ornamentation and significantly different dimensions compared to
 parental species. This suggests that species limits in the AVSC are
 maintained by both pre- and post-zygotic barriers and these species
 display a great potential for rapid adapta- tion and modulation of its
 virulence. This study highlights that a sufficient number of strains
 representing genetic diversity within a species is essential for
 meaningful species boundaries delimitation in cryptic species complexes.
 MSC-based delimitation methods are robust and suitable tools for
 evaluation of boundaries between these species.
description: Alignment - section
 Fumigati; concatenated data from benA, CaM, act and RPB2 loci, 76
 taxaCombined dataset of
 benA, CaM, act and RPB2 sequences for 76 taxa belonging to section
 Fumigati. Aspergillus clavatus NRRL 1 (sect. Clavati) represents an
 outgroup. BenA: positions 1-534; CaM: positions 535-1231; act: positions
 1232-1662; RPB2: positions 1663-2661.Fumigati benA caM actin RPB2 76
 taxa.fasPhylogeny of Aspergillus
 sect. Fumigati inferred from combined data: benA, CaM, act and
 RPB2Phylogenetic
 relationships of the section Fumigati members inferred from Bayesian
 analysis of the combined, 4-gene data set of β-tubulin (benA), calmodulin
 (CaM), actin (act) and RNA polymerase II second largest subunit (RPB2)
 genes. Bayesian posterior probability (PP) and Maximum likelihood
 bootstrap support (BS) are appended to nodes; only PP ≥ 95% and BS ≥ 70%
 and are shown; lower supports are indicated with a hyphen, whereas
 asterisks indicate full support (1.00 PP or 100% BS); ex-type strains are
 designated by a superscript T; species names in quotes are considered
 synonyms. The tree is rooted with Aspergillus clavatus NRRL 1. The
 reproductive mode of each species is designated by icons before the
 species name (see legend).Aspergillus section Fumigati
 phylogeny.pdfCombined alignment:
 benA, CaM, act and RPB2 loci; Aspergillus viridinutans
 complexCombined dataset of
 benA, CaM, act and RPB2 sequences for 110 taxa belongmembers of
 Aspergillus viridinutans complex. Aspergillus lentulus NRRL 35552
 represents an outgroup. BenA: positions 1-475; CaM: positions 476-1172;
 act: positions 1173-1516; RPB2: positions 1517-2483.BenA CaM actin RPB2
 viridinutans complex Dryad.fasPhylogeny of Aspergillus
 viridinutans species complex phylogeny inferred from combined data: BenA,
 CaM, act, RPB2Phylogenetic
 relationships of the section Aspergillus viridinutans species complex
 members inferred from Bayesian analysis of the combined, 4-gene data set
 of β-tubulin (benA), calmodulin (CaM), actin (act) and RNA polymerase II
 second largest subunit (RPB2) genes. Bayesian posterior probability (PP)
 and Maximum likelihood bootstrap support (BS) are appended to nodes; only
 PP ≥ 90% and BS ≥ 70% and are shown; lower supports are indicated with a
 hyphen, whereas asterisks indicate full support (1.00 PP or 100% BS);
 ex-type strains are designated by a superscript T; species names in quotes
 are considered synonyms. The tree is rooted with Aspergillus lentulus NRRL
 35552. The geographic origin, and reproductive mode with MAT idiomorph (if
 known) is designated by icons before the isolate number while substrate of
 origin is designated by icons after isolate number (see
 legend).Aspergillus viridinutans
 complex phylogeny.pdfAlignment - Aspergillus
 viridinutans complex, A. felis clade: concatenated data of act, benA, CaM,
 mcm7, RPB2 and tsr1Combined dataset of act,
 benA, CaM, mcm7, RPB2 and tsr1 sequences for 33 taxa belonging to
 Aspergillus viridinutans complex - A. felis clade only. act: positions
 1-329; benA: positions 330-803; CaM: positions 804-1484; mcm7: positions
 1485-2107; RPB2: positions 2108-3074; tsr1: positions
 3075-3835.actin benA CaM mcm7 RPB2 tsr1
 Dryad.fasSpecies delimitation in
 Aspergillus felis clade based on six genetic lociSchematic representation
 of results of species delimitation methods in Aspergillus felis clade
 based on six genetic loci. The results of multilocus method (STACEY) are
 compared to results of single-locus methods (mPTP, bGMYC, GMYC). The
 results of STACEY are shown as tree branches with different colours, while
 the results of single-locus methods are depicted with coloured bars
 highlighting congruence across methods. The displayed tree is derived from
 IQtree analysis based on a concatenated dataset and is used solely for the
 comprehensive presentation of the results from different methods. The
 species validation analysis results (BP&P) are appended to nodes and
 shown in gray bordered boxes; the values represent posterior probabilities
 calculated in three scenarios having different prior distributions of
 parameters θ (ancestral population size) and τ0 (root age). The top value
 represents the results of analysis with large ancestral population sizes
 and deep divergence: θ ~ G (1, 10) and τ0 ~ G (1, 10), the middle value );
 large ancestral populations sizes and shallow divergences among species: θ
 ~ G (1, 10) and τ0 ~ G (2, 2000) and the bottom value small ancestral
 population sizes and shallow divergences among species: θ ~ G (2, 2000)
 and τ0 ~ G (2, 2000).