Alternaria spp. from sect. Alternaria are frequently associated with hypersensitivity pneumonitis, asthma
and allergic fungal rhinitis and sinusitis. Since Alternaria is omnipresent in the outdoor environment, it is
thought that the indoor spore concentration is mainly influenced by the outdoor spore concentration.
However, few studies have investigated indoor Alternaria isolates, or attempted a phylogeographic or
population genetic approach to investigate their movement. Therefore, the aim of the current study
was to investigate the molecular diversity of indoor Alternaria isolates in the USA, and to test for recombination,
using these approaches. Alternaria isolates collected throughout the USA were identified using
ITS, gapdh and endoPG gene sequencing. This was followed by genotyping and population genetic inference
of isolates belonging to Alternaria sect. Alternaria together with 37 reference isolates, using five
microsatellite markers. Phylogenetic analyses revealed that species of Alternaria sect. Alternaria represented
98% (153 isolates) of the indoor isolates collected throughout the USA, of which 137 isolates could
be assigned to A. alternata, 15 to the A. arborescens species complex and a single isolate to A. burnsii. The
remaining 2% (3 isolates) represented sect. Infectoriae (single isolate) and sect. Pseudoulocladium
(2 isolates). Population assignment analyses of the 137 A. alternata isolates suggested that subpopulations
did not exist within the sample. The A. alternata isolates were thus divided into four artificial subpopulations
to represent four quadrants of the USA. Forty-four isolates representing the south-western
quadrant displayed the highest level of uniqueness based on private alleles, while the highest level of
gene flow was detected between the south-eastern (32 isolates) and south-western quadrants.
Genotypic diversity was high for all quadrants, and a test for linkage disequilibrium suggested that A.
alternata has a cryptic sexual cycle. These statistics could be correlated with environmental factors, suggesting
that indoor A. alternata isolates, although extremely diverse, have a continental distribution and
high levels of gene flow over the continent.