The use of parsimony network analysis for the formal delineation of phylogenetic species of yeasts: Candida apicola, Candida azyma, and Candida parazyma sp. nov., cosmopolitan yeasts associated with floricolous insects

Abstract

Parsimony network analysis of rDNA sequences was used to delimit phylogenetic species of yeasts in an objective, formal manner. Many strains assigned to Candida apicola (Starmerella clade), when compared to the type, fell outside the inclusion limits proposed by Kurtzman and Robnett (1998) based on a pair-wise comparison of the large subunit rRNA gene D1/D2 domains. However, when these sequences were analyzed jointly with ITS rDNA sequences by parsimony network analysis, 28 of the 30 strains formed a cohesive set. Two strains, MUCL 45721 and CBS 4353, were excluded from the species, but there was no evident justification to subdivide the rest. A similar analysis of 81 isolates originally assigned to Candida azyma (Wickerhamiella clade) yielded dramatically different results, giving rise to six independent networks corresponding to Candida azyma sensu stricto (18 strains), Candida azymoides (2 strains), a pair of isolates from Australian hibiscus flowers, a single isolate from the same substrate, a single isolate from Malaysian bertam palm nectar, and 57 isolates that are assigned to the new species Candida parazyma (type = UWOPS 91-652.1(T) = CBS 11563(T) = NRRL Y-48669(T)). The strains retained in C. azyma sensu stricto differed from one another by up to four substitutions in their D1/D2 sequences, but their polymorphism at the level of the ITS was considerable and suggested a history of divergence resulting from dispersal. Strains of C. parazyma fell into seven variant haplotypes based on sequences of the rDNA ITS and D1/D2 regions. The most abundant haplotype occurred across the global range of the species. Others were either endemic to Belize, Costa Rica, Rarotonga, or Tennessee, suggestive of vicariance, or occurred across remote localities, offering partial support to the notion of rapid dispersal.

Starmerella neotropicalis f. a., sp. nov., a yeast species found in bees and pollen

“…The analysis attempted a complete sampling of the described species most closely related to the type species of the genus Starmerella; the Starmerella 'sensu lato' subclade was represented only by Candida gropengiesseri and Candida magnoliae. All haplotypes of Candida apicola identified by Lachance et al (2010) were included. The root was placed on the branch leading to Candida blankii and Candida digboiensis.…”

“…kandeliae, Trichosporon mycotoxinivorans, Trichosporon sp., Wickerhamomyces anomalus and Zygosaccharomyces mellis. These species were identified by sequencing the D1/D2 domains of the large subunit (LSU) of the rRNA gene as described by Lachance et al (2010).…”

Zygosaccharomyces favi sp. nov., an obligate osmophilic yeast species from bee bread and honey

“…2). Unlike suggested by Lachance et al (2010Lachance et al ( , 2011b in this case gapped positions were not excluded from the analysis, because the aim was not to separate different species, but to demonstrate the intraspecies and intragenomic ITS heterogeneity (mainly indels) and the distribution of different ITS copies among the strains of the new species. In parsimony network the copy variants formed two groups, the first group consisted of copies belonging to strains NCAIM Y.02134 and NCAIM Y.02135 and one copy of NCAIM Y.02137, while the second of copies belonging to strains NCAIM Y.02136 and NCAIM Y.02137.…”

Saturnispora serradocipensis sp. nov. and Saturnispora gosingensis sp. nov., two ascomycetous yeasts from ephemeral habitats

“…Similar results were observed by Kurtzman (2006) when comparing the D1/D2 and ITS sequences of S. besseyi and S. ahearnii, which had nearly identical D1/D2 sequences but were divergent in ITS sequences. Additional information on the use of the Parsimony network analysis for yeast systematic can be found in Lachance et al (2010). The name Saturnispora serradocipensis sp.…”