Abstract
BackgroundThe taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. Species delineation in Ceratocystis primarily relied on genealogical concordance phylogenetic species recognition (GCPSR) using multiple standard molecular markers.ResultsQuestions have arisen regarding the utility of these markers e.g., ITS, BT and TEF1-α due to evidence of intragenomic variation in the ITS, as well as genealogical incongruence, especially for isolates residing in a group referred to as the Latin-American clade (LAC) of the species. This study applied a phylogenomics approach to investigate the extent of phylogenetic incongruence in Ceratocystis. Phylogenomic analyses of a total of 1121 shared BUSCO genes revealed widespread incongruence within Ceratocystis, particularly within the LAC, which was typified by three equally represented topologies. Comparative analyses of the individual gene trees revealed evolutionary patterns indicative of hybridization. The maximum likelihood phylogenetic tree generated from the concatenated dataset comprised of 1069 shared BUSCO genes provided improved phylogenetic resolution suggesting the need for multiple gene markers in the phylogeny of Ceratocystis.ConclusionThe incongruence observed among single gene phylogenies in this study call into question the utility of single or a few molecular markers for species delineation. Although this study provides evidence of interspecific hybridization, the role of hybridization as the source of discordance will require further research because the results could also be explained by high levels of shared ancestral polymorphism in this recently diverged lineage. This study also highlights the utility of BUSCO genes as a set of multiple orthologous genes for phylogenomic studies.
Highlights
The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate
The aim of this study was to use a phylogenomic approach to (i) identify a set of orthologous genes shared across the Ceratocystidaceae (ii) use these genes to identify the extent of discordance among gene trees, (iii) and analyse the alternative topologies within Ceratocystis, within the Latin-American clade (LAC)
Previous studies have failed to differentiate between C. manginecans, C. eucalypticola and C. fimbriata isolates using Biological Species Concept (BSC) [19] but the maximum likelihood (ML) phylogenetic tree placed C. fimbriata as a separate lineage from C. manginecans and C. eucalypticola
Summary
The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. It could be argued that the PSC offers the best possible approach because changes in gene sequences can be related to evolutionary time. Trait-based concepts typically lead to ambiguous outcomes due to convergent evolution of morphological traits and where cryptic species are commonly overlooked [2] In this regard, cryptic speciation is common in, but not limited to, groups that comprise large numbers of species such as the prokaryotes and fungi [5]
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