Diaporthe amygdali, a species complex or a complex species?. Issue 7 (July 2021)

• Record Type: Journal Article
• Authors: Hilário, Sandra; Santos, Liliana; Alves, Artur
• Is Part Of: Fungal biology. Volume 125:Issue 7(2021)
• Page Start: 505
• Page End: 518
• Publication Date: 2021-07
• Subjects: Coalescent models -- GMYC -- Phylogeny -- PTP -- Systematics -- Species delimitation; Mycology -- Periodicals; Fungi -- Periodicals; 579.505
• DOI: 10.1016/j.funbio.2021.01.006
• Languages: English
• ISSNs: 1878-6146

Abstract

Abstract: Delimitation of species boundaries within the fungal genus Diaporthe has been challenging, but the analyses of combined multilocus DNA sequences has become an important tool to infer phylogenetic relationships and to circumscribe species. However, analyses of congruence between individual gene genealogies and the application of the genealogical concordance principle have been somehow overlooked. We noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, commonly known as D. amygdali complex, occupy a monophyletic clade in Diaporthe phylogenies but the limits of all species within the complex are not entirely clear. To assess the boundaries of species within this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and coalescence-based models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). The incongruence detected between individual gene phylogenies, as well as the results of coalescent methods do not support the recognition of lineages within the complex as distinct species. Moreover, results support the absence of reproductive isolation and barriers to gene flow in this complex, thus providing further evidence that the D. amygdali species complex constitutes a single species. This study highlights the relevance of the application of the GCPSR principle, showing that concatenation analysis of multilocus DNA sequences, although being a powerful tool, might lead to an erroneous definition of species limits. Additionally, it further shows that coalescent methods are useful tools to assist in a more robust delimitation of species boundaries in the genus Diaporthe. Graphical abstract: Image 1 Highlights: Concatenation of multiple loci in Diaporthe tends to overestimate species diversity. GCPSR does not recognize distinct species within the Diaporthe amygdali complex. Coalescent models do not support lineages as distinct species within the complex. There are no reproductive and geographical barriers to gene flow in the complex. Diaporthe amygali complex constitutes a single species and not a complex of species.