Fungal species and their boundaries matter – Definitions, mechanisms and practical implications

Steenkamp, Emma Theodora; Wingfield, Michael J.; McTaggart, Alistair R.; Wingfield, Brenda D.

doi:10.1016/j.fbr.2017.11.002

Cited by 51 publications

(46 citation statements)

References 114 publications

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“…Schumer et al 8 suggests that in order to have evidence of true hybrid speciation, it is necessary to show that hybridization leads to reproductive isolation. This criterion is not readily applicable to fungi, as they can speciate without complete reproductive isolation 36,106 . Furthermore, hybridization and reproductive isolation are especially difficult to account for with lichen-forming fungi, which cannot be easily cultured in vitro for experimental testing.…”

Section: Discussionmentioning

confidence: 99%

Genome-scale data reveal the role of hybridization in lichen-forming fungi

Keuler

Garretson

Saunders

et al. 2020

Sci Rep

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Advancements in molecular genetics have revealed that hybridization may be common among plants, animals, and fungi, playing a role in evolutionary dynamics and speciation. While hybridization has been well-documented in pathogenic fungi, the effects of these processes on speciation in fungal lineages with different life histories and ecological niches are largely unexplored. Here we investigated the potential influence of hybridization on the emergence of morphologically and reproductively distinct asexual lichens. We focused on vagrant forms (growing obligately unattached to substrates) within a clade of rock-dwelling, sexually reproducing species in the Rhizoplaca melanophthalma (Lecanoraceae, Ascomycota) species complex. We used phylogenomic data from both mitochondrial and nuclear genomes to infer evolutionary relationships and potential patterns of introgression. We observed multiple instances of discordance between the mitochondrial and nuclear trees, including the clade comprising the asexual vagrant species R. arbuscula, R. haydenii, R. idahoensis, and a closely related rock-dwelling lineage. Despite well-supported phylogenies, we recovered strong evidence of a reticulated evolutionary history using a network approach that incorporates both incomplete lineage sorting and hybridization. these data suggest that the rock-dwelling western north American subalpine endemic R. shushanii is potentially the result of a hybrid speciation event, and introgression may have also played a role in other taxa, including vagrant species R. arbuscula, R. haydenii and R. idahoensis. We discuss the potential roles of hybridization in terms of generating asexuality and novel morphological traits in lichens. furthermore, our results highlight the need for additional study of reticulate phylogenies when investigating species boundaries and evolutionary history, even in cases with wellsupported topologies inferred from genome-scale data. open Scientific RepoRtS | (2020) 10:1497 | https://doi.org/10.1038/s41598-020-58279-x www.nature.com/scientificreports www.nature.com/scientificreports/ nuclear markers, which in turn can influence the genome in both adaptive and maladaptive ways 5,[19][20][21][22] . Adaptive introgression of mitochondrial DNA may play an important role in speciation and phylogeography 23,24 .While hybridization has been well-documented among pathogenic fungi 21,[25][26][27][28][29][30] , the role of hybridization on the process of speciation of fungal lineages with different life histories and ecological functions is not well understood, including among lichen-forming fungi. The role of gene flow and hybridization in lichen-forming fungal evolution has been a long-standing question [31][32][33][34][35] . Species boundaries in fungi, including symbiotic fungi such as lichen formers, have received substantial attention and become more robust with molecular sequence data 36 . However, processes involved in speciation in lichen-forming fungi have received far less attention. With a poor fossil record 37,38 and pote...

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Section: Discussionmentioning

confidence: 99%

Genome-scale data reveal the role of hybridization in lichen-forming fungi

Keuler

Garretson

Saunders

et al. 2020

Sci Rep

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“…A fungal hybrid is a product of sexual (or parasexual) recombination between non-conspecific parents (Steenkamp et al 2018). Fungal hybrids have been demonstrated by phylogenetic incongruence between loci (Cruywagen et al 2017), different copies of orthologous genes within one taxon (Morin et al 2009) and coalescence of gene regions (Stukenbrock et al 2012).…”

Section: Fungi Exchange Genetic Materialsmentioning

confidence: 99%

Fungal clones win the battle, but recombination wins the war

2019

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Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.

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“…The accumulation of such independently evolving regions may ultimately drive divergence of entire genomes. Overall, these processes may also be crucial for the formation and maintenance of species boundaries [62]. The whole divergence process can be enhanced even further by a range of additional factors; e.g., chromosome loss or large genomic rearrangements can interfere with complementary base pairing during homologous recombination [63], while geographical isolation becomes a physical barrier to gene flow [64].…”

Section: Rip May Contribute To Lineage-divergencementioning

confidence: 99%

Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives

et al. 2019

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The Repeat-Induced Point (RIP) mutation pathway is a fungal-specific genome defense mechanism that counteracts the deleterious effects of transposable elements. This pathway permanently mutates its target sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence of RIP in the pitch canker pathogen, Fusarium circinatum, and its close relatives in the Fusarium fujikuroi species complex (FFSC). Our results showed that the examined fungi all exhibited hallmarks of RIP, but that they differed in terms of the extent to which their genomes were affected by this pathway. RIP mutations constituted a large proportion of all the FFSC genomes, including both core and dispensable chromosomes, although the latter were generally more extensively affected by RIP. Large RIP-affected genomic regions were also much more gene sparse than the rest of the genome. Our data further showed that RIP-directed sequence diversification increased the variability between homologous regions of related species, and that RIP-affected regions can interfere with homologous recombination during meiosis, thereby contributing to post-mating segregation distortion. Taken together, these findings suggest that RIP can drive the independent divergence of chromosomes, alter chromosome architecture, and contribute to the divergence among F. circinatum and other members of this economically important group of fungi.

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Fungal species and their boundaries matter – Definitions, mechanisms and practical implications

Cited by 51 publications

References 114 publications

Genome-scale data reveal the role of hybridization in lichen-forming fungi

Genome-scale data reveal the role of hybridization in lichen-forming fungi

Fungal clones win the battle, but recombination wins the war

Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives

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