Abstract
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 well-supported topologies inferred from genome-scale data.
Highlights
For the mitochondrial genome dataset, metagenomic reads from each library were assembled using the SPAdes v3.12.0 assembler[72]
Metagenomic reads mapped to Benchmarking Universal Single-Copy Orthologs (BUSCO) genes larger than 1 kb resulted in an alignment of 1,620,052 bp; and from this alignment a total of 142,437 SNPs were extracted
Our results support the potential role of genomic combinatorial mechanisms in the diversification of symbiotic fungi
Summary
For the mitochondrial genome dataset, metagenomic reads from each library were assembled using the SPAdes v3.12.0 assembler[72]. We selected the longest mitochondrial assembly as a reference for phylogenomic assembly using REALPHY v1.12. The following parameters were implemented in REALPHY, implementing Bowtie v2.1.065 for read mapping: -readLength 100 -perBaseCov 5 -gapThreshold 0.2, with the remaining parameters set at default values. We generated additional mitochondrial datasets, inferring phylogenies from (i) concatenated CDS (protein coding sequence) regions, (ii) concatenated intronic regions, and (iii) complete, aligned mitochondrial contigs. We used DOGMA73 to initially demark mitochondrial genomic features. Multiple sequence alignments for individual CDSs and introns were performed using MAFFT74, with the resulting CDS and intron alignments concatenated separately and implementing the G-INS-I option. Complete mitochondrial contigs were aligned using MAFFT, implementing the E-INS-I option
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