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

This is data analyzed for manuscript title, "Genome-scale data reveal the role of hybridization in lichen-forming fungi", currently under review in Scientific Reports. The following datasets are included:rhizoplaca_RealPhy_BUSCO1kbplus.fa = the nuclear REALPHY dataset was generated using contigs >1kb from a draft genome assembly of R. melanophthalma as the reference RealPhy_BUSCO1kbplus_v1_ALN_SNPs.nex = the ‘BUSCO 1kb+ SNPs’ dataset represents all polymorphic sites from concatenated alignments of all BUSCO gene regions >1kb RealPhy_BUSCO1kbplus_v1_ALN_SNPs_SVDQRT.nex = the ‘BUSCO 1kb+ SNPs’ dataset represents all polymorphic sites from concatenated alignments of all BUSCO gene regions >1kb, with the SVDQRT "taxpartition species"mt_REALPHY_polymorphisms_move.phy = the mitochondrial REALPHY dataset was generated using the longest assembled mitochondrial contigrhizo_group_31_specimens_mtCONTIGs_MAFFT_aligned.fasta = Complete, mitochondrial contains assembled using Spadesphylonet_BUSCO407_r4_haydenii.nex = the ‘407 CEG trees’ are gene topologies inferred from 407 core eukaryotic gene regions passing quality filters, with phylonet MPL commands 407_BUSCO_trees_outgroupBSv1.tre = the ‘407 CEG trees’ are gene topologies inferred from 407 core eukaryotic gene regions passing quality filtersAbstract from manuscript: Advancements in molecular genetics have revealed that hybridization is 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 focus on vagrant forms (growing obligately unattached to substrates) within a clade of rock-dwelling, sexually reproducing species in the Rhizoplaca melanophthalma (Lecanoraceae, Ascomycota) group. We used phylogenomic data from both mitochondrial and nuclear genomes to infer evolutionary relationships and potential patterns of introgression. We were inferred well-supported phylogenies from both the mitochondrial and nuclear datasets. 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 reticulation 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.