Abstract
Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.
Highlights
Inference of evolutionary histories among these symbiotic fungi is of key importance to understanding processes that underlie diversification in this group
A total of 49.5 Gb of filtered PE reads were generated for this study, and the number of reads for each specimen is reported in Supplementary Table S1
An average of 70.8% of the reference genome was covered by each specimens within the R. melanophthalma complex in the RealPhy assembly, the proportion of genome coverage was much lower for P. peltata and R. subdiscrepans, at 4.7% and
Summary
Inference of evolutionary histories among these symbiotic fungi is of key importance to understanding processes that underlie diversification in this group. In order to evaluate the power of phylogenomic data for resolving relationships in problematic species groups of lichen-forming fungi, we investigated the Rhizoplaca melanophthalma species complex[19,20,21]. Previous studies of the R. melanophthalma group revealed apparent ILS for a number of taxa in this complex and a general pattern of incongruence among individual gene trees, potentially due to their recent diversification history[20,21]. We were interested in evaluating the performance of phylogenomic datasets at a variety of scales and using multiple analytical approaches, including concatenation and multispecies coalescent-based species tree methods, to infer evolutionary relationships in lichen-forming fungi. Our study highlights the promise of phylogenomic data for inferring robust phylogenies for lichen-forming fungi with recent diversification histories
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