A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia

Letharia, a genus of lichenized fungi described as a pair of sympatric species, one making abundant sexual structures and the other making few, was investigated as a model system in which to recognize species boundaries. Gene genealogies of 6 and 12 loci were used to estimate the evolutionary history of Letharia, based on the principles of lineage sorting of alleles in divergent lineages after genetic isolation. Instead of a species pair consisting of a putative clonal species derived from a progenitor sexual species, Letharia comprises at least six phylogenetic species. Judging by the presence of perennial apothecia and clonal reproductive structures, one species is exclusively sexual, three species are sexual and isidiate, and two species are sorediate and rarely sexual. Not all of these species would have been detected with a single gene genealogy, demonstrating the need for multiple independent loci in phylogenetic analysis to recognize recent speciation events. The results are concordant with aspects of both biological and phylogenetic species recognition. However, only phylogenetic species recognition can be applied to fungi like Letharia species that are difficult to cultivate and mate in the lab.