4.2 Concordance between the standard DNA barcoding marker and clades inferred from phylogenomic data
The standard DNA barcoding marker – the ITS – has been a powerful tool for understanding species diversity in lichen-forming fungi (Lücking et al., 2020; Schoch et al., 2012), although issues with using this marker in some clades have been demonstrated (Pino-Bodas et al., 2013). In taxonomically challenging groups, the ITS can provide an important first pass for grouping closely related species (Leavitt et al., 2013; Lücking et al., 2014; Moncada et al., 2020). Our results show that species partitions inferred from the ITS marker coincide with clades comprised of closely related species-level lineages in Niebla inferred from phylogenomic data (Fig. 2). These results suggest that in this speciose genus, the ITS can play a crucial role in assigning specimens to species complexes and provide guidance for future studies characterizing species-level diversity. However, our analyses of ITS alignments indicate that the ITS alone is not able to diagnose species-level lineage in Niebla . Extensive sampling of specimens representing ITS-delimited species, coupled with genome-scale data, will likely be essential to robustly characterize diversity in this genus. Similarly, focusing on specific habitats in Baja California supporting diverse Niebla communities, including Mesa Camacho, Mesa Santa Catarina, ridges between Punta Santa Rosalillita and Punta Negra, and Morro Santo Domingo, will be crucial to infer diversification processes in important genus of lichen-forming fungi occurring only in coastal fog deserts.
While the results of our analysis are somewhat ambiguous in terms of species delimitation, they provide a valuable perspective of the use of these empirical species delimitation methods in a non-model system. Furthermore, they add to the growing body of literature on the all-too-often “messy” species boundaries in organisms that further complicate our understanding of their complex evolutionary history. Future work should build upon the hypotheses presented here to add additional lines of evidence for specific species models in order to resolve the taxonomy in this group. Lichen-forming fungi are notoriously difficult to define in terms of species delimitation, and in some cases, traditional morphological and chemical characters used for taxonomy fail to reflect natural lineages (Lumbsch and Leavitt, 2011). Nevertheless, more thorough chemical investigations may clarify some species inNiebla . In addition, ecological and paleoclimatic feature should be considered in future work with speciation in Niebla.