Species delimitation among closely related species is challenging
because traditional phenotype-based approaches, e.g., morphology,
ecological, or chemical characteristics, often produce conflicting
results. With the advent of high-throughput sequencing, it has become
increasingly cost-effective to acquire genome-scale data which can
resolve previously ambiguous species boundaries. As the availability of
genome-scale data has increased, numerous species delimitation analyses,
such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been
developed to delimit species boundaries. However, even empirical
molecular species delimitation approaches can be biased by confounding
evolutionary factors, e.g., hybridization/introgression and incomplete
lineage sorting, and computational limitations. Here we investigate
species boundaries and the potential for micro-endemism in a lineage of
lichen-forming fungi, Niebla Rundel & Bowler in the family
Ramalinaceae. The species delimitation models tend to support more
specious groupings, but were unable to infer robust, consistent species
delimitations. The results of our study highlight the problem of
delimiting species, particularly in groups such as Niebla, with complex,
recent phylogeographic histories.
Species boundaries in the messy middle—A genome‐scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi