Data from: Species boundaries in the messy middle – testing the hypothesis of micro-endemism in a recently diverged lineage of coastal fog desert lichen fungi

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.