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

Abstract

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.

Introgressive Descent and Hypersexuality Drive The Evolution Of Sexual Parasitism and Morphological Reduction In a Fungal Species Complex

“…Second, they are only meaningful when populations don't deviate significantly from classical population genetics models (84). Both limitations have been systematically overlooked despite the growing evidence that species boundaries are semi-permeable (85) in lichenized (86)(87)(88) and non-lichenized fungi (89)(90)(91), and the evidence that the outcome of reproduction may not adhere to mendelian inheritance (92)(93)(94) or the simplistic expectations of Hardy-Weinberg equilibrium.…”

Species Delimitation in a Polyploid Group of Iberian Jasione (Campanulaceae) Unveils Coherence between Cryptic Speciation and Biogeographical Regionalization

“…The results of empirical methods for species delimitation based on nucleotidic information, regardless of the use of either single-locus sequences or genome-scale data, can be misled by some evolutionary processes specific to the group under study. Processes derived from hybridization events and introgression, and recent radiations and incomplete lineage sorting, can blur the inference [ 20 , 21 ]. Thus, complex phylogeographic histories and semipermeable species boundaries [ 21 ] make the accumulation of diverse lines of evidence important, particularly in close evolutionary entities within the same ploidy level.…”

“…Processes derived from hybridization events and introgression, and recent radiations and incomplete lineage sorting, can blur the inference [ 20 , 21 ]. Thus, complex phylogeographic histories and semipermeable species boundaries [ 21 ] make the accumulation of diverse lines of evidence important, particularly in close evolutionary entities within the same ploidy level. It is especially important at the beginning of the speciation process when different independent lines of evidence offer frequent conflicting signals.…”