Use of ddRAD-sequencing to diagnose cryptic species with low interspecific mitochondrial divergence

Abstract

Sister species that have diverged from each other recently can appear similar morphologically but typically have genetic features that can distinguish them due to a lack of gene flow. In the case of two sympatric species of bat (Myotis californicus and M. ciliolabrum) that are cryptic, they can be distinguished by features of their echolocation call, but no genetic marker has been discovered that can easily distinguish them. A simple diagnostic genetic marker, like a DNA sequence barcode, would assist researchers to identify species from wing punches or fecal pellets from a roost without the need to collect the bat. Despite research on their mitochondrial genome from specimens across their range, a barcoding approach does not seem to work for this complex. We tested the hypothesis that these two species can be diagnosed using a genomic approach. We used reduced representation genome sequencing (ddRAD-seq) to identify and analyze single nucleotide polymorphisms (SNPs) from individuals of M. californicus and M. ciliolabrum. Using principal component analysis, population structure analysis, and a RAxML phylogenetic tree, we found that the samples formed three distinct groups rather than the two we expected. We found more cryptic biological diversity than expected within the morphologically-similar complex. The two clusters recovered within M. ciliolabrum appear to be consistent with previously recognized subspecies