Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

The delimitation of species is an essential pursuit of biology, and proper
taxonomies are crucial for the assessment and conservation management of
organismal diversity. However, delimiting species can be hindered by a
number of factors including highly conserved morphologies (e.g. cryptic
species), differences in criteria of species concepts, and discordance
between gene topologies (e.g. mitonuclear discordance). Here we use a
taxonomically confounded species complex of toads in Central America that
exhibits extensive mitonuclear discordance to test delimitation
hypotheses. Our investigation integrates mitochondrial sequences, nuclear
SNPs, morphology, and macroecological data to determine which taxonomy
best explains the divergence and evolutionary relationships among these
toads. We found that a three species taxonomy following the distributions
of the nuclear SNP haplotypes offer the best explanation of the species in
this complex based off of the integrated data types. Due to the taxonomic
instability of this group we also discuss conservation concerns in the
face of improper taxonomic delimitation. Our study provides an empirical
hypothesis testing framework to assess species delimitation hypotheses in
the face of cryptic morphology and mitonuclear discordance and highlights
the importance that proper taxonomy has over conservation related actions.