Finding complexity in complexes: assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads

Mitonuclear discordance is a frequently encountered pattern in
phylogeographic studies and occurs when mitochondrial and nuclear DNA
display conflicting signals. Discordance among these genetic markers can
be caused by several factors including confounded taxonomies, gene flow,
and incomplete lineage sorting. In this study, we present a strong case of
mitonuclear discordance in a species complex of toads (Bufonidae: Incilius
coccifer complex) found in the Chortís Block of Central America. To
determine the cause of mitonuclear discordance in this complex, we used
spatially explicit genetic data to test species limits and relationships,
characterize demographic history, and quantify gene flow. We found
extensive mitonuclear discordance among the three recognized species
within this group, especially in populations within the Chortís Highlands
of Honduras. Our data reveal nuclear introgression within the Chortís
Highlands populations that was most likely driven by cyclical range
expansions due to climatic fluctuations. Though we determined
introgression occurred within the nuclear genome, our data suggest that it
is not the key factor in driving mitonuclear discordance in the entire
species complex. Rather, due to a lack of discernible geographic pattern
between mitochondrial and nuclear DNA, as well as a relatively recent
divergence time of this complex, we concluded that mitonuclear discordance
has been caused by incomplete lineage sorting. Our study provides a
framework to test sources of mitonuclear discordance and highlights the
importance of using multiple marker types to test species boundaries in
cryptic species.