Understanding cryptic diversity within the honeypot ant species complex of Myrmecocystus mendax

Cryptic species diversity, overlooked due to extreme morphological similarity, is a common phenomenon among ants. The “honeypot ant” genus Myrmecocystus (Wesmael, 1838; Formicinae: Lasiini) likely features multiple cryptic species, as previously suggested by phylogenetic studies based on ultraconserved elements (UCEs). Here, this work is expanded upon by examining 140 specimens and 2,508 UCE loci, with a particular focus on the M. mendax species complex from the southwestern USA and northern Mexico. Phylogenomic and population genomic analyses revealed five distinct M. mendax- like lineages and identified two potential cases of cryptic species diversity, one within samples matching the morphology of M. mendax and another within samples conforming to M. placodops . Most specimens morphologically identified as M. mendax formed a well-supported monophyletic group sister to M. melliger assigned individuals, with evidence for ongoing hybridization between both species in the Madrean Sky Islands along the USA-Mexico border. Patterns in the main M. mendax clade also suggest adaptive divergence across ecological gradients, warranting further investigation. Overall, these findings highlight the power of UCE-based genomic data in phylogenetic reconstructions and population genetic analyses to better resolve cryptic species diversity, and clarify complex evolutionary histories shaped by introgression and incomplete lineage sorting.