Species boundaries to the limit: validating species delimitation methods is critical to avoid taxonomic inflation in the genomic era

With the advent of molecular phylogenetics, the number of taxonomic studies unveiling and describing cryptic diversity has greatly increased. However, speciation between cryptic lineages is often defined without evaluating population structure or gene flow, which can lead to false claims of species status and, subsequently, taxonomic inflation. In the present study we focus on the intriguing case of the Arabian gecko Trachydactylus hajarensis (Squamata: Gekkonidae), a species for which cryptic diversity has been previously reported. We generated mitochondrial data (12S rDNA) and genome-wide SNP data (ddRADseq) for 52 specimens to determine phylogenomic relationships, population structure and gene flow within this species. Then, we applied species delimitation methods (SDMs) to evaluate several competing species hypotheses through the Multispecies Coalescent model. Results show that T. hajarensis is comprised by three well-defined lineages, two of them in the Hajar Mountains of eastern Arabia, and one in Masirah Island, in the southeastern coast of Oman. Even though high levels of past introgression and strong mitonuclear discordances were found, current gene flow is scarce with clear boundaries between populations and shallow levels of admixture in the contact zone between lineages. Surprisingly, species tree topology differed between methods and when different individuals were used in downsampled datasets. Conventional SDMs supported up to three putative new species within the group. However, after species validation with the genealogical divergence index (gdi), none of the putative species held. Overall, this study highlights the importance of sample choice, integrative analyses, and validation methods to not incur into taxonomic inflation, providing a set of already available tools to assess and validate population structure, gene flow, and SDMs before describing new species.