Molecular assessment of confiscated Sceloporus lizards (Squamata: Phrynosomatidae) reveals unresolved taxonomic affinities and genetic reference gaps in Honduras

Abstract

Molecular tools play a crucial role in biodiversity research and wildlife forensics, yet Central America remains underrepresented in genetic reference databases, particularly for reptiles. In Honduras, species of the genus Sceloporus are poorly studied despite their ecological relevance and increasing demand in the illegal pet trade. To address this knowledge gap, we analyzed mitochondrial COI sequences from seven confiscated Sceloporus individuals assigned to three morphotypes. Morphological examination identified three distinct morphotypes: two consistent with the published diagnoses of S. schmidti and S. hondurensis , and a third displaying atypical scale arrangements that did not conform to any recognized species diagnosis. Despite this morphological variation, the sequences showed very low nucleotide divergence (mean pairwise identity 99.4%) and formed a single strongly supported COI cluster, indicating very close mitochondrial affinity among the specimens and no COI differentiation corresponding to the morphotype assignments. This discordance between morphological assignment and mitochondrial variation was the most consistent pattern recovered. Comparisons with GenBank and BOLD returned sequences labeled as S. malachiticus as the closest available references, but identity values remained low (≤93.7%), indicating that the sampled individuals are not closely matched by any currently available public COI reference sequence. These results indicate an unresolved taxonomic affinity, with the closest currently available reference sequences assigned to the S. malachiticus complex, although a single mitochondrial marker and seven individuals cannot discriminate between an unsampled lineage, misidentified reference records, and incomplete database coverage. Our findings document substantial gaps in the regional molecular reference framework for Sceloporus and, to our knowledge, provide the first forensic genetic assessment of confiscated Sceloporus in Honduras.