Supplementary file 1_Molecular assessment of confiscated Sceloporus lizards (Squamata: Phrynosomatidae) reveals unresolved taxonomic affinities and genetic reference gaps in Honduras.docx

In Honduras, species of the genus Sceloporus are poorly studied despite their ecological relevance and increasing demand in the illegal pet trade.</p>Methods<p>To address this knowledge gap, we analyzed mitochondrial COI sequences from seven confiscated Sceloporus individuals assigned to three morphotypes.</p>Results<p>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.