Non-lethal scute transcriptomics reveals biomarker candidates for environmental stress in Mexican Morelet's crocodiles.

Aquatic ecosystems in southeastern Mexico face increasing chemical pollution, yet non-lethal molecular tools to monitor native reptile populations remain limited. We profiled RNA-seq from non-lethal caudal scute biopsies of 43 Morelet's crocodiles (Crocodylus moreletii) across six wild populations and a captive reference group. After mapping to the Alligator mississippiensis genome, 18,107 expressed genes were analyzed using PCA, DESeq2, WGCNA, and single-sample pathway scoring. Wild crocodiles showed a consistent shift along a dominant transcriptional axis contrasting dermal/ECM remodeling with epidermal-metabolic/barrier programs. A conserved core of DEGs and wild-associated modules were enriched for extracellular matrix organization, ER/secretory stress handling, vesicle trafficking and adhesion pathways, while union DEGs captured site-specific alterations in lipid metabolism, ion transport, neuronal signaling and developmental processes. Integrating network connectivity, differential expression strength, statistical support, and ROC performance, we prioritized 10 up-regulated genes as a preliminary scute biomarker panel that discriminates wild from captive individuals. This landscape-scale scute transcriptomic framework supports non-lethal omics-based biomonitoring in crocodilians and other non-model wildlife.