New Mitogenomic Resources for the Caiman yacare (Daudin, 1802) From Bolivia

This study addresses the evolutionary state of a newly discovered population of Caiman yacare outside the western edge of its range in Bolivia by providing new mitochondrial genomic resources. Despite their conservation importance, few complete mitochondrial genomes have been generated for South American crocodilians, and most of those available originate from captive individuals, thereby limiting their utility for conservation and taxonomic applications. To bridge this gap, we generated complete mitochondrial genomes for six wild individuals from this newly discovered population in Bolivia. These data complement previously available sequences and provide essential resources for conservation and forensic applications. Mitogenomes were assembled and annotated using MEGAHIT and MitoZ. Species delimitation analyses using five independent methods revealed seven mitochondrial lineages (MOTUs) within the genus Caiman, while C. yacare itself formed a single MOTU with two phylogroups of distinct geographic distributions. All six new genomes clustered within the Madeira phylogroup. Phylogenetic and coalescent analyses suggest that this newly documented population retains high haplotypic diversity despite being located at the margin of the species range distribution. This study provides the first mitogenomes of wild C. yacare and contributes valuable data for understanding population structure, lineage divergence, and for informing management strategies.