Molecular characterization of the spectacled caiman (Caiman crocodilus) in the upper Magdalena River basin, Colombia: Demographic and phylogeographic insights

Abstract

Maintenance of high levels of genetic diversity is crucial for the recovery of overexploited species and gaining knowledge of genetic diversity of natural populations is crucial to define effective conservation strategies. Spectacled caimans (Caiman crocodilus) were unsustainably exploited for decades in Colombia causing drastic population reductions with unknown effects on genetic structure. We molecularly characterized three spectacled caiman populations from the upper Magdalena River basin (UMRB), analyzing them within the context of the trans-Andean C. c. fuscus sensu stricto lineage, assessing nucleotide and genetic diversity, demographic history, and phylogeography at different scales. Seventeen of the 23 mitochondrial haplotypes currently described for Colombia are present in the UMRB, showing high levels of genetic diversity even when compared with the trans-Andean region (uncorrected genetic distances 0.00-0.87%). Mutational steps between closest haplotypes ranged from one to four while the most differentiated haplotypes were separated by 19 mutational steps across the whole trans-Andean region. Distribution of pairwise nucleotide differences and raggedness tests showed unimodal patterns of mismatch distribution curves fitting the sudden expansion model. Average time since demographic expansion for UMRB, Colombia, and trans-Andean region were inferred as 10,540, 7,591, and 7,071 years before present, respectively, placing the latest expansion close to the Pleistocene-Holocene boundary. Intriguingly, samples from Tolima were overall more related to those collected from Panama and Costa Rica (0.34 ± 0.15%) than the ones collected across Choco (0.45 ± 0.15%), Cauca (0.70 ± 0.09%), and Nariño (0.60 ± 0.14%) departments. We discuss our genetic findings in the context of the management policies carried out in the country during the last decades (unsustainable and sustainable use, and population restocking), evaluating the implications of these events for the genetic integrity and conservation of the species.

Key words:

• conservation genetics
• crocodylia
• genetic lineages
• genetic variability
• Tolima
• wildlife management

Acknowledgements

We thank the University of Ibague, University of Tolima, IUCN Crocodile Specialist Group, and the Asociación Colombiana de Herpetología for financial support. We also thank Sigifredo Clavijo and Yair Molina for their support during field and lab work. This project was approved by the University of Tolima research centre to capture, manipulate, and collect samples from spectacled caiman under its national permit (ANLA legal resolution 02191). We finally thank Chistopher Brochu, Lou Densmore, and Associate Editor David Gower for their comments that helped to improve the submitted manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supplemental material

Supplemental material for this article can be accessed here: https://doi.org/10.1080/14772000.2021.1968975.

Associate Editor: David Gower