Utilising mitochondrial barcode sequencing to evaluate phylogeographical structure and guide the release of illegally traded Amazon parrots

Abstract

Summary Amazon parrots stand out as one of the most illegally traded Psittacids in the neotropics. However, the lack of effective tools for determining the geographical origin of confiscated individuals has impeded the development of well-informed release programmes. In this study, we evaluated the efficacy of the cytochrome oxidase subunit I (COI) gene to identify phylogeographical groups and infer the origins of seized individuals across six Amazon parrot species. Through comprehensive genetic and phylogenetic analyses of 140 COI sequences from individuals with documented geographical origin, a genetic reference database was assembled. The most likely origin of 156 seized parrots was inferred by comparing their genotype to this database. Within the Yellow-headed Parrot Amazona ochrocephala species complex, our analyses revealed the presence of seven distinct phylogeographical groups, exposing a notable poaching impact in the Middle Magdalena’s river valley. For the Southern Mealy Amazon A. farinosa, three distinct genetic groups were identified, with seized individuals showing comparable proportions originating from both the Cis- and Trans-Andean regions. Noteworthy genetic differentiation was observed between individuals of Festive Amazon A. festiva from the Caquetá–Amazon Rivers and those from the Meta River, with two seized individuals assigned to the former. The Scaly-naped Amazon A. mercenaria exhibited genetic divergence between individuals from the central Andes and the Sierra Nevada de Santa Marta. In contrast, the Orange-winged Amazon A. amazonica and Red-lored Amazon A. autumnalis did not display significant phylogeographical structure. However, analyses of seized individuals of A. amazonica suggested a potential underestimation of its genetic diversity and structure. This study illustrates the utility of mitochondrial molecular markers in determining the most probable area of origin for confiscated Amazon parrots, aiding in release programmes and enhancing the monitoring of natural populations.