Mitochondrial markers (cytochrome c oxidase subunit I and 16S ribosomal RNA) as supporting biomarkers for wild bird identification

TL;DR

This study shows that mitochondrial markers COI and 16S rRNA can accurately identify psittacine birds, aiding in wildlife trafficking investigations and conservation.

Contribution

The study validates COI and 16S rRNA as reliable molecular tools for psittacine species identification in forensic and conservation contexts.

Findings

COI and 16S rRNA sequences achieved 100% concordance with morphological identification for six psittacine birds.

Phylogenetic analyses using both markers produced congruent results with high branch support (>90%).

Generated sequences were submitted to GenBank and BOLD, enhancing genetic databases for Neotropical avifauna.

Abstract

Illegal wildlife trafficking is a critical threat to biodiversity, particularly in megadiverse countries such as Colombia. Birds, notably psittacines, are among the most targeted taxa. Morphological identification is often insufficient, especially when dealing with cryptic species or degraded samples. This study aimed to assess the utility of mitochondrial markers cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) as molecular tools for species-level identification of psittacines housed at the Conservation Park of Medellín.

Six adult psittacines from the genera Ara and Pionus were selected based on availability. Blood samples were collected and genomic DNA was extracted using a commercial kit. Polymerase chain reaction amplification of partial COI and 16S rRNA gene fragments was performed, followed by Sanger sequencing. Sequence identity was confirmed using BLASTn and the Barcode of Life Data System (BOLD). Phylogenetic relationships were analyzed using Neighbor-Joining, Maximum Likelihood, and Bayesian Inference approaches.

Molecular results showed 100% concordance with prior morphological identification for all six individuals. COI and 16S rRNA sequences allowed clear species-level identification with similarity values >98%. Phylogenetic analyses for both markers yielded congruent tree topologies, with high branch support (>90%), further validating species identification. Maximum interspecific divergence for COI was observed between Ara macao and Pionus fuscus (0.15980), while 16S rRNA showed lower divergence values. All generated sequences were submitted to GenBank and BOLD in accordance with findable, accessible, interoperable, reusable principles.

This study confirms the robustness of COI and 16S rRNA mitochondrial markers in accurately identifying psittacine species. The integration of molecular and morphological approaches enhances forensic investigations, facilitates biodiversity conservation, and contributes to efforts against wildlife trafficking. Expanding genetic databases for Neotropical avifauna, especially for commonly trafficked species, is imperative. Future research should adopt integrative genomic approaches involving nuclear markers to overcome the maternal inheritance limitation of mitochondrial DNA.

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