Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

BACKGROUND

In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data.

OBJECTIVE

Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae).

METHODS

Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed.

RESULTS

The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively.

CONCLUSION

Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.

Not like night and day: the nocturnal letter-winged kite does not differ from diurnal congeners in orbit or endocast morphology

Nocturnal birds display diverse adaptations of the visual system to low-light conditions. The skulls of birds reflect many of these and are used increasingly to infer nocturnality in extinct species. However, it is unclear how reliable such assessments are, particularly in cases of recent evolutionary transitions to nocturnality. Here, we investigate a case of recently evolved nocturnality in the world's only nocturnal hawk, the letter-winged kite Elanus scriptus. We employed phylogenetically informed analyses of orbit, optic foramen and endocast measurements from three-dimensional reconstructions of micro-computed tomography scanned skulls of the letter-winged kite, two congeners, and 13 other accipitrid and falconid raptors. Contrary to earlier suggestions, the letter-winged kite was not unique in any of our metrics. However, all species of Elanus have significantly higher ratios of orbit versus optic foramen diameter, suggesting high visual sensitivity at the expense of acuity. In addition, visual system morphology varies greatly across accipitrid species, likely reflecting hunting styles. Overall, our results suggest that the transition to nocturnality can occur rapidly and without changes to key hard-tissue indicators of vision, but also that hard-tissue anatomy of the visual system may provide a means of inferring a range of raptor behaviours, well beyond nocturnality.

Characterization of the complete mitochondrial genome of Elanus caeruleus Desfontaines, 1789 (Accipitriformes: Accipitridae)

The complete mitochondrial genome of the Elanus caeruleus was sequenced via next-generation sequencing. The circular mitogenome is 18,898 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, a control region and a pseudo control region. The sequences (1210 bp) in the middle part of the two control regions are complete identical to each other. The gene order of the E. caeruleus mitogenome is identical to those of other Accipitridae species. The phylogenetic analysis indicated that E. caeruleus formed a basal lineage sister to other species within the Accipitridae family.