Genetic analysis reveals strong phylogeographical divergences within the Scarlet Macaw Ara macao

Scarlet Macaws Ara macao have the largest geographical distribution of any Neotropical psittacine, occupying a variety of lowland forest habitats from Mexico to Brazil. Two subspecies, Ara macao macao and Ara macao cyanoptera, are currently recognized based on wing chord length and plumage coloration, with formal descriptions suggesting genetic introgression in southern Nicaragua and northern Costa Rica. The present study aimed to investigate the extent of genetic diversification within A. macao by analysing mitochondrial sequence data from contemporary and historical samples. Phylogenetic reconstruction and population aggregation analysis confirmed two distinct phylogeographical groups, with a high degree of intraspecific genetic structure and no evidence of a putative hybrid zone. Whole mitochondrial genome sequencing further confirmed substantial divergence (~ 1.8%) between the cyanoptera and macao lineages. These results demonstrate a separation of A. macao into two distinct evolutionary entities and highlight a non-uniform distribution of intraspecific diversity, suggesting current conservation designations may warrant re-evaluation.