Phylogeography of the endangered Yellow-headed Parrot (Amazona oratrix)

Elucidating the historical processes that led populations to their current spatial and genetic arrangement is relevant in conserving threatened species. We interpreted the phylogeographic structure of the threatened Yellow-headed Parrot ( Amazona oratrix ) with mitochondrial markers and analyzed 98 samples from Mexico, Guatemala, and Belize. We performed analyses of genetic structure, genealogical relationships, demographic history, and divergence times and illustrated the phenotypic variation qualitatively of the sampled individuals. The studies revealed that 92% of the genetic variation is explained between the Mexican Tres Marías Islands, the Mexican Pacific Coast, and the Atlantic groups. These three groups were segregated into two main lineages (Pacific and Atlantic), separated by 26 mutations, leaving A . auropalliata within the Atlantic. We found that both lineages diverged 0.55 million years ago, from which the Atlantic lineage experienced population expansion, high levels of genetic diversity, and a low genetic structure with two phenotypes. The Pacific experienced demographic stability, low levels of diversity, and a genetic structure marked with two phenotypes. Our estimates indicate that this separation occurred in the Pleistocene when the Atlantic clade diverged from Panama and dispersed overland to the Gulf of Mexico. Simultaneously, the Pacific clade departed from the same area to Tres Marías Islands and the Mexican Pacific coast. We deduce that this long-distance event was probably produced by assisted dispersal, but other scenarios appear more parsimonious. We conclude that there is no gene flow between both lineages and that the phylogeographic structure resulted significantly from historical events and climatic changes during the Pleistocene. We propose undertaking other analyses in the future to compare our results and the paraphyletic relationships in A. oratrix. • Using mtDNA and populations not analyzed in previous studies, we found two genetic lineages in the Yellow-headed Parrot ( Amazona oratrix ). • The Atlantic lineage consisted of Amazona auropalliata and A. oratrix samples from the Gulf of Mexico, Belize, and Guatemala. • The Pacific lineage consisted of A. oratrix from the Tres Marias Islands and the Mexican Pacific coast. • Both lineages diverged 0.55 million years ago. • We propose that both lineages be considered as at least Evolutionarily Significant Units until more studies are available.