| Summary: | Advances in technology and molecular methodologies now provide an unprecedented view into the complex realm of natural populations by elucidating the degree and distribution of genetic variation, historical and contemporary processes driving differentiation, and individual behavior patterns. These critical biological parameters create a framework to enhance wildlife management initiatives, as illustrated here through the implementation of a model approach for the systematic genetic assessment of a group of scarlet macaws Ara macao under threat in La Selva Maya, a tri-national system of protected areas in Mexico, Guatemala, and Belize. A total of 2172 base pairs across four mitochondrial data partitions were employed to test the current hypothesis of subspecific diversification. Phylogenetic reconstruction uncovered two phylogeographic units exhibiting distinct and complex evolutionary histories, emphasizing the importance of Central American populations to intraspecific diversity. Focusing on A. m. cyanoptera, mitochondrial control region sequences of 850 base pairs were examined within a hierarchical context to investigate patterns of genetic substructure at varying spatial scales and extent of molecular variation, including potential temporal shifts in response to anthropogenic pressures. Population-level statistical tests detected evidence of recently restricted gene flow among nest sites in La Selva Maya, a stark contrast to the historical state of panmixia across the region; although overall levels of genetic variation remain high, a decrease in diversity was noted among modern samples originating in the Chiquibul Forest Reserve, Belize. Multilocus genotypes based on eight microsatellite markers were combined with haplotypic data to evaluate whether focal nest sites in the Maya Biosphere Reserve, Guatemala represent distinct genetic clusters. Results from population genetic analyses argue against the presence of site fidelity at fine geographic scales. Examination of pairwise relative relatedness indices supports the observation of genetic connectivity across local breeding areas, while also revealing important insights into recent demographic trends, movement patterns, and breeding behaviors. In summary, this work demonstrates the continuity of biological and ecological influences across individual, local, regional, and continental scales, thus creating an empirical framework to refine population management goals and prioritize mitigation strategies in order to maximize conservation outcomes and foster long-term survival of wild scarlet macaws in La Selva Maya.
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