An Evaluation of Genetic Diversity, Population Structure, and Effective Population Size of Red-and-Green Macaws (Ara chloropterus) and Scarlet Macaws (Ara macao) in Intact Peruvian Rainforest

Many Neotropical parrots are threatened or in danger of extinction due to exploitation and habitat destruction, but mitigating impacts is difficult because key components of their ecology, such as home range sizes, seasonal movements, effective population sizes, and dispersal patterns are not well-understood. We used non-invasive genetic sampling of feathers to evaluate the genetic diversity, population genetic structure, and the effective population size of Red-and-green Macaw (Ara chloropterus) and Scarlet Macaw (Ara macao) in intact rainforest in Peru. We sampled macaws from three to four locations across the Peruvian Amazon and generated genetic data for 12 nuclear microsatellite loci and 381 bp of the mitochondrial control region. Diversity was high across intact habitat for both macaws but was higher for Scarlet Macaw than for Red-and-green Macaw (He = 0.78 vs. 0.56, p = 0.0762; A = 5.6 vs. 3.9, p = 0.0256). For each species, Bayesian clustering analyses gave the greatest support for K = 1, suggesting one genetic group across the areas sampled. Pairwise FST values were low and not significantly different from zero, suggesting high gene flow across the region. Scarlet Macaws had higher overall FST values than Red-and-green Macaws, and more loci with differentiated allele frequencies, indicating that Scarlet Macaws may have more restricted gene flow than Red-and-green Macaws. Effective population size estimates for Scarlet Macaws were three to five times larger than for Red-and-green Macaws. These data provide baseline information on genetic diversity and population structure of macaws in intact habitat and can be used to inform conservation planning and as a reference to determine effects of human activities on macaw populations in Peru and throughout the Amazon Basin.