Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles.

Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean.

Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation.

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.

The Puerto Rican parrot reintroduction program: sustainable management of the aviary population.

The cornerstone of the recovery plan for the critically endangered Puerto Rican parrot (Amazona vitatta) is an actively managed, long-term reintroduction program. One captive population distributed across two aviaries in Puerto Rico is the sole source for release but its ability to persist as a managed resource has not been evaluated since 1989. We conducted an assessment for sustainable management of the aviary population while harvesting for release. To assess demographic rates such as population growth, vital rates, and age/sex structure, we compiled a studbook database on all living, dead, and released individuals in the aviary population. Using an individual-based risk assessment model we applied population specific data based on the management period from 1993 to 2012 to simulate future aviary population dynamics and evaluate future potential production. We modeled four potential management strategies to harvest parrots for proposed releases; these scenarios vary the number of parrots and the life stage. Our simulations revealed that the aviary population can be simultaneously managed for sustainability and harvesting of parrots for release. However, without cautious management, overharvesting can jeopardize sustainability of the aviary population. Our analysis of the aviary breeding program provides a rare opportunity to review progress relative to conservation program objectives after four decades of active management. The successful growth of the aviary population and its ability to serve as a sustainable source for reintroductions supports the 1973 decision to build a breeding program from a small population of 13 parrots.