BackgroundAmazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale.FindingsIn a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp), which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences.ConclusionsThe current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.
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.
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