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

The Recovery Program of the Puerto Rican Parrot at the Rio Abajo State Forest, Departamento de Recursos Naturales y Ambientales de Puerto Rico, Arecibo, PR 00613, USA

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Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA

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Program in Individualized Medicine (PrIMe), Pharmacogenomics Laboratory, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, 100 Grimes Way, Pullman, WA 99164, USA

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Genes 2019, 10(1), 54; https://doi.org/10.3390/genes10010054

Received: 15 October 2018 / Revised: 13 December 2018 / Accepted: 8 January 2019 / Published: 16 January 2019

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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Abstract

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. View Full-Text

Keywords: genomics; parrots; birds; heterozygosity; Puerto Rican parrot; Cuba; Hispaniola; conservation; demography

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MDPI and ACS Style

Kolchanova, S.; Kliver, S.; Komissarov, A.; Dobrinin, P.; Tamazian, G.; Grigorev, K.; Wolfsberger, W.W.; Majeske, A.J.; Velez-Valentin, J.; Valentin de la Rosa, R.; Paul-Murphy, J.R.; Guzman, D.S.-M.; Court, M.H.; Rodriguez-Flores, J.L.; Martínez-Cruzado, J.C.; Oleksyk, T.K. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes 2019, 10, 54. https://doi.org/10.3390/genes10010054

AMA Style

Kolchanova S, Kliver S, Komissarov A, Dobrinin P, Tamazian G, Grigorev K, Wolfsberger WW, Majeske AJ, Velez-Valentin J, Valentin de la Rosa R, Paul-Murphy JR, Guzman DS-M, Court MH, Rodriguez-Flores JL, Martínez-Cruzado JC, Oleksyk TK. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes. 2019; 10(1):54. https://doi.org/10.3390/genes10010054

Chicago/Turabian Style

Kolchanova, Sofiia, Sergei Kliver, Aleksei Komissarov, Pavel Dobrinin, Gaik Tamazian, Kirill Grigorev, Walter W. Wolfsberger, Audrey J. Majeske, Jafet Velez-Valentin, Ricardo Valentin de la Rosa, Joanne R. Paul-Murphy, David S.-M. Guzman, Michael H. Court, Juan L. Rodriguez-Flores, Juan C. Martínez-Cruzado, and Taras K. Oleksyk. 2019. "Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation" Genes 10, no. 1: 54. https://doi.org/10.3390/genes10010054

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

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