An Online mtDNA Tool for Identification of Neotropical Psittacid Species and Taxonomic Issues: A Study Case of the Amazona ochrocephala Complex

Anderson Vieira Chaves, R.O.P. Queiroz-Filho, Fabiano Augusto Assunção Silva, Cristina Yumi Miyaki, Fabrício Rodrigues dos Santos

Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Polícia Federal, Belo Horizonte, Brazil.
Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de S?o Paulo, S?o Paulo, Brazil.

DOI: 10.4236/nr.2014.511056                

Abstract

Parrots are among the most popular pets in the world and they are also some of the most illegally traded, particularly in Brazil. Some computational tools were recently developed by researchers based on molecular databases for taxonomy support, forensic identification and conservation purposes. In this study, the DNA Surveillance platform was used to build an online database tool for molecular identification of Brazilian Psittacids using DNA sequences of six mitochondrial genes. To illustrate possible taxonomic issues of the online tool due to interspecific hybridization or unresolved taxonomy, we focused on Amazona aestiva that is considered as one of the most common parrots in Brazil, commonly bred as pets, and considered to be part of a species complex with Amazona ochrocephala from South America. We provide three curated sequence databases, which allow the species identification of individuals or tissue samples of birds of the Psittacidae family using mitochondrial DNA markers, and a comprehensive description of a taxonomic issue involving the A. ochrocephala complex. The results obtained corroborate previous studies suggesting that these species are not reciprocally monophyletic, due to either an ancient hybridization in central Brazil, or, they maybe just are morpho-varieties of the same species. Alternatively, if A. aestiva and A. ochrocephala were considered as sister species, the data could be interpreted either as a result of secondary contact or incipient speciation. Beyond the use of mtDNA for species identification, the high mtDNA haplotype diversity observed in A. aestiva indicates its potential use in discrimination of lineages that could be an important auxiliary tool to certify the captive origin of legally commercialized parrots.

Keywords

Amazona aestiva, Illegal Trade of Birds, Psittaciformes, Phylogeography, DNA-Surveillance

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Snyder, N., McGowan, P., Gilardi, J. and Grajal, A. (2000) Parrots: Status Survey and Conservation Action Plan 2000-2004. IUCN, Gland, Switzerland and Cambridge.
[2]	Lopes, I.F., Del Lama, M.A. and Del Lama, S.N. (2007) Genetic Variability in three Amazon Parrot Species. Brazilian Journal of Biology, 67, 883-887. http://dx.doi.org/10.1590/S1519-69842007000500011.
[3]	IUCN (2007) The IUCN Red List of Threatened Species. http://www.iucnredlist.org
[4]	CITES (2013) Convention on International Trade of Endangered Species of Wild Flora and Fauna. http://www.cites.org
[5]	Russello, M.A. and Amato, G. (2004) A Molecular Phylogeny of Amazona: Implications for Neotropical Parrot Biogeography, Taxonomy, and Conservation. Molecular Phylogenetics and Evolution, 30, 421-437. http://dx.doi.org/10.1016/S1055-7903(03)00192-1
[6]	Eberhard, J.R. and Bermingham, E. (2004) Phylogeny and Biogeography of the Amazona ochrocephala (Aves: Psittacidae) Complex. The Auk, 121, 318-332. http://dx.doi.org/10.1642/0004-8038(2004)121[0318:PABOTA]2.0.CO;2
[7]	Ribas, C.C., Tavares, E.S., Yoshihara, C. and Miyaki, C.Y. (2007) Phylogeny and Biogeography of Yellow-Headed and Blue-Fronted Parrots (Amazona ochrocephala and Amazona aestiva) with Special Reference to the South American Taxa. Ibis, 149, 564-574. http://dx.doi.org/10.1111/j.1474-919X.2007.00681.x
[8]	Schunck, F., Somenzari, M., Lugarini, C. and Soares, E.S. (2001) Plano de Acao Nacional Para a Conservacao dos Papagaios da Mata Atlantica, Série Espécies Ameacadas No. 20, ICMBio, Brasília.
[9]	RENCTAS (2001) Rede Nacional de Combate ao Tráfico de Animais Silvestres, 1’ Relatório Nacional Sobre o Tráfico de Fauna Silvestre, Brasília. http://www.RENCTAS.org.br
[10]	IBAMA (2005) Relatório de Apreensoes em 2005. http://www.ibama.gov.br
[11]	Ratnasingham, S. and Hebert, P.D.N. (2007) BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes, 7, 355-364. http://dx.doi.org/10.1111/j.1471-8286.2007.01678.x
[12]	Baker, S.C. and Palumbi, S.R. (1994) Which Whales Are Hunted? A Molecular Genetic Approach to Monitoring Whaling. Science, 265, 1538-1539. http://dx.doi.org/10.1126/science.265.5178.1538
[13]	Baker, S.C., Cipriano, F. and Palumbi, S.R. (1996) Molecular Genetics Identification of Whale and Dolphin Products from Commercial Markets in Korea and Japan. Molecular Ecology, 5, 671-685. http://dx.doi.org/10.1111/j.1365-294X.1996.tb00362.x
[14]	Baker, S.C., Steel, D., Choi, Y., Lee, H., Kim, K.S., Choi, S.K., Ma, Y.U., Hamleton, C., Psihoyos, L., Brownell, R.L. and Funahashi, N. (2010) Genetic Evidence of Illegal Trade in Protected Whales Links Japan with the US and South Korea. Biology Letters, 6, 647-650. http://dx.doi.org/10.1098/rsbl.2010.0239
[15]	Cipriano, F. and Palumbi, S.R. (1999) Genetic Tracking of a Protected Whale. Nature, 397, 307-308. http://dx.doi.org/10.1038/16823
[16]	Baker, S.C., Dalebout, M.L., Lavery, S. and Ross, H.A. (2003) www.DNA-surveillance: Applied Molecular Taxonomy for Species Conservation and Discovery. Trends in Ecology & Evolution, 18, 271-272. http://dx.doi.org/10.1016/S0169-5347(03)00101-0
[17]	Robins, J.H., Hingston, M., Matisoo-Smith, E. and Ross, H.A. (2007) Identifying Rattus Species Using Mitochondrial DNA. Molecular Ecology Notes, 7, 717-729. http://dx.doi.org/10.1111/j.1471-8286.2007.01752.x
[18]	Chaves, P.B., Graeff, V., Lion, M.B., Oliveira, L.R. and Eizirik, E. (2012) DNA Barcoding Meets Molecular Scatology: Short mtDNA Sequences for Standardized Species Assignment of Carnivore Noninvasive Samples. Molecular Ecology Resources, 12, 18-35. http://dx.doi.org/10.1111/j.1755-0998.2011.03056.x.
[19]	Kerr, K.C.R., Lijtmaer, D.A., Barreria, A.S., Herbert, P.D.N. and Tubaro, P.L. (2009) Probing Evolutionary Patterns in Neotropical Birds through DNA Barcodes. PLoS ONE, 4, Article ID: e4379. http://dx.doi.org/10.1371/journal.pone.0004379
[20]	Caparroz, R., Seixas, G.H.F., Berkunsky, I. and Colevatti, R.G. (2009) The Role of Demography and Climatic Events in Shaping the Phylogeography of Amazona aestiva (Psitaciformes, Aves) and a Definition of Management Units for Conservation. Diversity and Distribution, 15, 459-468. http://dx.doi.org/10.1111/j.1472-4642.2009.00558.x
[21]	Chaves, A.V., Clozato, C.L., Lacerda, D.R., Sari, H.E.R. and Santos, F.R. (2008) Molecular Taxonomy of Brazilian Tyrant-Flycatchers (Passeriformes, Tyrannidae). Molecular Ecology Resources, 8, 1169-1177. http://dx.doi.org/10.1111/j.1755-0998.2008.02218.x
[22]	Sorenson, M.D. and Quinn, T.W. (1998) Numts: A Challenge for Avian Systematics and Population Biology. The Auk, 115, 214-221. http://dx.doi.org/10.2307/4089130
[23]	Sorenson, M.D. (2003) Avian mtDNA Primers. http://people.bu.edu/msoren/Bird.mt.Primers.pdf
[24]	Folmer, O., Black, M., Hoeh, W., Lutz, R. and Vrijenhoek, R. (1994) DNA Primers for Amplification of Mitochondrial Cytochrome C Oxidase Subunit I from Diverse Metazoan Invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
[25]	Ewing, B., Hillier, L., Wendi, M. and Green, P. (1998) Base-Calling of Automated Sequencer Tracer Using Phred. I. Accuracy Assessment. Genome Research, 8, 175-185. http://dx.doi.org/10.1101/gr.8.3.175
[26]	Gordon, D., Abajian, C. and Green, P. (1998) Consed: A Graphical Tool for Sequence Finishing. Genome Research, 8, 195-202. http://dx.doi.org/10.1101/gr.8.3.195
[27]	Edgar, R.C. (2004) MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic Acids Research, 32, 1792-1717. http://dx.doi.org/10.1093/nar/gkh340
[28]	Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739. http://dx.doi.org/10.1093/molbev/msr121
[29]	Excoffier, L., Laval, G. and Schneider, S. (2005) Arlequin Ver. 3.0: An Integrated Software Package for Population Genetics Data Analysis. Evolutionary Bioinformatics Online, 1, 47-50.
[30]	Rozas, J., Sánches-Delbarrio, J.C., Messeguer, X. and Rozas, R. (2003) DnaSP, DNA Polymorphism Analysis by the Coalescent and Other Methods. Bioinformatics, 19, 2496-2497. http://dx.doi.org/10.1093/bioinformatics/btg359
[31]	Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of Molecular Variance Inferred from Metric Distances among DNA Haplotypes: Application to Human Mitochondrial DNA 15 Restriction Data. Genetics, 131, 479-491.
[32]	Bandelt, H.J., Forster, P. and Rohl, A. (1999) Median-Joining Networks for Inferring Intraspecific Phylogenies. Molecular Biology and Evolution, 16, 37-48. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026036
[33]	Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007) Clustal W and Clustal X Version 2.0. Bioinformatics, 23, 2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404
[34]	Ross, H.A., Lento, G.M., Dalebout, M.L., Goode, M., Ewing, G., McLaren, P., Rodrigo, A.G., Lavery, S. and Baker, C.S. (2003) DNA Surveillance: Web-Based Molecular Identification of Whales, Dolphins, and Porpoises. Journal of Heredity, 94, 111-114. http://dx.doi.org/10.1093/jhered/esg027
[35]	Urantówka, A.D., Mackiewicz, P. and Strzala, T. (2014) Phylogeny of Amazona barbadensis and the Yellow-Headed Amazon Complex (Aves: Psittacidae): A New Look at South American Parrot Evolution. PLoS ONE, 9, Article ID: e97228. http://dx.doi.org/doi:10.1371/journal.pone.0097228
[36]	Clements, J.F., Schulenberg, T.S., Iliff, M.J., Sullivan, B.L., Wood, C.L. and Roberson, D. (2013) The eBird/Clements Checklist of Birds of the World: Version 6.8. http://www.birds.cornell.edu/clementschecklist/download
[37]	Souza, T.S. and Vilela, D.A.R. (2013) Espécies Ameacadas de Extincao víTimas do Tráfico e Criacao Ilegal de Animais Silvestres. Atualidades Ornitológicas, 176, 64-68.
[38]	Gogliath, M., Bisaggio, E.L., Ribeiro, L.B., Resgalla, A.E. and Borges, R.C. (2010) Avifauna Apreendida e Entregue Voluntariamente ao Centro de Triagem de Animais Silvestres (Cetas) do Ibama de Juiz de Fora, Minas Gerais. Atualidades Ornitológicas, 154, 55-59.
[39]	Pagano, I.S.A., Sousa, A.E.B.A., Wagner, P.G.C., and Ramos, R.T.C. (2009) Aves Depositadas no Centro de Triagem de Animais Silvestres do IBAMA na Paraíba: Uma Amostra do tráfico de aves Silvestres no Estado. Ornithologia, 3, 132-144.
[40]	Carvalho, C.B.V. (2012) Identificacao Genética de Aves Vítimas do Tráfico de Animais Silvestres. Atualidades Ornitológicas, 165, 40-44.