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

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 spe-* Corresponding author. A. V. Chaves et al. 635 cies 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.

Comparative mitogenomic analyses of Amazona parrots and Psittaciformes

“…H_14 contains the majority of COI’s from A. aestiva mitogenomes. The H9_clade1_SA, which is the haplotype closest to our sequence by the DNA Surveillance classification ( Figure 5 ), is part of clade 1, which according to Chaves et al (2014) , is related to the north-eastern group of Caparroz et al (2009) . The latter corresponds to the Brazil states Bahia, Tocantins, Minas Gerais, Distrito Federal, and Goiás.…”

“…Previous molecular phylogenies have shown that A. aestiva and A. ochrocephala are not reciprocally monophyletic ( Eberhard et al , 2004 ; Ribas et al , 2007 ; Caparroz et al , 2009 ; Chaves et al , 2014 ). Also, the parents of the specimen whose mitogenome is being described here were apprehended from the illegal trade and their origin is unknown.…”

“…The haplotype network was constructed by median joining using Network v 4.6 ( Bandelt et al , 1999 ). We also used the webpage DNA Surveillance for species identification of Brazilian parrots ( Baker et al , 2003 ; Chaves et al , 2014 ) to verify the species of our specimen based on their ND2 sequence. To ratify the other two approaches we aligned the COI gene sequences from 108 Amazona specimens ( ) using MUSCLE ( Edgar, 2004 ).…”

“…Furthermore, all 40 mitogenomes of Psittaciformes species available (as of October, 2017) were used in phylogenomic analyses. Finally, as previous genetic studies suggest that A. aestiva and A. ochrocephala are not reciprocally monophyletic ( Eberhard et al , 2004 ; Ribas et al , 2007 ; Caparroz et al , 2009 ; Chaves et al , 2014 ), we compared the sequence of the COI gene from the mitogenome described here with those of other individuals of A. aestiva and A. ochrocephala from various localities in South America to confirm if this individual has a typical A. aestiva sequence.…”