Comparative mitogenomic analyses of Amazona parrots and Psittaciformes

Lima, Nicholas Costa Barroso; Soares, André Elias Rodrigues; Almeida, Luiz Gonzaga Paula de; Costa, Igor Rodrigues da; Sato, Fernanda Midori; Schneider, P. J.; Aleixo, Alexandre; Schneider, Maria Paula Cruz; Santos, Fabrício R.; Mello, Claudio V.; Miyaki, Cristina Yumi; Vasconcelos, Ana Tereza Ribeiro de; Prosdocimi, Francisco

doi:10.1590/1678-4685-gmb-2017-0023

Cited by 5 publications

(3 citation statements)

References 56 publications

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“…To overcome this complexity, we used a combination of several next-generation sequencing technologies, producing a hybrid mitogenome assembly for this species. In this study, we have found that mitochondrial genomes of all representatives of the Greater Antillean amazons contain the nearly exact duplicated control region (CR) and a gene arrangement that is characteristic for all other amazon parrot mitogenomes analyzed so far [ 80 , 81 ].…”

Section: Resultsmentioning

confidence: 99%

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles

Kolchanova

Komissarov

Kliver

et al. 2021

Genes

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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.

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Section: Resultsmentioning

confidence: 99%

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles

Kolchanova

Komissarov

Kliver

et al. 2021

Genes

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“…In the domestic chicken, BTP is located downstream of CSB1 [ 51 ]. Amazona also has a similar region [ 35 ]. Although tandem repeats were found in domain III of Amazona genus [ 17 , 35 ], there were no tandem repeats in the Cacatua genus.…”

Section: Resultsmentioning

confidence: 99%

“…CRs were aligned with MAFFT [ 34 ]. Conserved motifs were identified by comparison with the mitogenomes of Amazona genus [ 17 , 35 ]. A phylogenetic analysis using CRs was conducted with Cacatuidae mitogenomes having duplicated CRs ( Table 1 ) [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

Characterization and Comparative Analysis of Complete Mitogenomes of Three Cacatua Parrots (Psittaciformes: Cacatuidae)

Kim

Choi

et al. 2021

Genes

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Cacatua alba, Cacatua galerita, and Cacatua goffiniana are parrots of the family Cacatuidae. Wild populations of these species are declining with C. alba listed by the International Union for the Conservation of Nature and Natural Resources (IUCN) as Endangered. In this study, complete mitogenomes were sequenced for a comparative analysis among the Cacatua species, and a detailed analysis of the control region. Mitogenome lengths of C. alba,C. galerita, and C. goffiniana were 18,894, 18,900, and 19,084 bp, respectively. They included 13 protein coding genes, two ribosomal RNA genes, 24 transfer RNA genes, three degenerated genes, and two control regions. Ten conserved motifs were found in three domains within each of the two control regions. For an evolution of duplicated control regions of Cacatua, domain I and the 3′ end of domain III experienced an independent evolution, while domain II and most of the regions of domain III was subjected to a concerted evolution. Based on a phylogenetic analysis of 37 mitochondrial genes, the genus Cacatua formed a well-supported, monophyletic, crown group within the Cacatuidae. Molecular dating results showed that Cacatua diverged from other genera of Cacatuinae in the middle of Miocene.

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