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Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups. [ABSTRACT FROM AUTHOR]

Background: Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the 'true' Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots' phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods. Results: Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration. Conclusions: Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree. [ABSTRACT FROM AUTHOR]

Vertebrate mitogenomes are thought to be selected for compactness. Therefore, the increasing number of avian mitogenomes comprising duplicated regions is surprising. Such regions were proposed for at least 26 parrot genera based on the length of PCR products. However, complete mitogenomes with the duplications were shown only for six genera. These duplications evolved probably from the ancestral tRNATHR/tRNAPRO/ND6/tRNAGLU/CR and were subjected to subsequent degeneration. Here, we report the mitogenome of Poicephalus gulielmi (the subfamily Psittacinae) with a unique duplication tRNATHR/pseudoND6/CR1/tRNAPRO/ND6/tRNAGLU/CR2. This region is different from all other identified regions and resembles mostly the arrangements in Amazona and Pionus from the subfamily Arinae. [ABSTRACT FROM AUTHOR]

Medium-sized neotropical parrots from Pionus genus are represented by at least eight species. However, their taxonomy should be revised because some external morphological characters together with genetic data recognize 19 taxa. At present, only two mitochondrial markers are available for most of these taxa and obtained phylogenies are not well resolved. Therefore, we sequenced Pionus chalcopterus chalcopterus mitogenome to gain more molecular data required for future studies of the taxonomical status and phylogenetic relationships between Pionus taxa. Performed phylogenetic analyses showed seven monophyletic clades including at least two sequences assigned to one species. However, not all subspecies sequences were monophyletic. [ABSTRACT FROM AUTHOR]

Recently resurrectedPsittacaragenus is one of the 19 recognized in parrot tribeArini. The status of taxa withinPsittacararemains controversial because some forms are treated as species or subspecies depending on authorities. Evolutionary history ofPsittacarais also unclear because related phylogenetic clades contain taxa from distant and non-overlapping regions. However, the basal placement ofPsittacara leucophthalmuswith wide South American distribution suggests that other taxa with restricted range could emerge by a local split of larger population. We sequencedP. leucophthalmusmitogenome to increase the set of sequences required to determine taxonomic level and phylogeny ofPsittacarataxa. [ABSTRACT FROM PUBLISHER]

Ariniwith 19 genera is the most diversified tribe of the neotropical parrots fromArinaesubfamily. So far, among this tribe, the genusAratingaappeared to be the most problematic for the taxonomists. The typical representative of this genus isAratinga solstitialis, whose complete mitochondrial genome were sequenced and compared with five other representatives ofArinimitogenomes. Despite the conservatism in their general organization, some changes in A + T% composition of individual genes, start/stop codon usage and intergenic regions accumulated during evolution. [ABSTRACT FROM PUBLISHER]

Six genera from Arini tribe form a morphologically diverse group named macaws, which differ from other Arini in the presence of bare facial area. Macaws are further distinguished by the bare face pattern, plumage colouration and body size. Six of the eight macaw species from Ara genus can be easily segregated into three pairs according to their colouration. An exception is Ara severus, which differs from others in their size and morphology. The lack of appropriate molecular markers precludes determination of its phylogenetic position. Therefore, the mitogenome of Ara severus presented in this report will be indispensable to refine these phylogenetic relationships. [ABSTRACT FROM AUTHOR]

Arini tribe with 19 genera is the most diversified tribe of neotropical parrots. Six of them are classified as macaws and nine as conures. The presence of bare facial area distinguishes macaws from conures and other members of this tribe. However, such morphological division seems to be disputable as the smallest macaw (monotypic Diopsittaca genus) turned out to be more closely related to three monotypic conures genera (Guaruba, Leptosittaca, Thectocercus) than to other macaws. We sequenced the complete mitochondrial genome of Guaruba guarouba to enrich the resource of molecular markers for examination of phylogenetic relationships between macaws and conures. [ABSTRACT FROM AUTHOR]

Six genera of the Arini tribe form morphologically diverse group termed as Macaws. The presence of bare facial area distinguishes them from other members of the tribe. Genera and species of Macaw group differ in pattern of this bare skin as well as in body size. The genus Ara contains eight extant species. Two of them are classified as medium-sized Macaws and other six species are classified as large Macaws. Based on morphological similarities and differences, large Macaw species can be segregated into three pairs according to their plumage coloration. So far, representative mitochondrial genomes were sequenced only for Ara glaucogularis (blue and yellow coloration), Ara macao (predominantly red/scarlet) and Ara militaris (predominantly green) species. Ara ararauna is the second of two Ara species with predominant blue and yellow plumage. Hitherto, close phylogenetic relation of these two species was shown using only ND2 genes or incomplete combined COI/Cytb/ND2 sequences. Therefore, Ara ararauna mitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships within Macaws group. [ABSTRACT FROM AUTHOR]

The presence of bare facial area distinguishes Macaws from other members of theArinitribe. Genera and species of the Macaw group differ in pattern of this bare skin as well as in body size. Individuals of the genera:Diopsittaca,Orthopsittaca,andPrimoliusare significantly smaller than the members of the genera:Anodorhynchus,Cyanopsitta,and the most species of the genusAra. The genusPrimoliuscontains three species:P. auricollis,P. couloni,andP. maracana, which are classified as medium-sized Macaws. So far, mitochondrial genome representative for the genus was sequenced only forPrimolius coulonispecies.Primolius maracanamitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships betweenPrimoliusspecies, as results of molecular researches seems to be inconsistent withPrimoliusspecies morphology. [ABSTRACT FROM PUBLISHER]

Androglossiniis one of four tribes recognized within a neotropical parrot subfamilyArinae. The tribe includes 10 genera of whichPionusis represented by eight species. However, its evolutionary diversification and relationship with otherAndroglossinimembers are still unclear. Depending on studied molecular markers,Pionusis closely related withAmazonagenus or two monotypic generaAlipiopsittaandGraydidascalusor the clade in whichAmazonagenus is sister toAlipiopsittaandGraydidascalus. Therefore, we sequencedPionus menstruus menstruusmitogenome to gain molecular data appropriate for future studies to resolve these discrepancies obtained in various phylogenetic analyses published so far. [ABSTRACT FROM PUBLISHER]

The Mitred Conure (Psittacara mitratus) is a species native to the forests and woodlands in the Andes in central Peru, south through west-central Bolivia, to northwestern Argentina. The genusPsittacarahave recently been distinguished on the basis of molecular revision of theAratingaspecies. In consequence, it became one of the nine genera, which form morphologically diverse group termed as Conures. Although, the number of species/subspecies belonging toPsittacararemains controversial, it is now believed that the genus is represented by 11 species. Taxonomic position of Mitred Conure was determined by molecular research and makes the species crucial for examination of evolutionary diversification of the genus. Therefore, we sequenced complete mitochondrial genome ofP. mitratusmitogenome to gain a source of comprehensive molecular data. It will be indispensable to refine the phylogenetic relationships within “Psittacaragroup” as well as within the tribe Arini. [ABSTRACT FROM AUTHOR]

According to some taxonomists the Red-throated Conure (Psittacara rubritorquis) is considered a subspecies of Green Conure (Psittacara holochlora). Some other classifications treatrubritorquisas a separate species based on relatively minor morphological differences between both species/subspecies. So far, taxonomic position ofP. rubritorquiswas determined by molecular researches using only ND2 gene sequence or incomplete combined mitochondrial ND2, COI and CYTB gene sequences. Obtained outcomes found thatP. rubritorquisshould be treated as a subspecies ofP. holochlora. However, the lack ofP. h. brewsteriiandP. h. strenuasamples as well as incompleteness of combined mitochondrial sequence do not exclude opposite scenario. Therefore, we sequencedP. rubritorquismitogenome to gain a source of molecular data appropriate for future examination of evolutionary diversification of theP. holochloragroup. [ABSTRACT FROM AUTHOR]