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The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus , as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately. [ABSTRACT FROM AUTHOR]

Mitogenomes are valuable data sources for phylogeographic and evolutionary studies of relatively closely related organisms. Here we describe eight complete sequences of moose mitogenomes belonging to the three clades of the European lineage and compare them with those of the Asian lineage. Mitochondrial genomes of moose and other cervids were used to infer highly resolved phylogenetic relationships and estimate divergence times. The analyses clearly distinguished two mtDNA lineages of moose and supported the division of the European lineage into three clades: East, West, and Central. The divergence of the European and Asian mtDNA lineages occurred in the Middle Pleistocene (ca. 443 kya), which significantly exceeds the fossil records of modern Alces alces dated to 100-200 kya. It indicates that the evolutionary history of the moose is more complex and could encompass inheritance of the ancestral variation. Our estimates also showed rapid diversification of present-day clades of the European lineage, which coincided with the transition from the Penultimate Glacial Period (MIS 6) and the Eemian interglacial (MIS 5) approximately 100 kya. Despite the strong division of the nucleotide sequences, we detected no evidence for the divergence ofamino acid sequences between Clade Central and Clade East. The recent diversification of A. alces clades, incombinationwiththeirevidentreciprocal monophyly, could be a result of low effective population size over its evolutionary history, augmented by severe bottlenecks during the Last Glacial Period. Our results are in agreement with the presence of different glacial refugia recently proposed for three identified clades of the European lineage and suggested the relict character of the Scandinavian (from Clade West) and the Biebrza moose population in northeastern Poland (belonging to Clade Central). [ABSTRACT FROM AUTHOR]

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]

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]

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]

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]