Adam Dawid Urantowka

Complete mitochondrial genome of endangered Socorro Conure (Aratinga brevipes) – taxonomic position of the species and its relationship with Green Conure

Abstract Socorro Conure (Aratinga brevipes.Aratinga holochlora brevipes) is a parrot endemic to the Island of Socorro. According to some taxonomists the species is considered a subspecies of Green Conure (Aratinga holochlora). Some other classifications treat brevipes as a separate species based on relatively minor morphological differences between both species/subspecies. However, taxonomic position of Aratinga brevipes was never determined by molecular research. We sequenced full mitochondrial genome of the species and constructed phylogenetic tree using sequences of mitochondrial ND2 gene from A. brevipes and some other representatives of Conures group. Our results showed, that despite Aratinga brevipes is closely related to Aratinga holochlora, this Conure should be treated as a separate species.

Complete mitochondrial genome of Blue-crowned Parakeet (Aratinga acuticaudata)—phylogenetic position of the species among parrots group called Conures

Blue-crowned Parakeet (Aratinga acuticaudata) is a South American parrot species with a taxonomic position not confirmed by molecular studies. We sequenced full mitochondrial genome and constructed phylogenetic tree using sequences of mitochondrial ND2 gene from A. acuticaudata and some other representatives of Conures group. Our results confirmed previously described distribution of Aratinga species into three clades, but surprisingly did not classify Blue-crowned Parakeet to any of them. We found that A. acuticaudata shares the closest relationship with Diopsittaca nobilis and forms a separate clade together with Guaruba guarouba and Leptosittaca branickii species with a significant node. Our results confirm lack of monophyly of the genus Aratinga and underline the need of its taxonomic revision.

Complete mitochondrial genome of endangered Yellow-shouldered Amazon (Amazona barbadensis): two control region copies in parrot species of the Amazona genus.

Amazona barbadensis is an endangered species of parrot living in northern coastal Venezuela and in several Caribbean islands. In this study, we sequenced full mitochondrial genome of the considered species. The total length of the mitogenome was 18,983 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, duplicated control region, and degenerate copies of ND6 and tRNA Glu genes. High degree of identity between two copies of control region suggests their coincident evolution and functionality. Comparative analysis of both the control region sequences from four Amazona species revealed their 89.1% over a region of 1300 bp and indicates the presence of distinctive parts of two control region copies.

The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes

BackgroundConures 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.ResultsSingle 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.ConclusionsPhylogenetic 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.

Complete mitochondrial genome of Critically Endangered Blue-throated Macaw (Ara glaucogularis): its comparison with partial mitogenome of Scarlet Macaw (Ara macao)

Abstract Blue-throated Macaw (Ara glaucogularis) is Critically Endangered species of parrot endemic to small Bolivian area. In this study, full mitochondrial genome of considered species was sequenced. It is 16,983 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. It`s comparison with published Ara macao mitogenome revealed their high degree of identity. On the other hand, analysis of both the genome compositions showed incompleteness of Ara macao CYTB gene. Hence, mitogenome of Ara macao species occurred only partial sequence. In consequence, Ara glaucogularis mitogenome is the first complete Macaw sequence, which will be indispensable to refine the phylogenetic relationships within the tribe Arini and will enrich the resource of markers for systematic, phylogenetic and population genetic studies.

Complete mitochondrial genome of endangered Maroon-fronted Parrot (Rhynchopsitta terrisi) – conspecific relation of the species with Thick-billed Parrot (Rhynchopsitta pachyrhyncha)

Abstract Maroon-fronted Parrot (Rhynchopsitta terrisi) is an endangered parrot endemic to pine-oak forests in north-eastern Mexico. According to all present classifications, R. terrisi as well as Rhynchopsitta pachyrhyncha are treated as a separate species based on some morphological and behavioral discrepancies. Despite this formal separation of the two species, some taxonomists conjecture their conspecific character. However, mutual taxonomic position of both species/subspecies was never verified by molecular research. We sequenced full mitochondrial genome of R. terrisi and constructed phylogenetic tree using sequences of mitochondrial ND2 gene from R. terrisi. R. pahyrchyncha and some other representative species of the tribe Arini. Our results indicated that in contrast to formal classification, both Rhynchopsitta taxa should be treated as subspecies.

Phylogeny of Amazona barbadensis and the Yellow-Headed Amazon Complex (Aves: Psittacidae): A New Look at South American Parrot Evolution

The Yellow-shouldered Amazon (Amazona barbadensis) is the sole parrot of the genus Amazona that inhabits only dry forests. Its population has been dropping; therefore it has been the topic of many studies and conservation efforts. However, the phylogenetic relationship of this species to potential relatives classified within the Yellow-Headed Amazon (YHA) complex are still not clear. Therefore, we used more extensive data sets, including the newly sequenced mitochondrial genome of A. barbadensis, to conduct phylogenetic analyses. Various combinations of genes and many phylogenetic approaches showed that A. barbadensis clustered significantly with A. ochrocephala ochrocephala from Colombia and Venezuela, which created the Northern South American (NSA) lineage, clearly separated from two other lineages within the YHA complex, the Central (CA) and South American (SA). Tree topology tests and exclusion of rapidly evolving sites provided support for a NSA+SA grouping. We propose an evolutionary scenario for the YHA complex and its colonization of the American mainland. The NSA lineage likely represents the most ancestral lineage, which derived from Lesser Antillean Amazons and colonized the northern coast of Venezuela about a million years ago. Then, Central America was colonized through the Isthmus of Panama, which led to the emergence of the CA lineage. The southward expansion to South America and the origin of the SA lineage happened almost simultaneously. However, more intensive or prolonged gene flow or migrations have led to much weaker geographic differentiation of genetic markers in the SA than in the CA lineage.

The first complete mitochondrial genome of Pyrrhura sp. – question about conspecificity in the light of hybridization between Pyrrhura molinae and Pyrrhura rupicola species

Abstract The genus Pyrrhura contains at least 24 species widespread mainly through South America. Pyrrhura molinae (Green-cheeked Conure) and Pyrrhura rupicola (Black-capped Conure) are treated as separate species based on morphological differences. Geographical ranges of these two species overlap in southern Peru. However, it is not clear if they occur there sympatrically or it is a hybridization zone. Some taxonomists conjecture their conspecific character, as possible hybrid individuals have been found in Puno region. We sequenced mitochondrial genome of specimen with phenotype typical for P. molinae. To confirm its species belonging, we aligned CYTB and control region (CR) sequences with adequate sequences of 21 Pyrrhura species. Surprisingly, analyzed P. molinae individual grouped together with two different individuals of P. rupicola species. Such incompatibility of genetic data with morphology may be only the result of these two species hybridization.

The first complete mitochondrial genome sequence from the blue-headed parrot (Pionus menstruus menstruus): a representative for the genus

Abstract Androglossini is one of four tribes recognized within a neotropical parrot subfamily Arinae. The tribe includes 10 genera of which Pionus is represented by eight species. However, its evolutionary diversification and relationship with other Androglossini members are still unclear. Depending on studied molecular markers, Pionus is closely related with Amazona genus or two monotypic genera Alipiopsitta and Graydidascalus or the clade in which Amazona genus is sister to Alipiopsitta and Graydidascalus. Therefore, we sequenced Pionus menstruus menstruus mitogenome to gain molecular data appropriate for future studies to resolve these discrepancies obtained in various phylogenetic analyses published so far.

The complete mitochondrial genome of red-fronted parrot (Poicephalus gulielmi) revealed a new gene rearrangement within the order Psittaciformes

Abstract 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.