Mitochondria and G-quadruplex evolution: an intertwined relationship

G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes.

Genetic Structure and Diversity of Two Populations of the Eastern Buzzard (Buteo japonicus japonicus and B. j. toyoshimai) in Japan

The nominotypical subspecies of the Eastern buzzard (Buteo japonicus japonicus; BJJ) is a common raptor inhabiting East Asia and Japan. Another subspecies, B. j. toyoshimai (BJT), inhabits only the Bonin Islands of the Ogasawara Islands, where there are only an estimated 85 breeding pairs. Because of this low population size, this subspecies is classified as endangered (class IB) in Japan. The aims of the present study were to examine genetic differences between BJJ and BJT, determine the genetic structure of the Eastern Buzzard, and assess genetic diversity within each subspecies. We sequenced 1526 bp within the control region of the mtDNA of 10 BJJ individuals during the breeding season in four sites; similarly, we sequenced 23 BJJ individuals during winter in three sites. We detected 24 haplotypes among the 33 individuals. In a similar analysis performed with 12 BJT individuals, three haplotypes were detected. The phylogenetic analysis showed that BJJ and BJT have diverged into distinct clades, supporting the genetic differentiation between the subspecies. Network and mismatch distribution analyses indicated that BJJ may have experienced population expansion. In addition, comparisons with other raptors revealed a high degree of genetic diversity in the BJJ population. In contrast, the genetic diversity of the BJT population is lower than that in other raptors. Our results indicated that it is necessary to protect BJT to prevent the reduction in its genetic diversity.

Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses

This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein-coding genes, 22 tRNA coding genes, two rRNA-coding genes, a control region (CR), and an extra pseudo-control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5' end of the domain I region, a long continuous poly-C sequence was found. Two tandem repeats were found in the pseudo-control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.

Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards

Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.

Complete mitochondrial genome of Himalayan buzzard (Buteo buteo burmanicus)

In this study, the complete sequence of the mitochondrial (mt) genome of Buteo buteo burmanicus was determined. This mitogenome was 18,231 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a control region (CR) and a pseudo-control region (ψCR). The overall base composition of the heavy strand was A, 30.8%; G, 13.2%; C, 31.8%; and T, 24.2%, with a slight AT bias of 65.1%. The complete mitogenomic data may provide more informative for phylogenetic approach for soft corals phylogeny especially for Buteo species.

Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae

In birds, the noncoding control region (CR) and its flanking genes are the only parts of the mitochondrial (mt) genome that have been modified by intragenomic rearrangements. In raptors, two noncoding regions are present: the CR has shifted to a new position with respect to the "ancestral avian gene order," whereas the pseudo-control region (PsiCR) is located at the original genomic position of the CR. As possible mechanisms for this rearrangement, duplication and transposition have been considered. During characterization of the mt gene order in Bonelli's eagle Hieraaetus fasciatus, we detected intragenomic sequence similarity between the two regions supporting the duplication hypothesis. We performed intra- and intergenomic sequence comparisons in H. fasciatus and other falconiform species to trace the evolution of the noncoding mtDNA regions in Falconiformes. We identified sections displaying different levels of similarity between the CR and PsiCR. On the basis of phylogenetic analyses, we outline an evolutionary scenario of the underlying mutation events involving duplication and homogenization processes followed by sporadic deletions. Apparently, homogenization may easily occur if sufficient sequence similarity between the CR and PsiCR exists. Moreover, homogenization itself allows perpetuation of this continued equalization, unless this process is stopped by deletion. The Pandionidae and the Aquilinae seem to be the only two lineages of Falconiformes where homology between both regionsis still detectable, whereas in other raptors no similarity was found so far. In these two lineages, the process of sequence degeneration may have slowed down by homogenization events retaining high sequence similarity at least in some sections.

Mitochondrial pseudo-control region in old world eagles (genus Aquila)

The mitochondrial pseudo-control region was analysed in five species of Aquila eagles. Indels caused great length differences in the nonrepetitive part of the region, whereas tandem repeat units were highly conserved among the genus. In a reconstructed phylogenetic tree, the clade formed by A. clanga and A. pomarina showed approximately the same distance to A. chrysaetos as did the clade A. heliaca/nipalensis. In Estonian subpopulations, 12 haplotypes were found among 51 A. pomarina individuals and 7 haplotypes among 8 A. clanga individuals. Nucleotide diversity in A. clanga was greater, and may be caused by decreased breeding density or by gene flow from other subpopulations.

Paraphyly of the Blue Tit (Parus caeruleus) suggested from cytochrome b sequences

The phylogenetic relationships of the Blue Tit-Azure Tit assemblage (genus Parus; Aves: Passeriformes) were studied using mitochondrial DNA sequences of 24 specimens representing seven subspecies from Eurasia and North Africa. Previous work based on comparative morphological and acoustic data suggested a division of the Blue Tit (Parus caeruleus) into two species. Our analyses clearly indicate that the Blue Tit represents a paraphyletic assemblage, including a European/Middle Asian clade that is the sister group to the Azure Tit (Parus cyanus) and a North African clade. The North African clade (teneriffae subspecies group) is a sister group to the European Blue Tit/Azure Tit clade. We suggest a division of the Blue Tit into two separate species, Eurasian Blue Tit (Parus caeruleus s. str.) and African Blue Tit (Parus teneriffae). However, our data give no support for assigning species rank to Parus cyanus flavipectus, a subspecies of the Azure Tit, as suggested by several authors on morphological grounds.

The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors

The complete sequence of the mitochondrial (mt) genome of Buteo buteo was determined. Its gene content and nucleotide composition are typical for avian genomes. Due to expanded noncoding sequences, Buteo possesses the longest mt genome sequenced so far (18,674 bp). The gene order comprising the control region and neighboring genes is identical to that of Falco peregrinus, suggesting that the corresponding rearrangement occurred before the falconid/accipitrid split. Phylogenetic analyses performed with the mt sequence of Buteo and nine other mt genomes suggest that for investigations at higher taxonomic levels (e.g., avian orders), concatenated rRNA and tRNA gene sequences are more informative than protein gene sequences with respect to resolution and bootstrap support. Phylogenetic analyses indicate an early split between Accipitridae and Falconidae, which, according to molecular dating of other avian divergence times, can be assumed to have taken place in the late Cretaceous 65-83 MYA.