The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses

Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini)

Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.

Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny

The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes-including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes-and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.

Characterization of the complete mitochondrial genome of Otus lettia: exploring the mitochondrial evolution and phylogeny of owls (Strigiformes)

Large-scale molecular phylogenetic studies of the avian order Strigiformes have been performed, and numerous mitochondrial genomes have been determined. However, their intergeneric relationships are still controversial, and few comprehensive comparative analyses of mitochondrial genomes have been conducted on Strigiformes. In this study, the mitochondrial genome of Otus lettia was determined and compared with other Strigiformes. The O. lettia mitochondrial genome was 16,951 bp in size. For Strigiformes, atp8 can be used as a suitable molecular marker for population genetic diversity, while cox1 is a candidate barcoding marker for species identification. All protein-coding genes may be under strong purifying selection pressure, and one extra cytosine insertion located in nad3 is common to all owls except Tyto longimembris, T. alba, and Athene noctua. Four different mitochondrial gene arrangement types were found among the Strigiformes mitogenomes, and their evolutionary relationship between each other can be perfectly explained by the tandem duplication and random loss model. The phylogenetic topologies using the mitochondrial genomes showed that target species O. lettia had a closer relationship with O. scops + O. sunia than O. bakkamoena, the genus Glaucidium was paraphyletic, and the Ninox clade was located at the basal position of Strigidae lineage. Our phylogenetic trees also supported the previous recommendations that Sceloglaux albifacies, Ciccaba nigrolineata, and Ketupa flavipes should be transferred to Ninox, Strix, and Bubo, respectively. These findings will be helpful in further unraveling the mitochondrial evolution and phylogeny of Strigiformes.

The complete mitochondrial genome of Gyps coprotheres (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors

Three species of Old World vultures on the Asian peninsula are slowly recovering from the lethal consequences of diclofenac. At present the reason for species sensitivity to diclofenac is unknown. Furthermore, it has since been demonstrated that other Old World vultures like the Cape (Gyps coprotheres; CGV) and griffon (G. fulvus) vultures are also susceptible to diclofenac toxicity. Oddly, the New World Turkey vulture (Cathartes aura) and pied crow (Corvus albus) are not susceptible to diclofenac toxicity. As a result of the latter, we postulate an evolutionary link to toxicity. As a first step in understanding the susceptibility to diclofenac toxicity, we use the CGV as a model species for phylogenetic evaluations, by comparing the relatedness of various raptor species known to be susceptible, non-susceptible and suspected by their relationship to the Cape vulture mitogenome. This was achieved by next generation sequencing and assembly. The Cape vulture mitogenome had a genome size of 16,908 bp. The mitogenome phylogenetic analysis indicated a close evolutionary relationship between Old World vultures and other members of the Accipitridae as indicated by bootstrap value of 100% on the phylogenetic trees. Based on this, we postulate that the other species could also be sensitive to the toxic effects of diclofenac. This warrants further investigations.

Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics

Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.

Biologia Futura: rapid diversification and behavioural adaptation of birds in response to Oligocene-Miocene climatic conditions

Our knowledge about the origin of landbirds (Telluraves) is increasing rapidly but new questions are arising because of the contradictory findings from previous studies. All of the major lineages in the highly diverse clade of Neoaves have a Gondwanan origin, although studies often disagree about the origin of different sub-lineages. Nevertheless, understanding the biogeographical histories of these groups (e.g. Accipitriformes, Passeriformes) is important when studying the evolution of variation in life history and behavioural traits. Therefore, we would like to find answers to questions such as which biogeographic changes affected the radiation of birds? When did the most influential climatic events affect the diversification of birds? What behavioural adaptations occurred in response to those large-scale changes? The major orogenetic events in Asia and South America formed specific corridors that enabled the radiation of birds. The climatic changes and habitat differentiation they caused during the Oligocene-Miocene era made the divergence of birds possible through their adaptation to newly available niches. Consequently, variation in life history and behavioural traits emerged as adaptive outcomes of changes in foraging, nestling and migratory behaviours.

Identification and comparative profiling of gonadal microRNAs in the adult pigeon (Columba livia)

1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.

Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics

Coturnix japonica (Japanese quail) has been extensively used as a model animal for biological studies. The Sox gene family, which was systematically characterized by a high-mobility group (HMG-box) in many animal species, encodes transcription factors that play central roles during multiple developmental processes. However, genome-wide investigations on the Sox gene family in birds are scarce. In the current study, we first performed a genome-wide study to explore the Sox gene family in galliform birds. Based on available genomic sequences retrieved from the NCBI database, we focused on the global identification of the Sox gene family in C. japonica and other species in Galliformes, and the evolutionary relationships of Sox genes. In our result, a total of 35 Sox genes in seven groups were identified in the C. japonica genome. Our results also revealed that dispersed gene duplications contributed the most to the expansion of the Sox gene family in Galliform birds. Evolutionary analyses indicated that Sox genes are an ancient gene family, and strong purifying selections played key roles in the evolution of CjSox genes of C. japonica. More interestingly, we observed that most Sox genes exhibited highly embryo-specific expression in both gonads. Our findings provided new insights into the molecular function and phylogeny of Sox gene family in birds.

Complete mitochondrial genome of Urocissa erythroryncha (Passeriformes: Corvidae)

The complete mitochondrial genome of Urocissa erythroryncha is 16930 bp in length. It was predicted to contain 13 PCGs, 22 tRNA genes, and 2 rRNA genes, and a putative control region. All of the PCGs initiated with ATG, except for MT-COX1 which began with GTG and MT-ND3 began with ATA, while stopped by three types of stop codons. Phylogenetic analysis showed that Urocissa erythroryncha and the other species of Corvidae were monophyletic group in this study. And the monophyly of the genus Pyrrhocorax was strongly supported. Moreover, our results also support a sister-group relationship between Corvidae and Muscicapidae.

Visual field shape and foraging ecology in diurnal raptors

Birds, particularly raptors, are believed to forage primarily using visual cues. However, raptor foraging tactics are highly diverse — from chasing mobile prey to scavenging — which may reflect adaptations of their visual systems. To investigate this, we studied the visual field configuration of 15 species of diurnal Accipitriformes that differ in such tactics, first focusing on the binocular field and blind area by using a single traits approach, and then exploring the shape of the binocular field with morphometric approaches. While the maximum binocular field width did not differ in species of different foraging tactics, the overall shape of their binocular fields did. In particular, raptors chasing terrestrial prey (ground predators) had a more protruding binocular field and a wider blind area above the head than did raptors chasing aerial or aquatic prey and obligate scavengers. Ground predators that forage on mammals from above have a wide but short bill — which increases ingestion rate — and large suborbital ridge to avoid sun glare. This may explain the protruding binocular field and the wide blind area above the head. By contrast, species from the two other groups have long but narrow bills used to pluck, flake or tear food and may need large visual coverage (and reduced suborbital ridges) to increase their foraging efficiency (e.g. using large visual coverage to follow the escaping prey in three dimensions or detect conspecifics). We propose that binocular field shape is associated with bill and suborbital ridge shape and, ultimately, foraging strategies.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

The complete mitochondrial genome of Anas crecca (Anseriformes: Anatidae)

The complete mitochondrial genome of Anas crecca is 16,596 bp in length. It was predicted to contain 13 PCGs, 22 tRNA genes, and 2 rRNA genes, and a putative control region. All of the PCGs initiate with ATG, except for MT-CO1, MT-CO2, and MT-ND5, which began with GTG. Four types of termination codons were identified. Phylogenetic analysis shows that A. crecca clustered with Anas acuta, and the monophyly of the genera Anser, Cygnus, Aythya, and Anas was strongly supported. Moreover, our results also support a sister-group relationship between Anas and Aythya.