Complete mitochondrial genome of Cabot's tragopan, Tragopan caboti (Galliformes: Phasianidae)

Description of the Three Complete Mitochondrial Genomes of Sitta (S. himalayensis, S. nagaensis, and S. yunnanensis) and Phylogenetic Relationship (Aves: Sittidae)

Nuthatches (genus Sitta; family Sittidae) are a passerine genus with a predominantly Nearctic and Eurasian distribution. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced the complete mitochondrial genomes of three Sitta species (S. himalayensis, S. nagaensis, and S. yunnanensis), which were 16,822–16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister group of Troglodytidae, and the genus Sitta can be divided into three major clades. We demonstrated the phylogenetic relationships within the genus Sitta (S. carolinensis + ((S. villosa + S. yunnanensis) + (S. himalayensis + (S. europaea + S. nagaensis)))).

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.

Complete mitogenomic and phylogenetic characteristics of the speckled wood-pigeon (Columba hodgsonii)

The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.

Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.

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.

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.

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.

The complete mitochondrial genome of the yellow-browed bunting, Emberiza chrysophrys (Passeriformes: Emberizidae), and phylogenetic relationships within the genus Emberiza

Mitochondrial genomes have proved to be powerful tools in resolving phylogenetic relationships. Emberiza chrysophrys (least concern species: IUCN 2013) is a passerine bird in the bunting family, Emberizidae. The complete mitochondrial genome of E. chrysophrys was sequenced. This circular mitochondrial genome was 16,803 bp in length, with an A+T content of 52.26%, containing 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a putative control region (CR). The CR of E. chrysophrys was divided into three conserved domains. Six conserved sequence boxes in the central conserved domain II were identified as F, E, D, C, b and B. An obvious positive AT-skew and negative GC-skew bias were found for all 28 genes encoded by the H strand, whereas it was the reverse in the remaining nine genes encoded by the L strand. Remarkable rate heterogeneity was present in the mitochondrial genome of E. chrysophrys. Notably, unusual slow rate of evolution in the mitochondrial CR of E. chrysophrys was detected, which is rarely seen in other birds. Phylogenetic analyses were carried out based on 13 PCGs that showed E. pusilla was the sister group of E. rustica, and the monophyly of Emberiza was established.

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

The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide'C'is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes.

Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae

The structure of the mitochondrial DNA control region in the Relict Gull (Larus relictus) was predicted and compared with data from the National Center for Biotechnology Information (NCBI) on five other gulls. The results showed that the control regions of the six gulls comprise three domains. Sequences of CSB-1-like (domain I) and CSB-1 (domain III) in L. relictus have the highest similarity with those in the other five gulls. The insertion fragments are located in downstream domain I of L. ridibundus, L. brunnicephalus, and L. saundersi. Seven conserved sequence boxes (additional box, F-box, E-box, D-box, C-box, bird-similarity-box, and B-box) are located in domain II in all six gulls. It is suggested that the CSB-2/3 sequence, the origin of H-strand replication, and bidirectional light- and heavy-strand transcription promoters in domain III of L. relictus have some distinguishing features to those of other gulls. Some repeat units are contained in the 3' end of the control region in the five gulls; however, no repeat units are found in the sequence CAAACAACAAA in L. relictus. The distribution of nucleotide diversity analysis will provide the useful information on the selected DNA fragment within the control region for genetic analyses among gulls.

Lack of Structural Variation but Extensive Length Polymorphisms and Heteroplasmic Length Variations in the Mitochondrial DNA Control Region of Highly Inbred Crested Ibis, Nipponia nippon

The animal mitochondrial DNA (mtDNA) length polymorphism and heteroplasmy are accepted to be universal. Here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtDNA control region of an endangered avian species - the Crested Ibis (Nipponia nippon). The complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the PCR fragments from captive birds with pedigrees, wild birds and a historical specimen. Our results demonstrated that there was no structural variation in the control region, however, different numbers of short tandem repeats with an identical motif of CA3CA2CA3 at the 3'-end of the control region determined the length polymorphisms among and heteroplasmy within individual birds. There were one to three predominant fragments in every bird; nevertheless multiple minor fragments coexist in all birds. These extremely high polymorphisms were suggested to have derived from the 'replication slippage' of a perfect microsatellite evolution following the step-wise mutational model. The patterns of heteroplasmy were found to be shifted between generations and among siblings but rather stable between blood and feather samples. This study provides the first evidence of a very extensive mtDNA length polymorphism and heteroplasmy in the highly inbred Crested Ibis which carries an mtDNA genome lack of structural genetic diversity. The analysis of pedigreed samples also sheds light on the transmission of mtDNA length heteroplasmy in birds following the genetic bottleneck theory. Further research focusing on the generation and transmission of particular mtDNA heteroplasmy patterns in single germ line of Crested Ibis is encouraged by this study.

The mitochondrial genome of the Cinnamon Bittern, Ixobrychus cinnamomeus (Pelecaniformes: Ardeidae): sequence, structure and phylogenetic analysis

Ixobrychus cinnamomeus is a member of the large wading bird family, known as Ardeidae. In the present study, we determined the complete mitochondrial genome of I. cinnamomeus for use in future phylogenetic analysis. This circular mitochondrial genome is 17,180 bp in length and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one putative control region. Three conserved domains and a minisatellite of 17 nucleotides with 22 tandem repeats were detected at the end of the control region. Phylogenetic relationships were reconstructed using the nucleotide and corresponding amino acid datasets of 12 concatenated protein-coding genes from the mitochondrial genome. Using maximum likelihood, maximum parsimony and Bayesian inference methods, the monophyly of Ciconiidae, Ardeidae and Threskiornithidae were confirmed; however, the monophyly of traditional Ciconiiformes and Pelecaniformes failed to be recovered. Although further studies are recommended to clarify relationships among and within the orders of Ciconiiformes, Pelecaniformes, Suliformes and Phaethontiformes, our results provide preliminary exploratory results that can be useful in the current understanding of avian phylogenetics.

DNA barcodes of Philippine accipitrids

DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster (white-bellied sea eagle), Ichthyophaga ichthyaetus (grey-headed fish eagle), Spilornis holospilus (crested serpent-eagle), Spizaetus philippensis (Philippine hawk-eagle), and Pithecophaga jefferyi (Philippine eagle), are reported for the first time. All individuals sampled are kept at the Philippine Eagle Center in Davao City, Philippines. Basic local alignment search tool results demonstrated that the COI sequences for these species were unique. The COI gene trees constructed using the maximum-likelihood and neighbour-joining (NJ) methods supported the monophyly of the booted eagles of the Aquilinae and the sea eagles of the Haliaeetinae but not the kites of the Milvinae.