Complete Mitochondrial Genome and Phylogenetic Analysis of the Blue Whistling Thrush (Myophonus caeruleus).

The blue whistling thrush (Myophonus caeruleus) is a bird belonging to the order Passeriformes and family Muscicapidae. M. caeruleus is widely distributed in China, Pakistan, India, and Myanmar and is a resident bird in the southern part of the Yangtze River in China and summer migratory bird in the northern part of the Yangtze River. At present, there are some controversies about the classification of M. caeruleus. We use complete mitochondrial genomes to provide insights into the phylogenetic position of M. caeruleus and its relationships among Muscicapidae. The mitochondrial genome (GenBank: MN564936) is 16,815 bp long and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region (D-loop). The thirteen PCGs started with GTG and ATG and ended with five types of stop codons. The nucleotide composition of T was 23.71%, that of C was 31.45%, that of A was 30.06%, and that of G was 14.78%. The secondary structures of 22 tRNAs were predicted, all of which could form typical cloverleaf structures. There were 24 mismatches, mainly G-U mismatches. Through phylogenetic tree reconstruction, it was found that Saxicola, Monticola, Oenanthe, and Phoenicurus were clustered into one clade, together with the sister group of Myophonus.

Molecular identification and phylogenetic analysis of the mitogenome in endangered giant nuthatch Sitta magna (Passeriformes, Sittidae).

The Giant Nuthatch Sitta magna (family Sittidae) is a passerine bird, the quantification of the number of habitats and species on a global scale remains low. Most species are restricted to low elevations in southwest China, eastern Myanmar, and northern Thailand. To characterize the mitochondrial genome sequence of S. magna and its phylogenetic relationships with other members within the genus Sitta, the mitochondrial genome of S. magna was sequenced using the whole genome shotgun method. The sequencing results showed that the mitochondrial genome was 16,829 bp long and consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (D-loop). All tRNAs were predicted to form a typical clover secondary structure. Among the 13 PCGs, only the start codon in COI was ATC, the start codon by the remaining 12 PCGs was ATG, and the stop codons were TAG, TAA, AGG, AGA, and TA. Bayesian inference and maximum likelihood phylogenetic analysis of the sequences of 17 species generated consistent well-supported phylogenies. The family Polioptilidae and the family Troglodytidae were closely related, and the family Sittidae was confined to a single branch. The genus Sitta in the family Sittidae was mainly clustered into three branches. Our findings provide new mitochondrial genomic data that could be used for phylogenetic and taxonomic studies; our results also certificate into the phylogenetic relationships within the genus Sitta ((S. himalayensi+(S. nagaensis + S. europaea))+(S. villosa + S. yunnanensis))+(S. carolinensis + S. magna).

Trophic Niche Differentiation in Two Sympatric Nuthatch Species (Sitta yunnanensis and Sitta nagaensis).

Sympatric closely related species may experience interspecific trophic competition due to ecological similarity; they may isolate in terms of diet or habitat use as a strategy to avoid competition. The body tissues of consumers contain stable isotope signatures information that can be applied to infer their dietary information. In this study, δ13C and δ15N stable isotopes were analyzed to determine the dietary information and trophic niches of sympatric coexisting Sitta yunnanensis and Sitta nagaensis. The results showed that the food sources of S. yunnanensis and S. nagaensis were from six orders, including Orthoptera, and the cumulative contribution rate was 99.97%, with the two species eating similar diets but at different rates. The larger δ13C of S. yunnanensis indicates that it had a wider range of habitats for feeding, while the difference in δ15N values was not significant (p > 0.05), indicating that both species feed on similar nutrient levels. As determined by Bayesian ellipses, the isotopic niches of S. yunnanensis and S. nagaensis were differentiated; the isotopic niche width of S. yunnanensis is 2.69‱2, which was larger than that of S. nagaensis (0.73‱2), indicates that differentiation between the two species in diet or habitat use reduced competition. Trophic niche differentiation and differences in foraging proportions may be the principal resource allocation mechanisms behind S. yunnanensis and S. nagaensis coexistence.

Three cases of collared owlet depredation on the green-backed tit within nest boxes.

The main cause of the reproductive failure of cavity-nesting birds is nest predation, even though cavity nests protect from numerous predators. To study the breeding biology of the green-backed tit (Parus monticolus) and to promote the reproduction of some other avian cavity breeders, we placed 245 nest boxes in the Zixi Mountain, southwest China. We collected breeding data by regularly checking the artificial nest boxes, three cases of green-backed tits being predated by collared owlet (Glaucidium brodiei) were confirmed by the video recordings. Larger mammals, chipmunks, squirrels, sparrowhawks, jays, and snakes have been identified as common predators of cavity-nesting birds in high-latitude regions of the northern hemisphere. Limited research in tropical and subtropical regions, particularly in Asia, has demonstrated squirrels and snakes as common predators of cavity-nesting birds. A gap in avian predators to cavity-nesting birds exists in the current knowledge. Hence the three cases of collared owlet's depredation reveal a new danger to green-backed tits, broadening our knowledge of the dynamics of cavity-nesting birds. In all three cases, the artificial box's entrance hole was only 5 × 5 cm in size and has not been expanded or poked. These findings provided evidence that the collared owlet is the predator of nestlings and adult green-backed tit breeding in artificial boxes, which emphasized a reevaluation of predator-prey interactions. Therefore, for effective breeding of the green-backed tit, we suggest to choose a hole size of 3 × 3 cm that is appropriate for its body size.

Morphological diversity and altitudinal differentiation of Aethopyga species.

The morphological characteristics of birds are an important tool for studying their adaptation and evolution. The morphological evolution of a clade is not only constrained by the phylogenetic relationship, but also influenced by ecological factors and interspecific competition. Aethopyga is a group of small nectar-eating birds with obvious sexual dimorphism. They have slender and decurved beaks, which reflect their unique diet and foraging mode. Traditional and geometric morphometrics were combined to characterize the body morphology and beak shape of six species of Aethopyga distributed in China. We aim to assess the roles of phylogeny, altitude, and species interactions to morphological evolution. The main distinguishing characteristic among these six species were overall body size, the ratio of body weight, culmen and tarsal length to body length, tail length and wing length, and beak shape (slender/straight vs. thick/decurved). Although these dimensions cannot distinguish all species, they can show a clear distribution trend, and there is a significant Mahalanobis distance between each pair of species. There were no significant phylogenetic signals in morphological traits. The results of PGLS analysis show that altitude is significantly correlated with log-transformed tarsus length and beak-shaped PC1 (slender/straight vs thick/decurved dimensions) across the six species analyzed. Mantel test shows that the distance matrix of beak morphological characteristics showed a significant correlation with the altitudinal distance matrix. The results indicated no significant phylogenetic signal in the morphological characteristics of six species. In terms of beak shape, species with greater overlap in elevation distribution have more similar morphological characteristics, that is, less morphological differentiation.

First Description of the Breeding Biology of the Spectacled Fulvetta (Fulvetta ruficapilla sordidior) in Southwest China.

The Spectacled Fulvetta (Fulvetta ruficapilla sordidior) is an endemic bird species to the southwest mountains of China, distributing from 1250 to 2500 m in the widespread broadleaved evergreen forest and occasionally in secondary scrubs. The present study describes its breeding biology for the first time. Fieldwork was conducted in the springs of 2017 and 2018 on Humashan Mountain, a hill mainly covered by secondary forest located at the eastern marginal of Kunming, the capital of Yunnan Province in Southwest China. This bird was found to initiate egg-laying mainly in March, and most nestlings fledged in late April and May. There were 16 nests found in total, which were located mainly in the dense shrubs at a height of 0.99 ± 0.40 m (n = 15). Of the 11 active nests, clutch size averaged 2.73 ± 0.45 (n = 11). Focal observations were made on nests; the incubation lasted for 13.67 ± 0.47 days (n = 3) with a notably high nest attendance, i.e., eggs were incubated 84.23% of the observation time. Nestlings fledged at 13.00 ± 0.71 days (n = 4), and parents feeding frequency increased as the nestlings grew. Overall, the cumulative hatching and fledgling rates were 71.43% and 35.71%, resulting in a nesting success rate of 45.45%.

Nest-Site Features and Breeding Ecology of Chestnut-Vented Nuthatch Sitta nagaensis in Southwestern China.

The breeding ecology of birds is the cornerstone of bird life-history theory, and breeding success directly affects the survival and development of populations. We studied the breeding ecology of a secondary cavity-nesting bird, the chestnut-vented nuthatch Sitta nagaensis, in southwestern China from March to June in 2020, 2021, and 2022. In total, 16 nests in nest boxes and 19 nests in natural cavities were studied. The nesting habitat was mainly Pinus yunnanensis forest (68.4%), and the nest trees were mainly P. yunnanensis and pear Pyrus spp. Cavities made by woodpeckers and knot holes were used as nest sites, and the nuthatches plastered the hole entrance with mud. The nesting material was mainly pine bark. The clutch size was 3.47 ± 0.56 (range 2-4, n = 30), with an incubation period of 16.06 ± 0.91 days (range 15-19 days, n = 18). The nestling period was 20.88 ± 1.90 days (range 18-23 days, n = 23), and both parents fed the nestlings.

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)))).

Identification and phylogenetic analysis in Pterorhinuschinensis (Aves, Passeriformes, Leiothrichidae) based on complete mitogenome.

The Black-throated Laughingthrush (Pterorhinuschinensis) is a bird belonging to the order Passeriformes and the family Leiothrichidae, and is found in Cambodia, China, Laos, Myanmar, Thailand and Vietnam. Pterorhinuschinensis was once classified as belonging to the genus Garrulax. However, recent research has reclassified it in the genus Pterorhinus. In this study, we sequenced and characterized the complete mitogenome of P.chinensis. The complete mitochondrial genome of P.chinensis is 17,827 bp in length. It consists of 13 PCGs, 22 tRNAs, two rRNAs, and two control regions. All genes are coded on the H-strand, except for one PCG (nad6) and eight tRNAs. All PCGs are initiated with ATG and stopped by five types of stop codons. Our comparative analyses show irregular gene rearrangement between trnT and trnP genes with another similar control region emerging between trnE and trnF genes compared with the ancestral mitochondrial gene order, called "duplicate CR gene order". The phylogenetic position of P.chinensis and phylogenetic relationships among members of Leiothrichidae are assessed based on complete mitogenomes. Phylogenetic relationships based on Bayesian inference and maximum likelihood methods showed that Garrulax and (Pterorhinus + Ianthocincla) formed a clade. Leiothrix and Liocichla also formed a clade. Our study provides support for the transfer of P.chinensis from Garrulax to Pterorhinus. Our results provide mitochondrial genome data to further understand the mitochondrial genome characteristics and taxonomic status of Leiothrichidae.

The New Mitogenome of Erpornis zantholeuca (Aves: Passeriformes): Sequence, Structure, and Phylogenetic Analyses.

White-bellied Erpornis (Erpornis zantholeuca) is a group of birds in the order Passeriformes, but its taxonomic status remains controversial. To understand the phylogenetic position of E. zantholeuca and phylogenetic relations within this family, we sequenced the complete mitochondrial genome of E. zantholeuca, which was 16,902 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the whole genome was 30.10% A, 30.48% C, 15.14% G, and 24.28% T and showed an elevated AT content (54.38%). All genes were encoded on the H-strand, with the exceptions of 8 tRNAs (trnQ, trnA, trnN, trnC, trnY, trnS2(UCN), trnP, trnE) and 1 PCG (Mt-ND6). Most PCGs used standard ATN as start codons, and TAN as stop codons. All tRNAs were predicted to form the typical cloverleaf secondary structures. The gene order of E. zantholeuca was consistent with that of Gallus gallus, which was considered to be a plesiomorphic or typical avian gene order. Phylogenetic relationships based on bayesian inference and maximum likelihood methods showed that E. zantholeuca was well supported as the sister group of (Vireo altiloquus + Vireo olivaceus). In addition, Pteruthius melanotis was sister to the other members of Vireonidae.

Analysis of complete mitochondrial genome sequence of bar-tailed Treecreeper certhia himalayana (psittaciformes: Certhiidae).

Bar-tailed Treecreeper Certhia himalayana usually lives in coniferous or mixed broadleaf-conifer forests, often crawling along the trunk. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of C. himalayana. The whole genome of C. himalayana was 16,852 bp in length, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 25.1% for A, 29.2% for T, 14.5% for C, 31.2% for G, with a GC content of 45.7%. A phylogenetic tree strongly supported that C. himalayana closely related with Family Troglodytidae by highly probability.

The first complete mitochondrial genome of Blossom-headed Parakeet Psittacula roseata (Psittaciformes: Psittacidae).

Blossom-headed Parakeet Psittacula roseate is listed as Near Threatened on the IUCN Red List of Threatened Species because of its habitat loss, and declining population. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of P. roseata. The whole genome of P. roseata was 16,814 bp in length, and contained 14 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 31.88% for A, 22.00% for T, 32.88% for C, 13.23% for G, with a GC content of 46.11%. A phylogenetic tree strongly supported that genus Psittacula closely related with genus Eclectus by highly probability.

The complete mitochondrial genome of Plautia crossota (Hemiptera: Pentatomidae).

In this study, we elucidated the complete mitochondrial genome (mitogenome) of Plautia crossota. The circular mitogenome is 16,809 bp long, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The overall base composition is as follows: A, 41.6%; T, 32.75%; C, 14.84%; G, 10.81%; a slight A + T bias of 74.35%. Phylogenetic analysis of 20 species of Pentatomoidea revealed that Plautia crossota was closer to Nezara viridula.

Sequence and phylogenetic analysis of the mitochondrial genome for red-breasted parakeet Psittacula alexandri (Psittaciformes: Psittacidae).

In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of Psittacula alexandri. The whole genome of P. alexandri was 16,883 bp in length, and contained 14 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control regions. The overall base composition of the mitochondrial DNA was 30.87% for A, 22.36% for T, 32.82% for C, and 13.95% for G, with a GC content of 46.77%. A phylogenetic tree strongly supported that P. alexandri closely related with Eclectus roratus by highly probability.

Complete mitochondrial genome of yellow-rumped honeyguide Indicator xanthonotus (Piciformes: Indicatoridae).

In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of Indicator xanthonotus. The whole genome of I. xanthonotus was 17,603 bp in length and contained 14 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and two non-coding control regions. The overall base composition of the mitochondrial DNA was 31.09% for A, 27.34% for T, 28.96% for C, and 12.61% for G, with a GC content of 41.57%. A phylogenetic tree strongly supported that I. xanthonotus clustered with another Piciformes species by high probability.

The complete mitochondrial genome and phylogenetic analysis of White-bellied Heron Ardea insignis (Pelecaniformes：Ardeidae).

The White-bellied Heron Ardea insignis is Critically Endangered wading bird. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of A. insignis. The whole genome of A. insignis was 18,656 bp in length and contained 14 protein-coding genes, 23 transfer RNA genes, two ribosome RNA genes, and two non-coding control regions. The overall base composition of the mitochondrial DNA was 30.86% for A, 24.60% for T, 30.48% for C, and 14.05% for G, with a GC content of 44.54%. A phylogenetic tree confirmed that A. insignis belonged to genus Ardea, family Ardeidae, and was sister to A. purpurea. This information will be useful in the current understanding of the phylogeny and evolution of Pelecaniformes.

The complete mitochondrial genome sequence of Ptyas mucosus.

The complete mitochondrial genome sequence of the Ptyas mucosus was sequenced and reported for the first time using muscle tissue. The total length is 17 151 bp and sequence analysis showed its structure is in accordance with other snakes. The complete mitochondrial genome contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes (PCGs), 2 control regions and 1 putative origin of L-strand replication. The gene order and nucleotide composition of P. mucosus are very similar with E. bimaculata, E. anomala and E. schrenckii. A phylogenetic tree of mitochondrial genomes indicated P. mucosus had the most closely relationship with E. bimaculata, and formed a monophyletic group with E. bimaculata, E. anomala and E. schrenckii.

Complete mitochondrial genome of a Wild Amur Moose (Alces alces cameloides).

In this study, the complete mitochondrial genome (mt DNA) of Amur Moose (Alces alces cameloides) was sequenced, using muscle tissue obtained from a male Amur moose. The total length of the mitochondrial genome is 16,305 bp. The genome structure of Amur moose is similar to other moose and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes, and 1 control region.