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

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.

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.