# Complete Mitochondrial Genome and Phylogenetic Analysis of Turdus pallidus (Passeriformes, Turdidae)

## TL;DR

This study sequenced the complete mitochondrial genome of Turdus pallidus, improving phylogenetic understanding of thrushes and highlighting the value of full mitogenomes in avian research.

## Contribution

The study provides the first complete mitochondrial genome of Turdus pallidus and enhances phylogenetic resolution within the genus Turdus.

## Key findings

- The complete mitochondrial genome of T. pallidus is 16,739 bp with typical gene content and structure.
- Phylogenetic analysis shows T. pallidus is most closely related to T. obscurus.
- Conserved genes like COX1 and CYTB are useful for deeper phylogenetic resolution, while ATP8 aids in closely related taxa.

## Abstract

Background: Thrushes (family Turdidae) are ecologically important passerine birds widely distributed across the Northern Hemisphere. However, the phylogenetic placement of several East Asian congeners, including Turdus pallidus, remains insufficiently resolved due to the limited resolution of partial mitochondrial or nuclear markers used in previous studies. Methods: In this work, we sequenced and annotated the complete mitochondrial genome of T. pallidus (16,739 bp) using high-throughput Illumina sequencing. The mitogenome exhibited the typical circular architecture and contained 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), with an overall GC content of 47.32%. Results: Most protein-coding genes initiated with the standard ATG codon, although lineage-specific deviations such as GTG in COX1 and ND2 were identified, and incomplete stop codons (T– or TA–) were observed, consistent with post-transcriptional polyadenylation. The 22 tRNA genes displayed typical cloverleaf secondary structures, except for trnS(AGN), which lacked a DHU arm, while rRNA genes were 977 bp (12S, 48.52% GC) and 1590 bp (16S, 44.65% GC), showing conserved stem regions but variable loop regions. Codon usage analysis revealed a strong bias toward A/T-ending codons, with a total of 3798 codons and an effective number of codons (ENC) of ~40, indicating moderate codon bias shaped by both mutational pressure and translational selection. Comparative analysis of evolutionary rates demonstrated that conserved genes such as COX1 and CYTB are suitable for resolving deeper relationships, whereas rapidly evolving genes like ATP8 provide resolution among closely related taxa. Conclusions: Phylogenetic reconstructions based on 13 mitochondrial protein-coding genes robustly supported the monophyly of Turdidae and recovered T. pallidus as most closely related to T. obscurus. Overall, this study provides a novel mitogenomic resource for T. pallidus, enhances phylogenetic resolution within Turdus, and underscores the value of complete mitochondrial genomes for molecular identification, conservation management, and avian evolutionary studies.