Saxicola is a genus of insectivorous birds widely distributed across Eurasia and Africa. Their mitochondrial genomes (mitogenomes), classification, phylogeny, and biogeography are underresearched. Here, we sequenced and/or assembled the mitogenomes of S. stejnegeri, S. torquatus, S. maurus, S. rubicola hibernans, S. r. rubicola and S. dacotiae for detailed comparative analysis, integrating them with published mitogenomes of members of Muscicapidae for phylogenetic reconstruction. Additionally, we estimated the divergence times and ancestral ranges for Saxicola using ND2 and Cytb. These mitogenomes, spanning 16,764 bp to 16,804 bp, exhibit typical gene arrangement, AT bias, and A/C skew tendencies. Among the 13 protein-coding genes, ND3 evolved the fastest, whereas COX1 evolved the slowest. The 22 tRNAs form the classic cloverleaf structure except trnS1 (AGY). The control region has three domains with 10 conserved elements. Mitogenomic phylogenetic analysis revealed the topology: (((((S. r. hibernans + S. r. rubicola) + S. dacotiae) + S. maurus) + S. torquatus) + S. stejnegeri), supporting the independent species status of S. stejnegeri rather than a subspecies of S. maurus. Ancestral range reconstruction indicated that Saxicola originated in the Indian subcontinent and mainland Southeast Asia during the late Miocene. These findings enhance our understanding of the classification, evolution, and geographical origin of Saxicola.

The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.

Background: A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially in the sex chromosome chain. Therefore, the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex. Results: Here, we present a new long reads–based chromosome-level short-beaked echidna (Tachyglossus aculeatus) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between 1 Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes. Conclusion: The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.

Archipelagos and oceanic islands have remarkably high levels of endemism, which is associated with rapid speciation. The Malayan pangolin (Manis javanica), one of critically endangered Asia pangolin species, occurs in southern Yunnan, China, and on oceanic islands via the Malay peninsula. The question of whether the distribution of Malayan pangolins between the mainland and nearby marine islands has led to deep population differentiation is not well addressed. In-depth investigation of population structure and genetic consequences is of vital importance for protection and conservation of Malayan pangolins. Here we carried out a large-scale population genomic analysis for Malayan pangolins, which revealed three highly distinct genetic populations. The largest population was found to be distributed over a wide area extending from mainland China to almost the whole of South East Asia. The other two smaller populations reported in this study were inferred from Borneo. In addition, based on multiple lines of genomic and skull morphological evidences, we confirmed the existence of a fifth Asian pangolin species (M. mysteria). Genetic diversity and genome-wide inbreeding were at moderate levels, indicating that anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins. However, Malayan pangolins from northeastern Borneo exhibited low genetic diversity, high levels of inbreeding and mutational load, thereby necessitating attention to their protection.

Turdus atrogularis is a species with a controversial taxonomic status. In this study, the first complete mitochondrial genome of T. atrogularis was sequenced and characterized. The mitochondrial genome (mitogenome) is 16,757 bp in length, with a higher AT content than GC content. The mitogenome consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region, without gene rearrangements relative to the ancestral avian gene order. Phylogenetic analysis indicates a very close genetic relationship between T. atrogularis and T. ruficollis. These findings provide valuable genetic resources for understanding the classification, phylogeny, and ecological conservation of T. atrogularis.