Mitochondrial Genomic Evidence of Selective Constraints in Small-Bodied Terrestrial Cetartiodactyla.

Body size may drive the molecular evolution of mitochondrial genes in response to changes in energy requirements across species of different sizes. In this study, we perform selection pressure analysis and phylogenetic independent contrasts (PIC) to investigate the association between molecular evolution of mitochondrial genome protein-coding genes (mtDNA PCGs) and body size in terrestrial Cetartiodactyla. Employing selection pressure analysis, we observe that the average non-synonymous/synonymous substitution rate ratio (ω) of mtDNA PCGs is significantly reduced in small-bodied species relative to their medium and large counterparts. PIC analysis further confirms that ω values are positively correlated with body size (R2 = 0.162, p = 0.0016). Our results suggest that mtDNA PCGs of small-bodied species experience much stronger purifying selection as they need to maintain a heightened metabolic rate. On the other hand, larger-bodied species may face less stringent selective pressures on their mtDNA PCGs, potentially due to reduced relative energy expenditure per unit mass. Furthermore, we identify several genes that undergo positive selection, possibly linked to species adaptation to specific environments. Therefore, despite purifying selection being the predominant force in the evolution of mtDNA PCGs, positive selection can also occur during the process of adaptive evolution.

An Efficient Improved Harris Hawks Optimizer and Its Application to Form Deviation-Zone Evaluation.

Evaluation of the deviation zone based on discrete measured points is crucial for quality control in manufacturing and metrology. However, deviation-zone evaluation is a highly nonlinear problem that is difficult to solve using traditional numerical optimization methods. Swarm intelligence has many advantages in solving this problem: it produces gradient-free, high-quality solutions and is characterized by its ease of implementation. Therefore, this study applies an improved Harris hawks algorithm (HHO) to tackle the problem. The average fitness is applied to replace the random operator in the exploration phase to solve the problem of conflicting exploration strategies due to randomness. In addition, the salp swarm algorithm (SSA) with a nonlinear inertia weight is embedded into the HHO, such that the superior explorative ability of SSA can fill the gap in the exploration of HHO. Finally, the optimal solution is greedily selected between SSA-based individuals and HHO-based individuals. The effectiveness of the proposed improved HHO optimizer is checked through a comparison with other swarm intelligence methods in typical benchmark problems. Moreover, the experimental results of form deviation-zone evaluation on primitive geometries show that the improved method can accurately solve various form deviations, providing an effective general solution for primitive geometries in the manufacturing and metrology fields.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila.

Aythya marila is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these Aythya species remains unclear due to the presence of extensive interspecific hybridization events within the Aythya genus. Here, we sequenced and annotated the complete mitochondrial genome of A. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for ND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were ATP8 and COI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in A. marila. FST analysis suggested a widespread gene exchange between A. baeri and A. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to A. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to A. fuligula. Overall, this study provides valuable information on the evolution of A. marila and new insights into the phylogeny of Anatidae.

A chromosome-level genome assembly of the yellow-throated marten (Martes flavigula).

The yellow-throated marten (Martes flavigula) is a medium-sized carnivore that is widely distributed across much of Asia and occupies an extensive variety of habitats. We reported a high-quality genome assembly of this organism that was generated using Oxford Nanopore and Hi-C technologies. The final genome sequences contained 215 contigs with a total size of 2,449.15 Mb and a contig N50 length of 68.60 Mb. Using Hi-C analysis, 2,419.20 Mb (98.78%) of the assembled sequences were anchored onto 21 linkage groups. Merqury evaluation suggested that the genome was 94.95% complete with a QV value of 43.75. Additionally, the genome was found to comprise approximately 39.74% repeat sequences, of which long interspersed elements (LINE) that accounted for 26.13% of the entire genome, were the most abundant. Of the 20,464 protein-coding genes, prediction and functional annotation was successfully performed for 20,322 (99.31%) genes. The high-quality, chromosome-level genome of the marten reported in this study will serve as a reference for future studies on genetic diversity, evolution, and conservation biology.

Chromosome-level genome assembly of the critically endangered Baer's pochard (Aythya baeri).

Baer's pochard (Aythya baeri) is a critically endangered species historically widespread throughout East Asia, whose population according to a recent estimate has decreased to between 150 and 700 individuals, and faces a long-term risk of extinction. However, the lack of a reference genome limits the study of conservation management and molecular biology of this species. We therefore report the first high-quality genome assembly of Baer's pochard. The genome has a total length of 1.14 Gb with a scaffold N50 of 85,749,954 bp and a contig N50 of 29,098,202 bp. We anchored 97.88% of the scaffold sequences onto 35 chromosomes based on the Hi-C data. BUSCO assessment indicated that 97.00% of the highly conserved Aves genes were completely present in the genome assembly. Furthermore, a total of 157.06 Mb of repetitive sequences were identified and 18,581 protein-coding genes were predicted in the genome, of which 99.00% were functionally annotated. This genome will be useful for understanding Baer's pochard genetic diversity and facilitate the conservation planning of this species.

Robust and Fast Normal Mollification via Consistent Neighborhood Reconstruction for Unorganized Point Clouds.

This paper introduces a robust normal estimation method for point cloud data that can handle both smooth and sharp features. Our method is based on the inclusion of neighborhood recognition into the normal mollification process in the neighborhood of the current point: First, the point cloud surfaces are assigned normals via a normal estimator of robust location (NERL), which guarantees the reliability of the smooth region normals, and then a robust feature point recognition method is proposed to identify points around sharp features accurately. Furthermore, Gaussian maps and clustering are adopted for feature points to seek a rough isotropic neighborhood for the first-stage normal mollification. In order to further deal with non-uniform sampling or various complex scenes efficiently, the second-stage normal mollification based on residual is proposed. The proposed method was experimentally validated on synthetic and real-world datasets and compared to state-of-the-art methods.

The Mechanisms of Fur Development and Color Formation in American Mink Revealed Using Comparative Transcriptomics.

American mink fur is an important economic product, but the molecular mechanisms underlying its color formation and fur development remain unclear. We used RNA-seq to analyze the skin transcriptomes of young and adult mink with two different hair colors. The mink comprised black adults (AB), white adults (AW), black juveniles (TB), and white juveniles (TW) (three each). Through pair comparison and cross-screening among different subgroups, we found that 13 KRTAP genes and five signaling pathways (the JAK-STAT signaling pathway (cfa04630), signaling pathways regulating pluripotency of stem cells (cfa04550), ECM-receptor interaction (cfa04512), focal adhesion (cfa04510), and the Ras signaling pathway (cfa04014)) were related to mink fur development. We also found that members of a tyrosinase family (TYR, TYRP1, and TYRP2) are involved in mink hair color formation. The expression levels of TYR were higher in young black mink than in young white mink, but this phenomenon was not observed in adult mink. Our study found significant differences in adult and juvenile mink skin transcriptomes, which may shed light on the mechanisms of mink fur development. At the same time, the skin transcriptomes of black and white mink also showed differences, with the results varying by age, suggesting that the genes regulating hair color are active in early development rather than in adulthood. The results of this study provide molecular support in breeding for mink coat color and improving fur quality.

Evolution of toll-like receptor gene family in amphibians.

The evolutionary position and lifestyle of amphibians highlights the important roles of the immune system in adaptive radiation and their adaptation to a complex pathogenic environment. Toll-like receptors (TLRs) are membrane-like sensors that recognize and bind conserved molecular motifs in pathogens to initiate downstream immune responses. To understand the evolutionary patterns of TLRs in amphibians, we analyzed TLR genes from the genomes and transcriptomes of 102 amphibian species. Phylogenetic results showed that 578 intact amphibian TLR sequences belonged to 16 TLR genes and were divided into seven subfamilies. The TLR4 subfamily was only identified in the Anura. Purification selection plays a leading role in amphibian TLR evolution and mean ω (dN/dS) values ranged from 0.252 for TLR7 to 0.381 for TLR19. Furthermore, the ω values of different domains were significantly different. We found positive selection patterns for 141 of 12,690 codons (1.1%) in all amphibian TLRs, most of which were located in leucine-rich repeats (LRRs). We also observed low to moderate levels of single-nucleotide polymorphisms (SNPs) in Pelophylax nigromaculatus and Bombina orientalis. This study provided critical primers, meaningful information regarding TLR gene family evolution in amphibians, and insights into the complex evolutionary patterns and implications of TLR polymorphisms.

A Method Based on Curvature and Hierarchical Strategy for Dynamic Point Cloud Compression in Augmented and Virtual Reality System.

As a kind of information-intensive 3D representation, point cloud rapidly develops in immersive applications, which has also sparked new attention in point cloud compression. The most popular dynamic methods ignore the characteristics of point clouds and use an exhaustive neighborhood search, which seriously impacts the encoder's runtime. Therefore, we propose an improved compression means for dynamic point cloud based on curvature estimation and hierarchical strategy to meet the demands in real-world scenarios. This method includes initial segmentation derived from the similarity between normals, curvature-based hierarchical refining process for iterating, and image generation and video compression technology based on de-redundancy without performance loss. The curvature-based hierarchical refining module divides the voxel point cloud into high-curvature points and low-curvature points and optimizes the initial clusters hierarchically. The experimental results show that our method achieved improved compression performance and faster runtime than traditional video-based dynamic point cloud compression.

Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes.

The silver fox and blue fox are economically important fur species and were domesticated by humans from their wild counterparts, the arctic fox and red fox, respectively. Farmed foxes show obvious differences from their wild counterparts, including differences in physiology, body size, energy metabolism, and immunity. However, the molecular mechanisms underlying these differences are presently unclear. In this study, we built transcriptome libraries from multiple pooled tissues for each species of farmed fox, used RNA-seq to obtain a comprehensive dataset, and performed selection analysis and sequence-level analyses of orthologous genes to identify the genes that may be influenced by human domestication. More than 153.3, 248.0, 81.6, and 65.8 million clean reads were obtained and assembled into a total of 118,577, 401,520, 79,900, and 186,988 unigenes with an average length range from 521 to 667 bp for AF, BF, RF, and SF, respectively. Selective pressure analysis showed that 11 and 14 positively selected genes were identified, respectively, in the two groups (AF vs. BF and RF vs. SF). Several of these genes were associated with natural immunity (CFI and LRRFIP1), protein synthesis (GOLGA4, CEP19 and SLC35A2), and DNA damage repair (MDC1). Further functional enrichment analyses demonstrated that two positively selected genes (ACO1 and ACAD10) were involved in metabolic process (GO:0008152, p-value = .032), representing a significant enrichment. Sequence analysis of 117 orthologous genes shared by the two groups showed that the LEMD2, RRBP1, and IGBP1 genes might be affected by artificial selection in farmed foxes, with mutation sites located within sequences that are otherwise highly conserved across most mammals. Our results provide a valuable transcriptomic resource for future genetic studies and improvement in the assisted breeding of foxes and other farmed animals.

Efficient point cloud segmentation approach using energy optimization with geometric features for 3D scene understanding.

Efficient and quick extraction of unknown objects in cluttered 3D scenes plays a significant role in robotics tasks such as object search, grasping, and manipulation. This paper describes a geometric-based unsupervised approach for the segmentation of cluttered scenes into objects. The proposed method first over-segments the raw point clouds into supervoxels to provide a more natural representation of 3D point clouds and reduce the computational cost with a minimal loss of geometric information. Then the fully connected local area linkage graph is used to distinguish between planar and nonplanar adjacent patches. Then the initial segmentation is completed utilizing the geometric features and local surface convexities. After the initial segmentation, many subgraphs are generated, each of which represents an individual object or part of it. Finally, we use the plane extracted from the scene to refine the initial segmentation result under the framework of global energy optimization. Experiments on the Object Cluttered Indoor Dataset dataset indicate that the proposed method can outperform the representative segmentation algorithms in terms of weighted overlap and accuracy, while our method has good robustness and real-time performance.

First Draft Genome of the Sable, Martes zibellina.

Members of genus Martes provide early warning signals about forest ecosystem health and are designated as a Management Indicator Species. As one of the most widespread members in Martes, the sable (Martes zibellina) is a circumboreal small predator found throughout all taiga zoogeographical zones of Eurasia and shows distinct population differentiation and morphological variations. To support further studies on striking local adaptation and population evolution, we present the first sable genome, assembled de novo from an individual originating in the Great Khingan Mountains (China). The assembled genome is 2.42 Gb, consisting of 15,814 scaffolds with a scaffold N50 of 5.20 Mb. Searches for complete Mammalia BUSCO (Benchmarking Universal Single-Copy Ortholog) gene groups found that 95.15% of the curated single-copy orthologs were assembled as complete, suggesting a high level of completeness of the genome. We totally predicted 19,413 protein-coding genes, and 0.82 Gb of repeat sequences was annotated. We also detected 1,257 olfactory receptor genes and found more functional olfactory receptor genes in sable than in other Mustelidae species, which provide a possible genetic explanation for the acute sense of smell of the sable for searching the preys under deep snow. Phylogenetic analyses revealed that the ferret (Mustela putorius furo) and sea otter (Enhydra lutris) form a clade that is sister to the sable, which was dated ∼16.4 Ma. Overall, our study provided the first reference genome for research in a broad range of areas including local adaptations, population evolution, conservation, and management for sable.

Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates.

Adaptation to a wide range of pathogenic environments is a major aspect of the ecological adaptations of vertebrates during evolution. Toll-like receptors (TLRs) are ancient membrane-bound sensors in animals and are best known for their roles in detecting and defense against invading pathogenic microorganisms. To understand the evolutionary history of the vertebrate TLR gene family, we first traced the origin of single-cysteine cluster TLRs that share the same protein architecture with vertebrate TLRs in early-branching animals and then analyzed all members of the TLR family in over 200 species covering all major vertebrate clades. Our results indicate that although the emergence of single-cysteine cluster TLRs predates the separation of bilaterians and cnidarians, most vertebrate TLR members originated shortly after vertebrate emergence. Phylogenetic analyses divided 1,726 vertebrate TLRs into 8 subfamilies, and TLR3 may represent the most ancient subfamily that emerged before the branching of deuterostomes. Our analysis reveals that purifying selection predominated in the evolution of all vertebrate TLRs, with mean dN/dS (ω) values ranging from 0.082 for TLR21 in birds to 0.434 for TLR11 in mammals. However, we did observe patterns of positive selection acting on specific codons (527 of 60,294 codons across all vertebrate TLRs, 8.7‰), which are significantly concentrated in ligand-binding extracellular domains and suggest host-pathogen coevolutionary interactions. Additionally, we found stronger positive selection acting on nonviral compared with viral TLRs, indicating the more essential nonredundant function of viral TLRs in host immunity. Taken together, our findings provide comprehensive insight into the complex evolutionary processes of the vertebrate TLR gene family, involving gene duplication, pseudogenization, purification, and positive selection.

Comparative Analyses of Fecal Microbiota in European Mouflon (Ovis orientalis musimon) and Blue Sheep (Pseudois nayaur) Living at Low or High Altitudes.

The gut microbiota is a complex and essential system organ that plays an integrative role in balancing key vital functions in the host. Knowledge of the impact of altitude on the gut microbiota of European mouflon (Ovis orientalis musimon) and blue sheep (Pseudois nayaur) is currently limited. In this study, we compared the characteristics of gut microbiota in 5 mouflon at low altitude (K group), 4 mouflon at high altitude (L group), 4 blue sheep at low altitude (M group), and 4 blue sheep at high altitude (N group). The V3-V4 region of the 16S rRNA gene was analyzed using high-throughput sequencing. Analyses based on the operational taxonomic units showed significant changes in the gut microbial communities between groups at different altitudes. At the phylum level, groups at the high altitudes had a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidetes than those at the low altitudes. A higher Firmicutes:Bacteroidetes ratio is beneficial to animals in terms of the gut microbiota-mediated energy harvest. The relative abundance of Proteobacteria was significantly higher in the gut microbiota of mouflon sheep at high altitudes. At the genus level, the Bacteroides:Prevotella ratio was significantly higher in the low-altitude group (than the high-altitude group) of mouflon sheep and the ratio was significantly higher in the high-altitude group (than the low-altitude group) in blue sheep. In addition, the Ruminococcaceae_UCG-005 related to cellulose and starch digestion was the predominant genus in blue sheep and the relative abundance of the genus was significant higher in the high-altitude group than the low-altitude group of blue sheep (P < 0.01). In conclusion, our results suggested that the gut microbiota of high-altitude groups of sheep had stronger abilities related to energy metabolism and the decomposition of substances, e.g., fiber and cellulose, and that such abilities are associated with high-altitude adaptation.

Adaptive evolution of the ACSL gene family in Carnivora.

Carnivores exhibit various fat contents and energy reserves to adapt to their environments. However, the molecular mechanisms underlying lipid metabolic differences among carnivores have not been well explored. Long-chain acyl-CoA synthetases (ACSLs) catalyze the initial step in lipid metabolism by activating fatty acids (FAs), and they drive acyl-CoAs toward anabolic lipid synthesis or catabolic ß-oxidation. We identified the sequences of the genes of the ACSL family (ACSL1, ACSL3, ACSL4, ACSL5 and ACSL6) in the sable (Martes zibellina) via transcriptome sequencing. The ACSL gene sequences of 13 other carnivores were obtained from NCBI. Phylogenetic results showed that unlike the widely accepted carnivore phylogeny, Canidae and Felidae tend to group together based on ACSL4 and ACSL6. The evolutionary analyses identified a series of positively selected amino acid residues in ACSL1, ACSL4 and ACSL5. Two radical amino acid substitutions detected in sable suggested potential insights into the molecular mechanism underlying the relatively low fat content in this animal. This is the first study to investigate the molecular mechanisms underlying the adaptive evolution of fat metabolism in carnivores. Overall, the ACSL genes were under different evolutionary forces in carnivores, and some genes have undergone adaptive evolution in lipid metabolism.

Changes in feeding habits promoted the differentiation of the composition and function of gut microbiotas between domestic dogs (Canis lupus familiaris) and gray wolves (Canis lupus).

Wolves (Canis lupus) and their domesticated and close relatives, dogs (Canis lupus familiaris), have great differences in their diets and living environments. To the best of our knowledge, the fundamental question of how the abundance and function of the gut microbiota of domestic dogs evolved to adapt to the changes in host feeding habits has yet to be addressed. In this study, our comparative analyses of gut metagenomes showed that the abundance of gut microbiota between the two species have some significant differences. Furthermore, a number of taxa observed in higher numbers in domestic dogs are related to carbohydrate metabolism, which may be because that there were more complicated polysaccharides in dogs diets than that in wolves diets. A significant difference in the abundance of genes encoding glycosyltransferase family 34 (GT34), carbohydrate-binding module family 25 (CBM25), and glycoside hydrolase family 13 (GH13) between the gut microbiota metagenomes of domestic dogs and gray wolves also supported this observation. Furthermore, the domestic dog gut microbiota has greater valine, leucine and isoleucine biosynthesis and nitrogen metabolism. This result showed that compared with wolves, the domestic dog diet contains a smaller amount of animal protein, which is consistent with the dietary composition of wolves and dogs. Our results indicate that the function and abundance of gut microbiota of domestic dogs has been adapted to domestication, which is of great significance for the ability of domestic dogs to adapt to changes in food composition.

Characterization of the peripheral blood transcriptome and adaptive evolution of the MHC I and TLR gene families in the wolf (Canis lupus).

BACKGROUND: The wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, because it is well adapted to various ecological niches and their corresponding pathogen environments. Immunological competence is a crucial factor involved in adapting to a changing environment and fighting pathogen infection in animals. In this study, the peripheral blood transcriptome of wolves was generated via RNA-seq to advance understanding of the wolf immunome, with a special focus on the major histocompatibility complex class I (MHC I) and toll-like receptor (TLR) gene families, which are involved in pathogen recognition and defense. RESULTS: The blood transcriptomic libraries of eight wolves originating from Tibet and Inner Mongolia were sequenced, and approximately 383 million reads were generated. Using a genome-guided assembly strategy, we obtained 123,851 unigenes, with a mean length of 845 bp and an N50 length of 1121 bp. On the basis of BLAST searches against the NCBI non-redundant protein database (Nr), a total of 36,192 (29.22%) unigenes were annotated. For functional classification, 24,663 unigenes were assigned to 13,016 Gene Ontology (GO) terms belonging to 51 sub-categories of the three main GO categories. Additionally, 7682 unigenes were classified into 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, in which the most represented functional sub-categories were signal transduction and the immune system, and 16,238 unigenes were functionally classified into 25 Eukaryotic Orthologous Groups (KOG) categories. We observed an overall higher ω (d N/d S) value at antigen-binding sites (ABSs) than at non-ABS regions as well as clear evidence of intergenic/intragenic recombination events at wolf MHC I loci. Additionally, our analysis revealed that carnivorous TLRs were dominated by purifying selection, with mean ω values at each TLR locus ranging from 0.173 to 0.527. However, we also found significant instances of positive selection that acted on several codons in pathogen recognition domains and were linked to species-specific differences in pathogen recognition. CONCLUSIONS: This study represents the first attempt to characterize the blood transcriptome of the wolf and to highlight the value of investigating the immune system. Balancing selection and recombination have contributed to the historical evolution of wolf MHC I genes. Moreover, TLRs in carnivores have undergone adaptive evolution against the background of purifying selection, and a high level of adaptive evolution was detected in the wolf TLR system.

The repertoire of bitter taste receptor genes in canids.

Bitter taste receptors (Tas2rs) play important roles in mammalian defense mechanisms by helping animals detect and avoid toxins in food. Although Tas2r genes have been widely studied in several mammals, minimal research has been performed in canids. To analyze the genetic basis of Tas2r genes in canids, we first identified Tas2r genes in the wolf, maned wolf, red fox, corsac fox, Tibetan fox, fennec fox, dhole and African hunting dog. A total of 183 Tas2r genes, consisting of 118 intact genes, 6 partial genes and 59 pseudogenes, were detected. Differences in the pseudogenes were observed among nine canid species. For example, Tas2r4 was a pseudogene in the dog but might play a functional role in other canid species. The Tas2r42 and Tas2r10 genes were pseudogenes in the maned wolf and dhole, respectively, and the Tas2r5 and Tas2r34 genes were pseudogenes in the African hunting dog; however, these genes were intact genes in other canid species. The differences in Tas2r pseudogenes among canids might suggest that the loss of intact Tas2r genes in canid species is species-dependent. We further compared the 183 Tas2r genes identified in this study with Tas2r genes from ten additional carnivorous species to evaluate the potential influence of diet on the evolution of the Tas2r gene repertoire. Phylogenetic analysis revealed that most of the Tas2r genes from the 18 species intermingled across the tree, suggesting that Tas2r genes are conserved among carnivores. Within canids, we found that some Tas2r genes corresponded to the traditional taxonomic groupings, while some did not. PIC analysis showed that the number of Tas2r genes in carnivores exhibited no positive correlation with diet composition, which might be due to the limited number of carnivores included in our study.

The complete mitochondrial genome of the Tibetan fox (Vulpes ferrilata) and implications for the phylogeny of Canidae.

Canidae is a family of carnivores comprises about 36 extant species that have been defined as three distinct monophyletic groups based on multi-gene data sets. The Tibetan fox (Vulpes ferrilata) is a member of the family Canidae that is endemic to the Tibetan Plateau and has seldom been in the focus of phylogenetic analyses. To clarify the phylogenic relationship of V. ferrilata between other canids, we sequenced the mitochondrial genome and firstly attempted to clarify the relative phylogenetic position of V. ferrilata in canids using the complete mitochondrial genome data. The mitochondrial genome of the Tibetan fox was 16,667 bp, including 37 genes (13 protein-coding genes, 2 rRNA, and 22 tRNA) and a control region. A comparison analysis among the sequenced data of canids indicated that they shared a similar arrangement, codon usage, and other aspects. A phylogenetic analysis on the basis of the nearly complete mtDNA genomes of canids agreed with three monophyletic clades, and the Tibetan fox was highly supported as a sister group of the corsac fox within Vulpes. The estimation of the divergence time suggested a recent split between the Tibetan fox and the corsac fox and rapid evolution in canids. There was no genetic evidence for positive selection related to high-altitude adaption for the Tibetan fox in mtDNA and following studies should pay more attention to the detection of positive signals in nuclear genes involved in energy and oxygen metabolisms.