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The genus Macaca is widely distributed, occupies a variety of habitats, shows diverse phenotypic characteristics, and is one of the best-studied genera of nonhuman primates. Here, we reported five re-sequencing Macaca genomes, including one M. cyclopis, one M. fuscata, one M. thibetana, one M. silenus, and one M. sylvanus. Together with published genomes of other macaque species, we combined 20 genome sequences of 10 macaque species to investigate the gene introgression and genetic differences among the species. The network analysis of the SNV-fragment trees indicates a reticular phylogeny of macaque species. Combining the results from various analytical methods, we identified extensive ancient introgression events among macaque species. The multiple introgression signals between different species groups were also observed, such as between fascicularis group species and silenus group species. However, gene flow signals between fascicularis and sinica group were not as strong as those between fascicularis group and silenus group. On the other hand, the unidirect gene flow in M. arctoides probably occurred between the progenitor of M. arctoides and the common ancestor of fascicularis group. Our study also shows that the genetic backgrounds and genetic diversity of different macaques vary dramatically among species, even among populations of the same species. In conclusion, using whole genome sequences and multiple methods, we have studied the evolutionary history of the genus Macaca and provided evidence for extensive introgression among the species., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The Chinese forest musk deer (Moschus berezovskii; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered. To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes. Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies. Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD. FMD-specific missense mutations were found in two PSGs (MHC class II antigen DRA and ADA) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases. Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion. Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD. Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA). Three different types of short tandem repeats in the N. rhombifolia control region (CR) were observed. The homologous alignments of these tandem repeats with other six cockroach mitogenome CRs revealed a low similarity. Three conserved sequence blocks (CSB) were detected in both cockroach mitochondrial CRs. CSB1 was specific for blattinine mitogenomes and was highly conserved with 95% similarity, speculating that this block was a possible molecular synapomorphy for this subfamily. CSB3 located nearby downstream of CSB1 and has more variations within blattinine mitogenomes compared with CSB1. The CSB3 was capable of forming stable stem-loop structure with a small T-stretch in the loop portion. We assessed the influence of four datasets and two inference methods on topology within Orthopteroidea. All genes excluding the third codon positions of PCGs could generate more stable topology, and higher posterior probabilities than bootstrap values were presented at some branch nodes. The phylogenetic analysis with different datasets and analytical methods supported the monophyly of Dictyoptera and supported strongly the proposal that Isoptera should be classified as a family (Termitidae) of the Blattaria. Specifically, Shelfordella lateralis was inserted in the clade Periplaneta. Considering the K2P genetic distance, morphological characters, and the phylogenetic trees, we suggested that S. lateralis should be placed in the genus Periplaneta.

Wood mice of the genus Apodemus are the most common small rodents in fields and broad-leaf forests in the temperate zone. In this study, we determined the complete mitochondrial genome of Apodemus latronum. It was endemic species to China, which mainly inhabited at the high land of the eastern Tibetan Plateau. The complete mitochondrial genome sequences of A. latronum was estimated to be 16,288 bases. Its organization and order were similar to that of typical vertebrate and other rodents' mitochondrial genomes, which consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Most protein-coding genes used ATG as the initiation codon. However, ND1, ND2 and ND5 began with ATA, whereas ND3 initiated with ATT. The termination codon also showed some degree of variation, and three types of stop codons were observed. The mitogenome sequence of A. latronum could provide helpful data to study the phylogeny of Apodemus.

The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.

Phylogeographical studies that focus on the southeastern margin of the Tibetan Plateau are limited. The complex terrain and unique geological history make it a particularly unusual region of the Tibetan Plateau. We carried out a phylogeographical study of two rodent species Neodon irene and Apodemus latronum using the mitochondrial cytochrome b gene sequences. High genetic diversities and deep phylogenetic splits were detected in both rodents. Some haplotypes from one sampling region fell into different evolutionary clades, but most haplotypes from the same sampling regions were clustered together with each other. The results of isolation by distance analysis further substantiated that their genetic diversities were structured along geography. Thus, there were high levels of geographical structure for both rodents. Demographic analyses implied a relatively constant population size for all samples of N. irene and A. latronum in history. However, clade B of N. irene and clade 3 of A. latronum experienced population expansions at 105-32 and 156-47 Kya, respectively. Through comparison with previous studies, we suggest the high mitochondrial DNA diversities in them are probably not a species-specific feature, but a common pattern for small mammals in this unique area. Details of the historical demography of these rodents revealed in this study could provide new insights into how rodents and possibly other small mammals in this region responded to the geological and climatic events.

The sugarcane borer, Diatraea saccharalis (F.), is an economically important pest of several major crops in North and South America. There is great concern over potential resistance development to the valuable transgenic Bacillus thuringiensis corn. Cost-effective monitoring methods, especially regarding molecular markers that could detect early changes in resistance allele frequency in field populations of D. saccharalis, are needed. This article reports the complete mitochondrial genome sequence of D. saccharalis (GenBank: FJ240227). The mitochondrial genome sequence of D. saccharalis has the typical metazoan mitogenome structure including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes, with a total size of 15,490 bp. The A+T content of the full mitogenome is 80.1% and the significant A+T bias is at the control region (94.9%), as compared to the extremely low G content (0.6%). In all 13 protein coding genes, 9 start with the common Met initiator codon (ATA or ATG) and 3 use ATT (Ile), whereas CGA (Arg) is used as a start codon in COI. Eleven of the 13 protein coding genes use complete termination codon (TAA), whereas COI and COII use incomplete ones, which terminated with a single T-nucleotide abutting on tRNA. There are seven major noncoding spacers (628 bp), including six intergenic spacers and an A+T-rich region, which are scattered in the mitogenome. Several microsatellite-like elements were observed in these noncoding regions. The complete mitochondrial sequences of D. saccharalis reported in this study can provide useful data in analyzing divergence of lepidopteran insects and in developing DNA-based diagnoses and genetic makers.

Although the subfamily Zapodinae (Rodentia, Dipodidae) contains only five species, the phylogeny and taxonomy of these species are still being disputed. First, whether Eozapus and Napaeozapus should be treated as independent genera or subgenera of Zapus has been argued for a long period. Second, the subspecific genetic differentiation of Chinese jumping mouse (Eozapus setchuanus) has not been studied in detail, neither from morphological nor molecular aspects. In this study, the phylogenetic relationship among all the five species of Zapodinae was reconstructed using DNA sequence data from the mitochondrial cytochrome b gene and the nuclear interphotoreceptor retinoid binding protein gene. Bayesian inference, maximum parsimony and maximum likelihood analyses were conducted. The results showed that two major clades could be recognized within Zapodinae. Eozapus setchuanus, is the species endemic to China, strongly formed a monophyletic clade. In the other clade, genus Zapus received significant support in all analyses to be the sister group of the genus Napaeozapus. By comparing genetic distances among these three genera, we conclude that both Eozapus and Napaeozapus should be considered as valid genera rather than subgenera of Zapus. Furthermore, we observed that the two subspecies of E. setchuanus did not form reciprocally monophyletic groups, thus the traditional taxonomy which divided E. setchuanus into two subspecies based on only one morphological character was questionable.

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.

The evolutionary history of the stump-tailed macaque ( Macaca arctoides ) and its genetic relationship to other macaques is a subject of continuing controversy. Here, we have reported the first genome sequences of two stump-tailed macaques and one Assamese macaque ( M. assamensis ). Additionally, we have investigated the genetic diversity between macaque species and analyzed ancient hybridization events. Genome-wide analyses demonstrated that the stump-tailed macaque is more closely related to sinica species than to fascicularis/mulatta species. This topology contradicts the mitochondrial sequence-based phylogeny that places the stump-tailed macaque into the fascicularis/mulatta group. However, our results further show that stump-tailed macaques have genetic backgrounds distinct from sinica species, and present evidence of gene flows with rhesus macaques. We suggest that an ancient introgression occurred after stump-tailed macaques diverged from sinica species. The distinct gene flow between proto-arctoides and proto-mulatta resulted in the transfer of rhesus macaque-type mitochondria into proto-arctoides . The rhesus macaque-type mitochondria remained in populations because of genetic drift during the bottleneck. The PSMC results and morphological and geographic evidence are consistent with the mitochondria capture pattern in the stump-tailed macaque. The molecular clock estimates suggest that the mitochondrial transference into stump-tailed macaques occurred 0.4–1.4 million years ago. Furthermore, we detected extensive admixtures between different macaque species, indicating that gene flow has played an important role in the evolutionary history of the genus Macaca . [ABSTRACT FROM AUTHOR]

The lineage of the Bar-backed Partridge () was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation. [ABSTRACT FROM AUTHOR]

The buff-throated partridge, Tetraophasis szechenyii Madarasz, 1885, is a species endemic to west China. The complete mitochondrial genome of this species was sequenced. It was 16,706 base pairs (bp) in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The phylogenetic relationships of the buff-throated partridge and 19 other Phasianidae species were inferred by Bayesian inference and maximum likelihood analyses based on 12 protein-coding genes. With the exception of a few nodes, most internal branches were supported by a high Bayesian posterior probability (BPP = 1.0). The resulting trees clarified the phylogenetic position of T. szechenyii within Phasianidae. The genetic diversity and population structure of the Pamulin population of T. szechenyii were examined based on the mitochondrial DNA CR. Nucleotide sequence analysis defined 18 haplotypes in 24 individuals. Haplotype diversity (h) was 0.953 and nucleotide diversity (π) was 0.0044. The results revealed that the genetic diversity of this population was not particularly low. Combined with the field work conducted by our lab, we found that members of the Pamuling population are cooperative breeders and the population may contain individuals from neighbouring groups. Our work provided genetic background information for the conservation and management of this species. [ABSTRACT FROM AUTHOR]

The Gracile shrew mole ( Uropsilus gracilis) belongs to the family Talpidae, which distributes in southwestern China, extending to northern Myanmar. In this study, the complete mitochondrial genome of U. gracilis was sequenced. It was determined to be of 16,533 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of U. gracilis and other 12 insectivores were used for phylogenetic analysis. Phylogenetic trees were constructed by using Bayesian and maximum likelihood methods, which showed that U. gracilis was clustered together with U. soricipes, and Urotrichus should be prior to Galemys. [ABSTRACT FROM AUTHOR]

The Chinese scrub vole ( Neodon irene) belongs to the subfamily Arvicolinae, which is restricted to mountain areas at high altitudes (2800-4000). In this study, we sequenced the complete mitochondrial genome of N. irene. It was determined to be 16,367 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of N. irene and other 22 rodents were used for phylogenetic analysis. Bayesian inference (BI) and maximum likelihood (ML) were used. Both the BI and ML trees demonstrated that Microtus rossiaemeridionalis and Microtus kikuchii did not cluster together with each other. On the contrary, M. rossiaemeridionalis showed close relationship with N. irene. In the present study, only one sequence from Neodon and two sequences from Microtus were included in the phylogenetic analysis which should contribute to the unusual relationship. Therefore, in order to better understand the phylogenetic relationship within Rodentia, more rodents' complete mitochondrial genomes are required. [ABSTRACT FROM AUTHOR]

Two novel mitogenomes of Eozapus setchuanus ( KJ648495 ) and Sicista concolor ( KJ648496 ) were reported and their total lengths were 16,630 bp and 16,493 bp, respectively. Both mitogenomes which were analogous to other rodent mitogenomes, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Specifically, the ND2 gene of S. concolor has three amino acids lesser than that of two other Dipodidae species ( E. setchuanus and Jaculus jaculus ) due to a premature termination codon in the 3′ end. We detected a tandem repeat cluster of 221 bp and 274 bp in the control region of S. concolor and E. setchuanus , respectively. Along with phylogenetic relationship analysis, we speculated that the tandem repeats in control regions might be common in Dipodinae species. Our phylogenetic analysis using concatenated mitochondrial gene datasets suggested five suborder and 16 family monophyletic groups in 54 rodent taxa sampled and strongly supported a basal position of the squirrel-related clade (PP = 1; BP = 100). Dipodidae had a sister-group relationship with Muroidea, and Sicistinae was in the base of Dipodidae clade. The complete mitochondrial genomes showed high resolution in deep-level phylogenetic relationship reconstructions of Rodentia. [ABSTRACT FROM AUTHOR]