Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae).

To enrich the mitogenomic database of Gerbillinae (Rodentia: Muridae), mitogenomes of three gerbils from different genera, Meriones tamariscinus (16,393 bp), Brachiones przewalskii (16,357 bp), and Rhombomys opimus (16,352 bp), were elaborated and compared with those of other gerbils in the present study. The three gerbil mitogenomes consisted of 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region. Here, gerbil mitogenomes have shown unique characteristics in terms of base composition, codon usage, non-coding region, and the replication origin of the light strand. There was no significant correlation between the nucleotide percentage of G + C and the phylogenetic status in gerbils, and between the GC content of PCGs and the leucine count. Phylogenetic relationships of the subfamily Gerbillinae were reconstructed by 7 gerbils that represented four genera based on concatenated mitochondrial DNA data using both Bayesian Inference and Maximum Likelihood. The phylogenetic analysis indicated that M. tamariscinus was phylogenetically distant from the genus Meriones, but has a close relationship with R. opimus. B. przewalskii was closely related to the genus Meriones rather than that of R. opimus.

A Data-Efficient Framework for the Identification of Vaginitis Based on Deep Learning.

Vaginitis is a gynecological disease affecting the health of millions of women all over the world. The traditional diagnosis of vaginitis is based on manual microscopy, which is time-consuming and tedious. The deep learning method offers a fast and reliable solution for an automatic early diagnosis of vaginitis. However, deep neural networks require massive well-annotated data. Manual annotation of microscopic images is highly cost extensive because it not only is a time-consuming process but also needs highly trained people (doctors, pathologists, or technicians). Most existing active learning approaches are not applicable in microscopic images due to the nature of complex backgrounds and numerous formed elements. To address the problem of high cost of labeling microscopic images, we present a data-efficient framework for the identification of vaginitis based on transfer learning and active learning strategies. The proposed informative sample selection strategy selected the minimal training subset, and then the pretrained convolutional neural network (CNN) was fine-tuned on the selected subset. The experiment results show that the proposed pipeline can save 37.5% annotation cost while maintaining competitive performance. The proposed promising novel framework can significantly save the annotation cost and has the potential of extending widely to other microscopic imaging applications, such as blood microscopic image analysis.

The uplift of the Qinghai-Tibet Plateau and glacial oscillations triggered the diversification of Tetraogallus (Galliformes, Phasianidae).

The Qinghai-Tibet Plateau (QTP) plays an important role in avian diversification. To reveal the relationship between the QTP uplift and avian diversification since the Late Cenozoic, here, we analyzed the phylogenetic relationship and biogeographical pattern of the genus Tetraogallus (Galliformes, Phasianidae) and the probable factors of speciation in the period of the QTP uplift inferred from concatenated data of four nuclear and five mitochondrial genes using the method of the Bayesian inference. Phylogenetic analysis indicated that T. himalayensis had a close relationship with T. altaicus and conflicted with the previous taxonomy of dark-bellied and white-bellied groups. The molecular clock showed that the speciation of Tetraogallus was profoundly affected by the uplift of the QTP and glacial oscillations. Biogeographic analysis suggested that the extant snowcocks originated from the QTP, and the QTP uplift and glacial oscillations triggered the diversification of Tetraogallus ancestor. Specifically, the uplift of the mountain provided a prerequisite for the colonization of snowcocks Tetraogallus as a result of the collision between the Indian and the Arab plates and the Eurasian plate, in which ecological isolation (the glacial and interglacial periods alternate) and geographical barrier had accelerated the Tetraogallus diversification process. Interestingly, we discovered hybrids between T. tibetanus and T. himalayensis for the first time and suggested that T. tibetanus and T. himalayensis hybridized after a second contact during the glacial period. Here, we proposed that the hybrid offspring was the ancestor of the T. altaicus. In conclusion, the uplift of QTP and glacial oscillations triggered the snowcocks colonization, and then, isolation and introgression hybridization promoted diversification.

Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae).

Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).

Phylogeography of the Tibetan hamster Cricetulus kamensis in response to uplift and environmental change in the Qinghai-Tibet Plateau.

AIM: The evolutionary process of an organism provides valuable data toward an understanding of the Earth evolution history. To investigate the relationship between the uplift of the Qinghai-Tibet Plateau (QTP) and mammalian evolution since the late Cenozoic, the geographic distribution of genetic variations in the Tibetan hamster Cricetulus kamensis was investigated using phylogeographical methods. In particular, population divergence, demographic history, genetic variation, and the prediction of species distribution area were investigated. LOCATION: The Qinghai-Tibet Plateau. METHODS: A total of 53 specimens, representing 13 geographic populations, were collected from the QTP. The phylogeographical pattern and demographic history of C. kamensis were analyzed, and the probable factors in the QTP uplift and the Quaternary glacial periods were inferred from one nuclear and four mitochondrial genes. Furthermore, the species distribution model (SDM) was used to predict changes in potentially suitable habitats since the last Interglacial. RESULTS: Phylogenetic analysis demonstrated that two major genetic differentiations of the C. kamensis population occurred during the Early Pleistocene that were influenced by the Qing-Zang tectonic movement from the Middle Pliocene to the Early Pleistocene. Genetic distance between two major clades indicated low genetic divergence. Demographic history analysis showed that the C. kamensis population was affected by the Quaternary glacial period. SDM analysis indicated that C. kamensis was endemic to the QTP and the suitable habitat was affected by climate change, especially during the Last Glacial Maximum (LGM). MAIN CONCLUSION: Our results indicated that the QTP uplift led to the population divergence of C. kamensis, and vicariance well accounted for the geographic distribution of genetic variation in C. kamensis as a result of genetic divergence and lack of gene flow. The genetic distance shows that C. alticola may be a subspecies of C. kamensis. Demographic history analysis suggests that the QTP was affected by the last glacial period. SDM analysis supports that almost the entire QTP is covered by a huge ice sheet during the LGM.

Mitochondrial genome of Cricetulus migratorius (Rodentia: Cricetidae): Insights into the characteristics of the mitochondrial genome and the phylogenetic relationships of Cricetulus species.

Cricetulus migratorius is widely distributed in the northwestern arid regions of China. Here, the complete mitochondrial genome (mitogenome) of C. migratorius is reported, to our knowledge, for the first time. It was found to be 16,246bp in length, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region, and showed characteristics typical of the vertebrate mitogenome. Comparative analyses of mitogenomes of Cricetulus species showed that hamster mitogenomes had the same arrangement and organizational structure. The base composition was AT-rich for all Cricetulus species. We elaborated the PCG sequence and found that the main differences in the start and stop codons were in the ND3 gene; the most frequently used codons were AUU (Ile) and CUA (Leu), and the AT-content at the 3rd position was lower than that at 1st and 2nd positions in all Cricetulus species. The second tRNAser had lost the dihydrouridine stem-loop structure, which is found in all Cricetulus species. We also elucidated the structure of the control region (the extended termination associated sequences, the central conserved sequences, and the conserved sequence blocks), and the putative origin of replication for the light strand in all Cricetulus species. Based on mitogenome data with four reconstructed methods, phylogenetic trees showed high resolution in the divergent clades within Cricetulus. The results indicated that Cricetulus kamensis is at basal position, and has the earliest split among all Cricetulus species. Cricetulus griseus and Cricetulus longicaudatus clustered in a subclade, and were separate from C. kamensis. As previous studies have shown, Tscherskia triton is part of Cricetulus with high support value. It is noteworthy that C. migratorius is a young species, and has a close relationship with Allocricetulus eversmanni within Cricetulus, which is closer to the subgenus Allocricetulus.

The complete mitochondrial genome of Allocricetulus eversmanni (Rodentia: Cricetidae).

Allocricetulus eversmanni is a unique species in the Allocricetulus, belonging to the Cricetinae group. Its complete mitochondrial genome was first obtained and the total length was 16,282 bp. Protein-coding genes approximately accounted for 69.6% of the complete genome. The heavy strand contained 30% A, 14.4% G, 27.9% C, 27.7% T. Compared with most other mammals, it had the same arrangement and similar length of vary genes or regions. The complete mitochondrial genome of A. eversmanni was conducive to more accurately locate its taxonomic status in Cricetinae and its evolutionary history. At the same time, it provided significant information about consummation of A. eversmanni gene pool.

Phylogenetic analysis of Dipus sagitta and Euchoreutes naso (Rodentia: Dipodidae) based on the mitochondrial genomes.

Dipus sagitta and Euchoreutes naso are both monotypic genus, both of them belong to the family of Dipodidae, and E. naso is an Endangered species (EN) defined by the World Conservation Union. The length of its complete mitochondrial sequence of D. sagitta and E. naso is 16,664 bp and 16,705 bp, respectively. Phylogenetic analysis displayed that D. sagitta, Jaculus jaculus, and E. naso were classified into the same cluster. This result was consistent with that of primary morphological taxonomy. The mitochondrial genome of D. sagitta and E. naso would be a key supplement for the gene pool of Rodentia and the conclusion of phylogenetic analysis was an important molecular evidence for the taxonomic status of the two species.

The complete mitochondrial genome of Meriones libycus (Rodentia: Cricetidae) and its phylogenetic analysis.

Meriones libycus belongs to the genus Meriones in Gerbillinae, its complete mitochondrial genome is 16,341 bp in length. The heavy strand contains 32.8% A, 13.1% G, 25.3% C, 28.8% T, protein-coding genes approximately accounting for 69.54%. Results of phylogenetic analysis showed that M. libycus and Meriones unguiculatus were clustered together, and it was consistent with that of primary morphological taxonomy. This study verifies the evolutionary status of M. libycus in Meriones at the molecular level. The mitochondrial genome would be a significant supplement for the gene pool of Rodentia and the conclusion of phylogenetic analysis could be an important molecular evidence for the classification of Gerbillinae.

The complete mitochondrial genome of Stylodipus telum (Rodentia: Dipodidae) and its phylogenetic analysis.

Stylodipus telum belongs to the genus Stylodipus in the subfamily of Dipodinae. We got its complete genome first and it is 16,696 bp in length, the heavy strand contains 31.0% A, 13.8% G, 27.3% C, 27.9% T. Among them, protein-coding genes take up approximately 67.90% of the complete sequence. Trees constructed through phylogenetic analysis showed S. telum and Jaculus jaculus were clustered in one branch belonging to the family Dipodinae. This conclusion was identical to the former result by the methods of morphological taxonomy, and it would be convenient for further research on S. telum and other jerboa.

The complete mitochondrial genome of Meriones meridianus (Rodentia: Cricetidae) and its phylogenetic analysis.

Meriones meridianus belongs to the genus Meriones in Gerbillinae. Total length of complete mitochondrial genome of M. meridianus is 16,376 bp and the heavy strand contains 32.8% A, 13.1% G, 25.3% C and 28.8% T. Sequences of protein-coding genes are 11,341 bp in length, accounting for 69.25%, approximately. Results of phylogenetic analysis shown that M. meridianus and Meriones unguiculatus were clustered in a single branch. This conclusion would be an important data for relevant studies about the genus Meriones, and mitochondrial genome would be an important supplement for the gene pool of Rodentia. It would play a pivotal role in researches about phylogeography and proteomics involving M. meridianus as well.

Past climate change and recent anthropogenic activities affect genetic structure and population demography of the greater long-tailed hamster in northern China.

The genetic diversity and the spatial structure of a species are likely consequences of both past and recent evolutionary processes, but relevant studies are still rare in East Asia where the Pleistocene climate has unique influences. In this study, we examined the impact of past climate change and recent anthropogenic activities on the genetic structure and population size of the greater long-tailed hamster (Tscherskia triton), an agricultural rodent pest species in northern China. DNA sequence data of 2 mitochondrial genes and genotypic data of 11 microsatellite DNA loci from 41 populations (545 individuals) were gathered. Phylogenetic and population genetic analyses, as well as species distribution modeling and coalescent simulations, were conducted to infer its historical and demographic patterns and processes. Two deeply diverged mitochondrial clades were recovered. A small one was restricted to the Shandong Peninsula while the main clade was further divided into 3 geographic clusters by their microsatellite DNA genotypes: Northwest, North-center and Northeast. Divergence dating indicated a Middle-to-Late Pleistocene divergence between the 2 clades. Demographic analysis indicated that all 3 and pooled populations showed consistent long-period expansions during last glacial period; but not during the Holocene, probably due to the impact of climate warming and human disturbances. Conflicting patterns between mtDNA and microsatellite markers imply an anthropogenic impact on North-center populations due to intensified agricultural cultivation in this region. Our study demonstrated that the impact of past glaciation on organisms in East Asia significantly differs from that of Europe and North America, and human activity is an important factor in determining the genetic diversity of a species, as well as its spatial structure.