The evolutionary shift from arboreal to fossorial lifestyles, coupled with deep hibernation and high-altitude hypoxia tolerance, represents a suite of extreme physiological adaptations unique to ground squirrels. To investigate the molecular basis of these interconnected traits, we generated a chromosome-level genome of the Himalayan marmot (Marmota himalayana) and conducted comparative analyses across 11 squirrel species. Evolutionary breakpoint regions distinguishing arboreal from fossorial taxa were enriched in bone morphogenesis and motor nervous system genes, providing testable hypotheses for the fossorial transition. Positively selected genes in hibernating ground squirrels included circadian regulators, and a hibernator-specific TIMELESS Leu173Phe mutation enhanced PER2 binding in co-immunoprecipitation assays, offering a candidate mechanism for circadian dampening during torpor. In M. himalayana, a fixed EPAS1 Thr478Met variant reduced protein expression under hypoxia while upregulating LDHA and VEGF, revealing a fine-tuned strategy for high-altitude adaptation. Together, these findings provide molecular insights into three key evolutionary innovations with TIMELESS and EPAS1 variants are supported by functional validations and the fossorial transition representing comparative genomic hypotheses awaiting further testing. The authors sequence the Himalayan marmot genome and compare 11 squirrel species, revealing candidate genes underlying fossorial transition, a hibernator-specific TIMELESS mutation enhancing PER2 binding, and an EPAS1 variant tuning hypoxia adaptation.

The evolutionary dynamics of immune adaptors in wildlife remain poorly understood, despite their critical role in host-pathogen interactions. In this study, we investigated the molecular evolution of five TIR domain-containing adaptors (MAL, MyD88, SARM, TRAM, and TRIF) in murid rodents across both interspecific and population levels to provide an integrative view of their evolutionary trajectories. Our analyses demonstrate that these adaptors are predominantly under purifying selection in murids, yet contain specific positively selected sites in MAL and MyD88, indicating localized adaptive fine-tuning. These positively selected amino acid sites exhibited substantial genetic divergence among murid species. Within populations, we observed reduced genetic diversity in the adaptor genes compared with noncoding regions across the whole genome in both Rattus tanezumi and Rattus norvegicus, and no significant signals of recent positive or negative selection were detected in either species. Notably, we identified identical or nearly identical allelic variants between these two rat species across all five adaptor genes. Collectively, this study delineates the evolution of immune adaptors in murids across both deep and recent timescales, advancing our understanding of adaptive evolution in multilevel immune systems.

The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts’ adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats. Analyses of gut microbiomes from sympatric animals of the Qinghai-Tibetan Plateau and comparison with Tibetan human gut microbiomes reveals the impact of host phylogeny on gut microbiota composition.

The ultrasonic vocalizations (USVs) of rodents play a substantial role in the communication and interaction between individuals; exhibit a high degree of complexity; and are influenced by a multitude of developmental, environmental, and phylogenetic factors. The functions of USVs are mainly studied in laboratory mice or rats. However, the behavioral relevance of USVs in wild rodents is poorly studied. In this work, we systematically investigated the vocal repertoire of the wild mouse Mus caroli and wild rat Rattus losea in multiple social or non-social contexts, e.g., pup-isolation, juvenile-play, paired opposite-sex encounter, female–female interaction, social-exploring, or foot-shock treatment. Unlike the laboratory mice, M. caroli, whose USVs were recorded during pup-isolation and courtship behaviors, did not produce any vocal sounds during juvenile-play and female–female interactions. R. losea, similar to laboratory rats, emitted USVs in all test situations. We found higher peak frequencies of USVs in both these two wild rodent species than in laboratory animals. Moreover, the parameters and structures of USVs varied significantly across different social or non-social contexts even within each species, confirming the context-sensitivity and complexity of vocal signals in rodents. We also noted a striking difference in call types between these two species: no downward type occurred in M. caroli, but no upward type occurred in R. losea, thereby highlighting the interspecific difference of vocal signals among rodents. Thus, the present study presents behavioral foundations of the vocalization context in wild mice and wild rats, and contributes to revealing the behavioral significance of widely used USVs in rodents.

Toll-like receptors (TLRs), the key sensor molecules in vertebrates, trigger the innate immunity and prime the adaptive immune system. The TLR family of rodents, the largest order of mammals, typically contains 13 TLR genes. However, a clear picture of the evolution of the rodent TLR family has not yet emerged and the TLR evolutionary patterns are unclear in rodent clades. Here, we analyzed the natural variation and the evolutionary processes acting on the TLR family in rodents at both the interspecific and population levels. Our results showed that rodent TLRs were dominated by purifying selection, but a series of positively selected sites (PSSs) primarily located in the ligand-binding domain was also identified. The numbers of PSSs differed among TLRs, and nonviral-sensing TLRs had more PSSs than those in viral-sensing TLRs. Gene-conversion events were found between TLR1 and TLR6 in most rodent species. Population genetic analyses showed that TLR2, TLR8, and TLR12 were under positive selection in Rattus norvegicus and R. tanezumi, whereas positive selection also acted on TLR5 and TLR9 in the former species, as well as TLR1 and TLR7 in the latter species. Moreover, we found that the proportion of polymorphisms with potentially functional change was much lower in viral-sensing TLRs than in nonviral-sensing TLRs in both of these rat species. Our findings revealed the first thorough insight into the evolution of the rodent TLR genetic variability and provided important novel insights into the evolutionary history of TLRs over long and short timescales.

H11N9 viruses in wild birds might have provided the NA gene of human H7N9 virus in early 2013 in China, which evolved with highly pathogenic strains in 2017 and caused severe fatalities. To investigate the prevalence and evolution of the H11N9 influenza viruses, 16,781 samples were collected and analyzed during 2016-2020. As a result, a novel strain of influenza A (H11N9) virus with several characteristics that increase virulence was isolated. This strain had reduced pathogenicity in chicken and mice and was able to replicate in mice without prior adaptation. Phylogenetic analyses showed that it was a sextuple-reassortant virus of H11N9, H3N8, H3N6, H7N9, H9N2, and H6N8 viruses present in China, similar to the H11N9 strains in Japan and Korea during the same period. This was the H11N9 strain isolated from China most recently, which add a record to viruses in wild birds. This study identified a new H11N9 reassortant in a wild bird with key mutation contributing to virulence. Therefore, comprehensive surveillance and enhanced biosecurity precautions are particularly important for the prediction and prevention of potential pandemics resulting from reassortant viruses with continuous evolution and expanding geographic distributions.

Pigeon paramyxovirus type I (PPMV-1) causes regular outbreaks in pigeons and even poses a pandemic threat among chickens and other birds. The birds infected with PPMV-1 mainly show a pathological damage in the respiratory system, digestive system, and nervous system. However, there were few reports on the efficiency of the virus entering the host via routes of different systems. In the present study, a PPMV-1 strain was obtained from a dead wild pigeon in 2016 in Beijing, China. The mean death time (MDT) and the intracerebral pathogenicity (ICPI) of our isolate showed medium virulence. Phylogenetic analysis based on F gene sequence showed that the isolate belonged to subgenotype VIb, class II, which dominated in China in recent years. Then, we evaluated the infection efficiency of different routes. Pigeons were randomly divided into five groups of six as follows: intracephalic (IC), intranasal (IN), and intraoral (IO) infection routes, cohabitation infection (CO), and negative control (N negative). All pigeons were inoculated with 100 μl·106 EID50 PPMV-1 virus. After infection, pathological lesions, virus shedding, body weight change, survival rate, and tissue tropism were tested to compare the efficiency of the different infected routes. The mortality of groups IC, IN, IO, and CO were 100, 66.7, 50, and 33.3%, respectively. Weight loss in group IC was higher than the other groups, followed by groups IN and IO. The lesions observed in PPMV-1-infected pigeons were severe, especially in the lung and intestine in group IC. Viral shedding was observed from 2 dpi in groups IC and IN, but the shedding rate was higher in group IN than group IC. The longest period was in group CO. Tissue tropism experiment showed that our isolate has a wide range of tissue distribution, and the virus titer in the heart and intestine of group IC and in the brain of group IN was higher. Our data may help us to evaluate the risk of transmission of PPMV-1.

As an economically important poultry pathogen, avian paramyxovirus serotype 4 (APMV-4) frequently reported and isolated from domestic and wild birds particularly waterfowls worldwide. However, evolutionary dynamics of APMV-4 based on genomic characteristics is lacking. In this study, APMV-4 strain designated JX-G13 was isolated from oropharyngeal and cloacal swab samples of wild birds in China. Phylogenetic analysis revealed APMV-4 strains were divided into four genetic genotypes and China isolates were mainly clustered into Genotype I. The MCMC tree indicated that APMV-4 diverged about 104 years ago with the evolutionary rate of 1.2927 x 10-3 substitutions/site/year. BSP analysis suggested that the effective population size of APMV-4 exhibited a steady state and decreased slowly after 2013. The F gene of APMV-4 was considered relatively conserved among isolates based on nucleotide diversity analysis. Although the F gene was under purifying selection, two positions (5 and 21) located in 3'-UTR were subject to positive selection. Our study firstly presented the evolutionary assessments on the genetic diversity of circulating APMV-4 from wild birds and domestic poultry.

Toll-like receptors (TLRs) are important initiators of innate immune responses that target host-pathogen interactions. However, further research into the molecular characteristics of TLRs in wild populations is required, as well as how TLRs genetically influenced pathogen infections in the brown rat (Rattus norvegicus). Here, we explored the genetic characterization and evolution of 2 sensing nucleic acid TLRs (TLR7 and TLR8) and 2 sensing non-nucleic acid TLRs (TLR2 and TLR4) in the wild brown rat, and assessed their associations with 2 RNA viruses (Seoul hantavirus and rat hepatitis E virus (HEV)) and 2 bacteria (Leptospira and Bartonella). In these 4 TLRs, we discovered a total of 16 variants. Furthermore, TLR8 had high genetic diversity among 7 variants, while TLR2 had low genetic diversity with only 1 variant. According to selective pressure analyses, TLR4, TLR7, and TLR8 genes evolved under purifying selection. Interestingly, significant associations were found between 3 TLR8 variants and HEV infection, as well as 1 TLR2 variant and Bartonella infection. Overall, our findings provided a glimpse into the genetic characterization of TLRs in the brown rat, and further demonstrated that TLR2 and TLR8 genetic variations were related to Bartonella and HEV infection, respectively. Especially, TLR8 may be a good candidate immune gene for future research on molecular ecology and functional adaptation in wild populations.

Infection with H5N6 highly pathogenic avian influenza virus caused high mortality in chickens, while ducks often appear to be asymptomatic. But, some recent H5Nx subtype viruses could cause high mortality in ducks. The variation between different species and the mechanisms by which some H5Nx viruses cause death in ducks requires investigation to identify the key processes in influenza susceptibility and pathogenesis. Here, we characterized two representative H5N6 viruses, A/ Pavo cristatus /Jiangxi/JA1/2016 (JA1) and A/ Anas crecca /shanghai/SH1/2016 (SH1), and compared their pathogenicity and expression profiles of immune-related genes in chickens and ducks to identify the elements of the host immune-related response that were involved in disease lethality. Results suggested that H5N6 HPAIVs had higher pathogenic and inflammatory effect in chickens than in ducks. Importantly, the TNF-α, IL-6, IFN-γ and iNOS levels were significantly higher in the lung of SH1 infected chickens compared to those of ducks. And we found higher systemic levels of IL-6 induced by JA1 in chickens than in ducks. In addition, our experiments demonstrated that JA1 was associated with greater pathogenicity in ducks were accompanied by the excessive expression of iNOS in the brain. These results are helpful to understand the relationship between the pathogenicity of H5N6 AIVs and inflammatory responses to them in chickens and ducks.

Commensal rats (Rattus spp.), which are globally distributed, harbour many pathogens responsible for significant human diseases. Despite this, we have a poor understanding of the epidemiology and genetic diversity of some recently neglected zoonotic pathogens, such as Leptospira spp., Bartonella spp. and hepatitis E virus (HEV), which constitute a major public health threat. Thus, we surveyed the occurrences, co-infection and genetic diversity of these pathogens in 129 urban rats from China. For Rattus tanezumi, the prevalences of Leptospira spp., Bartonella spp. and HEV infection were 6.67%, 0% and 46.67%, respectively. The prevalences of Leptospira spp., Bartonella spp. and HEV infection were 57.89%, 9.65% and 57.89% for Rattus norvegicus respectively. Leptospira spp. and HEV infections were more likely to occur in mature R. norvegicus. Phylogenetic analyses showed that pathogenic Leptospira interrogans and Leptospira borgpetersenii might exist. We also found that Bartonella spp. showed high similarity to Bartonella elizabethae, Bartonella rochalimae and Bartonella tribocorum, which are implicated in human disease. Dual and triple infections were both detected. Moreover, dual infections with Leptospira spp. and HEV represented the most frequent co-infection, and there was a significantly positive association between them. High genetic diversity was observed in genes segments from Leptospira, Bartonella and HEV. Our results first discover the occurrence of multiple co-infections and genetic diversity of Leptospira, Bartonella and HEV in commensal rats from China. Altogether, the present study provides an insight into evaluating the risk of rat-borne zoonoses in urban China.

Seoul virus (SEOV), which causes hemorrhagic fever with renal syndrome (HFRS) in humans, has spread all over the world, especially in mainland China. Understanding basic mechanisms of SEOV evolution is essential to better combat and prevent viral diseases. Here, we examined SEOV prevalence and evolution in the residential area of four districts in Guangzhou city, China. The carriage of SEOV was observed in 33.33% of the sampled rodents, with 35.96% of the sampled Rattus norvegicus and 13.33% of R. tanezumi. Based on the comprehensive analyses of large (L), medium (M), and small (S) segments, our study first demonstrated that the genetic characterization of urban SEOV was shaped by high nucleotide substitution rates, purifying selection, and recombination. Additionally, we detected mutational saturation in the S segment of SEOV, which may lead to the biases of genetic divergence and substitution rates in our study. Importantly, we have filled the gap of SEOV evolution in the urban area. The genetic variation of SEOV may highlight the risk of HFRS, which merits further investigation.

动物从环境中获取足够营养和能量的能力决定着其生存和繁殖.为探讨同域分布不同体型的鼠类对不同营养成分食物的摄食消化对策,以三种不同营养成分食物分别饲喂卡氏小鼠和黄毛鼠,在第10天和20天,以食物平衡法测定日摄食量、日粪便量、净摄入量和表观消化率.结果 发现,在整个驯化过程中,两种鼠的不同食物组间体重无显著差异,表明均能够适应食物营养的变化维持收支平衡.在驯化第10天时,高蛋白组卡氏小鼠的日摄食量显著高于高淀粉组,但两组与普通组均无差异;高蛋白组卡氏小鼠的日粪便量显著高于高淀粉组和普通组;而净摄入量无组间差异;高淀粉组和普通组的表观消化率显著高于高蛋白组.至第20天时,三组动物日摄食量无差异;高蛋白组的日粪便量高于高淀粉组和普通组.黄毛鼠仅在第10天时高淀粉组和普通组表观消化率高于高蛋白组,三组黄毛鼠其他消化参数在第10天和第20天均无显著组间差异.结果 表明,体型不同的鼠类因消化冗余能力的差异,面对相同的食物营养成分变化,会以不同的摄食消化策略调节适应.

Fertility control is considered as the second-generation pest rodent management strategy. Most previous studies have focused on the dosage-dependent effects of quinestrol and levonorgestrel compounds (EP-1) at a ratio of 1:2, but the ratio-dependent effects of EP-1 have not been fully investigated, especially in male rodents. To test the ratio-dependent antifertility effects of EP-1 with different ratios (1:2, 1:1, and 2:1) on male Swiss outbred strain of laboratory mice, forty male mice were randomly assigned into four groups (n = 10). Mice in the three treatment groups were provided one of the three EP-1 mixture compounds for 3 successive days via gavage at a dosage of 50 mg/kg(body weight), and then all mice were sacrificed 15 days after the gavage treatment. Reproductive organ weights, sperm density and motility, levels of testosterone (T), estradiol (E2), luteinizing hormone (LH), and follicle stimulating hormone (FSH) in serum and/or testis, and androgen receptor (AR), estrogen receptor α (ERα), estrogen receptor β (ERβ), luteinizing hormone receptor (LHR), and aromatase in testis were determined. Each of the ratios of quinestrol and levonorgestrel significantly decreased the density and motility of sperm and induced atrophy of the epididymis and seminal vesicle. The combination of compounds also significantly reduced serum T and LH levels, increased testicular T levels and decreased testicular estradiol ERβ and aromatase levels. EP-1 delivered at a ratio of 1:1 induced the most significant effects on the reproductive parameters assessed and shows the potential for use in fertility control of male rodents.

In May 2016,two rat species Rattus losea (1 male,1 female) with partial albinism were captured on a farmland in Feng Village,Zengcheng City,Guangdong Province.The two albinism positions are back and head.Their physical characteristics are described.Furthermore,the possible causes and the effects on organisms of partial albinism are discussed.

Ultrasonic pest repellers are important devices for the control of rodent pests by physical methods. However, scientific and uniform methods for evaluating the efficiency of ultrasonic repellers in repelling pest rats are lacking. In this study, we tested the efficiency of one ultrasonic pest repeller on adult male Rattus losea under laboratory condition by comparing the rat number and food intake in two adjacent rooms with open or close repellers. Results showed that rat number and food intake in the room with open repeller were significantly lowere by 27％ and 17％, respectively than that in the room with a closed repeller after 7 days. The tested repeller had some efficiency on R. losea, but isn't adequate for controlling rodent pests in room conditions.

Vocalizations are a crucial part of courtship and mating in a wide variety of species. Mating behavior, including courtship calls, is modulated by sex steroid hormones. Male mice produce courtship ultrasonic vocalizations to attract females during heterosexual encounters. However, rare is the knowledge on whether vocal behavior of mice changes under sterilant treatment which will affect gonadal hormone levels. In the present study, we treat male mice with quinestrol, which interferes with the release of the gonadotropin-releasing hormone (GnRH) and has a significant anti-fertility effect in rodents. We compared the differences in the syllable structures (including peak intensity, peak frequency, duration, and bandwidth), total number of calls, and harmonic syllable proportions between quinestrol treated and control male mice. Male mice treated with quinestrol produced more courtship calls and more harmonic syllables than control mice, whereas the parameters of call syllables showed no significant change between the two groups. The results indicate that normal male vocal behavior during sexual interactions could be retained or even reinforced after quinestrol treatment. In addition, female mice approached male mice treated with quinestrol more than control mice, suggesting that the treated male mice were more attractive to the female mice than the controls. Thus, competitive reproductive interference is enhanced. Further, findings provided behavior mechanism in vocal context of the fertility control in mice.

Fertility control reduces the birth rate of rodent populations and influences animal reproductive capability.By contrast,the effects of sterilants on individual behaviors may affect the social hierarchy of populations,and interfere with reproduction in normal animals.To understand the effects of cabergoline treatment dosage and treatment duration on the behavior of male Rattus losea,40 male rats were randomly divided into five groups and treated with 0,50,and 100 μg/kg cabergoline for 3 consecutive days.One male subject from the pre-treatment group (T750,T7100) was assigned to dyadic encounters with one subject from the control group (C) on the first day after the end of the three-day treatment.T2450 and T24100 rats encountered the same rat from C on the 18th day after the end of the three-day treatment.T750and T7100 were assigned to dyadic encounters with normal females on the fourth day after the end of the three-day treatment.T2450 and T24100 rats encountered normal females on the 21st day after the end of the three-day treatment.Social behaviors between the same sex and the opposite sex were observed for 30 min and videotaped.The results showed that cabergoline treatment negatively affected the investigative and aggressive behavior of male R.losea,and reduced the aggression duration and frequency of males toward females.The frequency of investigation,grooming and resting in males that encountered female counterparts were significantly different between pre-and post-treatment with 100 μμg/kg cabergoline.In conclusion,cabergoline treatment disturbs the inter-or intra-sexual social behaviors of R.losea.Furthermore,with longer duration post-treatment,the behavioral data in our experiment were not significantly different compared with pre-treatment.These results indicate that the effects of drug on social behavior of the male can gradually disappear after suspending cabergoline treatment.

The aim of this study was to assess the effects and reversibility of the synthetic estrogen compound, quinestrol, on the reproductive organs, steroid hormones, and drug-metabolizing enzymes CYP3A4 and CYP1A2 in liver and kidney over time after two quinestrol treatments in female Mongolian gerbils (Meriones unguiculatus). Female gerbils were treated with 4mg/kg quinestrol (9 gerbils/group, 3 treated group) (1 control group, 0mg/kg) for 3days and treated again after 25days. Animals were killed for collection of samples at 5, 10 and 15days after the second treatment ending. Two interval quinestrol treatments significantly increased uterine weight, with trend of increase over time, but no change could be detected in ovarian weights. Quinestrol treatment increased progesterone and estradiol levels, both with trend of decline over time. Quinestrol increased liver and kidney weights and total enzyme content of CYP3A4 and CYP1A2, with trend of decline over time. On the basis of reversible changes of detoxification enzymes or organs, interval quinestrol treatment effectively and reversibly influenced the reproductive hormone and organ to some extent.

To reduce errors in species recognition and the probability of interbreeding that lowers fitness, individuals within sympatric zones shift the signals to differentiate from those of other species. In the present study, the differences of the acoustic features of ultrasounds (courtship calls during heterosexual encounters) and audible calls (distress calls during tail-clamp stress) are compared among three sympatric Rattus species (Rattus andamanensis, R. norvegicus, and R. losea). Results showed that the three species have significantly different call parameters, including call duration, peak frequency, bandwidth, pitch, goodness of pitch, frequency modulation, and Wiener entropy. This study provides quantitative evidence for character displacement in the acoustic signals of closely related sympatric Rattus species. Results indicate that the divergence of acoustic signal has arrived at the quite meticulous degree of evolution. Therefore, the acoustic signal trait is likely involved in the evolution of species diversity in rodents.