Dispersal route of the Asian house rat (Rattus tanezumi) on mainland China: insights from microsatellite and mitochondrial DNA

Genomic and Phenotypic Adaptations of Rattus tanezumi to Cold Limit Its Further Northward Expansion and Range Overlap with R. norvegicus

Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric Rattus norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest, and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited higher brown adipose tissue activity and metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.

High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China

Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.

Population structure, dispersion patterns and genetic diversity of two major invasive and commensal zoonotic disease hosts (Rattus norvegicus and Rattus tanezumi) from the southeastern coast of China

Background: The invasive brownrat (Rattus norvegicus) and the Oriental rats (Rattus tanezumi) are common commensal murid that are important hosts for rodent-borne diseases in southeast Asia. Understanding their population structure and genetic diversity is essential to uncover their invasion biology and distribution dynamics that are essential for controlling rodent-borne diseases. Methods: TA total of 103 R. norvegicus and 85 R. tanezumi were collected from 13 to 9 coastal areas of six provincial monitoring sentinel sites, respectivelyto assess patterns in their microsatellite loci and their mitochondrial coxl gene region. Results: Eleven sampled populations of R. norvegicus were divided into two major clusters by region. The observed heterozygosity values of all regional populations were smaller than expected genetic diversity heterozygosity values and deviated from Hardy-Weinberg equilibrium Nine sample populations of R. tanezumi were divided into three clusters; two that included sample from Hainan and Fujian provinces, and one that included samples from the other provinces and cities. The genetic diversity of R. tanezumi was highest in samples from Jiangsu and Guangdong provinces. Conclusion: The data in this paper confirm the two invasive rodent species from the southeastern coastal region of China may have relied on maritime transport to spread from the southern region of China to the Yangtze River basin. R. tanezumi may then hanve migrated unidirectionally, along the southeastern provinces of China towards the north, while R. norvegicus spread in a complex and multidirectional manner in Hainan, Fujian, Zhejiang and Jiangsu Provinces of the country.

Genotypic detection of barriers to rat dispersal: Rattus rattus behind a peninsula predator-proof fence

Clear delimitation of management units is essential for effective management of invasive species. Analysis of population genetic structure of target species can improve identification and interpretation of natural and artificial barriers to dispersal. In Aotearoa New Zealand where the introduced ship rat (Rattus rattus) is a major threat to native biodiversity, effective suppression of pest numbers requires removal and limitation of reinvasion from outside the managed population. We contrasted population genetic structure in rat populations over a wide scale without known barriers, with structure over a fine scale with potential barriers to dispersal. MtDNA D-loop sequences and microsatellite genotypes resolved little genetic structure in southern North Island population samples of ship rat 100 km apart. In contrast, samples from major islands differed significantly for both mtDNA and nuclear markers. We also compared ship rats collected within a small peninsula reserve bounded by sea, suburbs and, more recently, a predator fence with rats in the surrounding forest. Here, mtDNA did not differ but genotypes from 14 nuclear loci were sufficient to distinguish the fenced population. This suggests that natural (sea) and artificial barriers (town, fence) are effectively limiting gene flow among ship rat populations over the short distance (~ 500 m) between the peninsula reserve and surrounding forest. The effectiveness of the fence alone is not clear given it is a recent feature and no historical samples exist; resampling population genetic diversity over time will improve understanding. Nonetheless, the current genetic isolation of the fenced rat population suggests that rat eradication is a sensible management option given that reinvasion appears to be limited and could probably be managed with a biosecurity programme.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10530-023-03004-8.

Infestation of Oriental House Rat (Rattus tanezumi) with Chigger Mites Varies along Environmental Gradients across Five Provincial Regions of Southwest China

Chigger mites are the exclusive vector of scrub typhus. Based on field investigations of 91 survey sites in 5 provincial regions of Southwest China, this paper reported variations of chigger infestation on the oriental house rat (Rattus tanezumi) along various environmental gradients. A total of 149 chigger species were identified from 2919 R. tanezumi in the 5 provincial regions, and Leptotrombidium deliense (a major vector of scrub typhus in China) was the first dominant chigger species, followed by Ascoschoengastia indica and Walchia ewingi. Rattus tanezumi had a stable overall prevalence (PM = 21.10%), mean abundance (MA = 7.01), and mean intensity (MI = 33.20) of chiggers with the same dominant mites in the whole Southwest China in comparison with a previous report in Yunnan Province, but chigger infestations on R. tanezumi varied along different environmental gradients. Rattus tanezumi in mountainous landscape had a higher infestation load of chiggers with higher species diversity than in flatland landscape. The infestation was higher at lower altitudes and latitudes. A high intensity of vegetation coverage was associated with high infestations. The results reflect the environmental heterogeneity of chiggers on the same host species. Warm climate and high relative humidity are beneficial to chigger infestation on R. tanezumi.

Comparative phylogeography of two commensal rat species (Rattus tanezumi and Rattus norvegicus) in China: Insights from mitochondrial DNA, microsatellite, and 2b-RAD data

Rattus norvegicus and Rattus tanezumi are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored. Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China with currently invading northward; northeast China was the natal region of R. norvegicus, while the spread of R. tanezumi in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b-RAD analyses. In neighbor-joining tree, individuals of R. tanezumi grouped into geographic-specific branches, and populations from southeast coast were ancestral groups, which confirmed the colonization route from southeast coast to central and western China. However, individuals of R. norvegicus were generally grouped into two clusters instead of geographic-specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that spread history of R. norvegicus in China was complex; in addition to on-land colonization, shipping transportation also have played great roles. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the R. norvegicus declined rapidly while the population of R. tanezumi continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation on phylogeography of two species in China.

Sustained population decline of rodents is linked to accelerated climate warming and human disturbance

Background

During the past three decades, sustained population decline or disappearance of cycles in small rodents have been observed. Both anthropogenic disturbance and climate warming are likely to be potential drivers of population decline, but quantitative analysis on their distinct effects is still lacking.

Results

Using time series monitoring of 115 populations (80 populations from 18 known rodent species, 35 mixed populations from unknown species) from 1980 in China (spanning 20–33 yrs), we analyzed association of human disturbances and climate warming with population dynamics of these rodent species. We found 54 of 115 populations showed a decreasing trend since 1980, and 16 of 115 showed an increasing trend. Human disturbances and climate warming showed significant positive associations with the population declines of most rodent species, and the population declines were more pronounced in habitats with more intensified human disturbance such as cities and farmlands or in high-latitude regions which experienced more increase of temperature.

Conclusions

Our results indicate that the large-scale sustained population decline of small mammals in various ecosystems driven by the rapid increase of both climate warming and human disturbance is likely a signal of ecosystem dysfunction or transition. There is an urgent need to assess the risks of accelerated climate warming and human disturbance imposes on our ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02056-z.

Distinct body-size responses to warming climate in three rodent species

In mammals, body-size responses to warming climates are diverse, and the mechanisms underlying these different responses have been little investigated. Using temporal and spatial datasets of three rodent species distributed across different climatic zones in China, we investigated temporal and spatial trends of body size (length and mass), identified the critical drivers of these trends, and inferred the potential causes underlying the distinct body-size responses to the critical drivers. We found that body mass of all species remained stable over time and across space. Body length, however, increased in one species over time and in two species across space. Generally, body-length variation was predicted best by minimum ambient temperature. Moreover, in two species, body length changed linearly with temperature differences between ancestral and colonization areas. These distinct temperature-length patterns may jointly be caused by species-specific temperature sensitivities and experienced magnitudes of warming. We hypothesize that species or populations distributed across distinct temperature gradients evolved different intrinsic temperature sensitivities, which affect how their body sizes respond to warming climates. Our results suggest that size trends associated with climate change should be explored at higher temporal and spatial resolutions, and include clades of species with similar distributions.

Predicting the potential distribution of a previously undetected cryptic invasive synanthropic Asian house rat (Rattus tanezumi) in South Africa

Three species of Rattus, Norway rat (R. norvergicus), black rat (R. rattus) and Asian house rat (R. tanezumi) are currently known to occur in South Africa. The latter two species are cryptic and form part of the Rattus rattus species complex. Historically, R. norvegicus has been reported to occur along the coast and in urban centres, R. rattus is widespread in most urban areas, except in the drier areas, while R. tanezumi was only recorded to occur in the country (and Africa) ca. 15 years ago, and its distribution remains unknown. The aim of this study was to predict the potential distribution of R. tanezumi in South Africa and assess how it overlaps with that of R. norvegicus and R. rattus using species distribution modelling. Rattus tanezumi was predicted to mainly occur in most inland urban areas and along the coast. The distribution of R. rattus was as expected, in contrast, the predicted range of R. norvegicus was not restricted to the coast but also included inland urban areas. All three species showed broad potential distributional ranges that overlapped extensively indicating that their establishment and spread may be influenced by similar factors such as proximity to urban areas and a wet and moderate climate. These results allow insights into assessing their risk of establishment and for formulating appropriate intervention strategies for their management and control.

Genetic diversity and population structure of the long-tailed hamster Cricetulus longicaudatus in Shanxi Province, China

The long-tailed hamster Cricetulus longicaudatus is a dominant rodent in farmland of Shanxi Province, China, but little is known about its genetic diversity and population structure. In this study, the genomic DNAs of individuals from 13 populations captured in different fields of Shanxi were extracted and amplified by six pairs of microsatellite primers and by universal primers for mtDNA COI gene sequences. Our data revealed significant departure from Hardy-Weinberg equilibrium in four of the 13 populations. In all 13 populations, the mean observed heterozygosity was significantly lower than the expected heterozygosity. Meanwhile, the mean inbreeding coefficient was statistically significant, which indicated non-random mating within populations. The pairwise genetic distance and natural logarithm of linear geographical distance were not significantly correlated for any C. longicaudatus populations. However, the correlation between genetic distance and resistance distance based on mountain landscape was significant, suggesting that the mountain landscape is an important factor affecting gene flow of C. longicaudatus. Pairwise F_ST analysis of population structure showed moderate to high genetic differentiation among populations, and all individuals could be divided into two gene clusters. Phylogenetic analysis based on COI sequences also showed that many individuals originated from a single haplotype, suggesting the existence of gene exchange among these populations at some time in the past. Our research should provide a scientific basis for the analysis of genetic differentiation and gene flow among populations of C. longicaudatus.

Genomic analysis unveils mechanisms of northward invasion and signatures of plateau adaptation in the Asian house rat

The Asian house rat (AHR), Rattus tanezumi, has recently invaded the northern half of China. The AHR is a highly adaptive rat species that has also successfully conquered the Qinghai-Tibet Plateau (QTP) and replaced the brown rat (BR), R. norvegicus, at the edge of the QTP. Here, we assembled a draft genome of the AHR and explored the mechanisms of its northward invasion and the genetic basis underlying plateau adaptation in this species. Population genomic analyses revealed that the northwardly invasive AHRs consisted of two independent and genetically distinct populations which might result from multiple independent primary invasion events. One invasive population exhibited reduced genetic diversity and distinct population structure compared with its source population, while the other displayed preserved genetic polymorphisms and little genetic differentiation from its source population. Genes involved in G-protein coupled receptors and carbohydrate metabolism may contribute to the local adaptation of northern AHRs. In particular, RTN4 was identified as a key gene for AHRs in the QTP that favours adaptation to high-altitude hypoxia. Coincidently, the physiological performance and transcriptome profiles of hypoxia-exposed rats both showed better hypoxia adaptation in AHRs than in BRs that failed to colonize the heart of the QTP, which may have facilitated the replacement of the BR population by the invading AHRs at the edge of the QTP. This study provides profound insights into the multiple origins of the northwardly invasive AHR and the great tolerance to hypoxia in this species.

Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene

Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima’s D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.

Distribution and Host Selection of Tropical Rat Mite, Ornithonyssus bacoti, in Yunnan Province of Southwest China

Simple Summary

The tropical rat mite (Ornithonyssus bacoti) is a transmission vector of rickettsia pox and a potential vector of hemorrhagic fever with renal syndrome (HFRS). This article reports the distribution and host selection of O. bacoti in Yunnan Province of Southwest China. The original data came from the investigations in 39 counties of Yunnan. The prevalence (P_M), mean abundance (MA) and mean intensity (MI) were calculated to reflect the infestations of the dominant rat hosts with O. bacoti mites. The patchiness index and Taylor’s power law were used to measure the spatial distribution of the mites. A total of 4121 O. bacoti mites were identified from 15 species of small mammal hosts in 27 of the 39 investigated counties, and 99.20% of them (4088/4121) were found on rodents. The majority of total O. bacoti mites was found in the flatland landscape (91.28%) and indoor habitat (73.48%). Moreover, 51.78% and 40.09% of O. bacoti mites were identified from Rattus tanezumi and R. norvegicus, the two synanthropic rat species. The mites had some host-specificity, with a preference to two dominant hosts (R. tanezumi and R. norvegicus), and they were of aggregated distribution on R. tanezumi.

Abstract

(1) Background: As a species of gamasid mite, the tropical rat mite (Ornithonyssus bacoti) is a common ectoparasite on rodents and some other small mammals. Besides stinging humans to cause dermatitis, O. bacoti can be a vector of rickettsia pox and a potential vector of hemorrhagic fever with renal syndrome (HFRS). (2) Objective: The present study was conducted to understand the host selection of O. bacoti on different animal hosts and the distribution in different environmental gradients in Yunnan Province of Southwest China. (3) Methods: The original data came from the investigations in 39 counties of Yunnan, between 1990 and 2015. The animal hosts, rodents and some other small mammals were mainly trapped with mouse traps. The O. bacoti mites on the body surface of animal hosts were collected and identified in a conventional way. The constituent ratio (Cr), prevalence (P_M), mean abundance (MA) and mean intensity (MI) were used to reflect infestations of animal hosts with O. bacoti mites. The patchiness index and Taylor’s power law were used to measure the spatial distribution pattern of O. bacoti mites on their hosts. (4) Results: A total of 4121 tropical rat mites (O. bacoti) were identified from 15 species and 14,739 individuals of hosts, and 99.20% of them were found on rodents. More than half of O. bacoti mites (51.78%) were identified from the Asian house rat (Rattus tanezumi), and 40.09% of the mites from the Norway rat (R. norvegicus) (p < 0.05). The infestations of R. tanezumi (P_M = 7.61%, MA = 0.40 and MI = 5.31) and R. norvegicus (P_M = 10.98, MA = 1.14 and MI = 10.39) with O. bacoti mites were significantly higher than those of other host species (p < 0.05). The infestations of two dominant rat hosts (R. tanezumi and R. norvegicus) with O. bacoti mites varied in different environmental gradients (latitudes, longitudes, altitudes, landscapes and habitats) and on different sexes and ages of the hosts. The prevalence of juvenile R. norvegicus rats with O. bacoti mites (P_M = 12.90%) was significantly higher than that of adult rats (P_M = 9.62%) (p < 0.05). The prevalence (P_M = 38.46%) and mean abundance (MA = 2.28 mites/host) of R. tanezumi rats with O. bacoti mites in the high latitude were higher than those in the low latitudes (p < 0.05). The majority of the total collected 4121 O. bacoti mites was found in the flatland landscape (91.28%) and indoor habitat (73.48%) (p < 0.05). The P_M (10.66%) and MA (0.49 mites/host) of R. tanezumi rats with O. bacoti mites were significantly higher in the indoor habitat than in the outdoor habitat (p < 0.05). The tropical rat mites showed an aggregated distribution pattern on their first dominant host, R. tanezumi. Conclusion: The tropical rat mite (O. bacoti) is a widely distributed species of gamasid mite in Yunnan Province, Southwest China, and its dominant hosts are two synanthropic species of rats, R. tanezumi and R. norvegicus. It is mainly distributed in the flatland landscape and indoor habitat. It has some host-specificity, with a preference to rodents, especially R. tanezumi and R. norvegicus. The O. bacoti mites are of aggregated distribution on R. tanezumi rats.