Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat

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.

Physiological strategies in wild rodents: immune defenses of commensal rats

The importance of issues associated with urban/commensal rats and mice (property damage, management costs, and health risks) press upon research on these animals. While the demography of commensal rodents is mostly studied, the need for understanding factors influencing their natural morbidity/mortality is also stressed. In this respect, more attention is expected to be paid to immunity, the physiological mechanism of defense against host survival threats (pathogens, parasites, diseases). Commensal rats and mice carry numerous pathogens that evoke diverse immune responses. The state of immunity in commensal house mice is studied in great detail, owing to the use of laboratory strains in biomedical research. Because commensal rats are, compared to mice, carriers of more zoonotic agents, rats' immunity is studied mainly in that context. Some of these zoonotic agents cause chronic, asymptomatic infections, which justified studies of immunological mechanisms of pathogen tolerance versus clearance regulation in rats. Occurrence of some infections in specific tissues/organs pressed upon analysis of local/regional immune responses and/or immunopathology. A survey of immunological activity/responses in commensal rats is given in this review, with mention of existing data in commensal mice. It should throw some light on the factors relevant to their morbidity and lifespan, supplementing the knowledge of commensal rodent ecology.

Fatty acid metabolism decreased while sexual selection increased in brown rats spreading south

For mammals that originate in the cold north, adapting to warmer environments is crucial for southwards invasion. The brown rat (Rattus norvegicus) originated in Northeast China and has become a global pest. R. n. humiliatus (RNH) spread from the northeast, where R. n. caraco (RNC) lives, to North China and diverged to form a subspecies. Genomic analyses revealed that subspecies differentiation was promoted by temperature but impeded by gene flow and that genes related to fatty acid metabolism were under the strongest selection. Transcriptome analyses revealed downregulated hepatic genes related to fatty acid metabolism and upregulated those related to pheromones in RNH vs. RNC. Similar patterns were observed in relation to cold/warm acclimation. RNH preferred mates with stronger pheromone signals intra-populationally and more genetic divergence inter-populationally. We concluded that RNH experienced reduced fat utilization and increased pheromone-mediated sexual selection during its invasion from the cold north to warm south.

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.

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.

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species

Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation.

Asian house rats may facilitate their invasive success through suppressing brown rats in chronic interaction

BACKGROUND

The Asian house rat (Rattus tanezumi) and the brown rat (Rattus norvegicus) are closely related species and are partially sympatric in southern China. Over the past 20 years, R. tanezumi has significantly expanded northward in China and partially replaced the native brown rat subspecies, R. n. humiliatus. Although invasive species are often more aggressive than native species, we did not observe interspecific physical aggression between R. tanezumi and R. n. humiliatus. Here, we focused on whether or not R. tanezumi was superior to R. n. humiliatus in terms of nonphysical competition, which is primarily mediated by chemical signals.

RESULTS

We performed two laboratory experiments to test different paradigms in domesticated R. tanezumi and R. n. humiliatus. In Experiment 1, we caged adult male rats of each species for 2 months in heterospecific or conspecific pairs, partitioned by perforated galvanized iron sheets, allowing exchange of chemical stimuli and ultrasonic vocalization. The sexual attractiveness of male urine odor showed a tendency (marginal significance) to increase in R. tanezumi caged with R. n. humiliatus, compared with those in conspecific pairs. Hippocampal glucocorticoid receptor (GR) and brain-derived nutrition factor (BDNF) mRNA were upregulated in R. n. humiliatus and R. tanezumi, respectively, when the rats were caged in heterospecific pairs. In Experiment 2, we kept juvenile male rats in individual cages in rooms with either the same or the different species for 2 months, allowing chemical interaction. The sexual attractiveness of male urine was significantly enhanced in R. tanezumi, but reduced in R. n. humiliatus by heterospecific cues and mRNA expression of hippocampal GR and BDNF were upregulated by heterospecific cues in R. n. humiliatus and R. tanezumi, respectively. Although not identical, the results from Experiments 1 and 2 were generally consistent.

CONCLUSIONS

The results of both experiments indicate that nonphysical/chronic interspecific stimuli, particularly scent signals, between R. n. humiliatus and R. tanezumi may negatively affect R. n. humiliatus and positively affect R. tanezumi. We infer that chronic interspecific interactions may have contributed to the invasion of R. tanezumi into the range of R. n. humiliatus in natural habitats.