New microsatellite markers for the bush rat,Rattus fuscipes greyii: characterization and cross‐species amplification

We describe here 16 new microsatellite markers for the bush rat, Rattus fuscipes greyii, and characterize their cross‐species amplification within the Australian Rattus and at a greater level of divergence in Rattus rattus and Rattus norvegicus. Within R. f. greyii, all of the loci are highly polymorphic, with six to 24 alleles per locus across the species range and expected heterozygosity ranging from 0.48 to 0.90 per locus within a sample of 24 rats from a large population on Kangaroo Island. Cross‐species amplification rates were approximately 87% within the Australian Rattus and approximately 50% within R. rattus and R. norvegicus. These loci are highly polymorphic with a high success rate of cross‐species amplification, making them potentially useful for a wide range of genetic studies.     

Isolation and characterization of microsatellites in Rattus rattus

We isolated and characterized 10 microsatellite loci in the black rat Rattus rattus (Muridae, Rodentia), a widespread invasive species largely known to cause serious problems in agriculture and human health. Polymorphism was studied in two populations, one from Madagascar and one from Senegal. It ranged from three to 12 alleles in Madagascar, and from two to five alleles in Senegal. Together with the loci previously adapted from Rattus norvegicus, this set of markers should allow the conduct of thorough studies on the genetic structure of natural populations of R. rattus.     

Enzyme polymorphism in Malayan rats of the Subgenus Rattus

Electrophoretic variation in nine red cell proteins was analysed in 256 specimens belonging to six species of Malayan Rattus (including one with two subspecies) of the subgenus Rattus. The average proportion of loci heterozygous per individual for the taxa analysed is 0.04. With the exception of Rattus rattus diardii, R. tiomanicus tiomanicus and R. t. jalorensis, individuals of the other species could be identified by specific electrophoretic phenotypes of one or more of the markers analysed. Relationships among the species studied were elucidated by the classical and phenetic approaches employing electrophoretic characters. The results obtained by the two approaches were similar in most respects and they corresponded better with results based on morphological characters than those based on cytological characters.     

Focus: Zoonotic Disease: Prevalence and Diversity of the Streptobacillus Rat-bite Fever Agent,in Three Invasive,Commensal Rattus Species from South Africa

Rat-bite fever is an over-looked, global zoonotic disease that has a mortality rate of up to 13%, if untreated. Historically, this rat-borne disease has been attributed to one of two causative agents, Streptobacillus moniliformis or Spirillum minus. Given the confirmed presence of multiple invasive Rattus host species, high rat densities in urban, informal human settlements and increasing reports of rat bites in South Africa, we undertook a retrospective assessment of Streptobacillus in rats sampled from 16 urban sites, in Gauteng, the smallest but most populous Province in South Africa. Using a multi-gene PCR-sequencing approach, we confirmed Streptobacillus presence in 50.9% of oral swabs from three rat species and the presence of two Streptobacillus species, viz. S. moniliformis and S. notomytis. The two members of the cryptic Rattus rattus species complex (R. rattus and R. tanezumi), which are morphologically indistinguishable from each other, had markedly different colonization rates. Whereas 48.6% of rats from this species complex were Streptobacillus-positive, only 32.3% of Rattus tanezumi were positive compared to 61.5% R. rattus. Rattus norvegicus had an intermediate prevalence of 55.6%. Phylogenetic analysis of four gene regions (16S rRNA, gyrB, groEL, recA) identified two discrete lineages; S. moniliformis occurred exclusively in R. norvegicus, and S. notomytis was restricted to the two members of the R. rattus species complex; this represents the first report of Streptobacillus in R. tanezumi. These results highlight a largely overlooked zoonotic threat posed by invasive rats and confirm the presence of two discrete and potentially host-specific Streptobacillus lineages in South Africa.     

Rat kappa-chain allotypes. III. Serological and genetic analysis of RI-1b cross-reactivity in Australian Rattus

The presence of rat kappa-chain allotype specificities (RI-1a and b) has been studied in 13 subspecies of the seven native Australian species of Rattus. RI-1a reactivity was not detected among these rats. On the other hand, extensive cross-reactivity was seen with RI-1b, some sera cross-reacting totally (R. leucopus cooktownensis), some not at all (R. colletti), and the remainder showing at least two distinct levels of partial cross-reactivity, confirming the existence of multiple specificities for RI-1b. Three subspecies show polymorphism with respect to RI-1b cross-reactivity (R. sordidus, R. colletti, and R. l. leucopus) and in one case (leucopus) breeding studies have indicated that there is allelic inheritance of this trait. The segregation of RI-1b reactivity has been studied in crosses and backcrosses made between species differing in their RI-1b reactivity, and the results are consistent with the existence of codominant alleles at a single locus. The fact that these species differ extensively in their karyotype opens the door to possible chromosomal localization of this and other genetic traits.     

Dual exposure of Rickettsia typhi and Orientia tsutsugamushi in the field‐collected Rattus rodents from Thailand

Field‐collected rodents and fleas from ten provinces covering four regions of Thailand were investigated for possible rickettsial pathogen infections. The 257 trapped‐rodents belonged to 12 species. Five species of Genus Rattus accounted for 93% of the total capture, of which Rattus exulans and Rattus norvegicus were the two major species caught. All flea specimens, removed from trapped rodents, were identified as Xenopsylla cheopis. The PCR technique was performed on ectoparasite specimens to detect the presence of murine typhus pathogen (Rickettsia typhi) and scrub typhus pathogen (Orientia tsutsugamushi). Thirteen flea specimens (2.6 %) were found to be positive for R. typhi but none for O. tsutsugamushi. An ELISA technique was used to detect the rodent's antibodies against R. typhi and O. tsutsugamushi. Sixty‐one rodent serum samples (23.7%) were positive for R. typhi specific IgM, IgG, or both, while 47 of the samples (18.3%) were positive for O. tsutsugamushi. Twenty serum samples from R. norvegicus (7.8%) had detectable antibodies against both R. typhi and O. tsutsugamushi. Our findings revealed the existence of the dual infection of rickettsial pathogens in the same natural hosts.     

Spatial autocorrelation analysis offers new insights into gene flow in the Australian bush rat,Rattus fuscipes

Dispersal is a fundamental process that influences the response of species to landscape change and habitat fragmentation. In an attempt to better understand dispersal in the Australian bush rat, Rattus fuscipes, we have combined a new multilocus autocorrelation method with hypervariable microsatellite genetic markers to investigate fine-scale (< or = 1 km) patterns of spatial distribution and spatial genetic structure. The study was conducted across eight trapping transects at four sites, with a total of 270 animals sampled. Spatial autocorrelation analysis of bush rat distribution revealed that, in general, animals occurred in groups or clusters of higher density (< or = 200 m across), with intervening gaps or lower density areas. Spatial genetic autocorrelation analysis, based on seven hypervariable microsatellite loci (He = 0.8) with a total of 80 alleles, revealed a consistent pattern of significant positive local genetic structure. This genetic pattern was consistent for all transects, and for adults and sub-adults, males and females. By testing for autocorrelation at multiple scales from 10 to 800 m we found that the extent of detectable positive spatial genetic structure exceeded 500 m. Further analyses detected significantly weaker spatial genetic structure in males compared with females, but no significant differences were detected between adults and sub adults. Results from Mantel tests and hierarchical AMOVA further support the conclusion that the distribution of bush rat genotypes is not random at the scale of our study. Instead, proximate bush rats are more genetically alike than more distant animals. We conclude that in bush rats, gene flow per generation is sufficiently restricted to generate the strong positive signal of local spatial genetic structure. Although our results are consistent with field data on animal movement, including the reported tendency for males to move further than females, we provide the first evidence for restricted gene flow in bush rats. Our study appears to be the first microsatellite-based study of fine-scale genetic variation in small mammals and the first to report consistent positive local genetic structure across sites, age-classes, and sexes. The combination of new forms of autocorrelation analyses, hypervariable genetic markers and fine-scale analysis (< 1 km) may thus offer new evolutionary insights that are overlooked by more traditional larger scaled (> 10 km) population genetic studies.     

Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar

Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague‐mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague‐mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague‐mediated selection.     

Small mammal responses to pyric successional changes in eucalypt forest

Sixteen 1-ha study plots covering five regeneration stages were simultaneously trapped five times over a 20-month period to provide data on small mammal response to vegetation changes following fire. Areas regenerating after fires from 9 years to 1 month before the investigation were sampled in a uniform open forest on a coastal sand plain. Two types of understorey were recognized: one dominated by true forest shrubs with which Rattus fuscipes, Antechinus stuartii and Sminthopsis murina were associated, and another dominated by heath elements where the addition of Pseudomys novaehollandiae and Mus musculus produced a significantly more diverse small mammal community. The two communities exhibited different responses to post-fire vegetation changes. Rattus fuscipes was the most abundant species and showed a logistic growth in biomass. No resident populations were established in the first 3 years, but a rapid increase in biomass occurred from 3 to 5 years to plateau after 8 years. Regeneration age had the greatest effect on R. fuscipes biomass mediated through the amount of accumulated leaf litter with additional variation being attributed to several vegetation structure variables and plant species diversity. A replacement sequence in time was observed for species reaching their maximum abundance (P. novaehollandiae and/or M. musculus → S. murina → A. stuartii → R. fuscipes) and was interpreted as species occupying stages in the succession when their optimal habitat requirements were fulfilled. These results have important implications for the design of management policies using fire or fire regimes as tools for habitat maintenance or alteration. A mosaic of forest patches of adequate size covering the entire range of seral stages is necessary to meet the optimum requirements of all the above species.     

Variation on islands: major histocompatibility complex (Mhc) polymorphism in populations of the Australian bush rat

Loss of genetic variation in small, isolated populations is commonly observed at neutral or nearly neutral loci. In this study, the loss of genetic variation was assessed in island populations for a locus of major histocompatibility complex (Mhc), a locus shown to be under the influence of balancing selection. A total of 36 alleles was found at the second exon of RT1.Ba in 14 island and two mainland populations of Rattus fuscipes greyii. Despite this high overall diversity, a substantial lack of variation was observed in the small island populations, with 13 islands supporting only one to two alleles. Two populations, Waldegrave and Williams Islands, showed moderately high levels of heterozygosity (52-56%) which were greater than expected under neutrality, suggesting the action of balancing selection. However, congruence between the level of variation at this Mhc locus and in previous allozyme electrophoresis and mitochondrial DNA studies highlights the dominant influence of genetic drift and population factors, such as bottlenecks and structuring in the founding population, in the loss of genetic variation in these small, isolated populations.     

Commensal Rats and Humans: Integrating Rodent Phylogeography and Zooarchaeology to Highlight Connections between Human Societies

Phylogeography and zooarchaeology are largely separate disciplines, yet each interrogates relationships between humans and commensal species. Knowledge gained about human history from studies of four commensal rats (Rattus rattus, R. tanezumi, R. exulans, and R. norvegicus) is outlined, and open questions about their spread alongside humans are identified. Limitations of phylogeographic and zooarchaeological studies are highlighted, then how integration would increase understanding of species’ demographic histories and resultant inferences about human societies is discussed. How rat expansions have informed the understanding of human migration, urban settlements, trade networks, and intra- and interspecific competition is reviewed. Since each rat species is associated with different human societies, they identify unique ecological and historical/cultural conditions that influenced their expansion. Finally, priority research areas including nuclear genome based phylogeographies are identified using archaeological evidence to understand R. norvegicus expansion across China, multi-wave colonization of R. rattus across Europe, and competition between R. rattus and R. norvegicus.     

中国拟家鼠分类与分布厘订

拟家鼠(Rattus pyctoris)由Hodgson在1845年命名,其模式产地为尼泊尔。该种的分类地位和是否在中国有分布都存在较大争议。近来有研究认为拟家鼠不分布于我国。2020年,在西藏吉隆县和札达县进行野外调查时采集到7号标本,皮毛、头骨和牙齿的形态特征与尼泊尔的拟家鼠相似,分子系统发育分析支持这些标本为单系(PP=1.0),与模式产地样品C_yt b基因的K2?P遗传距离为0~2.8%,确认这些标本为拟家鼠。这是第一次在我国境内采集到拟家鼠标本,丰富和完善了这个物种的生物地理资料。     

Similarity of giemsa banding patterns of chromosomes in several species of the Genus Rattus

Giemsa banding patterns of chromosomes in seven Rattus species were compared. Four species (R. rattus tanezumi, R. norvegicus, R. exulans and R. muelleri) had all 2n=42 and their karyotypes and banding patterns were similar, although slight differences were observed. Another subspecies (R. rattus rattus) and two other species (R. fuscipes and R. conatus) had fewer chromosomes than the above species by having large biarmed chromosomes developed probably by Robertsonian fusion. The origin of the arms of biarmed chromosomes was recognized by their characteristic banding patterns. The remaining species, R. sabanus, had a karyotype markedly different from the other species by having two small metacentrics although in the others their number was 7. Banding patterns of the chromosomes in this species, however, were also very similar to those of the other, and therefore the 7 small metacentrics seemed to have originated by pericentric inversion of small acrocentrics.Contribution No. 912 from the National Institute of Genetics, Japan. Supported by a grant-in-aid from the Ministry of Education of Japan, Nos. 90183, 90375 and 744002.     

社鼠和褐家鼠消化道长度和重量的季节变化

测定了浙江金华的社鼠和褐家鼠消化道长度和重量的季节变化。野生社鼠消化道各器官无论长度不审重量都有明显季差异,在寒冷的冬季具有相对较大的小肠、大肠、盲肠、雄性社鼠的消化道长度在秋季由于食物条件的改善而明显下降,但雌性社鼠由于在秋季仍有繁殖负担,其消化道长度下降不明显,而家栖的褐家鼠只有总消化道、小肠和大肠的长度有季节差异,冬、春季高于夏、秋季。消化道形态季节变化与温度、食物条件和繁殖有关。     

八种大鼠染色体银染核仁组织者的比较研究

本文对我国大鼠属(Rattus)8种鼠类的银染核仁组织者(NORs)进行了比较研究,结果表明:8种大鼠银染核仁组织者(Ag-NORs)的数目和分布均存在一定的差异,它们的NORs都呈现比较显著的多态性,并观察到了Ag-NORs的联合现象和异形现象。此外,将其银染核型差异数量化,通过模糊聚类分析,得到8种大鼠的聚类分析分支图,并结合它们的地理分布等对其分类地位进行了讨论。     

Mitochondrial DNA evidence for the spread of Pacific rats through Oceania

In the 10 years since we published our first full analysis of mitochondrial DNA (mtDNA) variation in Rattus exulans as a means for tracking human migration in Polynesia, we have extended the commensal approach through time and space with the use of ancient DNA (aDNA) and by analysing samples from across the Pacific. Not only can mtDNA phylogenies provide information regarding population origins and paths of migration, they have also provided information regarding degrees of contact and interaction between islands. An important extension of the R. exulans project is the creation and on-going development of a genetic database for the identification of Rattus species based on mtDNA sequences. The phylogenetic analysis of sequences from 18 species and 1 subspecies of Rattus thus far have raised some questions regarding species identification and species distributions in the Pacific.     

Dispersal strategies, secondary range expansion and invasion genetics of the nonindigenous round goby, Neogobius melanostomus, in Great Lakes tributaries

Dispersal strategies are important mechanisms underlying the spatial distribution and colonizing ability of all mobile species. In the current study, we use highly polymorphic microsatellite markers to evaluate local dispersal and colonization dynamics of the round goby (Neogobius melanostomus), an aquatic invader expanding its range from lake to river environments in its introduced North American range. Genetic structure, genotype assignment and genetic diversity were compared among 1262 round gobies from 20 river and four lake sites in three Great Lakes tributaries. Our results indicate that a combination of short-distance diffusion and long-distance dispersal, collectively referred to as 'stratified dispersal', is facilitating river colonization. Colonization proceeded upstream yearly (approximately 500 m/year; 2005-2009) in one of two temporal replicates while genetic structure was temporally stable. Contiguous dispersal from the lake was observed in all three rivers with a substantial portion of river fish (7.3%) identified as migrants. Genotype assignment indicated a separate introduction occurred upstream of the invasion front in one river. Genetic diversity was similar and relatively high among lake and recently colonized river populations, indicating that founder effects are mitigated through a dual-dispersal strategy. The remarkable success of round goby as an aquatic invader stresses the need for better diffusion models of secondary range expansion for presumably sessile invasive species.     

Is it worth eradicating the invasive pest Rattus norvegicus from Molène archipelago? Genetic structure as a decision-making tool

Genetic variability and structure were estimated by microsatellite analysis at 7 loci in brown rat populations (Rattus norvegicus) from the Iroise insular complex and neighbouring mainland (Brittany, France). Island genetic diversity is lower than on the mainland and a highly significant positive correlation was found between mean heterozygosity and the logarithm of island area, which is consistent with theoretical expectations. Rattus norvegicus populations are substructured at a kilometric scale, both on the islands and on the mainland. Intra-island structuration is extremely high, suggesting that no effective migration occurs between islands or with the mainland. Historical and genetical evidence suggest that R. norvegicus was introduced independently on Ouessant and Molène archipelago, with a low and a high founder effect respectively. These results are discussed in terms of recolonization probability of islands that have been cleared of R. norvegicus, which illustrates the usefulness of genetic markers in determining parameters of interest to the conservation biologist.     

Evolution of karyotypes and differentiation in 13 Rattus Species

Karyotypes of 13 Rattus species collected in Asia and Oceania were analysed with special interest to karyotype evolution and species differentiation. They were classified into three groups according to their karyotype similarity. Four species (R. annandalei, R. exulans, R. muelleri and R. norvegicus) with 2n=42 and a karyotype similar to some of the polymorphic karyotypes in the Asian black rats (R. rattus) are classified into the first group. Pericentric inversion of some acrocentrics seemed to have caused the differentiation of these species. The other four species (R. bowersii, R. fuscipes, R. leucopus and R. conatus) with similar karyotypes as the above group, but lower chromosome numbers than 2n=42 are classified into the second group. Robertsonian fusion in some acrocentrics observed in the first group are suggested to have caused the development of the species in this group. The remaining four species (R. sabanus, R. canus, R. huang and R. niviventer) with karyotypes markedly different from the above two in having a fewer number of small metacentrics are classified into the third group. They seemed to be more primitive karyotypes than the other Rattus species. By the comparison between the polymorphic karyotypes in the black rat, and karyotypes in its related species it was suggested that the former had occurred as primary events to the differentiation of the latter. Parallelism between the karyotype evolution and the species differentiation was discussed.Contribution No. 874 from the National Institute of Genetics, Japan. Supported by a grant-in-aid from the Ministry of Education of Japan (No. 92159 and 92332).