Evolutionary history of rat‐borne Bartonella: the importance of commensal rats in the dissemination of bacterial infections globally

Emerging pathogens that originate from invasive species have caused numerous significant epidemics. Some bacteria of genus Bartonella are rodent‐borne pathogens that can cause disease in humans and animals alike. We analyzed gltA sequences of 191 strains of rat‐associated bartonellae from 29 rodent species from 17 countries to test the hypotheses that this bacterial complex evolved and diversified in Southeast Asia before being disseminated by commensal rats Rattus rattus (black rat) and Rattus norvegicus (Norway rat) to other parts of the globe. The analysis suggests that there have been numerous dispersal events within Asia and introductions from Asia to other regions, with six major clades containing Southeast Asian isolates that appear to have been dispersed globally. Phylogeographic analyses support the hypotheses that these bacteria originated in Southeast Asia and commensal rodents (R. rattus and R. norvegicus) play key roles in the evolution and dissemination of this Bartonella complex throughout the world.     

Competition, coexistence, and adaptation amongst rodent invaders to Pacific and New Zealand islands

Variation in skull size was investigated for three species of rats (kiore –Rattus exulans Peale; ship rat –R. rattus L.; Norway rat –R. norvegicus Berkenhout) which were introduced by humans to various islands in New Zealand and other Pacific islands. Data from seventy-one islands and 882 specimens are examined for evidence of the effects of latitude, island size and interspecific competition among rats and the house mouse (Mus musculus L.) on skull size, using multiple regressions. For R. exulans, skull size increases with latitude as predicted by Bergmann's rule, but no such effect occurs for the other two rats. There was a positive relationship between island size and the number of species inhabiting it, and some species combinations were more likely to occur than others. For example, R. exulans and R. norvegicus were more likely to occur together, while R. rattus and R. exulans were rarely sympatric. R. exulans and R. rattus skull size was negatively correlated with the number of other rodents on the same island. R. exulans skull size increased on smaller islands in some island groups, perhaps because increased density and consequent increased intraspecific competition on smaller islands favours increased body size. This effect is more pronounced in tropical islands (Solomon islands), than in subtropical ones (Hawaiian islands) and less so in temperate New Zealand. Collectively the data demonstrate that rapid evolution of body size in predictable directions can follow within 150 years of the introduction of species to new receiving communities.     

Kiore (Rattus exulans) distribution and relative abundance on a small highly modified island

ABSTRACT

Kiore (Pacific rat; Rattus exulans) is both a target for eradication and a taonga or highly valued species in New Zealand, and its abundance and distribution vary considerably throughout the country. We investigated reports of an abundant kiore population on Slipper Island (Whakahau), off the east coast of New Zealand’s North Island, in March 2017. We trapped kiore to examine their distribution across a range of habitats with varying degrees of human activity. Kiore were captured in all habitats, with particularly high abundance at a campground with a fruiting fig tree (50 kiore per 100 trap nights corrected for sprung traps). We found no evidence of other rat species; Slipper Island appears to remain one of few New Zealand islands with kiore but without ship rats (Rattus rattus) and Norway rats (R. norvegicus), the two other rat species present in New Zealand. Slipper Island potentially provides opportunities to research kiore behaviour and population dynamics in a New Zealand commensal environment, and genetics of an isolated island population.     

Herbivory in invasive rats: criteria for food selection

Three species of rats (Rattus exulans, R. rattus, R. norvegicus) are widely invasive, having established populations in terrestrial habitats worldwide. These species exploit a wide variety of foods and can devastate native flora and fauna. Rats can consume a variety of plant parts, but may have the most dramatic effects on plant populations through consumption and destruction of seeds. The vulnerability of vegetation to rat consumption is influenced by many factors including size of plant part, and mechanical and chemical defenses. We reviewed the literature to find out what plant species and plant parts invasive rats are consuming and what characteristics these sources share that may influence selection by rats. Many of the studies we found were preformed in New Zealand and our analyses are, therefore, focused on this location. We also performed feeding trials in the laboratory with R. norvegicus to determine if seed hardness and palatability would influence rat consumptive choices. We found more reports of rat consumption of fruits and seeds versus vegetative plant parts, and smaller fruits and seeds versus larger. R. norvegicus are reported to consume proportionally more vegetative plant parts than either R. exulans or R. rattus, possibly due to their more ground dwelling habits. Large size and hard seed coats may deter rat feeding, but unpalatable chemicals may be even more effective deterrents to rats. Scientists and managers can better manage vegetation in rat invaded areas by understanding the criteria rats use to select food.     

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.     

Invasion genetics of a human commensal rodent: the black rat Rattus rattus in Madagascar

Studies focusing on geographical genetic patterns of commensal species and on human history complement each other and provide proxies to trace common colonization events. On Madagascar, the unintentional introduction and spread of the commensal species Rattus rattus by people may have left a living clue of human colonization patterns and history. In this study, we addressed this question by characterizing the genetic structure of natural populations of R. rattus using both microsatellites and mitochondrial sequences, on an extensive sampling across the island. Such data sets were analysed by a combination of methods using population genetics, phylogeography and approximate Bayesian computation. Our results indicated two introduction events to Madagascar from the same ancestral source of R. rattus, one in the extreme north of the island and the other further south. The latter was the source of a large spatial expansion, which may have initially started from an original point located on the southern coast. The inferred timing of introduction events—several centuries ago—is temporally congruent with the Arabian trade network in the Indian Ocean, which was flourishing from the middle of the first millennium.     

Genetics of the ceramide/sphingosine-1-phosphate rheostat in blood pressure regulation and hypertension

Background

South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present.

Results

To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species.

Conclusions

This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.     

Commensalism facilitates gene flow in mountains: a comparison between two Rattus species

Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20–640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.     

Genetic characterization of black rat (Rattus rattus) of the Canary Islands: origin and colonization

In the Canary Islands two invasive rat species, Rattus rattus and Rattus norvegicus are present, but little is known about the origin and colonization. To this end, a molecular study was performed on R. rattus from the Archipelago and from the nearest continents. Partial cytochrome b gene sequencing offered very low levels of haplotype and nucleotide diversities, with only seven haplotypes identified. All of them belong to the European Lineage I, specifically to the “ship rat” cluster. The haplotype network showed a star-like topology. Haplotype distribution showed a genetic subdivision between eastern and central/western islands, suggesting a double colonization event. This hypothesis is congruent with historical human colonization and it is similar to that proposed for the rodent parasite Hymenolepis diminuta. In addition, a possible role of the Canary Islands as a faunal link with the European and American continents is discussed.     

Intra- and Interspecific Variation of the Mitochondrial Genome in RATTUS NORVEGICUS and RATTUS RATTUS: Restriction Enzyme Analysis of Variant Mitochondrial DNA Molecules and Their Evolutionary Relationships

Restriction endonuclease analysis has revealed extensive mtDNA polymorphism in two species of rats, Rattus rattus and Rattus norvegicus. Sequence divergence values for the eight detected R. norvegicus variants range from 0.2% to 1.8% and for the eight R. rattus variants, from 0.2% to 9.6%. Three of the most closely related R. norvegicus mtDNA's appear to differ by deletions/insertions of about 4 base pairs apiece. Restriction sites for seven enzymes have been mapped for 11 of these variants. The 31 intraspecific and 41 interspecific variant sites appear to be evenly distributed on the mtDNA molecule outside of the rRNA cistrons. The location of sites present in all the DNAs suggests that the rRNA genes and possibly the light strand origin of replication may be more highly evolutionarily conserved than other parts of the molecule. The sequence divergences among the mtDNAs of animals whose geographic origins are separated by major barriers, such as oceans, were significantly greater than those among animals found within large land masses, such as the continental United States. Dendrograms (phenograms), which have been constructed to depict the relationships among the various DNAs, indicate that East Asian members of the R. rattus species are more closely related to American rats of this species than to other Asian R. rattus animals from Sri Lanka. Moreover, it appears that R. norvegicus comprises a group taxonomically distinct from any of the R. rattus subspecies.     

Invasion by Rattus rattus into native coastal forests of south‐eastern Australia: are native small mammals at risk?

The black rat, Rattus rattus, is an alien rodent in Australian ecosystems where niche overlap with native small mammals may lead to competition for resources and displacement of native species. In coastal habitats surrounding Jervis Bay in south‐eastern Australia, R. rattus co‐occurs with the native bush rat, Rattus fuscipes, and brown antechinus, Antechinus stuartii. Relative distributions and abundances, and fine‐scale space use suggest invasive and native rodents compete for use of space and habitat. Such competitive interactions were not evident between R. rattus and native A. stuartii, which was negatively influenced more by disturbance to habitat. Differences in rodent communities between spatially separate forests forming the northern and southern peninsulas of Jervis Bay potentially reflect symmetrical competition and differences in competitive outcomes. In southern forests, R. rattus was largely restricted to patches of disturbed forest associated with campgrounds. Competitive interference by native rodent populations inhabiting surrounding intact forests may have so far limited R. rattus colonization of these areas. In northern forests, R. rattus was the predominant rodent irrespective of disturbance, while populations of R. fuscipes were unusually low seemingly due to poor juvenile recruitment. Native individuals avoided areas frequented by adult R. rattus and given that species did not partition use of microhabitats, R. rattus most likely precluded R. fuscipes from suitable habitat and in doing so limited native populations. We discuss how natural disturbance of habitat and human activity have potentially facilitated successful invasion by R. rattus of the northern forests. Studies that manipulate rodent populations are required to support these interpretations of observed patterns.     

Black rat (Rattus rattus) genomic variability characterized by chromosome painting

Black rats are of outstanding interest in parasitology and infective disease analysis. We used chromosome paints from both the mouse(Mus musculus) and the Norway rat(Rattus norvegicus) to characterize the genome of two Black rat subspecies from Italy. Both subspecies have two large metacentrics (n. 1, 4) not present in the Norway rat (2n = 42).Rattus rattus rattus has a diploid number of 2n = 38, whileRattus rattus frugivorous has two small metacentric “supernumerary” or B chromosomes for a diploid number of 2n = 38 + 2B. The 21 mouse paints gave 38 signals on theR. r. rattus karyotype and 39 signals in theR. r. frugivorous karyotype. The two metacentrics, not present inR. norvegicus, were hybridized by mouse 16/1/17 and mouse 4/10/15. These chromosomes are homologous to: RRA1 = RNO 5/7, and RRA4 = RNO 9/11 and not “4/7” and “11/12” as previously reported. Furthermore, the synteny of Chr 13 of theR. r. frugivorous withR. norvegicus Chr 16 and mouse Chrs 8/14 is not complete, because there is a small pericentromeric insertion of RNO Chr 18 (mouse Chr 18). If we consider only the two metacentrics, RRA1 and RRA4, the principal differences betweenR. norvegicus andR. rattus, then we can propose the derived synteny of 124 genes in the black rat. A comparison of the Z index between rats and mice shows an acceleration of genomic evolution among genus, species, and subspecies. The chromosomal differences betweenR. r. rattus xR. r. frugivorous suggest that they may be classified as different species because hybrids would produce 50% unbalanced gametes.     

The morphology, distribution and conservation implications of introduced rats, Rattus spp. in the granitic Seychelles

There are no native land mammals in the Seychelles archipelago other than bats. Introduced rats have reduced the conservation value of most islands. This paper compares the results of rat‐trapping carried out on eight islands in the granitic Seychelles, between July 1999 and April 2000. Trapping was carried out in both the dry and wet seasons. Three introduced rodent species were caught, including two species of rat (ship rat Rattus rattus Linnaeus and Norway rat R. norvegicus Berkenhout), but only one Rattus species occurred on each island. Both rat species were smaller than European or Asian conspecifics, and there were variations in the size and appearance of rats on different islands. Inter‐island differences in size and pelage colour are discussed.     

Comparative phylogeography of invasive Rattus rattus and Rattus norvegicus in the U.S. reveals distinct colonization histories and dispersal

Invasive Rattus are arguably the most costly and destructive invasive species on the planet, but little is known concerning their invasion history and population structure in the U.S. We utilized both nuclear microsatellites and mitochondrial DNA sequences (mtDNA) to compare the colonization history, patterns of gene flow, and levels of genetic diversity of Rattus rattus and R. norvegicus in the U.S. Analyses of mtDNA suggest R. rattus is characterized by a single rapid expansion into the U.S. from one or two very closely related mtDNA lineages or geographic sources. For R. norvegicus, mtDNA analyses suggest at least four invasions distinct in space and/or time have occurred to establish its distribution in the U.S. Microsatellite analyses suggest for R. rattus that dispersal is characterized by an isolation-by-distance pattern, suggesting a relatively low frequency of long distance dispersal, and low levels of establishment for novel propagules. In contrast, microsatellite analyses of R. norvegicus suggest high frequencies of long distance dispersal and essentially panmixia among nearly all sampled populations, as well as a high frequency of novel propagules entering at the east and west coasts and assimilating into established populations. We discuss these results in the context of invasive Rattus management in the U.S. and their implications for invasive species in general, as well as the implications for managing the spread of rat-borne pathogens.     

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.     

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.     

Prickly coexistence or blunt competition? Opuntia refugia in an invaded rodent community

Endemic Nesoryzomys swarthi and invasive Rattus rattus exist in unlikely sympatry in Galápagos as female N. swarthi suffer from competition with R. rattus. This study evaluates the role of feeding habits in facilitating their co-occurrence. Spool-and-line tracking of 85 N. swarthi and 33 R. rattus was used to quantify their selected diets, foods of which were used in captive trials of 46 N. swarthi and 34 R. rattus to quantify their preferred diets. Selected diets were compared between species and seasons using niche measures, and contrasted to preferred diets to qualify inferences about competition. Diet overlap was highest in the wet season when food—particularly fruit—abundance was highest and R. rattus diet breadth was broadest. Preferred and selected diets were marginally correlated for R. rattus but uncorrelated for N. swarthi, suggesting that R. rattus interfere with N. swarthi foraging. Diet overlap was highest between female N. swarthi and R. rattus, perhaps due to female breeding requirements. Male N. swarthi avoided R. rattus-preferred foods, possibly to avoid aggressive encounters with R. rattus. During the dry season, when foods declined and the R. rattus population crashed, diet overlap was lowest as R. rattus diet narrowed in the absence of fruits. Female, and particularly male, N. swarthi diet broadened, with emphasis on acquiring Opuntia foods but N. swarthi-preferred and selected diets were uncorrelated, suggesting that their foraging was inhibited by R. rattus. In conclusion, the narrower diet breadth of R. rattus in contrast to N. swarthi suggests that this species may be less adapted to food acquisition at this site, particularly when fruits are absent. The year-round presence of R. rattus, however, appears to inhibit N. swarthi foraging for its preferred diet, and they instead specialise on Opuntia foods, which were uneaten by R. rattus and may provide N. swarthi with a localised competition refuge from encounters with R. rattus. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sexual-size dimorphism in two synanthropic rat species: Comparison and eco-evolutionary perspectives

Sexual dimorphism is a common trait in many mammal species and sexual-size dimorphism (SSD) represents its commonest form. Rattus rattus and Rattus norvegicus are two cosmopolitan, polygynous species, for which a male-biased SSD has been anecdotally reported, but never quantified. In this work, we assessed the occurrence of SSD in both species and we tested the hypothesis that R. norvegicus has a more evident SSD than R. rattus, in agreement with their body mass-testes size ratio, intra-male aggressive behaviour and mating system. We collected weight data of 40 (20 males and 20 females) adult R. rattus and 27 (13 males and 14 females) adult R. norvegicus from 4 localities in Italy characterized by different habitat typologies. We used a t-test based on Bayesian inference to compare the SSD in both species. The results were in line with our expectation supporting a higher SSD in R. norvegicus than in R. rattus. This study aimed to identify the eco-evolutionary drivers of SSD, and provides further support to well established life history theories on two widely distributed rodent species.     

A mathematical epidemiological model of gram-negative Bartonella bacteria: does differential ectoparasite load fully explain the differences in infection prevalence of Rattus rattus and Rattus norvegicus?

We postulate that the large difference in infection prevalence, 24% versus 5%, in R. norvegicus and R. rattus, respectively, between these two co-occurring host species may be due to differences in ectoparasite and potential vector infestation rates. A compartmental model, representative of an infectious system containing these two Rattus species and two ectoparasite vectors, was constructed and the coefficients of the forces of infection determined mathematically. The maximum difference obtained by the model in the prevalence of Bartonella in the two Rattus species amounts to 4.6%, compared to the observed mean difference of 19%. Results suggest the observed higher Bartonella infection prevalence in Rattus norvegicus compared to Rattus rattus, cannot be explained solely by higher ectoparasite load. The model also highlights the need for more detailed biological research on Bartonella infections in Rattus and the importance of the flea vector in the spread of this disease.     

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

Anthropophilic species (“commensal” species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their noncommensal counterparts. Using a next‐generation sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 noncommensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that, while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the noncommensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats.