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.     

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.     

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.     

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.     

Genetic Differentiation among Karyotypic Forms of the Black Rat, RATTUS RATTUS

The black rat, Rattus rattus, consists of five karyotypic forms—2n = 42 (high C-banding); 2n = 42 (low C-banding); 2n = 40; 2n = 38; 2n = 42 Mauritius. Here, we use isozyme electrophoresis and microcomplement fixation to elucidate the genetic distance and phylogenetic relationship among each of the various karyotypic forms of R. rattus and R. norvegicus . The results show that (1) the 2n = 42 Mauritius black rat (2n = 42Mau) is genetically very similar to the 2n = 38 form, suggesting that this island population has undergone very rapid chromosomal evolution; (2) the 2n = 40 form from the highlands of Sri Lanka is genetically distinct from the 2n = 38 form from the lowlands; the genetic difference is probably insufficient, however, to prevent future introgression; (3) the level of genetic differentiation occurring between the 2n = 42 forms on the one hand and the 2n = 38, 2n = 40 and 2n = 42 Mau forms on the other support the hybrid incompatability data in suggesting that the two groups are either full species or incipient species; (4) in contrast to data from amino acid composition of transferrin and from restriction endonuclease digests of mtDNA, the present data suggest that the various karyotypic forms of R. rattus are phylogenetically more closely related to each other than any is to R. norvegicus, and that they are related by a series 2n = 42 → 2n = 40 → 2n = 38; (5) the R. rattus/R. norvegicus divergence occurred 2–8 million years ago, whereas the various chromosomal forms of R. rattus diverged over the last 4 million years.     

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.     

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.     

Two sexes respond equally to food restriction in a sexually dimorphic but not body mass dimorphic jumping spider

Natural selection favors animals that evolve developmental and behavioral responses that buffer the negative effects of food restrictions. These buffering responses vary both between species and within species. Many studies have shown sex‐specific responses to environmental changes, usually in species with sexual size dimorphism (SSD), less found in species with weak or no SSD, which suggests that sizes of different sexes are experiencing different selections. However, previous studies usually investigated development and behavior separately, and the balanced situation where males and females of sexually dimorphic species respond in the same way to food restriction remains little known. Here, we investigated this in Phintelloides versicolor (Salticidae) that presents sexual dimorphism in color and shape but weak SSD. We examined whether food restriction induced the same responses in males and females in development duration, adult body size and weight, daily time allocated to foraging, and hunting. We found food restriction induced similar responses in both sexes: both exhibited longer development duration, smaller adult body size and weight, higher probability of staying outside nests and noticing prey immediately, and higher hunting success. However, there were sexual differences regardless of food condition: females showed faster development, smaller adult body size, higher probability of staying outside of nests, and higher hunting success. These indicated the differential selection on male and female sizes of P. versicolor could be under a balanced situation, where males and females show equal developmental and behavioral plasticity to environmental constraints.     

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.     

Attack and defense in laboratory and wild Norway and black rats

Intra- and interspecific agonistic encounters in Long-Evans and field-trapped Rattus norvegicus and Rattus rattus showed a consistency in the form and character of attack and defensive behaviors. Colony alpha males exhibited high levels of lateral attack, on-top, and chasing behaviors which resulted in a high percentage of bites on the intruder's back. Bites directed to the back were countered by intruders through the utilization of boxing, on-back, and flight defense. These findings indicate that agonistic interactions in Rattus are underlined by back-attack and back-defense strategies. A sex difference in biting was also consistent across strains: males bit the back and flanks and females the head of an anesthetized stranger which suggest differences in the motivation of male and female attack.     

Adult sex ratio,sexual dimorphism and sexual selection in a Mesozoic reptile

The evolutionary history of sexual selection in the geologic past is poorly documented based on quantification, largely because of difficulty in sexing fossil specimens. Even such essential ecological parameters as adult sex ratio (ASR) and sexual size dimorphism (SSD) are rarely quantified, despite their implications for sexual selection. To enable their estimation, we propose a method for unbiased sex identification based on sexual shape dimorphism, using size-independent principal components of phenotypic data. We applied the method to test sexual selection in Keichousaurus hui, a Middle Triassic (about 237 Ma) sauropterygian with an unusually large sample size for a fossil reptile. Keichousaurus hui exhibited SSD biased towards males, as in the majority of extant reptiles, to a minor degree (sexual dimorphism index −0.087). The ASR is about 60% females, suggesting higher mortality of males over females. Both values support sexual selection of males in this species. The method may be applied to other fossil species. We also used the Gompertz allometric equation to study the sexual shape dimorphism of K. hui and found that two sexes had largely homogeneous phenotypes at birth except in the humeral width, contrary to previous suggestions derived from the standard allometric equation.     

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.     

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.     

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.     

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.     

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.     

GEOTROPIC ORIENTATION OF YOUNG RATS

The geotropic orientation of Rattus rattus (roof rat) obeys the equations previously found applicable for Rattus norvegicus. The former is more sensitive, geotiopically, and the numerical values of the constants in the equations for the two forms are found to differ significantly. Certain consequences of this difference are pointed out.     

Ecology of cutaneous leishmaniasis in Sinai: linking parasites,vectors and hosts

Cutaneous leishmaniasis (CL) is a neglected clinical form of public health importance that is quite prevalent in the northern and eastern parts of Egypt. A comprehensive study over seven years (January 2005-December 2011) was conducted to track CL transmission with respect to both sandfly vectors and animal reservoirs. The study identified six sandfly species collected from different districts in North Sinai: Phlebotomus papatasi, Phlebotomus kazeruni, Phlebotomus sergenti, Phlebotomus alexandri, Sergentomyia antennata and Sergentomyia clydei. Leishmania (-)-like flagellates were identified in 15 P. papatasi individuals (0.5% of 3,008 dissected females). Rodent populations were sampled in the same districts where sandflies were collected and eight species were identified: Rattus norvegicus (n = 39), Rattus rattus frugivorous (n = 13), Rattus rattus alexandrinus (n = 4), Gerbillus pyramidum floweri (n = 38), Gerbillus andersoni (n = 28), Mus musculus (n = 5), Meriones sacramenti (n = 22) and Meriones crassus (n = 10). Thirty-two rodents were found to be positive for Leishmania infection (20.12% of 159 examined rodents). Only Leishmania major was isolated and identified in 100% of the parasite samples. The diversity of both the vector and rodent populations was examined using diversity indices and clustering approaches.     

Review of negative effects of introduced rodents on small mammals on islands

In this first comprehensive review of negative effects of introduced rodents on insular small mammals, the focal species Rattus rattus, R. norvegicus, R. exulans and Mus musculus are implicated in at least 11 extinctions. Furthermore, removal experiments, eradication campaigns and control programmes provide evidence for negative effects on extant populations. While data are currently insufficient for meaningful generalisation with regard to the most threatening rodents, the most threatened small mammals, and the true extent of the problem, it is interesting that R. rattus is implicated in the majority of impacts. This may be explained by its extensive distribution and ecological plasticity. I conclude with methodological recommendations to guide data collection for impact quantification and the study of impact mechanism. This information should facilitate the prioritisation and justification of eradication campaigns, control programmes and biosecurity measures while ensuring that much-needed attention is paid to the conservation of insular small mammals.     

Shifts from native to invasive small mammals across gradients from tropical forest to urban habitat in Borneo

Urbanization has paved the way for the spread of commensal rodents at global scale. However, it is largely unknown how these species use tropical anthropogenic landscapes originally covered with forests and inhabited by diverse small mammal assemblages. We surveyed non-flying small mammals in various urban and suburban habitat types and adjacent forest in the tropical town of Kota Kinabalu in Borneo. We used occupancy and polynomial regression models to determine variation in species occurrences along gradients of land-use intensity. Müller’s sundamys (Sundamys muelleri) was the only native small mammal species found in urban and suburban landscapes with a continuous decrease in occurrence probability from forests to urban habitats. The invasive Asian black rat (Rattus rattus species complex) and the invasive Asian house shrew (Suncus murinus) had the highest occurrence probabilities in habitats of intermediate land-use intensity, but Asian black rats are also likely to occasionally invade forested habitats and occupied urban habitats in sympatry with the Norway rat (Rattus norvegicus). In urban and suburban habitats, fallow land possibly favoured the occurrence of S. muelleri and S. murinus. Other native small mammal species (Muridae, Sciuridae, Tupaiidae) were found only in forested areas. Our study shows that native small mammals found in forest are largely replaced by invasive species in urban and suburban habitats. Due to their occurrence in habitats of various land use intensities, S. muelleri and R. rattus comprise central links between forest wildlife and urban species, an association that is important to consider in studies of parasite and disease transmission dynamics.