Origin of agouti-melanistic polymorphism in Wild Black Rats (Rattus rattus) inferred from Mc1r gene sequences

We examined nucleotide changes that underlie coat color variation in Black Rats (the Rattus rattus species complex), which show polymorphism in dorsal fur color, including either grayish brown (agouti) or black (melanistic) forms. We examined the full coding sequence of a gene known to produce melanism in other vertebrates-melanocortin-1-receptor gene Mc1r (954 bp) -using samples of both R. rattus (with 2n = 38) and its close relative Asian Black Rat (R. tanezumi; 2n = 42). We used 61 specimens from Japan with karyotype-known individuals and four samples from Pakistan. We found 11 allele sequences and constructed a network tree that shows two distinct clusters, with allelic segregation according to karyotype and by inference, representing the two species. We found that a nucleotide substitution from G to A at site 280, producing an amino acid change from glutamic acid to lysine, was associated with the dominant trait of the melanistic form of the coat color in R. rattus. Notably, the derived SNP 280A was found in a single allele, with the ancestral SNP 280G present in seven alleles. By contrast, all three alleles for R. tanezumi retain the ancestral SNP 280G. These results suggest a possible recent origin of melanism in R. rattus.     

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.     

Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes

The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.     

Characterization of third beta-chain variant in Rattus rattus rufescens

Different molecular forms of hemoglobins of locally available murines, represented by Rattus rattus rufescens, have been investigated and the probable genetic mechanisms leading to the observed heterogenicity in the hemoglobin phenotypes are discussed. Each fraction was isolated in chromatographically pure form, identified and characterised structurally to establish their alpha- and non-alpha-chain constitution. Six molecular forms of component hemoglobins were identified from a wild population of R. rattus rufescens. The present study suggests five different globin chains in the hemoglobin of house rats (Rattus rattus rufescens). There are apparently two alpha-chains, namely alpha I and alpha II, and three different beta-chains, viz. beta I, beta II and beta III. The invariable presence, though at varying concentrations, of all these five globin chains implicates a gene duplication at the alpha-chain loci and a gene triplication at the beta-chain loci, the latter being a rather rare and unique genetic event.     

The tick Ixodes granulatus infests Rattus rattus populating a small island offshore of Singapore

The ixodid tick Ixodes granulosus Supino 1897 was found infesting Rattus rattus in Semakau island, one of the small offshore islands fringing Singapore to the south. None of the examined R. rattus from the other islands fringing Singapore, or from Singapore island were found infested. Ixodes granulatus occurs, however, on Singapore island on Rattus annandalei, resident of undisturbed forested habitats. We speculate that invading black rats in Semakau replaced autochthonous sylvatic rodent population and contracted their associate tick population.     

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.     

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.     

Seasonal studies on commensal rats and their ectoparasites in a rural area of Egypt: the relationship of ectoparasites to the species, locality, and relative abundance of the host.

The present study was carried out in 3 villages, namely Kafr Ayoub Soliman, Kafr Ibrahim El-Aidi, and El-Sa'adat, Sharqiya Governorate, Egypt. A total of 519 rats was collected from the 3 study sites: 46.6% Rattus rattus, and 53.4% Rattus norvegicus. A total of 20,643 ectoparasites was recovered from R. rattus: 33.3% mites, 33.8% fleas, and 32.9% lice. From R. norvegicus a total of 40,997 ectoparasites was recovered: 28.9% mites, 31% fleas, and 40.1% lice. Three common mite species were recovered from both rat hosts, i.e., Ornithonyssus bacoti, Radfordia ensifera, and Laelaps nuttalli. Three common flea species were also recovered from both rat hosts, i.e., Echidnophaga gallinacea, Leptopsylla segnis, and Xenopsylla cheopis. Polyplax spinulosa was the only dominant louse species that infested both rat hosts. Rats did not show a definite breeding season, and the seasonal rat indices were generally low in different study sites. There were no significant differences between the prevalence of each of mites, fleas, and lice in both rat species. The total general indices of mites and fleas, on the other hand, was significantly higher in R. norvegicus. The general index of X. cheopis was high and ranged between 5.9 in R. rattus and 14.5 in R. norvegicus. Season-related changes were observed in the general index of each of L. segnis infesting both rat species and R. ensifera and O. bacoti infesting R. norvegicus. The prevalence and general indices of some ectoparasites showed differences related to the locality of their rat hosts. Seasonal changes in the general indices of some ectoparasites paralleled seasonal changes in the relative abundance of their rat hosts.     

Epizootiological and epidemiological study of hantavirus infection in Japan

Epizootiological surveys on hantavirus infections in rodents were carried out in various areas of Japan, including the four major islands of Hokkaido, Honshu, Shikoku, and Kyushu from 2000 to 2003. A total of 1,221 rodents and insectivores were captured. Seropositive animals were found in Apodemus (A.) speciosus (5/482, 1.0%), Rattus (R.) norvegicus (4/364, 1.1%), R. rattus (3/45, 6.7%), and Clethrionomys (C.) rufocanus (7/197, 3.6%). The partial S segment was amplified from one seropositive R. rattus captured at Hakodate. The nucleotide sequence showed 96% identity with the Seoul virus (SEOV) prototype strain SR-11. In addition, we conducted an epidemiological survey on human hantavirus infection in a high-risk population, the personnel of the Japan Ground Self-defense Force on Hokkaido. One out of 207 human blood samples was positive for anti-hantavirus antibody by IFA, ELISA, and WB analysis. The result of the serotype specific ELISA indicates that this individual acquired SEOV infection. This study indicates that A. speciosus, R. norvegicus, R. rattus, and C. rufocanus carry hantaviruses as the reservoir animals in Japan. Infected R. rattus and R. norvegicus in port areas could be the sources of human SEOV infection and a threat to travelers and individuals working in seaports.     

Patterns of parasite species richness of Western Palaeartic micro-mammals: island effects

We investigate the patterns of parasite species richness of small mammals of the Western Palaearctic, and the effects of insularity. We compiled 28 studies dealing with 16 species of mammals. There was a significant effect of area size on the total parasite species richness, controlling for host sample size. Four mammal species were sufficiently sampled. Two are associated with humans: Mus musculus, and Rattus rattus , and two are not associated with humans, Apodemus sylvaticus and Clethrionomys glaerolus. We show that there is an effect of insularity on parasite species richness of A. sylvaticus . Rodents associated with humans show no effect of insularity on parasite species richness. These rodents appear to reflect a more complex pattern of parasite species richness, probably because of their close association with humans. Host specificity of parasites significantly decreases on islands, with the exception of Rattus rattus . We use parasitological data in order to explore the geographical connections between host populations. We show that parasites may help to resolve these connections but we emphasise that parasites are better geographic than phylogenetic markers.     

Vocalizations of nine species of rat (Rattus; Muridae)

The sounds produced by seven species of Rattus native to Australia and the Black rat ( R. rattus ) and the Brown rat ( R. norvegicus ), were investigated in the laboratory. Both audible and ultrasonic sounds were recorded and the ontogeny of the different vocalizations investigated. All nine species had the same basic repertoire of seven more or less discrete calls. Some calls varied more between the different species than did others. Similarly there were species' differences in the ease with which some calls could be elicited. Two major continua were identified, one audible and one ultrasonic. An attempt was made to put the vocalizations recorded into an evolutionary perspective.     

Patterns in size and shedding of Fasciola hepatica eggs by naturally and experimentally infected murid rodents

Using samples collected on the island of Corsica, a comparative study was done of the morphometry of Fasciola hepatica eggs shed by cattle and by naturally and experimentally infected murid rodents (wild Mus musculus and Rattus rattus and Rattus norvegicus Wistar laboratory strain). Eggs shed by murids are smaller in size than those shed by naturally infected cattle. A second study analyzed the number of F. hepatica eggs shed in murid feces at different time intervals, i.e., months, days, and 6-hr periods, by the Kato-Katz technique. Both experimentally and naturally infected black rats (R. rattus) were used, and Wistar rats were experimentally infected and included for comparison. The present studies prove that black rats R. rattus are able to shed eggs independently from the liver fluke isolate and that egg shedding occurs throughout the life of this host species, uninterrupted during all the months analyzed in a 2-yr period. Moreover, the results suggest that this shedding is continuous, with eggs appearing in the feces daily. The results on egg shedding by wild black rats R. rattus reach their maximum shedding in spring and autumn and a maximum during twilight hr. These chronobiological patterns appear to favor parasite transmission, both seasonally and daily.     

Ag-NOR chromosomal association patterns in Rattus rattus (Rafinesque, 1814) and Rattus norvegicus (Berkenhout, 1796) from the southern Iberian peninsula

A high frequency of satellite association phenomena in a number of specimens of Rattus rattus and R. norvegicus, captured on the coastal fringe of Málaga province (Southern Spain), was found. Only Ag-NOR bearing chromosomes participated in associations in both species. R. rattus is characterized by 14/18 heterologous and R. norvegicus by 5/5 and 13/13 homologous association types.     

Population distribution and zoonotic potential of gastrointestinal helminths of wild rats Rattus rattus and R. norvegicus from Jamaica

The population distribution and zoonotic potential of gastrointestinal helminths in a naturally infected population of wild rats (Rattus rattus and Rattus norvegicus) in Jamaica are described. One hundred and thirty (29.7%) of 437 rats captured in the study were infected: 104 (35%) of 297 R. rattus compared with 26 (18.6%) of 140 R. norvegicus. Nine species of gastrointestinal helminths were recovered: Raillietina sp. (0.2%), Trichuris sp. (0.2%), Rictularia sp. (0.7%), Syphacia obvelata (1.1%), Strongyloides ratti (1.4%), Hymenolepis diminuta (3.8%), Protospirura muricola (4.3%), Moniliformis moniliformis (11.2%), and Nippostrongylus brasiliensis (14.2%). In a logistic model, the single risk factor identified for both M. moniliformis and P. muricola was R. rattus, compared with R. norvegicus (OR = 8.369 and 9.714, respectively). In comparison, the risk factor predicted for infection with N. brasiliensis was the northeastern section of Jamaica (OR = 11.000) compared with western Jamaica. Rictularia sp. represents a new geographic distribution record for the Caribbean region. Hymenolepis diminuta, M. moniliformis, Raillietina sp., and Rictularia sp. are potentially zoonotic, but only human infection with H. diminuta has been previously reported in the Caribbean.     

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.     

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.     

Invasion facilitates hybridization with introgression in the Rattus rattus species complex

Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south‐eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.     

Nesting, overwintering, and conservation of the Crab Plover Dromas ardeola in central Eritrea

We describe 30 new nesting sites of the Crab Plover Dromas ardeola , the main breeding grounds of which were largely unknown, and for which fewer than 30 colonies had been confirmed since 1970. Our survey included 90 islands, 53% of those existing, in the Dahlak and Howakil archipelagoes, and off the coast of central Eritrea. Colony size varied between 20 and 400 nests. We estimate the numbers of Crab Plovers breeding in central Eritrea at 5000–6000 pairs, i.e. about 50% of the known world breeding population. We describe two cases of probable replacement clutches, a feature unrecorded in this species. Black Rats Rattus rattus seem unable to open Crab Plover eggs, and do not seem to be a threat. Crab Plover colonies are traditionally exploited by local fishermen for collection of eggs, an activity that has increased recently. Our new records solve only partially the problem of the 'missing' colonies that are required to account for the world wintering population of 60 000–80 000 birds, and thus other breeding sites remain to be discovered, probably in southern Eritrea, Sudan and Somalia. We estimated that there are 4800–6500 Crab Plovers overwintering within central Eritrea, making it an important wintering ground for the species.     

Multiple paternity in wild populations of invasive

Multiple paternity within litters has been recorded among a variety of small mammal species, including some species of rodents. Although multiple mating has been observed in wild Rattus populations, whether such mating results in litters with multiple paternities has not been established previously. For studies involving invasive species, awareness is useful of the level of genetic diversity a single pregnant invader can bring to a population. Multiple paternity is a means of providing additional genetic diversity to founding populations of rats on islands, which might improve population fitness. We used a genetic approach to confirm that multiple paternity occurs in wild populations of two rat species (Rattus norvegicus and R. rattus) in New?Zealand. This was accomplished by genotyping litters of embryos in pregnant females, and subtracting the known maternal alleles to find the number of paternal alleles necessary to form the litter. The number of paternal contributors cannot be overestimated by this method, befitting a conservative approach to the detection of multiple paternity, but can be underestimated. We used simulations to investigate the level of underestimation likely under two possible scenarios involving multiple paternity.