GENETIC DIFFERENTIATION AMONG KARYOTYPIC FORMS OF THE BLACK RAT, RATTUS RATTUS

New record of the Oriental house rat, Rattus tanezumi, in Nepal inferred from mitochondrial Cytochrome B gene sequences

This study determines the presence of R. tanezumi from in Nepal using morphological and molecular analyses. Morphologically, it is indistinguishable with R. rattus owing to similar fur colour and morphometric data. However, molecular identification and phylogenetic analysis using sequences of the mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene revealed two different species R. rattus and R. tanezumi from collected specimens. The genetic distance between R. rattus and R. tanezumi was found 0.043. In phylogenetic tree, the clade of R. tanezumi is distinguished into two sub-clades, R. tanezumi found in Nepal, and East Asian countries, China, Laos, Thailand, Viet Nam, and South Korea have genetic distance 0.031, suggesting the different lineages of R. tanezumi. This study confirmed the R. tanezumi present in Nepal. Our findings suggest that morphological analysis and molecular study should be carried out simultaneously for accurate identification of small sized cryptic mammals like R. tanezumi and R. rattus.

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.

A review of the evidence for potential impacts of black rats (Rattus rattus) on wildlife and humans in Australia

The black rat (Rattus rattus) is among the world’s worst invasive species, having spread across the globe in close association with the spread of human settlement. It is the source of some of the worst diseases affecting humans and is thought to have had a devastating impact on native wildlife, especially in island ecosystems. Black rat is likely to have arrived in Australia with the first European settlers, making it among the first of many alien species to invade the continent, and it is now widespread. Yet, its impacts on local wildlife have largely been overlooked. Here, we review the potential for black rat impacts in Australia in terms of its role as a source of disease and threats to wildlife and humans. We first summarise the global evidence for black rat impacts as background to the potential threats it poses and then focus specifically on emerging evidence available for Australian systems. We found a significant gap in our understanding of the ecology of black rats and the ecological role that it plays in Australia. This is despite its role as a source of a diverse range of diseases affecting humans and wildlife and its actions as a predator and competitor of native wildlife in Australia and elsewhere.

Multiple geographic origins of commensalism and complex dispersal history of Black Rats

The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.

Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences

Microtus is one of the most taxonomically diverse mammalian genera, including over 60 extant species. These rodents have evolved rapidly, as the genus originated less than 2 million years ago. If these numbers are taken at face value, then an average of 30 microtine speciation events have occurred every million years. One explanation for the rapid rate of cladogenesis in Microtus could be the karyotypic differentiation exhibited across the genus: diploid numbers range from 17 to 64. Despite the striking chromosomal variability within Microtus, phenotypic variation is unremarkable. To determine whether nucleotide substitution rates are also elevated in voles, we sequenced the entire mitochondrial DNA (mtDNA) genome of the Eurasian sibling vole (Microtus rossiaemeridionalis). We compared this genome to another previously sequenced vole mtDNA genome (Microtus kikuchii) and performed pairwise sequence comparisons with the mtDNA genomes of ten additional mammalian genera. We found that microtine mtDNA genomes are evolving more rapidly than any other mammalian lineage we sampled, as gauged by the rate of nucleotide substitution across the entire mtDNA genome as well as at each individual protein-coding gene. Additionally, we compared substitution rates within the cytochrome b gene to seven other rodent genera and found that Microtus mtDNA is evolving fastest. The root cause of accelerated evolution in Microtus remains uncertain, but merits further investigation.

Preliminary genetic characterization of two lineages of black rats (Rattus rattus sensu lato) in Japan, with evidence for introgression at several localities

We conducted a pilot survey of genetic diversity among 37 karyotyped individuals of the black rat Rattus rattus (sensu lato) from six localities on the Japanese Islands, using complete gene sequences of mitochondrial cytochrome b (cyt b) and nuclear interphotoreceptor retinoid binding protein (IRBP). Our sampling included two previously documented karyotypic groups: 'Oceanian' with 2n = 38 and 'Asian' with 2n = 42. Cyt b sequences for most individuals clustered according to their karyotypic groups, with an average between-group divergence of 3.8%. One exception was that individuals from Kagoshima (Kyushu Island) showed 'Asian' karyotypes combined with a cyt b haplotype that differed by a single nucleotide substitution from the haplotype of the 'Oceanian' karyotypic group. Six IRBP haplotypes were identified. They belonged to three distinct IRBP lineages (I-III), with an average inter-lineage divergence of 1%. Among homozygous individuals, these lineages showed good association with the karyotypic groups: IRBP lineage I occurred only with 'Oceanian' karyotypes, while IRBP lineages II and III both occurred with 'Asian' karyotypes. Individuals from Kagoshima all possessed IRBP of 'Asian' lineages, despite the presence of an 'Oceanian' mitochondrial type. The Chichijima population (Ogasawara Islands) featured exclusively 'Asian' karyotypes and cyt b sequences, but various combinations of all three IRBP lineages. The Kagoshima and Chichijima populations thus provide strong evidence of viable hybridization and genetic introgression between the two karyotypic groups, but with variable genetic outcomes. Our results demonstrate the potential of combined analysis of karyotypes and mitochondrial and nuclear gene sequences to elucidate the complex dispersal and population history of the black rat.

Concordant divergence in proteins and mitochondrial DNA between two vole species in the genus Clethrionomys

The bank vole (Clethrionomys glareolus) and the northern red-backed vole (C. rutilus) are two closely related species where interspecific crosses result in fertile female but sterile male offspring. Mitochondrial DNA (mtDNA) from C. rutilus has passed the species barrier and is found in C. glareolus from northern Fennoscandia. The present report shows that the genetic distance between the two species, calculated from enzyme data (Nei's D), is 0.64. Isoelectric focusing of muscle proteins resolved around 55 bands, of which each species had 6 or 7 bands not present in the other species. Sequence divergence of mtDNA from the two species is 13.9%. A comparison between protein and mtDNA distances in other species pairs reveals a high correlation between the two measures, indicating that differences in mtDNA between taxa are not random when compared to divergence in protein-coding nuclear genes. The relationship between genetic divergence in proteins and that in mtDNA between Clethrionomys glareolus and C. rutilus is similar to that found in other species pairs. It is also shown that despite large differences on the protein level it is still, in some cases, possible for species pairs to produce fertile hybrid females.

Transfer of mitochondrial DNA from the northern red-backed vole (Clethrionomys rutilus) to the bank vole (C. glareolus)

Using a silver staining method to detect DNA fragments produced by restriction enzymes, it was possible to compare mitochondrial DNAs (mtDNAs) from 85 individuals of the bank vole (Clethrionomys glareolus) trapped at 25 localities in Fennoscandia. There are two distinctly different mtDNA lineages, one occurring in southern and central Fennoscandia and the other in the northern parts. A fragment comparison method shows about 12.7% nucleotide sequence divergence between these two lineages. This major difference between animals of the same species could theoretically be explained by intraspecific lineage survivorship independent of species hybridization, or by introduction of an atypical mtDNA via hybridization with a closely related species. Analysis of mtDNAs from the two other Clethrionomys species present in Fennoscandia (C. rutilus and C. rufocanus) shows that the mtDNA of northern C. glareolus is very similar to that of C. rutilus and that the mtDNA lineages of these two species cluster together in a phenogram, with small genetic distances among them. By contrast, electrophoresis of proteins encoded by 17 nuclear loci reveals fixed allelic differences between these two species at 8 loci. Hence the presence of two distinctly different mtDNA lineages within C. glareolus may be a consequence of a limited episode of hybridization between C. glareolus and C. rutilus, probably during the postglacial recolonization of Fennoscandia 8000-13,000 years ago.

Morphological and biochemical correlates in the characterization of Sarcocystis spp

Isoenzyme electrophoretic techniques were applied to the characterization of seven Sarcocystis spp. that had been identified by conventional morphological studies. Cystozoites were harvested from macroscopic cysts from sheep, cattle, and mice and from microscopic cysts from sheep, cattle, and goats. Soluble cystozoite extracts were subjected to cellulose acetate gel electrophoresis and characterized at 15 of the 39 enzyme loci examined. Genetic relationships among isolates were examined by simple phenetic clustering. Two different morphological types of macroscopic cysts from sheep, identified as S. gigantea (syn. S. ovifelis) and S. medusiformis, consistently differed at 40% of the loci examined. Such genetic divergence confirms their separate morphotypic classification. Both differed from microscopic cyst isolates from sheep at 87% of the loci examined; however, two different morphotypes of microscopic cysts were found in the sheep sampled (thick-walled and thin-walled cysts). Until sufficient numbers of each type can be isolated and examined separately, both were regarded as belonging to the species S. tenella (syn. S. ovicanis). Macroscopic and microscopic cysts from cattle consistently differed at 80% of the loci thereby supporting their separate classification as S. hirsuta (syn. S. bovifelis) and S. cruzi (syn. S. bovicanis), respectively. Isolates from goats (microscopic cysts identified as S. capracanis) differed from S. tenella and S. cruzi at 20% and 47% of the loci, respectively. All macroscopic cyst isolates from the various host animal species (including S. muris from mice) differed from each other at nearly all loci. Isoenzyme electrophoretic techniques therefore provided genetic evidence supporting the classification of these various Sarcocystis spp. by their morphological characteristics.