Geographical Distribution of Twelve Transferrin Alleles in Black Rats of Asia and Oceania

About 450 black rats (Rattus rattus) were collected from 25 localities in Asia and Oceania. Their serum transferrins were analyzed by a newly developed thin layer acrylamide gel electrophoresis accompanied with acrinol pretreatment, exhibiting 12 transferrin bands. Generally, Asian type rats (2N=42) had fast-moving transferrins (R-series), Ceylon type (2N=40) moderately moving ones and Oceanian type (2N=38) slowly moving ones (C-series). Exceptionally, in northern India and Pakistan all Asian-type rats had C-series Tf. The possibility that divergence of R-series Tf and C-series Tf had preceded the karyotypic differentiation from 42 to 38 is proposed. In combination with the previous molecular data, the time of the divergence is roughly estimated between the order of a million years and ten thousand years.     

Polymorphisms of mitochondrial DNAs in Norway rats (Rattus norvegicus): Cleavage site variations and length polymorphism of restriction fragments

Summary Extensive polymorphism was found in mitochondrial DNAs (mtDNAs) of Norway rats (Rattus norvegicus). The restriction endonuclease cleavage patterns of mtDNAs of laboratory rats, wild rats, tumor cells, and culture cells were compared The polymorphism is defined by two criteria; one is cleavage site variation and the other is length polymorphism of restriction fragments. The cleavage site variation may be caused by point mutation, and the length polymorphism by sequence deletions or insertions. At least five types, types A-E, were identified by cleavage site variations, and two groups, a and b, were identified by length polymorphism of one HpaII fragment, Hpa5. All types except type C belonged to either group-a or group-b, whereas both groups were found in type C. Differentiation of polymorphic Norway rat mtDNA types and the experimental use of the polymorphism are discussed.     

Frequencies of chromosome polymorphism in pairs no. 1, 9, and 13 in three geographical variants of black rats,Rattus rattus

Frequencies of the acrocentric and subtelocentric polymorphism in pairs no. 1, 9 and 13 chromosomes have been examined in 358 black rats, Rattus rattus, distributed over several countries of Asia, Australia and United States. The black rats are divided into three geographical types by the different chromosome numbers, such as Asian (2n=42), Ceylon (2n=40) and Oceanian types (2n=38). Pairs no. 13 polymorphism was found widely in these all types, but the pair no. 1 and 9 polymorphisms were found in only Asian type black rats. In the Asian type rats, however, those distributed in northern India and Pakistan showed always the subtelocentric pairs no. 1 and 9 like as those in Ceylon and Oceanian type black rats. This finding supports that the Ceylon and Oceanien type rats have developed in India or Pakistan from the Asian type. The present study also suggests that inversion of the pair no. 13 could have occurred in earlier period than those of the pairs no. 1 and 9.     

Cytogenetical survey of black rats,Rattus rattus,in southwest and Central Asia,with special regard to the evolutional relationship between three geographical types

A chromosome survey of the black rat, Rattus rattus, was made from animals collected at different localities in Southwest and Central Asia. Asian type black rats (2 n=42) were distributed in northern India, northern Pakistan, while the Oceanian type rats (2 n=38) were found in southern India, southern Pakistan and Central Asia. A border line of distribution of rats with Asian and Oceanian types can be drawn dividing India and Pakistan into northern and southern parts. A hybrid type between Asian and Oceanian types was found in Karachi, Pakistan. Rats with 40 chromosomes, probably a transient type from Asian to Oceanian type, were found in Sri Lanka (Ceylon). It is suggested that these three geographic variants have developed via sequential events of Robertsonian fusion of acrocentric chromosomes in Asian type black rats. This fusion probably took place somewhere in southern India. The Oceanian type black rats that thus developed in southern India migrated widely to the rest of the world through Central Asia and Europe accompanying the movement of mankind.     

Habitat use by three rat species (

The relative abundance of ship rats (Rattus rattus), Norway rats (R. norvegicus), and Pacific rats (R. exulans), was measured in four vegetation types on Stewart Island/Rakiura, over six consecutive seasons. Ship rats were found in all four vegetation types and dominated in podocarp-broadleaf forest and riparian shrubland. Norway rats were most common in subalpine shrubland and Pacific rats dominated in manuka (Leptospermum scoparium) shrubland. Analysis of micro-habitat affinities for the three species showed that ship rats were habitat generalists. Norway rats were associated with plants of damp sites. Pacific rats showed a significant positive relationship with increasing amounts of the ground cover wire rush, (Empodisma minus). Reasons for the observed habitat use on Stewart Island could include physiological adaptation to cold and wet conditions in Norway rats; the avoidance of predation or inter-specific competition by Pacific rats; and possibly preference for more structurally complex vegetation types by ship rats.     

Effect of sex, size, and age of commensal rat hosts on the infestation parameters of their ectoparasites in a rural area of Egypt.

The present study was carried out in the Bilbeis area, Sharqiya Governorate, Egypt. A total of 127 male and 115 female black rats Rattus rattus and 124 male and 153 female Norway rats R. norvegicus was collected during the study period. A total of 20,643 and 40,997 ectoparasites was recovered from R. rattus and R. norvegicus, respectively. Three common mite species were recovered from both rat hosts: Ornithonyssus bacoti, Radfordia ensifera, and Laelaps nuttalli. Three common flea species were also recovered from both rat hosts: Echidnophaga gallinacea, Leptopsylla segnis, and Xenopsylla cheopis. Polyplax spinulosa was the only louse species that infested both rat hosts. Rats that lived more than 12 mo formed about 24 and 14% of the populations of the black and Norway rats, respectively. The prevalences and general indices of many ectoparasites were significantly higher on males than on females of both rat hosts. Seasonal differences in prevalences and general indices of many ectoparasites were recorded between the 2 sexes of both rat species. Prevalences and general indices of most ectoparasites on both rat species showed a tendency to increase with increasing size and age of rat hosts. The type and degree of correlation between prevalences and general indices on the one hand and each of body size and age on the other hand differed among the species of ectoparasites.     

Rat mitochondrial DNA polymorphism: sequence analysis of a hypervariable site for insertions/deletions

Three closely related variants of rat (Rattus norvegicus) mtDNA have been shown to differ in the number of T residues found in a run of Ts (light strand) which spans the junction between the tRNACys and tRNATyr genes. The number of Ts in the repeat varies from 6 to 8 in these DNAs. Another, less closely related, R. norvegicus variant has a run of 5 Ts at this site and in the related species, Rattus rattus, a run of 4 Ts is found. In R. norvegicus mtDNA runs of 5 As and 5 Gs are found just to the 3' side of the variable T repeat, and it is suggested that the three runs of repeated nucleotides may stabilize heteroduplexes which result from strand slippage and which give rise to the insertions and/or deletions. Among 17 mtDNA clones derived from an individual with the 8T repeat, one clone was found which possessed a 9T repeat. This variant may represent an additional DNA type originally present within the individual.     

Patterns of polymorphism and gene flow of gender-associated mitochondrial DNA lineages in European mussel populations

Mussels of the genus Mytilus have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally and the F type is transmitted maternally. RFLP analysis is used to assess phylogenetic relationships and nucleotide diversity and divergence for both mtDNA genomes in European populations of M. edulis and Atlantic and Mediterranean forms of M. galloprovincialis. Ten restriction endonucleases were used to assay variation in regions of the ND2 and COIII genes for a total of 77 individuals. F and M genomes show a concordant phylogenetic split into two major divergent clades, one specific to Mediterranean M. galloprovincialis and the other containing haplotypes from the three taxa. For both genomes, the geographical distribution of mtDNA variation suggests: (i) extensive levels of mtDNA introgression; (ii) asymmetric mtDNA gene flow from Atlantic to Mediterranean populations; and (iii) recurrent historical hybridization events. Significantly higher mtDNA diversity and divergence are observed for the M than F genome in all three Mytilus taxa, although the evolutionary forces responsible for these differences cannot be resolved. The extensive mtDNA gene flow between European Mytilus taxa conflicts with the restricted mtDNA introgression observed in American mussels , implying geographical variation in the nature of nuclear/mtDNA interactions regulating biparental inheritance.     

Length of polymorphisms of restriction fragments of rat mitochondrial DNAs

Differences were found in the HpaII cleavage patterns of two types of rat (Rattus norvegicus) mtDNA, types A and B. One HpaII fragment, Hpa5, of type A was about 30 base pairs smaller than that of type B, but no 30-base pair fragment was detectable in an HpaII digest of type A mtDNA. Moreover, one HaeIII fragment, which is overlapped by Hpa5 in the cleavage map, was also about 30-base pairs smaller in type A than in type B. Thus, the length polymorphism of Hpa5 in the two types is probably not caused by HpaII site gain or loss, but by sequence deletion or insertion.     

Interpretation of mtDNA RFLP variability among <Emphasis Type="Italic">Aspergillus tubingensis</Emphasis> isolates

Aspergillus tubingensis isolates collected from distant geographic areas were earlier classified into six groups on the basis of the mtDNA RFLP variability they exhibited (mtDNA types 2a-2f). In the present work, we investigated the reason for the intraspecific mtDNA variability and we describe here how this fungus, with a relatively small mitochondrial genome, can display intraspecific polymorphism due to intron acquisition and also sporadic point mutations affecting the recognition motifs of the restriction enzymes employed in the RFLP analysis. Three different LAGLI-DADG type group I introns were identified in the cox1 gene amongst the six mtDNA RFLP types. MtDNAs of types 2b and 2d contain all of the three introns, mtDNA of type 2f carries only one, and the other mtDNA types contain two introns each. Comparative analysis showed that the first and second introns of mtDNAs of types 2b and 2d are well distributed among fungi, indicating their active horizontal transfer capacity. The third intron occurs rarely among fungi and is restricted to a limited number of fungal species, namely to A. tubingensis and the yeast Candida stellata. It is interesting that this intron is present in a small mitochondrial genome such as that of A. tubingensis and, considering its rarity, its presence amongst black Aspergillus isolates is recommended to be considered as a tool to establish taxonomical unit(s) or to track down evolutionary divergence of closely related taxonomical units.     

The heterogeneity of rat-liver mitochondrial DNA

Two types of mitochondrial DNA (mtDNA) can be distinquished in an inbred strain of rats of the Wistar type. The population of DNA molecules of the liver of one single rat is homogeneous. This was shown for a number of 100 animals and confirms the data of other investigators. The two types of mitochondrial DNA, designated A and B, differ in their number of cleavage sites for the restriction endonucleases Eco RI (2sites), Hind II (1 site) and Hha I (1 site). No differences were found for the restriction enzymes Bam HI, Hap II, Hind III and Hpa I. The degree of sequence divergence of the two types of DNA is calculated to be roughly 5% on the basis of these observations. From 20 rats part of the liver was taken and the mtDNA was characterized. Heterologous and homologous crosses between type A and type B rats were made. Analysis of the offspring revealed strictly maternal inheritance of the A and B mtDNA traits. For purposes of base-sequence analysis and RNA.DNA hybridization the strain could easily be "purified" genetically.     

The Complete Mitochondrial Genome of the Hagfish Myxine glutinosa: Unique Features of the Control Region

The complete sequence of the mitochondrial DNA of the hagfish Myxine glutinosa has been determined. The hagfish mtDNA (18,909 bp) is the longest vertebrate mtDNA determined so far. The gene arrangement conforms to the consensus vertebrate type and differs from that of lampreys. The exceptionally long (3628-bp) control region of the hagfish contains the typical conserved elements found in other vertebrate mtDNAs but is characterized by a large number of putative hairpins, which can potentially fold into a highly compact secondary structure that appears to be unique to hagfish. The comparison of the mtDNAs of two M. glutinosa specimens, excluding the control region, shows a 0.6% divergence at the nucleotide level as a sample of intraspecies polymorphism. Received: 21 August 2000 / Accepted: 2 March 2001     

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.     

Mitochondrial genomes in intraspecies mammalian cell hybrids display codominant or dominant/recessive behavior

A unique type of nonstochastic mitochondrial DNA (mtDNA) segregation was found in mammalian cells. In human cell hybrids isolated from the fusion of HeLa cells with 23, GM639, A549, or 293 cells, HeLa mtDNA was always lost from the hybrids, whereas both parental mtDNAs were maintained in hybrids of HeLa X 143BTK-. Similar phenomena were observed in mouse cell hybrids isolated by the fusion of cells with different mtDNA types. Types 1, 2, and 3, can be distinguished from each other by restriction fragment-length polymorphisms. The mouse cell hybrids between cells with type 1 and type 2 mtDNA always lost type 2 mtDNA, whereas the hybrids between cells with type 2 and type 3 mtDNA retained both types stably. These observations suggest that either a codominant or a dominant/recessive relationship may be present in intraspecies mitochondrial genomes of human and mouse cells. When the mitochondrial genomes in cell hybrids are codominant, stochastic segregation occurs while nonstochastic segregation occurs when they are in the dominant/recessive relationship. These concepts may help elucidate organelle heredity in animals.     

Phylogenetic relationships of Sakhalin taimen Parahucho perryi inferred from PCR-RFLP analysis of mitochondrial DNA

RFLP analysis of three amplified mtDNA fragments (Cytb/D-loop, ND1/ND2, and ND3/ND4L/ND4) was performed in the following taxa: Parahucho perryi, Hucho taimen, Brachymystax lenok, B. tumensis, Salmo salar, Salvelinus leucomaenis, and S. levanidovi. For mtDNA of P. perryi, a substantial decrease in the haplotype and nucleotide diversity was observed as a result of random genetic drift, caused by a reduction in the effective population size. Nucleotide divergence estimates between the mtDNA haplotypes were determined. Sakhalin taimen P. perryi was found to be approximately equally diverged from S. salar and from the charrs of the genus Salvelinus, by 11.0 and 10.0%, respectively. The divergence between P. perryi and H. taimen constituted 14.6%, between P. perryi and lenoks of the genus Brachymystax, 14.2%, and between H. taimen and Brachymystax, 7.7%. The analysis of possible phylogenetic relationships of the mtDNA from P. perryi among the group of taxa examined confirmed validity of the genus Parahucho. Phylogenetic reconstructions performed showed that robustness of the trees constructed for the complex of phylogenetically informative characters over three mtDNA fragments was considerably higher than that of the trees constructed for individual genes.     

Evolutionary history of the hybridogenetic hybrid frog Rana esculenta as deduced from mtDNA analyses [published erratum appears in Mol Biol Evol 1986 Sep;3(5):463]

mtDNA of the hybridogenetic hybrid frog Rana esculenta from Switzerland, Austria, and Poland was compared to mtDNA of the parental species R. ridibunda and R. lessonae using electrophoretic analysis of restriction enzyme fragments. Two mtDNA phenotypes, with 3.4% sequence divergence, are present in R. lessonae: type C is found in Poland, and type D is found in Switzerland. Rana ridibunda from Poland has either of two mtDNA phenotypes: type A is the typical ridibunda mtDNA, and type B is a lessonae mitochondrial genome, introgressed into R. ridibunda, that differs from type C mtDNA of R. lessonae by only 0.3%. Each of the three lessonae genomes differs from A, the typical ridibunda mtDNA, by approximately 8%. All four types of mtDNA (A and B of R. ridibunda, C and D of R. lessonae) are found in R. esculenta. Of 62 R. esculenta from Poland, 58 had type C, three had type A, and one had type B mtDNA. All nine R. esculenta from Switzerland had type D mtDNA. All three R. esculenta from Austria, from a population in which males of R. esculenta are rare, had ridibunda mtDNA, two having type B and one having type A. Both field observations and studies of mating preference indicate that the primary hybridizations that produce R. esculenta are between R. ridibunda females and R. lessonae males; thereafter, R. esculenta lineages are usually maintained by matings of R. esculenta females with R. lessonae males. The presence of ridibunda mtDNA in the three R. esculenta sampled from Austria, its occasional presence in R. esculenta populations in Poland, and its absence from R. esculenta in Switzerland support both the direction of the original hybridization and the rarity of formation of new R. esculenta lineages. The preponderance of R. esculenta individuals with lessonae mtDNA in our samples from central Europe suggests that most lineages have gone through at least one mating between an R. lessonae female and an R. esculenta male. This reveals a greater reproductive role for R. esculenta males than their partial sterility and infrequent matings would suggest.      

Genetic monitoring of laboratory rat strains by restriction fragment length polymorphisms of mitochondrial DNA

Restriction fragment length polymorphisms of rat mitochondrial DNA (mtDNA) were examined using various kinds of laboratory rat strains in Japan. The results show that mtDNA of laboratory rats, Rattus norvegicus, are highly polymorphic; at least 7 types, Aa, Ba, Bb, Cb, Dc, Eb, and Fa, were found with the use of 6 restriction enzymes, EcoR I, Hind II, Hha I, Hpa II, Taq I, and Hinf I. Types Aa, Ba, and Eb were distributed widely in several strains, whereas types Ba, Cb, Dc and Fa were limited to some specific strains. These results indicate that restriction fragment length polymorphisms of mtDNA can be applied to genetic monitoring of laboratory rat strains.     

The type I Lanyu pig has a maternal genetic lineage distinct from Asian and European pigs

The Lanyu pig is an indigenous breed from Lanyu Islet, located south-east of Taiwan, with phenotypic characteristics distinctive from other pig breeds in Asia and Europe. Based on geographic considerations, the Lanyu pig may have originated from mainland China, Austronesia or the Ryukyu Islands. In the present study, polymorphism of the mitochondrial DNA control region sequence was used to clarify phylogenetic relationships among two herds of Lanyu pigs imported before 1980 from Lanyu Islet into Taiwan and reared in isolation on two different farms. Two distinct mitochondrial control region haplotypes were found. The type I Lanyu sequence appeared independently as a unique clade different from Asian and European pig sequences, while the type II Lanyu sequence was clustered within the major Asian clade. The pairwise distances between the major Asian clade vs. the type I Lanyu and European clades were 0.01726 +/- 0.00275 and 0.01975 +/- 0.00212 changes per site respectively. Estimates of divergence time suggest that the type I Lanyu sequence split from the major Asian pig clade in prehistoric times. The type II Lanyu mtDNA shares a close genetic lineage with Japanese Satsuma and New Zealand Kune Kune mtDNA with pairwise distances of 0.00095 +/- 0.00000 and 0.00192 +/- 0.00000 respectively, indicating gene flow between Lanyu Islet, Japan and Oceania in recent times. Together these results indicate that the type I Lanyu pig has a genetic lineage separate from Asian-type pigs, while the type II Lanyu sequence may represent a more recent introgression of modern Asian pigs.     

The Use of Restriction Endonucleases to Measure Mitochondrial DNA Sequence Relatedness in Natural Populations. I. Population Structure and Evolution in the Genus Peromyscus

In this study we introduce to natural population analysis a molecular technique that involves the use of restriction endonucleases to compare mitochondrial DNA (mtDNA) sequences. We have examined the fragment patterns produced by six restriction endonucleases acting upon mtDNA isolated from 23 samples of three species of the rodent Peromyscus. Our observations confirm the following conclusions derived from previous experiments with laboratory animals: (1) mtDNA within an individual homogeneous; (2) at least the majority of mtDNA present in an individual is inherited from the female parent. Our experiments demonstrate for the first time that there is detectable heterogeneity in mtDNA sequences within and among natural geographic populations of a species and that this heterogeneity can readily be used to estimate relatedness between individuals and populations. Individuals collected within a single locale show less than 0.5% sequence divergence, while those collected from conspecific populations separated by 50 ti 500 miles differ by approximately 1.5%. The mtDNAs of the closely related sibling species P. polionotus and P. maniculatus differ from each other by 13 to 17%; nonsibling species differ by more than 20%. Qualitative and quantitative approaches to analysis of digestion patterns are suggested. The results indicate that restriction analysis of mtNDA may become the most sensitive and powerful technique yet available for reconstructing evolutionary relationships among conspecific organisms.     

Rodent-Borne <Emphasis Type="Italic">Bartonella</Emphasis> Infection Varies According to Host Species Within and Among Cities

It is becoming increasingly likely that rodents will drive future disease epidemics with the continued expansion of cities worldwide. Though transmission risk is a growing concern, relatively little is known about pathogens carried by urban rats. Here, we assess whether the diversity and prevalence of Bartonella bacteria differ according to the (co)occurrence of rat hosts across New Orleans, LA (NO), where both Norway (Rattus norvegicus) and roof rats (Rattus rattus) are found, relative to New York City (NYC) which only harbors Norway rats. We detected human pathogenic Bartonella species in both NYC and New Orleans rodents. We found that Norway rats in New Orleans harbored a more diverse assemblage of Bartonella than Norway rats in NYC and that Norway rats harbored a more diverse and distinct assemblage of Bartonella compared to roof rats in New Orleans. Additionally, Norway rats were more likely to be infected with Bartonella than roof rats in New Orleans. Flea infestation appears to be an important predictor of Bartonella infection in Norway rats across both cities. These findings illustrate that pathogen infections can be heterogeneous in urban rodents and indicate that further study of host species interactions could clarify variation in spillover risk across cities.