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.     

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.     

Variation of C-bands in the chromosomes of several subspecies of Rattus rattus

All subspecies of black rats (Rattus rattus) used in the present study are characterized by having large and clear C-bands at the centromeric region. The appearance of the bands, however, is different in the subspecies. Chromosome pair No. 1 in Asian type black rats (2n=42), which are characterized by an acrocentric and subtelocentric polymorphism, showed C-band polymorphism. In Phillipine rats (R. rattus mindanensis) the pair was subtelocentric with C-bands, but in Malayan black rats (R. rattus diardii) it was usually acrocentric with C-bands. In Hong-Kong (R. rattus flavipectus) and Japanese black rats (R. rattus tanezumi) it was polymorphic with respect to the presence of acrocentrics with C-bands or subtelocentrics without C-bands. The other chromosomes pairs showed clear C-bands, but in Hong-Kong black rats the pairs No. 2 and 5 were polymorphic with and without C-bands. In Japanese black rats, 6 chromosome pairs (No. 3, 4, 7, 9, 11 and 13) were polymorphic in regard to presence and absence of C-bands, but the other 5 chromosome pairs (No. 2, 5, 6, 8 and 10) showed always absence of C-bands. Only pair No. 12 usually showed C-bands. C-bands in small metacentric pairs (No. 14 to 20) in Asian type black rats generally large in size, but those in the Oceanian (2n=38) and Ceylon type black rats (2n=40) were small. In the hybrids between Asian and Oceanian type rats, heteromorphic C-bands, one large and the other small, were observed. Based on the consideration of karyotype evolution in the black rats, the C-band is suggested to have a tendency toward the diminution as far as the related species are concerned.     

Evolutionary aspects of variant types of rat mitochondrial DNA'S.

Mitochondrial DNA's (mtDNAs) were prepared from various kinds of individual Norway rats, Rattus norvegicus, and from three types of individual black rats, Rattus rattus, (Asian type, Ceylon type, and Oceanian type). Intra- and interspecies divergence of their mtDNA sequences were calculated based on changes in restriction endonuclease cleavage sites. The extent of intraspecies divergence of black rats (about 8%) is much larger than that of Norway rats (1%) and the mtDNA of Asian-type black rats resembles the mtDNA of Norway rats more closely than it resembles the mtDNA of other types of black rats. These results strongly suggest that during the course of intraspecies differentiation of black rats, probably long after the separation of the three types of black rats, some Asian-type black rats were isolated sexually and formed a new species, Norway rats. On the basis of our observations we propose a hypothetical process to explain the evolution of animal mtDNA.     

Karyotypes and serum transferrin patterns of hybrids between Asian and Oceanian black rats,Rattus rattus

Karyotypes and serum transferrin patterns were examined in Asian and Oceanian black rats (R. rattus). Japanese R. r. tanezumi and Malayan R. r. diardii had 2n=42, but Australian and New Guinea R. r. rattus showed 2n=38 chromosomes. F₁ hybrids between Japanese and Australian rats and Malayan and New Guinea rats had 2n=40 chromosomes which consists of the two genomes of both parents. Although various matings between the F₁ hybrids were made, only one F₂ male rat with 2n=39 chromosomes was obtained. The F₁ hybrids seem to be semisterile. Parental transferrin phenotypes were TfR in Japanese rats and TfCD in Oceanian rats. F₁ hybrids examined showed TfRD in both male and female and one F₂ hybrid had TfR type transferrin. Based on the above investigations, it is suggested that Asian and Oceanian black rats are geographically isolated and evolved different chromosomal and serum transferrin characteristics, but the sexual isolation of the two groups is incomplete at the present time.Contribution No. 826 from the National Institute of Genetics, Japan. Supported by a grant-in-aid from the Ministry of Education of Japan (Scientific Expedition in 1968, No. 8801 in 1969 and No. 9001 in 1970).     

High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from central Asia and West Asia into India

Linguistic evidence suggests that West Asia and Central Asia have been the two major geographical sources of genes in the contemporary Indian gene pool. To test the nature and extent of similarities in the gene pools of these regions we have collected DNA samples from four ethnic populations of northern India, and have screened these samples for a set of 18 Y-chromosome polymorphic markers (12 unique event polymorphisms and six short tandem repeats). These data from Indian populations have been analysed in conjunction with published data from several West Asian and Central Asian populations. Our analyses have revealed traces of population movement from Central Asia and West Asia into India. Two haplogroups, HG-3 and HG-9, which are known to have arisen in the Central Asian region, are found in reasonably high frequencies (41.7% and 14.3% respectively) in the study populations. The ages estimated for these two haplogroups are less in the Indian populations than those estimated from data on Middle Eastern populations. A neighbour-joining tree based on Y-haplogroup frequencies shows that the North Indians are genetically placed between the West Asian and Central Asian populations. This is consistent with gene flow from West Asia and Central Asia into India.     

Karyotypic differences of black rats,Rattus rattus,collected in various localities of East and Southeast Asia and Oceania

Karyotypes of several subspecies of black rats, Rattus rattus, collected in different localities of Asia and Oceania were examined with special emphasis on the relationship between the chromosome polymorphism and differentiation of the subspecies. Subspecies of black rats (R. rattus) collected were as follows; tanezumi from Japan; flavipectus and sladeni from Hong Kong; diardii, jalorensis from Kuala Lumpur, Malaysia; argentiventer from Kuala Lumpur, and Java and Celebes, Indonesia; mindanensis from Luzon and Mindanao, Philippines; and rattus from Australia, New Zealand, and New Guinea. Subspecies in Formosa, Korea and Thailand were not determined. All black rats collected in the above Asian districts had 42 diploid chromosomes, while those in Oceania had 38. The rats collected in Japan (tanezumi), Korea, Formosa, Thailand and Malaysia (diardii) had A/A No. 1 pair or polymorphic No. 1 (A/A, A/S and S/S) pairs, while those collected in Java and Celebes (argentiventer), Luzon and Mindanao (mindanensis) showed a higher frequency of S/S No. 1 pair. From the higher occurrence of No. 1 A/A pair of black rats in the Asian continent where the black rats originated, it is suggested that the original type of No. 1 chromosome pair of the black rats is A/A, and a pericentric inversion occurred in the acrocentric No. 1 chromosome and thus rats with subtelocentric No. 1 pair formed.—Black rats with 38 chromosomes were observed in Australia, New Guinea and New Zealand. These karyotypes seem to have developed by Robertsonian fusion of 4 acrocentric pairs (No. 4 and 7, and No. 11 and 12) in black rats of the Asian type. A relationship between body size and chromosome constitution was observed in subspecies of the black rats.Contribution No. 831 from the National Institute of Genetics, Japan. Supported by a grant-in-aid from the Ministry of Education of Japan (Scientific Expedition in 1968, No. 8801 in 1969, and No. 9001 in 1970).     

Range-habitat relationships of vascular plant species at the taiga forest-steppe borderline in the western Khentey Mountains,northern Mongolia

World distribution of 488 out of 619 vascular plant species known from an area of 500 km² within the western Khentey Mountains, northern Mongolia is analyzed. Most species belong to Eastern Asian (29%) or Asian, Eurasian, or circumpolar temperate species (24%) supporting the classification of the Khentey Mountains as part of the temperate zone of Eurasia. Seventeen percent of species are boreal plants. Circumpolar temperate-boreal (9%), Central (-Eastern) Asian (9%), Continental mountain species (5%), Middle-Central Asian (3%), arctic-alpine (3%) as well as Western Eurasian and western Siberian species are of lower significance for the flora of the western Khentey Mountains. Eastern Asian species occur in all types of habitats, whereas plants of other distribution types are focused on certain habitats. Boreal species preferably grow in the dark taiga, which prevails in the upper montane belt and on northern and eastern slopes of the most humid parts of the lower montane belt. Temperate and temperate-boreal species prefer subtaiga forests, which are found on northern and eastern slopes in drier parts of the lower montane belt as well as in upper parts of sun-exposed, southern and western slopes of the lower montane belt. Central (-Eastern) Asian and Middle-Central Asian species primarily inhabit forest steppe habitats, such as meadow and mountain steppes, Ulmus pumila open woodlands and dry Pinus sylvestris forests on steep, southern slopes.     

A shared Y-chromosomal heritage between Muslims and Hindus in India

Arab forces conquered the Indus Delta region in 711 AD and, although a Muslim state was established there, their influence was barely felt in the rest of South Asia at that time. By the end of the tenth century, Central Asian Muslims moved into India from the northwest and expanded throughout the subcontinent. Muslim communities are now the largest minority religion in India, comprising more than 138 million people in a predominantly Hindu population of over one billion. It is unclear whether the Muslim expansion in India was a purely cultural phenomenon or had a genetic impact on the local population. To address this question from a male perspective, we typed eight microsatellite loci and 16 binary markers from the Y chromosome in 246 Muslims from Andhra Pradesh, and compared them to published data on 4,204 males from East Asia, Central Asia, other parts of India, Sri Lanka, Pakistan, Iran, the Middle East, Turkey, Egypt and Morocco. We find that the Muslim populations in general are genetically closer to their non-Muslim geographical neighbors than to other Muslims in India, and that there is a highly significant correlation between genetics and geography (but not religion). Our findings indicate that, despite the documented practice of marriage between Muslim men and Hindu women, Islamization in India did not involve large-scale replacement of Hindu Y chromosomes. The Muslim expansion in India was predominantly a cultural change and was not accompanied by significant gene flow, as seen in other places, such as China and Central Asia.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Ramana Gutala and Denise R. Carvalho-Silva contributed equally to the article.     

Genetic studies of human diversity in East Asia

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.     

A Fossil Species of Eremophila and Other Larks (Aves,Alaudidae) from the upper Pliocene of the Selenga River Valley (Central Asia)

We describe lark (Alaudidae) fossils from the upper Pliocene of the Beregovaya (southern Transbaikalia) and Shaamar (northern Mongolia) localities. The presence of 4 extinct forms in these localities is established, including the new fossil horned lark Eremophila orkhonensis (Zelenkov et Kurochkin, 2012), comb. nov. This is the oldest member of Eremophila in the fossil record, indicating a possible Central Asian origin of the genus. Two other larks Alaudala aff. A. rufescens and Calandrella aff. C. brachydactyla also probably represent extinct forms. The paper describes in detail the osteology of larks and compares it with other passerines in its size class. The evolutionary history of Eremophila is discussed, and the environmental preferences of larks and their relationship to the late Pliocene landscapes of Central Asia are considered.     

Genetic variation and phylogeography of central Asian and other house mice,including a major new mitochondrial lineage in Yemen.

The mitochondrial DNA (mtDNA) control region and flanking tRNAs were sequenced from 76 mice collected at 60 localities extending from Egypt through Turkey, Yemen, Iran, Afghanistan, Pakistan, and Nepal to eastern Asia. Segments of the Y chromosome and of a processed p53 pseudogene (Psip53) were amplified from many of these mice and from others collected elsewhere in Eurasia and North Africa. The 251 mtDNA types, including 54 new ones reported here, now identified from commensal house mice (Mus musculus group) by sequencing this segment can be organized into four major lineages-domesticus, musculus, castaneus, and a new lineage found in Yemen. Evolutionary tree analysis suggested the domesticus mtDNAs as the sister group to the other three commensal mtDNA lineages and the Yemeni mtDNAs as the next oldest lineage. Using this tree and the phylogeographic approach, we derived a new model for the origin and radiation of commensal house mice whose main features are an origin in west-central Asia (within the present-day range of M. domesticus) and the sequential spreading of mice first to the southern Arabian Peninsula, thence eastward and northward into south-central Asia, and later from south-central Asia to north-central Asia (and thence into most of northern Eurasia) and to southeastern Asia. Y chromosomes with and without an 18-bp deletion in the Zfy-2 gene were detected among mice from Iran and Afghanistan, while only undeleted Ys were found in Turkey, Yemen, Pakistan, and Nepal. Polymorphism for the presence of a Psip53 was observed in Georgia, Iran, Turkmenistan, Afghanistan, and Pakistan. Sequencing of a 128-bp Psip53 segment from 79 commensal mice revealed 12 variable sites and implicated >/=14 alleles. The allele that appeared to be phylogenetically ancestral was widespread, and the greatest diversity was observed in Turkey, Afghanistan, Pakistan, and Nepal. Two mice provided evidence for a second Psip53 locus in some commensal populations.     

Genetic Evidence of an East Asian Origin and Paleolithic Northward Migration of Y-chromosome Haplogroup N

The Y-chromosome haplogroup N-M231 (Hg N) is distributed widely in eastern and central Asia, Siberia, as well as in eastern and northern Europe. Previous studies suggested a counterclockwise prehistoric migration of Hg N from eastern Asia to eastern and northern Europe. However, the root of this Y chromosome lineage and its detailed dispersal pattern across eastern Asia are still unclear. We analyzed haplogroup profiles and phylogeographic patterns of 1,570 Hg N individuals from 20,826 males in 359 populations across Eurasia. We first genotyped 6,371 males from 169 populations in China and Cambodia, and generated data of 360 Hg N individuals, and then combined published data on 1,210 Hg N individuals from Japanese, Southeast Asian, Siberian, European and Central Asian populations. The results showed that the sub-haplogroups of Hg N have a distinct geographical distribution. The highest Y-STR diversity of the ancestral Hg N sub-haplogroups was observed in the southern part of mainland East Asia, and further phylogeographic analyses supports an origin of Hg N in southern China. Combined with previous data, we propose that the early northward dispersal of Hg N started from southern China about 21 thousand years ago (kya), expanding into northern China 12–18 kya, and reaching further north to Siberia about 12–14 kya before a population expansion and westward migration into Central Asia and eastern/northern Europe around 8.0–10.0 kya. This northward migration of Hg N likewise coincides with retreating ice sheets after the Last Glacial Maximum (22–18 kya) in mainland East Asia.     

The 9-bp deletion between the mitochondrial lysine tRNA and COII genes in tribal populations of India

A 9-base-pair (bp) deletion located between the lysine tRNA (MTTK) and COII (MTCOX*2) genes in the human mitochondrial genome is a valuable marker for tracing population relationships. Previous research has shown that the 9-bp deletion is associated with two major clusters of control region sequences; one occurs in sub-Saharan Africa, while the other is associated with Asian populations and populations of Asian origin. We surveyed 898 individuals from 16 tribal populations in India and found 6 individuals with the 9-bp deletion. Sequences of the first hypervariable segment (HV1) of the mtDNA control region from these 9-bp deletion-bearing mtDNAs were compared to those previously reported from Asian and African populations. Phylogenetic analysis indicates three distinct clusters of tribal Indian 9-bp deletion mtDNA types. One cluster, found in northeast India, includes southeast Asian and Indonesian mtDNA types. The remaining two clusters appear to have unique origins in southern India. These data provide further evidence of past migrations from Asia into the northeast corner of the Indian subcontinent.     

DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan

Background

Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan.

Methods/Principal Findings

Sequence diversity in the DNA barcode region (mtCOI-5′) was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3′ to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage “Pakistan”. The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and “Pakistan” were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan.

Conclusions

DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.     

胶蚧属昆虫的自然分布扩散及地理起源(半翅目:胶蚧科)

在对南亚、东南亚及邻近地区胶蚧属昆虫分布资料归纳的基础上,结合近年实地调查资料,提出了胶蚧属昆虫的自然分布、扩散路线及地理起源。结果如下:胶蚧属昆虫主要分布在南亚、东南亚及邻近地区,主要包括中国、印度、巴基斯坦、孟加拉国、尼泊尔、不丹、缅甸、泰国、老挝、越南、马来西亚、印度尼西亚、菲律宾、澳大利亚等地。胶蚧属昆虫有2个分布区,即南亚分布区和东南亚分布区。国际流域恒河、印度河、布拉马普特拉河、萨尔温江-怒江、澜沧江-湄公河、元江-红河及它们的部分支流是胶蚧属昆虫扩散的通道。南亚扩散路线以印度为中心,分别向北、向西和向东3个方向扩散;东南亚扩散路线以马来西亚为中心,向北扩散。胶蚧属昆虫有2个地理起源,南亚范围以印度为中心,东南亚范围内以马来西亚为中心。胶蚧属昆虫的寄主植物是其分布扩散的先决条件,气候条件是限制分布扩散的关键因子。     

Banding pattern analysis of polymorphic karyotypes in the black rat by a new differential staining technique

Polymorphic karyotypes of black rats (Rattus rattus) collected in Japan, Australia and India were analysed by a new differential staining technique by which banding patterns in the metaphase chromosomes are revealed. The technique consists in two steps: immersion of slides in a mixture of 2 x SSC and 0.1% (w/v) SDS (sodium dodecyl sulfate) for a few seconds at room temperature, and staining in Giemsa. By this treatment characteristic banding patterns were obtained in each chromosome pair. From the banding pattern analysis, subtelocentric pairs No. 1 and 9, which are polymorphic in respect to the acrocentrics and the subtelocentrics, were proven to have originated by pericentric inversion in the acrocentrics. The origin of two large metacentrics observed in Australian and Indian black rats was confirmed to have been developed by Robertsonian fusion of the acrocentrics No. 4 and 7 and No. 11 and 12 present in the Asian type black rat.Contribution No. 873 from the National Institute of Genetics, Japan. Supported by a grant-in-aid from the Ministry of Education of Japan (Nos. 92159 and 92332).     

Japanese barnyard millet (Echinochloa utilis,poaceae) in Japan

Two species are included in barnyard millet:Echinochloa utilis andE. frumentacea. These differ from each other in their genomic constitution and phylogeny. The former species originated fromE. crus-galli probably in eastern Asia, and is grown in Japan, Korea, and the northeastern part of China; the latter originated fromE. colona probably in tropical Asia, and is grown in Pakistan, India, and Nepal. “Japanese barnyard millet” is suggested as a suitable English common name forE. utilis; “Indian barnyard millet,” forE. frumentacea. In the past, Japanese barnyard millet was important in Japan as the staple food crop in districts where soil, weather conditions and irrigation systems were not suitable for paddy rice cultivation. When the rice crop suffered serious cool weather damage, the millet relieved people from starvation, especially in northeastern Japan. But the acreage devoted to the millet gradually decreased during and after the 1880s. Only the northern part of Iwate Prefecture is an exclusive Japanese barnyard millet cropping region at present. The breeding of cool- weather- resistant rice varieties and improvements in rice- growing techniques are mainly responsible for the decrease in acreage of the millet.     

Early Paleogene decapod crustaceans from the Sulaiman and Kirthar Ranges,Pakistan

A set of Paleocene and Eocene decapod crustaceans is described from the Sulaiman and Kirthar Ranges of Pakistan. The fossil crabs Proxicarpilius planifrons Collins and Morris, 1978 and Pakicarcinus orientalis (Collins and Morris, 1978), already known in the Eocene of northern Pakistan, are reported for the first time in the Paleocene of southern Pakistan, enlarging the stratigraphic and the palaeobiogeographical ranges of these species. The callianassid genus Calliax de Saint Laurent, 1973 is reported for the first time in the Paleocene of southern Pakistan; this is the oldest record for the genus.     

First record of Entelodontidae (Mammalia,Artiodactyla) from the late Eocene of Southeast Asia

We describe two entelodontid upper premolars that were recovered from the late Eocene of the Krabi coal mine in southern Thailand. The size and morphology of the material suggest that it can be referred to Entelodon aff. E. gobiensis, a species known from the late Eocene to the early Oligocene of northern Asia and southern China. The Thai material documents for the first time the southernmost occurrence of entelodontids in Asia during the Paleogene and also suggests that Eocene Southeast Asian mammal localities might potentially yield further entelodontid remains mostly associated with selenodont ungulates.