A new insight into cattle's maternal origin in six Asian countries

The domestication of cattle fuelled the development of agricultural society in the history of human being.The evolution and genetic relationship of cattle can be elucidated by investigating the variation of mitochondrial DNA (mtDNA) D-loop sequence.In this study,we built a cattle phylogeny with a pool of 856 individual D-loop sequences,of which 264 Chinese cattle D-loop sequences were obtained in this study (141 ones were first analyzed,and 123 were first submitted) and the rest sequences of cattle from six Asian countries (Japan,Korea,Mongolia,Nepal,India and China) were retrieved from GenBank.Our results indicated that cattle from six Asian countries fell into three clades,Bos taurus (taurine),Bos indicus (zebu) and yak.Four main haplogroups T1A,T2,T3 (including T3A and T3B) and T5 were found in taurine,and two haplogroups I1 and I2 in zebu.Furthermore,we found that I1 and I2 haplogroups were separated by four variable sites rather than five ones and four haplogroups or sub-haplogroups of T1A,T3A,T3B and T5 were found for the first time in these Asian cattle.These data brought us a new insight into cattle's genetic structure in these six Asian countries.The geographical distribution of haplogroups was also outlined to provide systematic information on cattle genetic resources.     

Origin and phylogeographical structure of Chinese cattle

Complete mitochondrial D-loop sequences of 231 samples were used to explore the origin and genetic diversity of Chinese cattle. Phylogenetical analysis of these sequences revealed both Bos taurus and Bos indicus mitochondrial types in Chinese cattle. Four of the previously identified mitochondrial DNA lineages (T1–T4) were identified in the Bos taurus type, including lineage T1, which was found for the first time in Chinese cattle. Two lineages (I1 and I2) were identified in the Bos indicus type. Our results support the suggestion that the Yunnan-Guizhou Plateau is the domestication site of Chinese zebu. We also found evidence that Tibetan cattle originated from taurine and zebu cattle. The distribution pattern of Chinese cattle breeds was closely related to the geographical and climatic background. It was possible to divide Chinese cattle in this study into two major groups: northern and southern cattle.     

贵州黄牛mtDNA D-loop 遗传多样性研究

对贵州4个地方黄牛品种共计82个个体的线粒体DNA D-loop区全序列910 bp进行分析,检测到31种单倍型,其核苷酸多态位点65个,约占所测核苷酸总长的7.14%,其中有62个转换,2个颠换,1个转换/颠换共存。贵州4个黄牛品种mtDNA D-loop区核苷酸多样度（π值）为2.16%～2.61%,单倍型多样度（H）为0.695～0.909,表明贵州黄牛mtDNA遗传多样性比较丰富。根据单倍型构建了贵州4个黄牛品种的NJ分子系统树。聚类表明,贵州黄牛有普通牛和瘤牛2大母系起源,其影响较为均一。并探讨了用核苷酸多样度π值的大小来衡量黄牛群体遗传分化程度的可行性。      

Phylogenetic relationships of Northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-loop sequence polymorphism

Phylogenetic relationships of Northeast Asian cattle to various other cattle breeds including Bos taurus, Bos indicus, and Bison bison were assessed using mtDNA D-loop sequences. A neighbor-joining tree was constructed using sequences determined for 4 Cheju Black, 4 Cheju Yellow, 4 Korean Yellow cattle (Bos taurus), and 2 American Brahman cattle (Bos indicus), and also published sequences for 31 Japanese Black cattle, 45 European breed cattle, 6 African zebus, 2 African taurines, and 6 Indian zebus. Five American bisons (Bison bison) were used as an outgroup. The neighbor-joining tree showed that American bisons and Indian zebus are clearly separate from other cattle breeds, respectively, and African cattle clustered together, although with a low bootstrap probability (<50%). Results indicate that cattle in Northeast Asia, Europe, and Africa are closely related to each other–suggesting their recent divergence, but are separate from Indian zebus.     

中国黄牛mtDNA D-loop遗传多样性及起源

黄牛自古以来就是我国一个重要的畜种,其经济、文化价值很高。我国是世界上黄牛品种资源最丰富的国家之一。据《中国牛品种志》介绍,把一些地区同种异名的黄牛品种合并以后,尚有28个地方黄牛品种,按照其地理分布区域分为北方黄牛、中原黄牛和南方黄牛三大类型(邱怀,1986)。如果把中国地方黄牛品种分得更细,则有49个固有品种(常洪,1995)。关于中国黄牛的起源,历来有不同的观点。一般认为,中国黄牛是多元起源的,但究竟起源于哪几个牛种,观点不一(陈宏等,1993;于汝梁等,1993;Yu et al.,1999;陈幼春,1990)。主要的观点有:(1)中国黄牛主要起源于…     

中国17个黄牛品种mtDNA变异特征与多态性分析

中国黄牛品种资源丰富,尚有28个地方固有品种.为了进一步深入了解这些宝贵遗传资源,本研究通过mtDNA变异特征与多态性分析揭示这些来自中国不同地域地方黄牛的母系起源与分子系统学特征.在17个品种84个体的mtDNA D-loop全序列中,一共检测到了102个核苷酸替代突变位.由此定义的53个单倍型被类聚为2个明显的单倍群：普通牛和瘤牛.mtDNA D-loop全序列变异的第一个特征是转换发生的频率远高于颠换;第二个特征是缺失与替代突变共存;第三个特征是缺失突变率比较高.所有D-loop全序列的核苷酸多样性和单倍型多样性分别为0.026 78±0.000 50和0.919±0.027.普通牛D-loop单倍型在北方牛种群中占有优势(80%～100%),而瘤牛单倍型在南方牛种群中占有优势(42.9%～100%),2种不同单倍型在中原牛种群中的分布也存在差异.2种不同单倍型在中国不同地域17个黄牛品种中的差异性分布揭示出了瘤牛mtDNA基因在中国黄牛中自南而北、由高到低的流动模式,这种基因流动模式的形成可能是由历史事件、地理隔离以及气候环境差异等造成的.     

A comprehensive evaluation of cattle introgression into US federal bison herds

Genetic introgression, especially from interspecies hybridization, is a significant threat to species conservation worldwide. In this study, 11 US federal bison populations were comprehensively examined for evidence of both mitochondrial and nuclear domestic cattle (Bos taurus) introgression. Mitochondrial introgression was examined using established polymerase chain reaction methods and confirmed through analysis of D-loop sequences. Nuclear introgression was assessed in 14 chromosomal regions through examination of microsatellite electromorph and sequence differences between bison and domestic cattle. Only one population was identified with domestic cattle mitochondrial DNA introgression. In contrast, evidence of nuclear introgression was found in 7 (63.6%) of the examined populations. Historic accounts of bison transfers among populations were corroborated with evidence of introgressed DNA transmission. While neither nuclear nor mitochondrial domestic cattle introgression was detected in bison from Grand Teton National Park, Sully's Hill National Game Preserve, Wind Cave National Park, or Yellowstone National Park, adequate sample sizes were available only from the last 2 populations to allow for statistical confidence (>90%) in nuclear introgression detection limits. The identification of genetically unique and undisturbed populations is critical to species conservation efforts, and this study serves as a model for the genetic evaluation of interspecies introgression.     

海南长臂猿线粒体D-loop区序列分析及种群复壮

海南长臂猿(Nomascus hainanus)是世界上最濒危的灵长类动物之一, 但目前有关海南长臂猿的种群遗传学方面的信息以及种群复壮所面临的困难未见报道。为更好地保护该极危物种, 作者以粪便为研究材料, 首次在分子生物学水平上测定了海南长臂猿1个群体(B群)共6个个体的线粒体D-loop区基因序列。结果显示: 202 bp的D-loop区基因共检测到5个变异位点, 4个单倍型, 单倍型多样性(h)为0.6000, 核苷酸多样性(π)为0.00829, 表明海南长臂猿B群的遗传多样性较低; 与此同时, 海南长臂猿还面临着种群数量过小, 性比失衡, 以及栖息地质量低下等严峻的问题。     

Genetic Stability of Progeny from an Artificial Allotetraploid Carp Using Sperm from Five Fish Species

Microsatellite markers and D-loop sequences of mtDNA from a female allotetraploid parent carp and her progenies of generations 1 and 2 induced by sperm of five distant fish species were analyzed. Eleven microsatellite markers were used to identify 48 alleles from the allotetraploid female. The same number of alleles (48) appeared in the first and second generations of the gynogenetic offspring, regardless of the source of the sperm used as an activator. The mtDNA D-loop analysis was performed on the female tetraploid parent, 25 gynogenetic offspring, and 5 sperm-donor species. Fourteen variable sites from the 1,018 bp sequences were observed in the offspring as compared to the female tetraploid parent. Results from D-loop sequence and microsatellite marker analysis showed exclusive maternal transmission, and no genetic information was derived from the father. Our study suggests that progenies of artificial tetraploid carp are genetically stable, which is important for genetic breeding of this tetraploid fish.     

Molecular genetic analysis of ancient cattle bones excavated from archaeological sites in Jeju, Korea

Ancient cattle bones were excavated from archaeological sites in Jeju, Korea. We used molecular genetic techniques to identify the species and establish its relationship to extant cattle breeds. Ancient DNA was extracted from four sources: a humerus (Gonae site, A.D. 700-800), two fragments of radius, and a tooth (Kwakji site, A.D. 0-900). The mitochondrial DNA (mtDNA) D-loop regions were cloned, sequenced, and compared with previously reported sequences of various cattle breeds (9 Asian, 8 European, and 3 African). The results revealed that these bones were of the breed, Bos taurus, and a phylogenetic tree indicated that the four cattle bones formed a monophyletic group with Jeju native black cattle. However, the patterns of sequence variation and reports from archaeological sites suggest that a few wild cattle, with a different maternal lineage, may have existed on Jeju Island. Our results will contribute to further studies of the origin of Jeju native cattle and the possible existence of local wild cattle.     

野牦牛线粒体基因组序列测定及其系统进化

野牦牛属高寒地区的特有物种,是我国最珍贵的野生动物遗传资源之一,已被列为国家一级重点保护动物。对野牦牛mtDNA进行全序列测定和结构分析,并基于线粒体基因组序列对其系统发生进行了探讨。结果表明:(1)野牦牛线粒体基因组全序列的大小为16 322 bp,整个基因组由37个编码基因和D-loop区组成;22个tRNA基因序列长度为1 524 bp、2个RNA基因序列长度为2 528 bp、13个编码蛋白基因序列长度为11420 bp、D-loop区长度为892 bp。基因组中无间隔序列,基因间排列紧密,基因内无内含子。(2)野牦牛具有较丰富的遗传多样性。(3)分子系统发生关系显示牦牛为牛亚科中的一个独立属,即牦牛属(Poephagus),牦牛属包括家牦牛(Poephagus grunniens)和野牦牛(Poephagus mutus)2个种。野牦牛线粒体基因组全序列的获得和结构解析对研究牦牛的起源、演化和分类,以及野牦牛遗传资源的保护、开发和利用均具有重要的理论和实际意义。     

African matrilineages in American Creole cattle: evidence of two independent continental sources

In order to clarify the historical origin and phylogeographic affinities of Creole cattle matrilineages throughout the American continent, we analysed published D-loop mtDNA sequences (n = 454) from Creole, Iberian and African cattle breeds. The Western European T3 haplogroup was the most common in American Creole cattle (63.6%), followed by the African T1 (32.4%) and the Near Eastern T2 haplogroups (4%). None of the sequences were found in Bos indicus types. Within the African T1 haplogroup there were two subclades, T1a and T1*, whose geographic distribution in America was clearly disjointed. T1a is a highly divergent clade originally reported for Creole cattle from Brazil and the Lesser Antilles, but whose geographic distribution in Africa remains unknown. In contrast, lineages attributable to T1* are restricted in America to the region colonized by the Spaniards. We propose a new hypothesis for the origins of Creole cattle that summarizes all previously published historical and genetic data. While the African T1* fraction in Creole cattle may have arrived in America through the Iberian breeds, the divergent T1a lineages may have been introduced by Portuguese and other European crowns from some unknown, not-yet-sampled African location. Additional molecular studies will be required for pinpointing the specific African regional source.     

Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

The tribe Bovini contains a number of commercially and culturally important species, such as cattle. Understanding their evolutionary time scale is important for distinguishing between post-glacial and domestication-associated population expansions, but estimates of bovine divergence times have been hindered by a lack of reliable calibration points. We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. By employing the radiocarbon dates as internal calibrations, we co-estimate the bovine phylogeny and divergence times in a relaxed-clock framework. The analysis yields evidence for significant population expansions in both taurine and zebu cattle, European aurochs and yak clades. The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence.     

High frequency of mitochondrial DNA D-loop mutations in Ewing’s sarcoma

Somatic mutations and polymorphisms in the noncoding displacement (D)-loop of mitochondrial DNA (mtDNA) are present in a variety of human cancers. To investigate whether Ewing’s sarcoma (EWS) harbors genetic alterations within the D-loop region and their potential association with EWS carcinogenesis, we analyzed and compared the complete mtDNA D-loop sequences from 17 pairs of tumor tissues and corresponding peripheral blood samples using the direct DNA sequencing method. Our results revealed that 12 of the 17 EWS tumor specimens (70.6%) carried 19 somatic mutations in the D-loop of mtDNA, including 11 single-base substitutions, 3 insertions and 5 deletions. Among the tested 17 patients, we screened a total of 40 germline polymorphisms including one novel sequence variant in the D-loop fragment. Most of these identified mutations and germline variations were clustered within two hypervariable segments (HVS1 and HVS2) as well as the homopolymeric C stretch between nucleotide position 303 and 309. In addition, there was no significant correlation between mtDNA D-loop mutations and various clinicopathological factors of EWS. In conclusion, our study reports for the first time that mtDNA D-loop mutations occur at a high frequency in EWS. These data provide evidence of mtDNA alterations’ possible involvement in the initiation and/or progression of this rare malignancy.     

Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: comparison of mitochondrial D-loop region sequences

To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705-824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.     

Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequences

In this study, we assessed the maternal origin of six Hungarian indigenous chicken breeds using mitochondrial DNA information. Sequences of Hungarian chickens were compared with the D-loop chicken sequences annotated in the GenBank and to nine previously described reference haplotypes representing the main haplogroups of chicken. The first 530 bases of the D-loop region were sequenced in 74 chickens of nine populations. Eleven haplotypes (HIC1-HIC11) were observed from 17 variable sites. Three sequences (HIC3, HIC8 and HIC9) of our chickens were found as unique to Hungary when searched against the NCBI GenBank database. Hungarian domestic chicken mtDNA sequences could be assigned into three clades and probably two maternal lineages. Results indicated that 86% of the Hungarian haplotypes are related to the reference sequence that likely originated from the Indian subcontinent, while the minor part of our sequences presumably derive from South East Asia, China and Japan.     

Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs

The nucleotide sequences of the D-loop region and its flanking genes of the mitochondrial DNA (mtDNA) from Japanese pond frogs were determined by the methods of PCR, cloning, and sequencing. The frogs belonged to two species, one subspecies, and one local race. The gene arrangements adjacent to the D-loop region were analyzed. The frogs shared a unique mitochondrial gene order that was found in Rana catesbeiana; i.e., cyt b--D-loop region--tRNA(Leu(CUN))--tRNA(Thr)--tRNA(Pro)--tRNA(Phe)--12S rRNA. The arrangements of the three tRNA genes of these frogs were different from those of X. laevis, a species which has the same overall structure as in mammals. Highly repetitive sequences with repeat units (16-bp or 17-bp sequence specific for each taxon) were found in the D-loop region. The length of repetitive sequences varied from 0.6 kbp to 1.2 kbp, and caused the extensive size variation in mtDNA. Several short sequence elements such as putative TAS, OH, CSB-1, and CSB-2 were found in the D-loop region of these frogs. The sequences of these short regulatory elements were conserved in R. catesbeiana, X. laevis, and also in human. The comparison of sequence divergences of the D-loop region and its adjacent genes among various taxa revealed that the rates of nucleotide substitutions depend on genes. The nucleotide sequences of the 3'-side segment of the D-loop region were the most variable among taxa, whereas those of the tRNA and 12S rRNA genes were the most conservative.     

Two Genetically Distinct Lineages of the Sika Deer, Cervus nippon, in Japanese Islands: Comparison of Mitochondrial D-Loop Region Sequences

To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705–824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.     

A phylogenetic study of the genus Apodemus by sequencing the mitochondrial DNA control region

The sequences of the mitochondrial DNA control region (D-loop) and flanking tRNA genes (about 1000 bp) of 20 samples of wood mice (genus Apodemus ) were analyzed in order to clarify the relationships between different species belonging to the genus. The phylogenetic trees obtained using different methods showed similar topologies with distinct Karstomys ( Apodemus epimelas and Apodemus mystacinus ) and Sylvaemus ( Apodemus alpicola , Apodemus flavicollis , Apodemus hermonensis , Apodemus sylvaticus and Apodemus uralensis ) subtrees. Within Sylvaemus all species appeared to be closely related to each other, probably as result of a bush-like radiation event. Nevertheless, A. hermonensis seemed to be the first diverging branch followed by A. sylvaticus ; A. alpicola and A. flavicollis appeared to be very closely related. Three individuals of uncertain taxonomical status were included in the analysis: hypotheses as to their status are discussed. Further phylogenetic analysis was carried out combining the D-loop sequences of part of the samples of certain taxonomical status with 12S rRNA and cytochrome b sequences obtained by other researchers. Furthermore, I present a structure analysis of the D-loop in Apodemus as compared other rodent species.     

Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation

To determine the origin and genetic diversity of Chinese cattle, we analyzed the complete mtDNA D-loop sequences of 84 cattle from 14 breeds/populations from southwest and west China, together with the available cattle sequences in GenBank. Our results showed that the Chinese cattle samples converged into two main groups, which correspond to the two species Bos taurus and Bos indicus. Although a dominant lineage was clearly discerned in both B. taurus and B. indicus mtDNAs, network analysis of the lineages in each of the two species further revealed multiple clades that presented regional difference. The B. taurus samples in China could be grouped into clades T2, T3, and T4, whereas B. indicus harbored two clades I1 and I2. Age estimation of these discerned clades showed a time range of 14,100-44,500 years before present (YBP). The phylogenetic pattern of Chinese cattle was consistent with the recently described cattle matrilineal pool from northeast Asia, but suggested that B. indicus contributed more to the cattle from south and southwest China. The genetic diversity of Chinese cattle varied among the breeds studied.