Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus

The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequence

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F-1 hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e., represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau, On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister tars of one steppe? dweller and one shrub dweller is very low. These findings support the hypothesis that pikes have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution. (C) 2000 Academic Press.

Genetic characterization of three Ompok species using mitochondrial DNA sequences

Partial sequences of cytochrome b (Cyt b) and 16S ribosomal RNA (16S rRNA) mitochondrial genes were used for species identification and estimating phylogenetic relationship among three commercially important Ompok species viz. O. Pabda, O. pabo and O. bimaculatus. The sequence analysis of Cyt b (1118bp) and 16S rRNA (569 & 570bp) genes revealed that O. pabda, O. pabo & 0. bimaculatus were genetically distinct species and they exhibited identical phylogenetic relationship. The present study discussed usefulness of mtDNA genes (Cyt b & 16S rRNA) in resolving taxonomic ambiguity and estimating phylogenetics relationship.

Mitochondrial DNA D2loop Variation and Genetic Background of Brahman Cattle

对10 头原种婆罗门牛mtDNA D2loop 全序列912 bp 测序, 婆罗门牛遗传多样性丰富, 检测到的9 种单 倍型兼有瘤牛( B . indicus) 与普通牛( B . taurus) 的遗传背景, 核苷酸变异率为6125 % , 单倍型多态度为01978 ± 01054 , 核苷酸多态度为01014 30 ±01008 68。所有单倍型聚为明显的两大分支, 婆罗门牛的大部分单倍型为普通 牛单倍型类群, 并占绝对优势(90 %) , 仅Brah26 与亚洲瘤牛聚在一起, 属于亚洲瘤牛线粒体单倍型, 表明婆罗门 牛的确是集亚洲瘤牛、欧洲普通牛等优良特性于一身(易产犊、产肉性能好、耐热与体表寄生虫等) 的瘤牛品种之 一。育种学家引种瘤牛的目的是改善当地牛的生产力与适应性, 现代普通牛表现出明显又普遍的瘤牛渐渗现象。 对现代的瘤牛品种而言, 除亚洲瘤牛品种外, 普通牛对其他瘤牛品种育成的贡献同样高。支持瘤牛( B . indicus ) 为独立驯化、起源于印度次大陆的假说。

Molecular Phylogeny of Slow Lorises ( Nycticebus) Revealed by D2loop Sequences and Complete Cytochrome bGene Sequences of Mitochondrial DNA

本研究测定了懒猴属( Nycticebus) D 环的部分序列和细胞色素b 基因的全序列(1 140 bp) , 分析了 该属物种之间的系统发育进化关系。在DNA 水平上, 序列分析结果一致地提供了新的分类学证据: 支持Rata2 jszczak 和Groves 的观点, 即N1intermedus 只是N1 pygmaeus 的成体(Ratajszczak , 1998 ; Groves , 1971) 。对两种 序列的数据做了联合及个别分析, 获得相似的系统树, 支持懒猴属由两个单系群组成: 第一群由N1 pygmaeus 聚成, 第二群由N1coucang 聚成。该结果也提供了新的分子遗传证据, 支持懒猴属由N1coucang 和 N1 pygmaeus 两物种组成。

A Molecular Phylogeny of Macaca Based on Mitochondrial Control Region Sequences

通过线粒体部分控制区DNA 序列数据探讨7 种猕猴属物种的分子系统发育关系。结果表明熊猴的 核苷酸多样度最高, 而藏酋猴核苷酸多样度较低。基于控制区序列数据所构建的最大似然树, 不考虑食蟹猴的 位置, 7 种猕猴物种可粗略地分为3 个种组, 即狮尾猴组(包括北平顶猴) 、头巾猴组(包括红面猴、熊猴和藏 酋猴) 和食蟹猴组(包括恒河猴和台湾猴) 。与前人( Fooden & Lanyon , 1989 ; Tosi et al , 2003a ; Deinard & Smith , 2001 ; Evans et al , 1999 ; Hayasaka et al , 1996 ; Morales &Melnick , 1998) 的结果不同, 我们的结果支 持食蟹猴比北平顶猴分化早的假设; 东部恒河猴(相对于台湾猴) 和东部熊猴(相对于藏酋猴) 出现并系。与 Y染色体、等位酶、核基因以及部分形态学数据推测的结果(Delson , 1980 ; Fooden &Lanyon , 1989 ; Fooden , 1990 ; Tosi et al , 2000 , 2003a , b ; Deinard & Smith , 2001) 一致, 红面猴应归于头巾猴组, 但此结论与前人 (Hayasaka et al , 1996 ; Morales &Melnick , 1998 ; Tosi et al , 2003a) 依据线粒体得到的结果有较大分歧。

Study on Mitochondrial DNA Cytochrome b Gene of Chinese sea bass, Lateolabrax sp.

参考鳗鲡等鱼类线粒体 DNA序列进行了中国花鲈线粒体 DNA细胞色素 b基因片断的引物设计、PCR扩增及其序列测定。得到中国花鲈的碱基序列为 4 10 bp,其 A、T、G、C含量分别为 10 1bp(2 4 .6 3% )、112 bp(2 7.32 % )、72 bp(17.56 % )、12 5bp(30 .4 9% ) ,与鳗鲡等其他鱼类相同基因片断序列碱基含量相似。

GENETIC DIVERSITY IN THE CHINESE PANGOLIN (MANIS-PENTADACTYLA) - INFERRED FROM RESTRICTION ENZYME ANALYSIS OF MITOCHONDRIAL DNAS

Two different forms of Chinese pangolins can be recognized according to the color of their scales, i.e., brown and dusky. We analyzed mitochondrial DNA (mtDNA) purified from the livers of seven dusky and six brown Chinese pangolins from the same locality, using cleavage patterns from 19 restriction enzymes. From the 19 6-bp recognition enzymes used, 51-56 sites were observed. By combining the cleavage patterns for each enzyme, the 13 samples were classified into four restriction types: two in dusky and two in brown Chinese pangolins. The estimated number of nucleotide substitutions per site in dusky and brown types is 0.002, and that between dusky and brown types is 0.012. Divergence between brown and dusky forms began 0.6 Myr ago, provided the mean rate of sequence divergence is 0.02 per Myr in mtDNA. Our results suggest that there is considerable divergence in Chinese pangolins, and brown and dusky Chinese pangolins may be quite different forms or, at least, belong to different maternal groups.

PHYLOGENY OF RHESUS-MONKEYS (MACACA-MULATTA) AS REVEALED BY MITOCHONDRIAL-DNA RESTRICTION ENZYME ANALYSIS

Mitochondrial DNA, purified from 36 samples of 23 local populations which are widely distributed in Vietnam, Burma, and 10 provinces of China, has been analyzed to model the phylogeny of rhesus monkeys. The 20 local populations of China may represent nearly all major populations in China. Using 20 restriction endonucleases of 6-bp recognition, we observed a total of 50-61 sites in the various samples. By combining the cleavage patterns for each enzyme, the 36 samples were classified into 23 restriction types, each of which was found exclusively in the respective population from which samples were obtained By combining the earlier study of Indian rhesus monkeys, phylogenetic trees, which have been constructed on the basis of genetic distance, indicate that rhesus monkeys in China, Vietnam, India, and Burma can be divided into seven groups. Integrating morphological and geographical data, we suggest that rhesus monkeys in China, Vietnam, and Burma may be classified into six subspecies-M. m. mulatta, M. m. brevicaudus, M. m. lasiotis, M. m. littoralis, M. m. vestita, and M. m. tcheliensis-and rhesus monkeys in India may be another valid subspecies. M. m. tcheliensis is the most endangered subspecies in China. Divergence among subspecies may have begun 0.9-1.6 Ma. The radiation of rhesus monkeys in China may have spread from the southwest toward the east. The taxonomic status of the Hainan monkey and the Taiwan monkey require further investigation.

PHYLOGENETIC-RELATIONSHIPS OF MACAQUES AS INFERRED FROM RESTRICTION-ENDONUCLEASE ANALYSIS OF MITOCHONDRIAL-DNA

Mitochondrial DNAs (mtDNAs) purified from 25 samples of 6 species of macaques, Macaca mulatta, M. fascicularis, M. arctoides, M. nemestrina, M. assamensis and M. thibetana, were analyzed to study the phyletic relationships among the species. A total of 36-46 sites was observed in each sample. By combining the cleavage patterns for each of the endonucleases, the 25 samples were classified into 11 restriction types. When data on M. fuscata and M. cyclopis collected by other authors were added to our own, the resultant molecular phylogenetic trees indicated that the 8 species may be divided into 4 groups: (1) M. mulatta, M. fuscata, M. cyclopis and M. fascicularis; (2) M. arctoides, (3) M. nemestrina; (4) M. assamensis and M. thibetana. Our results suggest that within both the fascicularis and sinica groups genetic distances are small between members and that the status of the species within the groups may require further investigation.

PHYLOGENY OF THE SLOW LORISES (GENUS NYCTICEBUS) - AN APPROACH USING MITOCHONDRIAL-DNA RESTRICTION ENZYME ANALYSIS

Mitochondrial DNA polymorphisms in 15 specimens of three species of slow lorises-Nycticebus coucang, N. intermedius, and N. pygmaeus-were analyzed in order to study the evolutionary relationships among the species. Eight restriction types were observed in the samples. Phylogenetic trees constructed on the basis of genetic distances showed that the slow lorises sort into two clusters: four types of N. coucang and three types of N. intermedius plus one type of N. pygmaeus. Our results suggest that there are two valid species in the genus Nycticebus-N. coucang and N. pygmaeus-and that N. intermedius should be included within N. pygmaeus. Divergence between the two species may have begun 2.7 Ma (million years ago). Evolution of gross morphology, chromosomes, and mitochondrial DNA in the slow lorises appears to be concordant.

DIFFERENT RATES OF MITOCHONDRIAL-DNA SEQUENCE EVOLUTION IN KIRK DIK-DIK (MADOQUA-KIRKII) POPULATIONS

We have investigated evolutionary rates of the mitochondrial genome among individuals of Madoqua kirkii using the relative rate test. Our results demonstrate that individuals of two chromosome races, East African cytotype A and Southwest African cytotype D, evolve about 2.3 times faster than East African cytotype B. Cytogenetic changes, DNA repair efficiency, mutagens, and more likely, hitherto unrecognized factors will account for the rate difference we have observed. Our results suggest additional caution when using molecular clocks in the estimation of divergence time, even within lineages of closely related taxa. Rate heterogeneity in microevolutionary timescales represents a potentially important aspect of basic evolutionary processes and may provide additional insights into factors which affect genome evolution. (C) 1995 Academic Press, Inc.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

A phylogeny of Chinese leaf monkeys using mitochondrial ND3-ND4 gene sequences

The phylogeny of Chinese leaf monkeys, especially the snub-nosed monkeys (Rhinopithecus), has not been thoroughly investigated using molecular sequence data, perhaps due to their rarity in the wild and their poor representation in institutional collections. Despite several proposed classifications, systematic relationships of these species remain poorly defined and this has hindered their conservation. To clarify the phylogenetic relationships of the leaf monkey clade in China, we sequenced the mitochondrial ND3, ND4L, ND4, tRNA(Arg), tRNA(His), tRNA(Ser), and tRNA(Leu) genes for Rhinopithecus bieti, R. roxellana, Trachypithecus francoisi, T. f. leucocephalus, and T. phayrei as well as Pygathrix nemaeus and Colobus guereza. We included a rotal of 2252 characters for each individual, excluding gaps in primary sequences. Our interpretation of the results from character- and distance-based phylogenetic analyses suggest that (1) Pygathrix nemaeus is sister to Rhinopithecus rather than to Trachypithecus though it is quite divergent from the former; (2) the Yunnan snub-nosed monkey, Rhinopithecus bieti, represents a valid species; (3) the white-headed leaf monkey is not a distinct species, but instead is a subspecies of Trachypithecus francoisi (T. f. leucocephalus), though it should still be considered a separate evolutionarily significant unit (ESU); and (4) because two individuals of the Phayrei's leaf monkey, T. phayrei, are genetically distinct from one another, a more extensive revision of the taxonomy of this putative species in China is needed. These results, plus ongoing work on the molecular systematics of the entire Asian leaf monkey radiation, can provide a sound basis for identifying the appropriate units of conservation for this endangered group of primates.