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.

Extraction, PCR amplification, and sequencing of mitochondrial DNA from scent mark and feces in the giant panda

To expand the feasibility of applying simple, efficient, non-invasive DNA preparation methods using samples that can be obtained from giant pandas living in the wild, we investigated the use of scent markings and fecal samples. Giant panda-specific oligonucleotide primers were used to amplify a portion of the mitochondrial DNA control region as well as a portion of the mitochondrial DNA cytochrome b gene and tRNA(Thr) gene region. A 196 base pair (bp) fragment in the control region and a 449 bp fragment in the cytochrome b gene and tRNA(Thr) gene were successfully amplified. Sequencing of polymerase chain reaction (PCR) products demonstrated that the two fragments are giant panda sequences. Furthermore, under simulated field conditions we found that DNA can be extracted from fecal samples aged as long as 3 months. Our results suggest that the scent mark and fecal samples are simple, efficient, and easily prepared DNA sources. (C) 1998 Wiley-Liss, Inc.

Mitochondrial cytochrome b gene sequences of Old World monkeys: With special reference on evolution of Asian colobines

The classification and phylogenetic relationships of the Old World monkeys are still controversial. For Asian colobines, from three to nine genera were recognized by different primatologists. In the present study, we have sequenced a 424 bp mitochondrial tRNA(Thr) gene and cytochrome b gene fragment from Macaca mulatta, Mandrillus sphinx, Mandrillus leucophaeus, Semnopithecus entellus, Trachypithecus vetulus, T. johnii, T. phayrei, T. francoisi, Pygathrix nemaeus, Rhinopithecus roxellanae, R. bieti, R. avunculus, Nasalis larvatus, and Colobus polykomos in order to gain independent information on the classification and phylogenetic relationships of those species. Phylogenetic trees were constructed with parsimony analysis by weighting transversions 5 or 10 fold greater than transitions. Our results support the following conclusions: (1) the Old World monkeys are divided into two subfamilies; (2) that among the colobines, Colobus, the African group, diverged first, and Nasalis and Rhinopithecus form a sister clade to Pygathrix; (3) that there are two clades within leaf monkeys, i.e. 1) S. entellus, T. johnii, and T. vetulus, and 2) T, phayrei and T. francoisi; (4) that Rhinopithecus avunculus, R. roxellanae, and R. bieti are closely related to each other, and they should be placed into the same subgenus; (5) that Rhinopithecus is a distinct genus; and (6) that the ancestors of Asian colobines migrated from Africa to Asia during the late Pliocene or early Pleistocene.

Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genesis strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five, distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D, sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The Kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D.. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D, nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous. (C) 1999 Academic Press.

Mitochondrial cytochrome b sequences variation of Protura and molecular systematics of Apterygota

Mitochondrial cytochrome b genes of about 450 bp fragments from 3 proturan species, 5 collembolan species and 2 dipluran species have been sequenced. The number of nucleotide substitutions and Kimura 2-parameter distances have also been calculated, and a series of molecular phylogenetic trees reconstructed by using parsimony and distance methods. The proturan, collembolan and dipluran species have evolved monophyletic groups. The results suggest that Protura and Collembola are sister groups, while Diplura is more or less demonstrating a closer phylogenetic relationship to the pterygotan insects. The phylogeny and their systematic position of protura and other groups are also discussed.