Cytogenetics, morphology and evolution of four subspecies of the Giant Sheep argali (Ovis ammon) of Asia

Dalai-lamae (Ovis ammon dalai-lamae), Gobi (O. a. darwini), Kara Tau (O. a. nigrimontana) and Tibetan (O. a. hodgsoni) argali share a 2n = 56 diploid chromosome number and a karyotype consisting of 2 pairs of biarmed and 25 pairs of acrocentric autosomes, a large acrocentric X and a minute Y chromosome. The Giemsa-banding patterns of the largest pair of biarmed chromosomes were identical to those of the largest biarmed chromosomes in all wild sheep and domestic sheep of the genus Ovis. The banding patterns of the second pair of biarmed chromosomes (metacentric) were identical to the third pair of biarmed chromosomes in Ovis with 2n = 54 and to the third largest pair of chromosomes in the 2n = 52 karyotype of Siberian snow sheep (O. nivicola). The G-banded karyotypes of dalai-lamae, darwini, hodgsoni and nigrimontana are consistent with all subspecies of argali (O. ammon), except that the Y chromosome is acrocentric instead of metacentric as typical of the argaliform wild sheep and Ovis. The Dalai-lamae and Tibetan argali specimens exhibit the light-colored, long-haired ruffs and body coloration typical of argalis from the Tibetan Plateau. The Gobi argali, from the extreme western Gobi, is similar to the dark phase argali.

Genetic divergence of orangutan subspecies (Pongo pygmaeus)

Microsatellites and mitochondrial DNA sequences were studied for the two subspecies of orangutans (Pongo pygmaeus), which are located in Borneo (P. p, pygmaeus) and Sumatra (P. p. abelii), respectively. Both subspecies possess marked genetic diversity. Ge

Differentiation of subspecies of asiatic striped squirrels (Tamiops swinhoei) (Milne-Edwards) (Rodentia : Sciuridae) in China with description of a new subspecies

Based on the pelage characteristics and results of multivariate and univariate analyses, a new subspecies is described in this study, and a taxonomic revision of Tamiops swinhoei from China is presented. In total, 123 specimens of Tamiops swinhoei were in

Geographic variation of the Anderson's Niviventer (Niviventer andersoni) (Thomas, 1911) (Rodentia: Muridae) of two new subspecies in China verified with cranial morphometric variables and pelage characteristics

A total of 66 specimens of Niviventer andersoni with intact skulls was investigated on pelage characteristics and cranial morphometric variables. The data were subjected to principal component analyses as well as to discriminant analyses, and measurement

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

PCR-RFLP analysis of mitochondrial DNA ND5/6 region among 3 subspecies of common carp (Cyprinus carpio L.) and its application to genetic discrimination of subspecies

Mitochondrial DNA ND5/6 region was studied by PCR-RFLP analysis among ten representative strains belonging to three subspecies (Cyprinus carpio carpio, Cyprinus carpio haematopterus and Cyprinus carpio rubrofuscus) of common carp (Cyprinus carpio L.). A total of 2.4 kb fragment was amplified and subjected to restriction endonuclease analysis with nine restriction endonucleases subsequently. The results indicated that each subspecies owned one hyplotype and four restriction enzymes (Dde I, HaeIII, Taq I and Mbo I) produced diagnostic restriction sites which could be used for discriminating the three subspecies and as molecular genetic markers for assistant selective breeding of common carp.

Phylogenetic relationships among two species of golden monkey and three species of leaf monkey inferred from rDNA variation

Restriction maps of rDNA repeats of five species of Colobinae and three outgroup taxa, Hylobates leucogenys, Macaca mulatta, and Macaca irus, were constructed using 15 restriction endonucleases and cloned 18S and 28S rRNA gene probes. The site variation between Rhinopithecus roxellana and Rhinopithecus bieti is comparable to that between Presbytis francoisi and Presbytis phayrei, implying that R. bieti is a valid species rather than a subspecies of R. roxellana. Phylogenetic analysis on the 47 informative sites supports the case for Rhinopithecus being an independent genus and closely related to Presbytis. Furthermore, branch lengths of the tree seem to support the hypothesis that the leaf monkeys share some ancestral traits as well as some automorphic characters.

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

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.

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.

Genetic diversity in crucian carp (Carassius auratus)

A survey of restriction fragment polymorphism in mitochondrial DNA of three subspecies of Carassius auratus throughout four provinces in China was undertaken using 17 restriction enzymes. Two carp, Cyprinus carpio rubbrofuscus and Cyprinus carpio carpio, were included as the outgroup. A total of 16 haplotypes was observed: 5 in tetraploids of C. auratus auratus; 8 in hexaploids of C. auratus auratus; and 2 in C. auratus gibelio and C. auratus cuvieri, respectively. The tetraploids and hexaploids share three common haplotypes as I, V, and VI. C. a. Cuvieri may have diverged first among the three subspecies. Interestingly, C. a. auratus and C. a. cuvieri did not form monophyletic clades, which indicated that the classification of carassius auratus required further studies. The current hypothesis, that hexaploids originated from tetraploids by a polyploidy event, is less favorable, based on the distribution of haplotypes and the lower diversity in tetraploids than in hexaploids. Our data also indicate that divergence of hexaploids and tetraploids might be recent and mtDNA polymorphism existed before the divergence. Meanwhile, genetic isolation exists between the hexaploids and the tetraploids.

Genetic diversity and taxonomic implication of Cordyceps sinensis as revealed by RAPD markers

Random amplified polymorphic DNA (RAPD) markers are used to investigate genetic variation and evolutionary relationships of 29 samples of Cordyceps sinensis from different geographical populations on the Qinghai-Tibet plateau. Out of 137 RAPD bands scored, 100 are polymorphic. A correlation is revealed between geographical distance and genetic distance. The molecular phylogenetic tree suggests that the 29 samples are divided into three notable clusters, corresponding to the geographical populations, i.e., the north population (NP), middle population (MP), and south population (SP). The NP consists of 7 northern samples from Menyuan, Maqu, and Luqu, the MP consists of 8 samples from Yushu and Chengduo, and the SP consists of 14 samples from Byma Snow Mountain, Renzhi Snow Moutain, Chongcaoxiwa, and Dacaodi. It is demonstrated that extensive genetic diversity is found among different geographical populations of C. sinensis. The genetic diversity pattern of C. sinensis may be caused by the founder effects. The taxonomic status of NP, MP, and SP populations should be that they are different subspecies rather than different species.

Taxonomic status of the white-head langur (Trachypithecus francoisi leucoscephalus) inferred from allozyme electrophoresis and random amplified polymorphism DNA (RAPD)

Six sample specimens of Trachypithecus francoisi and 3 of T. leucocephalus were analyzed by use of allozyme electrophoresis and random amplified polymorphism DNA (RAPD) in order to clarify the challenged taxonomic status of the white-head langur. Among the 44 loci surveyed, only 1 locus (PGM-2) was found to be polymorphic. Nei's genetic distance was 0.0025. In total, thirty 10-mer arbitrary primers were used for RAPD analysis, of which 22 generated clear bands. Phylogenetic trees were constructed based on genetic distances using neighbor-joining and UPGMA methods. The results show that T. francoisi and T: leucocephalus are not monophyletic. T. francoisi from Guangxi, China and Vietnam could not be clearly distinguished, and they are not divided into 2 clusters. A t-test was performed to evaluate between genetic distances within and between T. leucocephalus and T. francoisi taxa groups. The statistical test shows that the taxa group within T: leucocephalus and T: francoisi does not significantly differ from that between T: leucocephalus and T: francoisi at the 5% level. Our results suggest that the level of genetic differentiation between T, leucocephalus and T. francoisi is relatively low. Recent gene flow might exist between T. francoisi and T. leucocephalus. Combining morphological features, geographical distribution, allozyme data, RAPD data, and mtDNA sequences, we suggest that the white-head langur might be a subspecies of T. francoisi.

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation

Background: Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family repre