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 of Chinese native pigs inferred from protein electrophoresis

We examined protein polymorphism of 20 native pig breeds in China and 3 introduced pig breeds. Thirty loci have been investigated, among which six loci were found to be polymorphic. Especially, the polymorphism of malate dehydrogenase (MDH), adenylate kinase (AK), and two new alleles of adenosine deaminase (ADA) had not been reported in domestic pigs and wild pigs. The percentage of polymorphic loci (P), the mean heterozygosity (H), and the mean number of alleles (A) are 0.200, 0.065, and 1.300, respectively. The degree of genetic variability of Chinese pigs as a whole was higher than that of goats, lower than that of cattle and horses, and similar to that of sheep. Using the gene frequencies of the 30 loci, Nei's genetic distance among the 20 native breeds in China and 3 introduced pig breeds was calculated by the formula of Nei. The program NEIGHBOR in PHYLIP 3.5c was chosen to construct an UPGMA tree and a NJ tree. Our results show that, of the total genetic variation found in the native pig breeds in China, 31% (0.31) is ascribable to genetic differences among breeds. About 69% of the total genetic variation is found within breeds. Most breeds are in linkage disequilibrium. The patterns of genetic similarities between the Chinese native pig breeds were not in agreement with the proposed pig type classification.

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion:haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modem humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVS1 diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

Frequency of the mtDNA 9-bp deletion in Chinese ethnic groups

The 9-bp deletion in the COII/tRNA(Lys) intergenic region (region V) of human mitochondrial DNA was screened in 1521 Chinese from 16 ethnic groups and 9 Hen geographic groups. The highest frequency was found in populations of Miao (32.4%) and Bouyei (30.8

Melanocortin-1 receptor gene variants in four Chinese ethnic populations

There is strong relationship between melanocortin-1 receptor (MC1R) gene variants and human hair color and skin type. Based on a sequencing study of MC1R gene in 50 individuals from the Uygur, Tibetan, Wa and Dai ethnic populations, we discuss the occurre

The origin and genetic diversity of Chinese native chicken breeds

The first 539 bases of mitochondrial DNA D-loop region of six Chinese native chicken breeds (Gallus gallus domesticus) were sequenced and compared to those of the red junglefowl (Gallus gallus), the gray junglefowl (Gallus sonneratii), the green junglefow

Length polymorphism of thymidylate synthase regulatory region in Chinese populations and evolution of the novel alleles

The tandemly repeated 28-bp sequence in the 5'-terminal regulatory, region of human thymidylate synthase (TSER), which has been reported to be polymorphic in different populations, was surveyed in 668 Chinese from 9 Han groups, 8 ethnic populations, and 3

Genetic relationship of Chinese ethnic populations revealed by mtDNA sequence diversity

The origin and demographic history of the ethnic populations of China have not been clearly resolved. In this study, we examined the hypervariable segment I sequences (HVSI) of the mitochondrial DNA control region in 372 individuals from nine Chinese popu

Phylogeographic differentiation of mitochondrial DNA in Han Chinese

To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171-10659 of the coding region,

Mitochondrial DNA variation, effective female population size and population history of the endangered Chinese sturgeon, Acipenser sinensis

The anadromous Chinese sturgeon (Acipenser sinensis), mainly endemic to the Yangtze River in China, is an endangered fish species. The natural population has declined since the Gezhouba Dam blocked its migratory route to the spawning grounds in 1981. In the near future, the completion of the Three Gorges Dam, the world's largest hydroelectric project, may further impact this species by altering the water flow of the Yangtze River. Little is currently known about the population genetic structure of the Chinese sturgeon. In this study, DNA sequence data were determined from the control region (D-loop) of the mitochondrial genome of adult sturgeons (n = 106) that were collected between 1995-2000. The molecular data were used to investigate genetic variation, effective female population size and population history of the Chinese sturgeon in the Yangtze River. Our results indicate that the reduction in abundance did not change genetic variation of the Chinese sturgeon, and that the population underwent an expansion in the past. AMOVA analysis indicated that 98.7% of the genetic variability occurred within each year's spawning populations, the year of collection had little influence on the diversity of annual temporary samples. The relative large effective female population size (N-ef) indicates that good potential exists for the recovery of this species in the future. Strikingly, the ratio of N-ef to the census female population size (N-f) is unusually high (0.77-0.93). This may be the result of a current bottleneck in the population of the Chinese sturgeon that is likely caused by human intervention.

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals, collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058 bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML. and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species. (C) 2003 Elsevier Science (USA). All rights reserved.