Polymorphism in mitochondrial DNA (mtDNA) of yak (Bos grunniens)

Mitochondrial DNAs (mtDNA) from 21 yaks (Bos grunniens) were assayed for restriction fragment length polymorphisms by using 20 restriction endonucleases, six of which (AvaI, AvaII, BglII, EcoRI, HindIII, and HpaI) detected polymorphism. Four different mtD

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.

Mitochondrial DNA control region and cytochrome b sequence variation in the genus Mystacoleucus Gunther (Pisces : Cyprinidae : Barbinae) from China

Mitochondrial DNA (mtDNA) hypervariable segment I sequences (HVSI, 471 bp) of the control region and partial cytochrome b sequences (Cytb, 403 bp) were analyzed in three tentative species of the genus Mystacoleucus in China (M. chilopterus, M. marginatus, and M. lepturus). Not more than two mutations were found in both the HVSI and Cytb fragments among the samples from M. chilopterus and M. marginatus. However, M. lepturus differed from each of them by at least 25 mutations in Cytb and 51 mutations in HVSI. Moreover, the HVSI sequence variation within M. lepturus was larger than that between M. chilopterus and M. marginatus. Given that M. chilopterus and M. marginatus are very similar in morphology, it is reasonable to consider M. chilopterus and M. marginatus as conspecific. Our results also suggest a recent radiation of M. marginatus from downstream to upstream of the Lancangjiang (Mekong) River.

Molecular phylogeny of wood mice (Apodemus, Muridae) in East Asia

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear IRBP (1152 bp) genes were used to assess the evolutionary history of Apodemus, using the complete set of Asian species. Our results indicate that speciation in Asia involved three radiations, which supports an earlier study. The initial radiation yielded A. argenteus (Japanese endemic), A. gurkha (Nepalese endemic), and the ancestral lineage of the remaining Asian species. This lineage subsequently diverged into four groups: agrarius-chevrieri (agrarius group), draco-latronum-semotus (draco group), A. peninsulae, and A. speciosus (Japanese endemic). The final step consisted of divergence within two species groups as a consequence of the geography of the Yunnan-Guizhou plateau and Taiwan. The ecological ability of two Apodemus-species to inhabit one locality via niche partitioning likely drove the second radiation and shaped the basic geographical pattern seen today: A. argenteus and A. speciosus in Japan, A. agrarius and A. peninsulae in northern China, and the A. agrarius and A. draco groups in southern China. The three radiations are estimated to have occurred 7.5, 6.6, and 1.8-0.8 Mya respectively, using the IRBP clock, based on rat-mouse divergence 12 Mya. (C) 2003 The Linnean Society of London.

Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China

To study the mitochondrial DNA (mtDNA) polymorphisms in a total of 232 individuals from five ethnic populations (Daur, n=45; Ewenki, n=47; Korean, n=48; Mongolian, n=48; Oroqen, n=44) in northern China, we analyzed the control region sequences and typed for a number of characteristic mutations in coding regions (especially the region 14576-16047), by direct sequencing or restriction-fragment-length-polymorphism (RFLP) analysis. With the exception of 14 individuals belonging to the European-specific haplogroups R2, H, J, and T, the mtDNAs considered could be assigned into the East Asian-specific haplogroups described recently. The polymorphisms in cytochrome b sequence were found to be very informative for defining or supporting the haplogroups status of East Asian mtDNAs in addition to the reported regions 10171-10659 and 14055-14590 in our previous study. The haplogroup distribution frequencies varied in the five ethnic populations, but in general they all harbored a large amount of north-prevalent haplogroups, such as D, G, C, and Z, and thus were in agreement with their ethnohistory of northern origin. The two populations (Ewenki and Oroqen) with small population census also show concordant features in their matrilineal genetic structures, with lower genetic diversities observed.

Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences

The now-emerging mitochondrial DNA ( mtDNA) population genomics provides information for reconstructing a well-resolved mtDNA phylogeny and for discerning the phylogenetic status of the subcontinentally specific haplogroups. Although several major East Asian mtDNA haplogroups have been identified in studies elsewhere, some of the most basal haplogroups, as well as numerous minor subhaplogroups, were not yet determined or fully characterized. To fill the lacunae, we selected 48 mtDNAs from >2,000 samples across China for complete sequencing that cover virtually all ( sub) haplogroups discernible to date in East Asia. This East Asian mtDNA phylogeny can henceforth serve as a solid basis for phylogeographic analyses of mtDNAs, as well as for studies of mitochondrial diseases in East and Southeast Asia.

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.

Adaptive diversification of bitter taste receptor genes in mammalian evolution

The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome sequences, respectively, in addition to the 23 and 6 previously known T2R genes from the two species. A phylogenetic analysis of the T2R genes suggests that they can be classified into three main groups, which are designated A, B, and C. Interestingly, while the one-to-one gene orthology between the human and mouse is common to group B and C genes, group A genes show a pattern of species- or lineage-specific duplication. It is possible that group B and C genes are necessary for detecting bitter tastants common to both humans and mice, whereas group A genes are used for species-specific bitter tastants. The analysis also reveals that phylogenetically closely related T2R genes are close in their chromosomal locations, demonstrating tandem gene duplication as the primary source of new T2Rs. For closely related paralogous genes, a rate of nonsynonymous nucleotide substitution significantly higher than the rate of synonymous substitution was observed in the extracellular regions of T2Rs, which are presumably involved in tastant-binding. This suggests the role of positive selection in the diversification of newly duplicated T2R genes. Because many natural poisonous substances are bitter, we conjecture that the mammalian T2R genes are under diversifying selection for the ability to recognize a diverse array of poisons that the organisms may encounter in exploring new habitats and diets.

Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis

A fragment of mitochondrial DNA (mtDNA) control region (similar to700 bp) was sequenced in 104 individuals from 20 breeds (three Chinese domestic breeds, five recently derived breeds and 12 introduced breeds) of domestic rabbits, Oryctolagus cuniculus . Nineteen sites were polymorphic, with 18 transitions and one insertion/deletion, and eight haplotypes (A1, A2, A3, A4, A5, A6, A7 and A8) were identified. Haplotype A1 was the most common and occurred in 89 individuals. In the 25 Chinese rabbits, only haplotype A1 was observed, while four haplotypes (A1, A3, A5 and A6) were found in 26 recently derived individuals. Haplotype A2 was shared by seven individuals among three introduced strains. The other six haplotypes accounted for 0. 96-1. 92% of the animals. Combined with the published sequences of European rabbits, a reduced median-joining network was constructed. The Chinese rabbit mtDNAs were scattered into two clusters of European rabbits. These results suggest that the (so-called) Chinese rabbits were introduced from Europe. Genetic diversity in Chinese rabbits was very low.

Evolution and biogeography of talpid moles from continental East Asia and the Japanese islands inferred from mitochondrial and nuclear gene sequences

We sequenced the cytochrome b gene from two little-studied mammal species from the highlands of Southwest China, the long-tailed mole Scaptonyx fusicaudus and the gracile shrew-like mole Uropsilus gracilis. This data was used to examine the phylogenetic r

Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes

Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon1 of the IRBP gene (approximate to1.3 kb) and first intron

Phylogenetic relationships of 12 Penaeoidea shrimp species deduced from mitochondrial DNA sequences

DNA sequences of an 847 bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene and a 514 bp fragment of 16s rRNA gene were determined to examine the phylogenetic relationships of 12 Penaeoidea shrimp species (Penaeus chinensis, Penaeus japon