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.

Molecular systematics of Xenocyprinae (Teleostei : Cyprinidae): Taxonomy, biogeography, and coevolution of a special group restricted in east Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structu

Intra- and interspecific variation of the CCR5 gene in higher primates

We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light on its functional role. The comparison of differences between intraspecific polymorphisms and interspecific fixed substitutions provides useful information regarding modes of selection during the course of evolution. There is marked polymorphism in the CCR5 gene sequence within different primate species, whereas sequence divergence between different species is small. By using contingency tests, we compared synonymous (SS) and nonsynonymous (NS) CCR5 mutations occurring within and between a broad range of primates. Our results demonstrate that CCR5 evolution did not follow expectations, of strict neutrality at the level of the whole gene. The proportion of NS to SS at the intraspecific level was significantly higher than that observed at the interspecific level. These results suggest that most CCR5 NS polymorphisms are slightly deleterious. However, at domains more closely correlated with its known biological functions, there was no obvious evidence to support deviation from neutrality.

Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia)

Oriental voles of the genus Eothenomys are predominantly distributed along the Southeastern shoulder of the Qinghai-Tibetan Plateau. Based on phylogenetic analyses of the mitochondrial cytochrome b gene (1143 bp) obtained from 23 specimens (eight species)

Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes

The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ tw

Moderate mutation rate in the SARS coronavirus genome and its implications

Background: The outbreak of severe acute respiratory syndrome (SARS) caused a severe global epidemic in 2003 which led to hundreds of deaths and many thousands of hospitalizations. The virus causing SARS was identified as a novel coronavirus (SARS-CoV) an

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history. (c) 2005 Elsevier Inc. All rights reserved.

Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences

In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (+/- 0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65 +/- 1.15 MYA similar to 1.12 +/- 10.47 MYA). (c) 2005 Elsevier Inc. All rights reserved.

Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis)

Climatic oscillations during the Pleistocene ice ages produced great changes in species' geographical distribution and abundance, which could be expected to have genetic consequences. Living in the temperate upwelling zones of the northwestern Pacific, Ja

Molecular phylogeny of the Drosophila virilis section (Diptera : Drosophilidae) based on mitochondrial and nuclear sequences

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the

Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific

The Quaternary cold periods in the Northwestern Pacific are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in marine fishes. To estimate the demographic history and genetic structure of Lateolabrax macula

Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia : Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis

With modified DNA extraction and Purification protocols, the complete cytochrome b gene sequences (1140 bp) were determined from degraded museum specimens. Molecular analysis and morphological examination of cranial characteristics of the giant flying squirrels of Petaurista philippensis complex (P. grandis, P. hainana, and P. yunanensis) and other Petaurista species yielded new insights into long-standing controversies in the Petaurista systematics. Patterns of genetic variations and morphological differences observed in this study indicate that P. hainana, P. albiventer, and P. yunanensis can be recognized as distinct species, and P. grandis and P. petaurista are conspecific populations. Phylogenetic relationships reconstructed by using parsimony, likelihood, and Bayesian methods reveal that, with P. leucogenys as the basal branch, all Petaurista groups formed two distinct clades. Petaurista philippensis, P. hainana, P. yunanensis, and P. albiventer are clustered in the same clade, while P. grandis shows a close relationship to P. petaurista. Deduced divergence times based on Bayesian analysis and the transversional substitution at the third codon suggest that the retreating of glaciers and upheavals or movements of tectonic plates in the Pliocene-Pleistocene were the major factors responsible for the present geographical distributions of Petaurista groups. (c) 2005 Elsevier Inc. All rights reserved.

Phylogeny of Raninae (Anura : Ranidae) inferred from mitochondrial and nuclear sequences

Phylogenetic relationships among representative species of the subfamily Raninae were investigated using approximately 2000 base pairs of DNA sequences from two mitochondrial (12S rRNA, 16S rRNA) and two nuclear (tyrosinase, rhodopsin) genes. Phylogenetic

Genetic differentiation and cryptic speciation in natural populations of Drosophila lacertosa

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two ge

Mitochondrial variation of the "eyed" turtles (Sacalia) based on known-locality and trade specimens

Bryan L. Stuart is thanked for his hard work to collect wild specimens, as well as providing insightful and useful comments on the data. We thank Abigail Wolf of the Field Museum for providing photographs of specimens. Robert Murphy of the Royal Ontario M