Blind equalization and sequence estimation using Markov chain Monte Carlo methods

This paper discusses the problem of restoring a digital input signal that has been degraded by an unknown FIR filter in noise, using the Gibbs sampler. A method for drawing a random sample of a sequence of bits is presented; this is shown to have faster convergence than a scheme by Chen and Li, which draws bits independently. ©1998 IEEE.

Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations

The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 5

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

Molecular Cloning and Sequence Analysis of Two cDNAs Encoding Metalloproteinase2disintegrin from Trimeresurus jerdonii

　从菜花烙铁头蛇的毒腺中,利用RT2PCR 进行体外扩增,克隆到2 个金属蛋白酶2去整合素基 因,命名为TJM21、TJM22. TJM21 cDNA 全长为1 528 bp ,编码481 个氨基酸;TJM22 cDNA 全长为1 578 bp ,编码484 个氨基酸. TJM21 和TJM22 都属于Ⅱ型蛇毒金属蛋白酶,由信号肽、前肽、金属蛋白酶、 间隔肽和去整合素5 部分组成. Ⅱ型蛇毒金属蛋白酶氨基酸序列的比较及进化分析显示,它可进一 步分为两类,一类包括大多数Ⅱ型蛇毒金属蛋白酶(其中含有TJM21) ,而TJM22 和agkistin 则组成了 另一类. 并且TJM22 和agkistin 的第407 位和第426 位残基都是半胱氨酸,而在其它Ⅱ型金属蛋白酶 的相应位置,407 位是丝氨酸,426 位则缺失. TJM22 和agkistin 均有可与整合素α2 Ⅰ区域特异性结合 的片段QPNRKRHDNAQ(残基276～284) ,这个片段在其它Ⅱ型金属蛋白酶中并没有发现. 因此推 断, TJM22 和agkistin 可能属于一类新型的Ⅱ型蛇毒金属蛋白酶.

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.

Sequence variation and genetic diversity in the giant panda

About 336-444 bp mitochondrial D-loop region and tRNA gene were sequenced for 40 individuals of the giant panda which were collected from Mabian, Meigu, Yuexi, Baoxing, Pingwu, Qingchuan, Nanping and Baishuijiang, respectively. 9 haplotypes were found in 21 founders. The results showed that the giant panda has low genetic variations, and that there is no notable genetic isolation among geographical populations. The ancestor of the living giant panda population perhaps appeared in the late Pleistocene, and unfortunately, might have suffered bottle-neck attacks. Afterwards, its genetic diversity seemed to recover to same extent.

Sequence evolution of the CCR5 chemokine receptor gene in primates

The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellanae, Rhinopithecus bieti, Rhinopithecus avunculus, Macaca assamensis, and Macaca arctoides. When compared with CCR5 sequences from humans and other primates, our results demonstrate that:(1) nucleotide and amino acid sequences of CCR5 among primates are highly homologous, with variations slightly concentrated on the amino and carboxyl termini; and (2) site Asp13, which is critical for CD4-independent binding of SIV gp120 to Macaca mulatta CCR5, was also present in all other nonhuman primates tested here, suggesting that those nonhuman primate CCR5s might also bind SIV gp120 without the presence of CD4. The topologies of CCR5 gene trees constructed here conflict with the putative opinion that the snub-nosed langurs compose a monophyletic group, suggesting that the CCR5 gene may not be a good genetic marker for low-level phylogenetic analysis. The evolutionary rate of CCR5 was calculated, and our results suggest a slowdown in primates after they diverged from rodents. The synonymous mutation rate of CCR5 in primates is constant, about 1.1 x 10(-9) synonymous mutations per site per year. Comparisons of K-a and K-s suggest that the CCR5 genes have undergone negative or purifying selection. K-a/K-s ratios from cercopithecines and colobines are significantly different, implying that selective pressures have played different roles in the two lineages.

Sequence of mitochondrial DNA cytochrome oxidase II in Cryptopygus nanjiensis and phylogeny of apterygota

The mitochondrial cytochrome oxidase II (Co II) from four different apterygotens Cryptopygus nanjiensis (Collembola), Neanura latior (Collembola), Gracilentulus maijiawensis (Protura) and Lepidocampa weberi (Diplura) were sequenced. Their A+T content, number of nucleotide substitutions, TV/TV ratio; and Tamura-Nei's distance were calculated. A series of phylogenetic trees were constructed by parsimony and distance methods using a crustacean Artemia franciscana as outgroup, Finally the evolutionary trend A+T content of CO II genetic divergence and phylogenetic relationship of apterygotan groups were discussed.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Mitochondrial cytochrome b gene sequence diversity in the Korean hare, Lepus coreanus Thomas (Mammalia, Lagomorpha)

Partial sequences of the mitochondrial cytochrome b gene of the Korean hare (Lepus coreanus) were analyzed to determine the degree of genetic diversity. Nine haPlotyes were observed, and the maximum Tamura-Nei nucleotide distance among them was 2.8%, indicating that genetic diversity of L. coreanus is moderate. In order to clarify the Korean hare's taxonomic status and relationship with the Manchurian hare (L. mandshuricus) and the Chinese hare (L. sinensis), these nine haplotypes of the Korean hare were compared with 13 haplotypes from five other species of eastern Asian Lepus including L. mandshwicus and L. sinensis. The Korean hare was distinct in its cytochrome b gene, and it is confirmed that L. coreanus is a valid species, as noted by Jones and Johnson (1965, Univ. Kansas Publ. (Mus. Nat. Hist.) 16:357). Further analyses of mtDNA cytochrome b gene with additional specimens of L. coreanus from North Korea and other species of Lepus from eastern Asia are needed to clarify the taxonomic status of the divergent mtDNA clades of L. mandshuricus and L. sinensis.