Bacterial RNA polymerase (RNAP) is an effective target for antibacterial treatment. In order to search new potential targets in RNAP of Mycobacterium, we detected adaptive selections of RNAP related genes in 13 strains of Mycobacterium by phylogenetic analysis. We first collected sequences of 17 genes including rpoA, rpoB, rpoC, rpoZ, and sigma factor A-M. Then maximum likelihood trees were constructed, followed by positive selection detection. We found that sigG shows positive selection along the clade (M. tuberculosis, M. bovis), suggesting its important evolutionary role and its potential to be a new antibacterial target. Moreover, the regions near 933Cys and 935His on the rpoB subunit of M. tuberculosis showed significant positive selection, which could also be a new attractive target for anti-tuberculosis drugs.

The adaptive evolution of the rbcL gene in 14 species of Ephedra and 9 other gymnosperms was tested by the PAML program. Three large-scale selections were found in the catalytic region of the RbcL protein by branch model. Species in Ephedra with positive selection at the 365th codon site in rbcL gene were detected by branch-site model. 3D structure modeling showed that the 365th codon could change the spatial structure of the β-sheet (βG, βH, or βE) of the RbcL protein. These changes may be associated with the adaptation of the protein in Ephedra to the environment.

Incarvillea younghusbandii Sprague (Bignoniaceae) is a perennial herbaceous plant endemic to Qinghai-Tibetan Plateau. As a species of medical and horticulture importance, L younghusbandii is threatened by over exploitation and habitat fragmentation. In this study, we analyze the genetic diversity and population structure of I. younghusbandii using amplified fragment length polymorphism (AFLP) markers. Our data reveal very low levels of genetic diversity in seven natural populations across Tibet. Specifically, at population level, the average Nei's genetic diversity index (H-E) and Shannon's diversity index (1) were 0.063 and 0.096, respectively. In contrast, high genetic differentiation among populations (Gst = 0.6238, Phi(ST) = 0.614) is detected. The results of Neighbor-joining cluster, PCO, and STRUCTURE assignment reveal consistent pattern, suggesting seven well-defined genetic groups that are concordant with their geographical origins. The possible mechanisms and implications of these findings for conservation are discussed. (C) 2009 Elsevier Ltd. All rights reserved.

Araucariaceae is one of the most primitive families of the living conifers, and its phylogenetic relationships and divergence times are critically important issues. The DNA sequences of 8 genes, i.e., nuclear ribosomal 18S and 26S rRNA, chloroplast 16S rRNA, rbcL, matK and rps4, and mitochondrial coxI and atp1, obtained from this study and GenBank were used for constructing the molecular phylogenetic trees of Araucariaceae, indicating that the phylogenetic relationships among the three genera of this family should be ((Wollemia, Agathis), Araucaria). On the basis of the fossil calibrations of Wollemia and the two tribes Araucaria and Eutacta of the genus Araucaria, the divergence time of Araucariaceae was estimated to be (308 ± 53) million years ago, that is, the origin of the family was in the Late Carboniferous rather than Triassic as a traditional view. With the same gene combination, the divergence times of the genera Araucaria and Agathis were (246 ± 47) and (61 ± 15) Ma, respectively. Statistical analyses on the phylogenetic trees generated by using different genes and comparisons of the divergence times estimated by using those genes suggested that the chloroplast matK and rps4 genes are most suitable for investigating the phylogenetic relationships and divergence times of the family Araucariaceae.

南洋杉科是最原始的松杉纲类群之一,其系统发育关系与起源(分支)时间研究具有极为重要的意义.利用自行测定和GenBank中获得的核核糖体18S和26S,叶绿体16S,rbcL,matK和rps4以及线粒体cox 1和atp1等8个基因的DNA序列,构建了南洋杉科的分子系统树,确定该科属间系统发育关系应为((瓦勒迈杉属,贝壳杉属),南洋杉属).以瓦勒迈杉属和南洋杉属Araucaria族和Eutacta族的化石记录作为时间标定,估计南洋杉科的起源在(308±53)百万年前,即该科在石炭纪晚期起源,而非以往认为的三叠纪.用相同基因组合还估计出南洋杉属起源于(246±47)百万年前,贝壳杉属起源于(61±15)百万年前.对不同基因所构建的系统树进行统计分析并对它们所估计的起源时间进行比较表明,叶绿体matK和rps4基因较为适合南洋杉科的系统发育与起源时间估计研究.