Wallace's Line and plant distributions: two or three phytogeographical areas and where to group Java?

Wallace's Line or its variants divide the Malay Archipelago or Malesia into a western and eastern area, but is this suitable for plant distributions? Indeed, all boundaries satisfactorily divide Malesia into two parts, stopping far more species east or west of a line than disperse over the boundary. However, phenetic analyses (principal components analysis, nonmetric multidimensional scaling analysis and the unweighted pair group method with arithmetic mean) of 7340 species distributions revealed a stronger partitioning of Malesia into three instead of two regions: the western Sunda Shelf minus Java (Malay Peninsula, Sumatra, Borneo), central Wallacea (Philippines, Sulawesi, Lesser Sunda Islands, Moluccas, with Java), and the eastern Sahul Shelf (New Guinea). Java always appears to be part of Wallacea, probably because of its mainly dry monsoon climate. The three phytogeographic areas equal the present climatic division of Malesia. An everwet climate exists on the Sunda and Sahul Shelves, whereas most of Wallacea has a yearly dry monsoon. During glacial maxima, the Sunda and Sahul Shelves became land areas connected with Asia and Australia, respectively, whereas sea barriers remained within Wallacea. Consequently, the flora of the two shelves is more homogeneous than the Wallacean flora. Wallacea is a distinct area because it comprises many endemic, drought tolerant floristic elements. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 531–545.     

菊花起源的RAPD分析

利用ＲＡＰＤ分析技术,选取２２个２０个碱基长度的随机引物,对７种野生菊花、１４种栽培菊花和５个种间杂种进行了随机扩增。通过实验建立了ＰＣＲ随机扩增实验体系。在观察到的２２４个扩增条带中,３４条（１５％）表现多态性。利用ＵＰＧＭＡ法对扩增数据进行分析,结果表明：在７种野生种中,Ｄｅｎｄｒａｎｔｈｅｍａｉｎｄｉｃｕｍ、Ｄ．ｖｅｓｔｉｔｕｍ和Ｄ．ｎａｎｋｉｎｇｅｎｓｅ与栽培菊花亲缘关系最近,而Ｄ．ｚａｗａｄｓｋｉ与栽培菊花亲缘关系最远。前３种野菊与栽培菊花间的遗传距离小于０．４０,而Ｄ．ｚａｗａｄｓｋｉ与栽培菊花间的遗传距离大于０．５０。根据上述数据及以往研究结果,使用ＲＡＰＤ数据对菊花起源问题进行了探讨,提出栽培菊花主要起源于Ｄ．ｉｎｄｉｃｕｍ、Ｄ．ｖｅｓｔｉｔｕｍ和Ｄ．ｎａｎｋｉｎｇｅｎｓｅ．     

Polymorphism of BMP4 gene in Indian goat breeds differing in prolificacy

Bone morphogenetic proteins (BMPs) are members of the TGF-β (transforming growth factor-beta) superfamily, of which BMP4 is the most important due to its crucial role in follicular growth and differentiation, cumulus expansion and ovulation. Reproduction is a crucial trait in goat breeding and based on the important role of BMP4 gene in reproduction it was considered as a possible candidate gene for the prolificacy of goats. The objective of the present study was to detect polymorphism in intronic, exonic and 3′ un-translated regions of BMP4 gene in Indian goats. Nine different goat breeds (Barbari, Beetal, Black Bengal, Malabari, Jakhrana (Twinning > 40%), Osmanabadi, Sangamneri (Twinning 20–30%), Sirohi and Ganjam (Twinning < 10%)) differing in prolificacy and geographic distribution were employed for polymorphism scanning. Cattle sequence (AC_000167.1) was used to design primers for the amplification of a targeted region followed by direct DNA sequencing to identify the genetic variations. Single nucleotide polymorphisms (SNPs) were not detected in exon 3, the intronic region and the 3′ flanking region. A SNP (G1534A) was identified in exon 2. It was a non-synonymous mutation resulting in an arginine to lysine change in a corresponding protein sequence. G to A transition at the 1534 locus revealed two genotypes GG and GA in the nine investigated goat breeds. The GG genotype was predominant with a genotype frequency of 0.98. The GA genotype was present in the Black Bengal as well as Jakhrana breed with a genotype frequency of 0.02. A microsatellite was identified in the 3′ flanking region, only 20 nucleotides downstream from the termination site of the coding region, as a short sequence with more than nineteen continuous and repeated CA dinucleotides. Since the gene is highly evolutionarily conserved, identification of a non-synonymous SNP (G1534A) in the coding region gains further importance. To our knowledge, this is the first report of a mutation in the coding region of the caprine BMP4 gene. But whether the reproduction trait of goat is associated with the BMP4 polymorphism, needs to be further defined by association studies in more populations so as to delineate an effect on it.     

Rh系统单倍型在中国人群中的分布

对中国已发表的125个人群Rh血型系统表型分布频率数据进行了收集和整理。用累积计算法（Counting method)重新计算单倍型频率,通过各单倍型的分布差异分析中国不同地区不同种族、人群的遗传差异,分组比较了不同地区汉族和少数民族人群的基因多样度和基因分化度,结果表明南方少数民族和北方少数民族民族亚群体基因多样度有明显差异,用不同方法计算中小组遗传距离并进行聚类分析。最后,计算了除维吾尔族和哈萨克族外的68个人群间的遗传距离并聚类比较,结果表明Rh基因单倍型的分布与地理分布基本相符。     

Species Delimitation of Pterygiella (Orobanchaceae), a Genus Endemic to Southwestern China on the Basis of Morphometric and Molecular Analyses

Pterygiella, a genus endemic to southwestern China, belongs to hemiparasitic rhinanthoid Orobanchaceae. Since P.bartschioides was segregated as an independent genus of its own, i.e. Xizangia, the genus was treated to include four species, P.duclouxii, P.nigrescens, P.cylindrica, and P.suffruticosa. However, the discriminative characters are obscure among these species, and the delimitation of the two varieties in P.duclouxii remains problematic. To revise the taxonomy of the genus, thirteen populations from the four species were collected for both morphometric and molecular systematic analyses. Principal component analysis (PCA) and cluster analysis via unweighted pair group method with an arithmetic average (UPGMA) were used. In addition, four chloroplast sequences (i.e., atpB rbcL, psbA trnH, trnD trnT and trnS trnG) and nuclear ITS region were studied. The results showed that Pterygiella includes only three species, namely P.nigrescens, P.duclouxii, and P.cylindrica, while P.suffruticosa should be merged into P.cylindrica as a variety. The previous delimitation of the two varieties within P.duclouxii was probably caused by imperfect analysis of morphological characters. Thus, a lectotype was designated for P.duclouxii and the plants formerly treated as P.duclouxii that bear eglandular stem hairs should be put into P.nigrescens, while the individuals with glabrous stem should remain in P.duclouxii. A new key to the three species in the genus reflecting the results of this study was presented, and a taxonomic revision was given.     

Intra-specific hybridization: generator of genetic diversification and heterosis in Andrographis paniculata Nees. A bridge from extinction to survival

Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant species. Self-pollinated mating system, being an introduced species and experiencing a bottleneck as well as over exploitation cause such a consequence. Inter and intra-specific hybridizations have been suggested as essential techniques for generating genetic diversity. To test the effect of intra-specific hybridization on diversification and heterosis of AP, seven accessions were outcrossed manually in all 21 possible combinations. Three types of markers including morphological, phytochemical and RAPD markers were employed to evaluate the mentioned hypothesis. The results revealed that hybridization acted as a powerful engine for diversification of AP as it caused heterotic expression of the studied traits, simultaneously. Initially, it seems that additive and non-additive gene effects both can be considered as the genetic basis of heterosis in AP for the investigated traits. Agronomic and morphological traits were differentiated from each other, while positive heterosis was recorded mainly for agronomic traits but not for the morphological traits. Intra-specific hybridization increased the genetic diversity in AP population. Nevertheless, a part of this variation could also be attributed to the negative heterosis. The current exploration demonstrated the first ever conducted manual intra-specific hybridization among AP accessions in a mass scale. However, the 17 RAPD primers produced a monomorph pattern, but perhaps increasing the number of markers can feature a new genetic profile in this plant.     

石竹科繁缕属与孩儿参属的数量分类

石竹科繁缕属(Stellaria L.)和孩儿参属(Pseudostellaria Pax)的关系一直备受关注。为了弄清它们之间的关系及属下分类等问题,选择繁缕属22种和孩儿参属8种,共30种植物51个形态特征,利用NTSYS-pc 2.10e软件中的UPGMA聚类分析方法和主坐标分析方法,对这2个属进行数值分类学研究。结果表明,繁缕属与孩儿参属是2个自然类群,除繁缕属的繁缕(S.media(L.)Cyr.)和鸡肠繁缕(S.neglecta Weihe ex Bluff et Fingerh)在聚类中不能分开外,其它物种都能很好地分开。两属有较近的关系,其中巫山繁缕(S.wushanensis Williams)是过渡种。此外,数量分类结果建议将细叶孩儿参(P.sylvatica(Maxim.)Pax)作为一个独立组处理。对性状的主坐标排序分析显示,根的形状、叶缘质地、花的形态(是否具花瓣、花瓣长度、花瓣裂数、深裂还是浅裂)和种子表面纹饰(是否具齿轮状、疣状突起)等在繁缕属与孩儿参属的分类中具有重要作用。     

Genetic diversity and relationships in some <Emphasis Type="Italic">Vicia</Emphasis> species as determined by SDS-PAGE of seed proteins

To evaluate the genetic diversity of some Vicia species, seed proteins of 160 accessions (30 of Vicia faba, 15 of V. narbonensis, 82 of V. sativa and 25 of V. ervilia and 8 accessions of other Vicia species) were analysed by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The dendrogram showed that the two outcrossing species V. faba and V. villosa were the most distant among all species (average percent disagreement value PDV 0.47 and 0.45, respectively). The tree was divided into small clusters of two species each. V. narbonensis fell in one cluster with V. michausai (at PDV = 0.35) and V. lutea (var. hirta) fell in one cluster with V. serococorpes (at PDV = 0.32) whereas, V. ervilia fell in one cluster with V. sativa (at PDV = 0.27). The V. sativa subspecies, however, were closely related (PDV < 0.1). In general, this study did not prove any relationship between the studied storage proteins and the geographical distribution or ecological needs of the studied accessions.     

Comparative genomic analysis of Lactococcus garvieae phage WP-2, a new member of Picovirinae subfamily of Podoviridae

To date, a few numbers of bacteriophages that infect Lactococcus garvieae have been identified, but their complete genome sequences have not yet been investigated. For the first time, herein, the complete DNA sequence of a new phage of L. garvieae (phage WP-2) is reported and analyzed. The morphological characteristics indicated that the phage had a small isometric head along with a short and non-contractile tail, suggesting that WP-2 belongs to the family Podoviridae. Bioinformatic analysis revealed that phage WP-2 can be classified as a new member of Ahjdlikevirus in the Picovirinae subfamily because it had a small dsDNA of 18,899 bp with 24 open reading frames and a protein-primed DNA polymerase. The phage nucleotide sequence and predicted protein products have been identified to share very limited evidence of homology with complete genome and proteome of other phages. To our knowledge, this is the first Ahjdlikevirus bacteriophage which can infect a member of the Lactococcus genus.     

Trypanosoma cruzi: exploring the nuclear genome of zymodeme 3 stocks by chromosome size polymorphism

Chagas disease is emerging in the Brazilian Amazon. We evaluated the position of eight zymodeme 3 isolates from Amazonian sylvatic vectors and one human case in relation to Trypanosoma cruzi I and II major groups and hybrid strains by chromosome size polymorphism. Nineteen isolates were analyzed by mapping nine coding sequences on chromosomal bands (0.6-3.3Mbp). Numerical analysis was based on the absolute chromosomal size difference index (aCSDI). A dendrogram was obtained applying the minimum evolution criterion and considering the aCSDI values to estimate the branch lengths. The isolates were distributed in four groups. Group A clustered hybrid isolates; Groups B and C, T. cruzi II and T. cruzi I isolates, respectively. Seven Z3 stocks were clustered in Group D, which showed low intra-group diversity and was the most divergent. The proportion of two different-sized homologous chromosomes was determined. Wild vectors harboring Z3 stocks constitute a potential reservoir of human infection in the Amazon.