Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

The monophyly of Diplura and its phylogenetic relationship with other hexapods are important for understanding the phylogeny of Hexapoda. The complete 18SrRNA gene and partial 28SrRNA gene (D3-D5 region) from 2 dipluran species (Campodeidae and Japygidae), 2 proturan species, 3 collembolan species, and 1 locust species were sequenced. Combining related sequences in GenBank, phylogenetic trees of Hexapoda were constructed by MP method using a crustacean Artemia salina as an outgroup. The results indicated that: (i) the integrated data of 18SrDNA and 28SrDNA could provide better phylogenetic information, which well supported the monophyly of Diplura; (ii) Diplura had a close phylogenetic relationship to Protura with high bootstrap support.

The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes

Many efforts based on complete mitochondrial DNA (mtDNA) genomes have been made to depict the global mtDNA landscape, but the phylogeny of Indian macrohaplogroup M has not yet been resolved in detail. To fill this lacuna, we took the same strategy as in o

More evidence for non-maternal inheritance of mitochondrial DNA?

Background: A single case of paternal co-transmission ofmitochondrial DNA (mtDNA) in humans has been reported so far. Objective: To find potential instances of non-maternal inheritance of mtDNA. Methods: Published medical case studies (of single patients) were searched for irregular mtDNA patterns by comparing the given haplotype information for different clones or tissues with the worldwide mtDNA database as known to date-a method that has proved robust and reliable for the detection of flawed mtDNA sequence data. Results: More than 20 studies were found reporting clear cut instances with mtDNAs of different ancestries in single individuals. As examples, cases are reviewed from recent published reports which, at face value, may be taken as evidence for paternal inheritance of mtDNA or recombination. Conclusions: Multiple types (or recombinant types) of quite dissimilar mitochondrial DNA from different parts of the known mtDNA phylogeny are often reported in single individuals. From re-analyses and corrigenda of forensic mtDNA data, it is apparent that the phenomenon of mixed or mosaic mtDNA can be ascribed solely to contamination and sample mix up.

胡蜂属Vespa linnaeus的系统发育研究

报道胡蜂属Vespa Linnaeus的系统发育研究结果。运用PAUP(SWOFFORD,1993)软件程序对胡蜂属系统发育关系进行研究,结果将胡蜂属分为2个大的类群,即树巢胡蜂类群(Wood-nesting groups),地巢胡蜂类群(earth-nesting groups),各分为4个亚群。文中还给出了胡蜂属18种的系统发育和包括1个新种的形态描述。

Phylogenetic relationships of the mustache toads inferred from mtDNA sequences

Species of the genus Vibrissaphora are unique among all annurans in that males exhibit external cornified spines in the maxillary region during the breeding season. They were separated from species of the genus Leptobrachium based on this unique character. We construct a phylogeny using the 16S, ND4, and cytochrome b mitochondrial genes of 42 individuals from eight species of Vibrissaphora and five species of Leptobrachium from mainland China, Southeast Asia, and Hainan Island. Species of both Oreolalax and Scutiger were used as outgroups. The results indicate that: L. huashen and L. chapaense form a clade that is nested within Vibrissaphora, and L. hainanense is the sister taxon to the clade comprising all Vibrissaphora plus L. chapaense and L. huashen; V. boringiae is grouped with a clade consisting of V. leishanensis, V. liui, and V. yaoshanensis; and V. yaoshanensis is a species separate from V. liui. We propsed taxonomix changes that reflect these findings. Also based on the resulting phylogenetic trees, we propose that the mustache toads originated in the trans-Himalayan region of southwest China, and that the evolution of maxillary spines, large body size, and reverse sexual size dimorphism in these frogs was influenced by intrasexual selection due to adopting a resource-defense polygyny matting system.

茸卷象属（Coleoptera：Attelabidae）分类与系统发育研究及寄主识别机制初探

本文选取卷叶象甲科昆虫为研究对象，以形态分类学为基础，辅之以分子生 物学手段，对中国特有的茸卷象属（Euscelophilus）进行了系统发育学的研究。 并在此基础上，对该属昆虫进行了亚显微结构的研究，该研究不仅对其分类学观 点进行了验证，对属内分种的有效形态学性状进行了补充，而且从感受器亚显微 形态的角度讨论了卷象与寄主植物的化学识别机制，明晰了其结构基础。最后， 本文首次从力学角度对卷象与其寄主植物的物理识别机制进行了探讨。 在分类学研究中，本文首先整理了中国卷叶象甲鉴定科、亚科、族、属的检 索表，同时对其中的18 个常见属的分种检索表进行了整理，并对其中中国特有 属Euscelophilus 进行了深入的分类学研究。将Euscelophilidius、Cureuscelophilus 两属和Euscelophiloides 亚属定义为Euscelophilus 的新异名，并提供了该属物种 检索表，同时为该属新增三个物种，分别是Euselophilus longispinus Xie & Liang, sp. n.，Euselophilus gaoligongensis Xie & Liang, sp. n.和Euselophilus caperratus Xie & Liang, sp. n.，并对两物种E. denticulatus 和 E. gibbicollis 的雄性外生殖器 进行了描绘。 分子生物学研究以该属内9 种和4 个外群种共23 个个体为材料，对其COII 基因进行了扩增，并对所得的核苷酸序列使用PAUP 和贝叶斯两种方法构建分子 系统发育树。结果表明，中国茸卷象属是一个单系群，其内部可分为三支，分别 以E. niger，E. gibbicollis 和E. rugolosus 为代表，建议将该属分为三个亚属，对 于该属有争议的物种T. (E.) qinni，依照本研究获得的数据，建议将其移回 Euscelophilus 属。亚显微结构研究选取本属内8 个物种作为研究对象，分别对其头部、胸部、 腹部及前足的形态性状，使用扫描电子显微镜进行了观察拍照。同时，选取了复 眼、触角、下唇须、外颚叶、腹部、跗节等部位分布的各种感受器进行了亚显微 结构的研究。结果表明，形态相似的近缘物种在亚显微结构上可显示出更大的形 状差异，同时，首次证明额的形态特征可作为该属内分种的有效依据。感受器结 构研究表明卷象识别寄主植物的主要感受器为毛状、锥状、乳突状化学感受器， 其次为刺状、毛状的听觉（物理）感受器以及六棱形小眼组成的视觉感受器（复 眼）。 力学研究部分选取Apoderus 属一种卷象及其寄主植物马桑（Coriaria nepalensis Wall.）为研究对象，首先以人工模拟卷叶的形式对卷象卷叶所需的力 进行了分析，其次以纳米压痕手段对卷象上颚和马桑叶片的硬度和弹性模量分别 进行了研究。结果表明，先切叶后卷叶是更省力更进化的卷叶模式，同时卷象选 择寄主植物的机制中，两者的物理性能呈一定的相关性。

Generic allocation of Indian and Sri Lankan Philautus (Anura: Rhacophoridae) inferred from 12S and 16S rRNA genes

The generic allocation of Indian and Sri Lankan Philautus needs further examination. In this study, a comprehensive understanding of the phylogeny of Indian and Sri Lankan Philautus is obtained based on 125 and 16S rRNA genes. All phylogenetic analyses indicate that Indian-Sri Lankan Philautus, Philautus menglaensis, Philautus longchuanensis, and Philautus gryllus form a well supported clade, separate from Philautus of Sunda Islands that form another well supported clade representing true Philautus. This result supports the designation of the genus Pseudophilautus to accommodate the Indian and Sri Lankan species. Pseudophilautus consists of two major lineages, one comprises the majority of Indian species, Chinese species, and Southeast Asian species, and one comprises all Sri Lankan species and a few Indian species. Pseudophilautus may have originated in South Asia and dispersed into Southeast Asia and China. Based on the results, we further suggest that Philautus cf. gryllus (MNHN1997.5460) belongs to the genus Kurixalus. (C) 2010 Published by Elsevier Ltd.

中国鸟类的DNA分类及系统发育研究概述

鸟类分类是鸟类学其他研究领域的基础,近年来分子技术的发展,以及计算机技术的应用为鸟类分类学和鸟类系统演化研究提供了新的研究手段,给传统的系统分类研究带来了新的机遇.Tautz等于2002年首先提出运用DNA序列作为生物分类系统的主要平台,即DNA分类学(DNA Taxonomy).而Hebert等于2003年则首次提出了DNA条形码(DNA Barcoding)的概念,并对其物种分类和鉴定意义予以肯定,建议利用线粒体细胞色素C氧化酶亚单位Ⅰ(COI)的特定区段来做DNA条形编码的基础.在鸟类DNA分类方面,国内学者应用线粒体基因Cut b,COI,c-mos,c-myc,12s rRNA,16s rRNA,ND2,ND3,CR,RAG-1以及核基因myoglobin introⅡ等不同片段对很多类群进行了分类探讨和系统发育研究.但是主要集中在鸡形目及雀形目鸟类.中国是鸟类多样性极其丰富的国家,近年来很多亚种、种及以上分类阶元依然存在问题,因此,中国鸟类物种的分类地位、系统发育与演化关系等依然有很多问题等待深入研究.目前国内基于COI的鸟类分类及系统发育研究有了一些报道,但是真正的DNA条形码工作尚需继续、深入地开展.

High Altitude Adaptation and Phylogenetic Analysis of Tibetan Horse Based on the Mitochondrial Genome

研究测定了西藏那曲(4,500 m)、云南中甸(3,300 m)、云南德钦(3,300 m)地区3匹藏马线粒体全基因组序列.3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短.藏马基因组在DNA序列上的两两相似性达99.3%.通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象.这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色.此外,利用7匹藏马的D-loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源.

鲤科的科下类群及其宗系发生关系

<正> 鲤科为鲤形目中最大的科,拥有275属1600种(Pattern 1975)。早在100多年前Bleeker(1863)已对该科进行了较细的类群划分,嗣后,其他作者也先后做过这方面的工作。Regan(1911)发现某些骨骼性状在宗系发生(phylogeny)上具有一定的重要性,而另一些性状则对划分类群没有意义。Berg(1912,1940)依据较特别的外部形态来规定

Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau

National Natural Science Foundation of China (NSFC) [30225008, 30300036, 30530120]; Key Innovation Plan [KSCX2-SW-106]; National Basic Research Project in China [2005cb422005]; National Natural Science Foundation of China [30600062]

Morphological and molecular phylogenetic analysis of two Saprolegnia sp (Oomycetes) isolated from silver crucian carp and zebra fish

Two Saprolegnia isolates, JY isolated from silver crucian carp (Carassius auratus gibelio Bloch) and BMY isolated from zebra fish (Brachydanio rerio Hamilton) came from infections occurring concurrently in different locations in China. To confirm whether the two isolates were from the same Saprolegnia clone, comparative studies have been carried out based on their morphological, physiological and molecular characteristics. Observations showed that morphologically (both asexual and sexual organs) the two isolates were broadly similar and both isolates under-went repeated zoospore emergence. Comparing 704 base pairs of internal transcribed spacer (ITS) region and the 5.8S rDNA, we found isolates JY and BMY shared an identical ITS sequence with a minor variation (99.6 % similarity). Forty available sequences for representatives Saprolegnia spp. belonged to four phylogenetically separate clades. The two studied isolates fell within clade I that comprised a group of isolates which showed almost an identical ITS sequence but had been identified as a number of different morphological species. our findings suggest that isolates JY and BMY appear to belong to the S. ferax clade and this clade (1) contains a number of closely related phylogenetic species. This is distinct from the more common fish pathogenic isolates, which belong to the S. parasitica clade (III) and are characterized by having cysts decorated by bundles of long hooked hairs and two further clades (II and IV) containing largely saprotrophic or soil born species. (C) 2009 Published by Elsevier Ltd on behalf of The British Mycological Society.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.