The phylogenetic relationship of the family Lutjanidae based on analyses of AFLP and mitochondrial 12S rRNA sequences

Fishes of the family Lutjanidae are commercially important in South China Sea. However, the phylogeny of Lutjanids is still unclear and there are many controversies over it. Herein, studies about the phylogeny of Lutjanids were performed based on Amplified Fragment Length Polymorphism （AFLP） analysis of genome DNA and sequence analysis of mitochondrial 12S rRNA gene, and 10 Lutjanidae species and 1 Lethrinidae species were employed. The topologies of minimum evolution （ME） trees based on the two analyses respectively were congruent except for positions of genera Pristipomoides and Caesio. The optimal substitution model TrN ＋ G for DNA sequences of 12S rRNA genes in Lutjanids was obtained using MODELTEST 3.6 software and maximum likelihood （ML） analysis supports the topology displayed by the ME tree. The test of log-likelihood suggests that the use of molecular clock calibrations to estimate species divergence time appeared valid. Phylogenetic analyses using AFLP data and DNA sequences of mitochondrial 12S rRNA genes indicated the monophyly of Lutjanus genra. However, further studies are required to reveal the phylogenetic relationship among other genera. In addition, the results demonstrated that AFLP genetic marker was suitable for the phylogenetic analysis of Lutjanids.     

Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes

Partial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich unpaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in unpaired regions. The overall substitution rate in unpaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two majorlineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by “glyptosternoids Pseudecheneis“. The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data. Pseudecheneis is shown to be a sister taxon of Glaridoglanis. Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

PIXE and INAA studies on ancient potteries from Guangfulin relics in Shanghai

This paper reports the study of ancient potteries unearthed from the Guangfulin site in Shanghai. From the external features of these potteries, archeologists can classify them into two different cultural types: Liangzhu culture (local culture) and a new culture which might be derived elsewhere, but they can not recognize whether they were produced in the same place. Proton induced X-ray emission (PIXE) and instrumental neutron activation analysis (INAA) were used to measure the chemical compositions of the samples and the results were analyzed using multivariate statistics. We found that the two methods can complement each other and their database can be mutually referenced in the study of ancient potteries. Experimental results show that the compositions of the potteries from the two cultural types are different, which means that the materials for ancient potteries of new culture originate from elsewhere. This supports the archaeologists’ speculation that a group of ancient people migrated to Shanghai from some other places 4000 years ago.     

Molecular phylogeny of the specialized schizothoracine fishes （Teleostei： Cyprinidae）,with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochrome b gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies of Ptychobarbus form a monophyly. But three species of Gymnodiptychus do not form a monophyly. Gd.integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes while Gdo pachycheilus has a close relation with Gd. dybowskii, and both of them are as a sister group of Diptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene(about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic.Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 m during the late Pliocene(about 2.6 MaBP).     

Reappraisal of phylogenetic status and genetic diversity analysis of Asian population of Lentinula edodes

Phylogenetic relationship within the Lentinula genus is constructed based on the sequenced ITS fragments of the 60 Chinese wild L. edodes isolates and the sequence data of 48 isolates of different species from other districts downloaded from the GenBank. The 108 isolates of Lentinula genus are divided into two branches and seven groups, one branch and two groups in the New World, and the other branch and five groups in the Old World, and the isolates clustering of different groups corresponds obviously with the classification of the morphological species. Asian isolates are partitioned in group Ⅰ and Ⅴ, two of the five groups of the Old World, by which the germplasm resources status represented is of great importance shown by the phylogenetic analysis. Group Ⅴ which fills up the blank of geographic distribution has become one of the mainstream groups with an increased isolate number, while group Ⅰ has a tendency to dissimilate into two subgroups (Ia and Ib) with a huge isolate quantity and a coverage of most tested districts, suggesting that China (or Asia) is an important genetic diversity center of the natural population of Lentinula genus. Genetic analysis of Asian isolates based on groups Ia, Ib and group Ⅴ indicates that the diversity of the east coastal-land, northwestern highland and southwestern China and Himalayas districts is the most plentiful, which is the three priorities in diversity protection of Asian Lentinula population.     

Molecular phylogenetic evidence that the Chinese viviparid genus Margarya (Gastropoda: Viviparidae) is polyphyletic

We investigated the phylogeny of the viviparid genus Margarya,endemic to Yunnan,China,using two mitochondrial gene fragments(COI and 16S rRNA).The molecular phylogeny based on the combined dataset indicates that Margarya is polyphyletic,as two of the three well-supported clades containing species of Margarya also comprise species from other viviparid genera.In one clade,sequences of four species of Margarya even cluster indiscriminately with those of two species of Cipangopaludina,indicating that the current state of Asian viviparid taxonomy needs to be revised.Additionally,these data suggest that shell evolution in viviparids is complex,as even the large and strongly sculptured shells of Margarya,which are outstanding among Asian viviparids,can apparently be easily converted to simple smooth shells.The molecular data also indicate that the species status of the six extant species of Margarya should be re-assessed.     

Molecular biological research on Foraminifera

As one of the most important groups in micropaleontology, Foraminifera is traditionally described to have a membranous, agglutinated or carbonate shell according to its morphology, which resembles the marine granuloreticuloseans. However, recent molecular analyses on its ribosomal RNA gene have disclosed the existence of the naked, and also freshwater and terrestrial species. Foraminiferal SSU rDNA sequence suggests that this group is positioned at the base of the Eukaryotes phylogenetic trees, between Euglenoida and Diplomonadida. Existence of a large amount of genetic types in planktonic foraminifera suggests an underestimation of the biodiversity for the nearly 50 species in world oceans and their close relationship with the ocean environment, such as bio-geographic distribution and water currents. This provides a more reliable proxy for future paleoenvironmental study.     

Genomic and genic sequence variation in synthetic hexaploid wheat （AABBDD） as compared to their parental species

In order to understand the genomic changes during the evolution of hexaploid wheat, two sets of synthetic hexaploid wheat from hybridization between maternal tetraploid wheat （AABB） and paternal diploid goat grass （DD） were used for DNA-AFLP and single strand conformation polymorphism （SSCP） analysis to determine the genomic and genic variation in the synthetic hexaploid wheat. Results indicated that more DNA sequences from paternal diploid species were eliminated in the synthetic hexaploid wheat than from maternal tetraploid wheat, suggesting that genome from parental species of lower ploidity tends to be eliminated preferentially. However, sequence variation detected by SSCP procedure was much lower than those detected by DNA-AFLP, which indicated that much less variation in the genic regions occurred in the synthetic hexaploid wheat, and sequence variations detected by DNA-AFLP could be derived mostly from non-coding regions and repetitive sequences. Our results also indicated that sequence variation in 4 genes can be detected in hybrid F1, which suggested that this type of sequence variation could be resulted from distant hybridization. It was interesting to note that 3 out of the 4 genes were mapped and clustered on the long arm of chromosome 2D, which indicated that variation in genic sequences in synthetic hexaploid wheat might not be a randomized process.     

Testing relative evolutionary rates and estimating divergence times among six genera of Rhizophoraceae using cpDNA and nrDNA sequences

The molecular phylogenetic trees of 10 species representing 6 genera of the family Rhizophoraceae have been constructed using the sequences of chloroplast genesmatK andrbcL as well as the ITS regions of nuclear ribosomal DNA. Relative-rate tests between lineages in these phylogenetic trees have been performed. On the basis of the results of the relative-rate tests and related molecular evolutionary rate data, the divergence times between the lineages are estimated as follows: (i) the first divergence time in these genera is 132.25 million years ago (mya); (ii) the average divergence time between two tribes, i.e. inland Legnotideae (exceptCarallia brachiata) and mangrove Rhizophoreae, is 64.13 mya; and (iii) the average divergence time between two inland species,C. garciniaefolia andC. pectinifolia, is 19.92 mya.     

The discovery of aeschnidiid nymphs (Aeschnidiidae, Odonata, Insecta)

Aeschnidiid nymphs are here first identified and described, and its phylogenetic relationship and bioecological characteristics are deduced. The nymphs known from China, Mongolia, Russia and Brazil and arranged in the family Aeschnidiidae are, in fact, unrelated to this group. All the known five Chinese species in four genera which were erected based on fossil nymphs and placed in the family Gomphidae may be transferred in Aeschnidiidae and merged into one alone, theSinaeschnidia cancellosa. It is a geographically widespread species from the “Jehol biota” of East Asia and appeared in the latest Late Jurassic age.     

Phylogenetic investigation on five genera of tintinnid ciliates （Ciliophora, Choreotrichia）, based on the small subunit ribosomal RNA gene sequences

The phylogenetic relationship among tintinnid ciliates are relatively poorly studied based on molecular data. In the present work, seven species belonging to five genera of the order Tintinnida (Amphorellopsis acuta, Codonellopsis nipponica, Favella taraikaensis, Stenosemella nivalis, Tintinnopsis beroidea, Tintinnopsis cylindrica and Tintinnopsis lohmanni) were analyzed using the information on their small subunit ribosomal RNA gene sequences. Phylogenetic trees were constructed using Bayesian inference (BI), maximum parsimony (MP), neighbor-joining (NJ), and least-squares (LS) methods. Generally, similar topologies were revealed with high or moderate supports, in which the main results show that (1) all tintinnids analyzed belong to a single assemblage; (2) congeners in Tintinnopsis do not cluster together, which indicates that the lorica-based definition for this genus is not consistent with the SSU rRNA phylogeny; (3) A. acuta groups with Tintinnidium mucicola but not with Eutintinnus, indicating that the traditional family Tintinnidae might be a paraphyletic group; (4) Stenosemella and Codonellopsis are clearly most related and possibly even merged into one genus regarding their similar morphology and molecular analyses, and possession of a hyaline collar is the only characteristic of the genus.     

基于线粒体蛋白编码基因探讨飞虱科Delphacidae13属系统发育关系

飞虱科昆虫隶属于半翅目蜡蝉总科,是世界上最重要的农业害虫之一.昆虫的线粒体基因是昆虫分子与进化研究中常用且有效的分子标记.本研究基于线粒体蛋白编码基因探讨了飞虱科13属18种的系统发育关系,分别采用距离法、最大似然法和贝叶斯法构建的系统发育树得到的结论是一致的,即在飞虱科13属中,Ugyops属较为原始,处于系统树的基...     

六种鱼巴亚科鱼类线粒体细胞色素b基因序列分析

 测定了鱼巴亚科云南光唇鱼(Acrossocheilus yunnanensis)、宽头四须鱼巴(Barbodes laticeps)、抚仙金线鱼巴(Sinocyclocheilus tingi)和滇池金线鱼巴(Sinocyclocheilus grahami)4种鱼类线粒体细胞色素b基因DNA序列402bp,结合已知的云南倒刺鱼巴(Spinibarb denticulatus yunnanensis)和细尾长臀鱼巴(Mystacoleucus lepturus)的同源序列,组成1个6种代表鱼巴亚科5属鱼类的数据集.选用已知的云南鲴(Xenocypris yunnanensis)作为外群,采用邻接法、最大简约法和最大似然法构建了分子系统树.结果显示:倒刺鱼巴属(Spinibarbus)和光唇鱼属(Acrossocheilus)有较近的亲缘关系,四须鱼巴属(Barbodes)和长臀鱼巴属(Mystacoleucus)有较近的亲缘关系,而金线鱼巴属(Sinocyclocheilus)和它们的关系不能确定.上述结果与它们的地理分布基本吻合.     

青海柯柯盐湖16株细菌的ARDRA筛选及系统发育初步分析

 从青海柯柯盐湖泥样中分离的16株细菌,用2种限制性内切酶酶切进行ARDRA分析,其中12株菌的酶切带谱有较大差异.根据这12株菌的16SrDNA序列进行系统发育分析结果表明,12株菌有11株分布于芽孢杆菌科中的Halobacillus,Gracibacillus,Amphibacillus,Virgibacillus,Bacillus,Salibacillus和1个潜在的新属中,另1株属于Proteobacteria的Gamma亚群Halomonadaceae科,Halomonas属.而且16SrDNA系统发育分析提示这些菌株中存在3个新种和1个新属的可能.本研究得出的结论为:应用ARDRA来初步筛选菌株是可行的;青海柯柯盐湖这一极端环境中存在较丰富的新的芽孢菌种类.     

中国南方沿海13种石斑鱼类的分子系统进化关系分析

石斑鱼类(Groupers)是世界性海洋经济鱼类,也是中国南方沿海省份重要的海水增养殖对象,其种类繁多,由于缺乏明显的种间外部形态区别特征,石斑鱼的分类一直是鱼类系统分类学的一个难题,存在着较多的争议和混淆。为了从分子水平揭示石斑鱼类的系统进化关系,应用线粒体细胞色素b基因(Cyt b)及两个核糖体RNA基因(16S和12S)序列联合构建系统进化树对中国近海石斑鱼亚科3属13种进行种类鉴定及亲缘关系分析,探讨了石斑鱼类的分子系统进化。结果表明:①线粒体基因序列在石斑鱼类种间存在较大的变异,种内变异极小,是进行石斑鱼类种类鉴定较为适宜的分子标记;②所研究的3属13种石斑鱼类中,石斑鱼属与九棘鲈属的亲缘关系较近,与鳃棘鲈属的较远;③赤点石斑鱼和青石斑鱼、蜂巢石斑鱼与鲑点石斑鱼、斜带石斑鱼与棕斑石斑鱼两两间具有较近的亲缘关系。     

广西兰科植物的物种多样性及区系特征研究

广西是我国兰科植物生物多样性特别丰富的省区之一,同时也是兰科植物生物多样性受威胁特别严重的省区之一。摸清广西兰科植物资源的家底,分析广西兰科植物资源的优势以及广西兰科植物的区系特征,有助于为广西兰科植物就地保护和迁地保护提供科学依据。通过整理广西兰科植物近20年的文献资料,对广西目前兰科植物资源的状况进行编目和分析。结果表明：广西已发现野生兰科植物129属510种,分别占中国兰科植物总属数和总种数的67.89%和31.88%,其中石斛属Dendrobium、羊耳蒜属Liparis、石豆兰属Bulbophyllum、兰属Cymbidium、虾脊兰属Calanthe和玉凤花属Habenaria是本区兰科植物中的优势属。从区系来看,广西兰科热带分布类型94属,占广西兰科植物总属数的72.87%,其中热带亚洲分布有44属,占广西兰科植物总属数的34.11%;广西兰科植物以热带成分为主,受温带成分影响,保留了较多特有性、古老残遗性的特点。     

井冈山自然保护区井冈山杜鹃种群与群落特征研究

以井冈山自然保护区井冈山杜鹃群落5个样地调查资料为基础,对其种群及群落特征进行了研究。结果表明:井冈山杜鹃种群径级结构为金字塔型,生命期望值基本随径级增加而呈递减趋势,存活曲线为近直线型,空间分布格局为集群分布,种群属于增长型种群。群落有维管植物29科42属53种,其中蕨类植物5科5属5种,裸子植物2科2属2种,被子植物22科35属46种。群落区系起源古老,成分较复杂,科、属区系成分均具有明显的热带性质。群落除Pielou指数较高外,其它3种多样性指数均较低;测度井冈山杜鹃群落物种多样性时,各种多样性指数未表现出相同的变化趋势。井冈山杜鹃本身的生物学特性及其群落所处的严酷环境是导致其种群濒危的主要原因。     

Phylogeny of fireflies (Coleoptera: Lampyridae) inferred from mitochondrial 16S ribosomal DNA，with references to morphological and ethological traits

We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of China. Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and Chinese species were reconstructed by neighbor-joining, maximum parsimony and Bayesian methods. All reconstructions agree on most nodes of the trees. Monophyly of Lampyridae is not supported because Rhagophthalmus ohbai in Rhagophthalmidae is included within it. Lamprigera, a genus placed unreliably in Lampyrinae, shows a close relationship to Amydetinae. Monophyly of Luciolinae is not supported because Pristolycus sagulatus (Lampyrinae) is included within it. In the Luciolinae, monophyly of Curtos and Hotaria is well established, respectively, but both morphological and molecular data continue to indicate that Luciola is not monophyletic and its subdivision is indeed necessary. Within the Lampyrinae, both Pyrocoelia and Diaphanes are not monophyletic, but monophyly of Pyrocoelia+Diaphanes is well supported. Phylogeny of Diaphanes is discussed for the first time. Generic placement of a newly discovered species (Diaphanes pectinealis Li et Liang) sharing some characters of Pyrocoelia and Diaphanes challenges the delimitation of these two similar genera. With references to the firefly mating systems, we suggest that more emphases should be placed on those sexually selected characters such as antennal structure in taxonomy of Lampyridae.