利用TrnL-F序列探讨苎麻属植物的系统发育关系

目的:探讨苎麻属植物的系统发育关系。方法:对10个种和8个变种苎麻属植物的TrnL-F序列进行PCR扩增和T/A克隆产物序列测定;选取雾水葛属的植物作为参考外类群,同样也测定其TrnL-F全序列;根据TrnL-F区碱基序列的差异计算种间的遗传距离,采用UPGMA法进行系统发育分析并得到系统发育树。结果:野线麻、福州苎麻、赤麻、悬铃叶苎麻、序叶苎麻、白面苎麻、束序苎麻、密球苎麻、疏毛水苎麻、圆叶水苎麻、灰绿水苎麻和糙叶水苎麻聚成一支;帚序苎麻、黔桂苎麻、苎麻、微绿苎麻、贴毛苎麻和青叶苎麻聚为另一支;雾水葛单独聚成一类,与苎麻属的其他种在一级分支中即分开,与其他种的亲缘关系较远。结论:帚序苎麻组和苎麻组植物具有较近的亲缘关系。     

稻族的系统发育及其研究进展

稻族Oryzeae是禾本科Poaceae中包含多种经济植物的重要类群, 现有大约12个属, 广布全球的热带和温带地区。由于其重要的经济价值和在理论研究上的代表性, 稻属Oryza及其近缘属的研究受到了广泛关注。虽然形态学和初步的分子证据表明稻族是一个单系类群, 但稻族内各属的分类处理和属间系统发育关系以及稻族的起源、地理分布式样和机制等方面仍存在许多悬而未决的问题。本文简要回顾了稻族系统学研究的历史, 包括稻族的建立及其在禾本科中的系统位置、稻族的族下划分、稻族各属的界定及其系统发育关系。目前已有的研究结果表明: 稻族是单系类群, 可分为两个主要分支, 相当于传统的两个亚族(Zizaniinae和Oryzinae), 但稻族单性花小穗是多次起源的, 不宜作为划分亚族的依据; 一些单型属(Hydrochloa、Porteresia和Prosphytochloa)的建立得不到分子证据的支持; 根据分子钟原理估计稻族两个主要分支(亚族)的分歧时间在大约2000万年前, 而稻属和近缘属假稻属Leersia的分歧时间为1400万年; 稻属内主要类群的分歧时间在900万年前左右。此外, 本文还对稻族的生物地理学问题进行了初步探讨, 对稻族系统发育和进化研究中存在的问题及未来研究方向进行了讨论。     

基于rbcL序列试论鸢尾属部分物种间的系统发育关系

选用叶绿体rbcL基因对鸢尾属植物的分类和系统发育进行了分析。以雄黄兰为外类群,对21份鸢尾属材料和GenBank下载的共49条序列采用最大简约法构建系统进化树,探讨了鸢尾属的分类系统。针对有争议的物种,聚类结果表明：马蔺与白花马蔺关系较远;扁竹兰和蝴蝶花亲缘关系较扇形鸢尾近;细锐果鸢尾和锐果鸢尾亲缘关系近,大锐果鸢尾较之远;四川鸢尾和薄叶鸢尾聚类近;西伯利亚鸢尾系内物种间聚类复杂,亲缘关系不清楚。     

蝽科部分昆虫细胞色素b基因序列及其系统发育关系的探讨

以线粒体细胞色素b(Cyt b)基因作为分子标记,对蝽科蝽亚科3种、益蝽亚科2种、荔蝽亚科1种、盾蝽亚科2种昆虫进行序列测定,获得Cyt b基因432bp的序列片段,该片段中碱基T、C、A、G的平均含量分别为31．3％、12．4％、37．6％和18．7％,A T平均含量为68．9％,明显高于G C含量(30．1％);密码子第三位点A T含量更高达82．7％。属和种间序列变异大,碱基替换多发生在第三位点。以筛豆龟蝽(Megacopta cribraria)为外群构建系统发育树,结合形态特征与序列变异率,赞同将盾蝽亚科、荔蝽亚科从蝽科划分出来并提升为科的观点,它们之间的系统关系为：盾蝽科与荔蝽科形成姊妹群,较蝽科发育得早;蝽科作为一个单系群,是蝽总科中最为进化的类群。     

基于线粒体细胞色素b基因序列的虹雉属鸟类的系统发育关系

通过雉科虹雉属(Lophophorus)、角雉属(Tragopan)、勺鸡属(Pucrasia)和血雉属(Ithaginis)7种鸟类的细胞色素b(cyt b)基因序列比较,构建的虹雉属及其近缘属的分子系统树表明：①3种虹雉构成一个单系群(monophyletic group),虹雉属与角雉属、勺鸡属构成一个单系群;②虹雉属内分为白尾梢虹雉,以及棕尾虹雉和绿尾虹雉两个演化枝。综合分子系统学、地理分布格局和形态学的证据,推测虹雉属鸟类起源于中国的横断山脉,其中繁衍生活在原地的一枝演化为白尾梢虹雉;另一枝则分别进入喜马拉雅山区(西)和中国西南部(东),向西的演化为棕尾虹雉,向东的则为绿尾虹雉。     

从细胞色素b部分序列探讨石斑鱼属的分子系统发育关系

石斑鱼的分类在学术界尚存在很多争议。本文采用PCR技术,测定了分布于中国的点带石斑鱼(Epinepheluscoioiaes)、青石斑鱼(E.awoara)、六带石斑鱼(E.sexfasciatus)、褐石斑鱼(E.brunneus),长棘石斑鱼(E.longispinis),吻斑石斑鱼(E.spilotoceps),巨石斑鱼(E.tauvina)以及石斑鱼亚科侧牙鲈属的侧牙鲈(Variola louti)的线粒体细胞色素b基因402bp的序列,结合GenBank提供的7种中国无记录的石斑鱼:青铜石斑鱼(E.aeneus)、海丰石斑鱼(E.haifensis)、犬牙石斑鱼(E.caninus)、东大西洋石斑鱼(E.marginatus)、白斑石斑鱼(E.multinotatus)、德氏石斑鱼(E.drummondhayi)、淡点石斑鱼(E.labriformis),把这14种石斑鱼作为内群,对他们的序列组成和结构特点进行了分析;并以同为科(Serranidae)、石斑鱼亚科(Epinephelinae)的侧牙鲈属(Variola)的侧牙鲈作外群,分别用MP法、NJ法对内、外群构建了分子系统树,结果表明:(1)14种石斑鱼402bp的mtDNA Cytb部分序列的碱基组成上,A+T的含量为53.6%高于G+C含量(46.4%),序列中转换颠换比为4.78,没有突变饱和;(2)青石斑鱼与六带石斑鱼、点带石斑鱼与巨石斑鱼、长棘石斑鱼与吻斑石斑鱼分别聚在一起,与形态分类结果一致;(3)系统树中,大西洋与太平洋种类各枝交替汇合,表明石斑鱼的Cytb序列有严格的保守性,也可能是协同进化的结果;(4)揭示在良种选配或遗传管理时,避免居于同枝的石斑鱼混交,将大西洋种类与太平洋种类杂交可能是遗传改良的一种途径。       

我国沿海棱鳀属鱼类的物种鉴定与系统发育

利用DNA条形码技术对中国沿海分布的6种棱鳀属(Thryssa)鱼类样品进行了物种鉴定, 并每种取5尾用于探讨该属系统发育关系。结果显示: 棱鳀属鱼类的主要形态鉴别特征为上颌骨伸达位置和第一鳃耙的下鳃耙数量。在525 bp的目的片段上有175个变异位点, 其中简约信息位点172个, 单一信息位点3个, 无插入缺失现象, 转换数为182, 颠换数为57。A+T含量明显高于G+C含量, 并且表现出明显的反G偏倚。结合GenBank中相关的同源序列进行比较发现, 所有序列明显分为10个组群, 表明已提交的棱鳀属鱼类COI基因序列中仍存在一定的问题。从各组群间的遗传距离和氨基酸遗传差异水平可以看出, 10个组群应为不同的有效种, 但是否存在隐存种还有待于进一步确定。从NJ树上可以看出, 长颌棱鳀(T. setirostris)是最先分化出的物种, 保持着最原始的特征, 而中颌棱鳀(T. mystax)与黄吻棱鳀(T. vitrirostris)聚类到一起, 二者间存在共享单倍型。棱鳀属鱼类最早分化于中新世早期。在今后的研究中仍需要结合更多的分子标记对中颌棱鳀和黄吻棱鳀的分类地位作进一步的探讨。     

基于ITS序列探讨忍冬属的系统发育关系

以七子花(Heptacodium miconioides)为外类群,运用MEGA软件对20种忍冬属植物进行系统发育分析,采用邻接法(NJ)和最大简约法(MP)构建系统发育树,从分子系统学角度探讨忍冬属下的亲缘关系.结果表明:(1)在NJ和MP系统树中,没有形成系统树的基部分支,忍冬亚属(Subg.Chamaecerasus)和轮花亚属(Subg.Lonicera)没有形成姐妹群关系.(2)在各系统树中,囊管组内的各种没有聚为一支,故认为对囊管组的划分应进一步探讨.(3)忍冬属ITS区(ITS1+ITS2)的信息位点达到11.0%,信息位点比较丰富,证明ITS序列可以为解决忍冬属植物的系统发育问题提供较强的证据.     

基于多个叶绿体基因序列片段重建广义苋科系统发育关系

苋科(Amaranthaceae sensu lato)是石竹目(Caryophyllales)第二大科, 目前被普遍接受的苋科为其广义概念, 含狭义苋科(Amaranthaceae sensu stricto)和藜科(Chenopodiaceae)。然而到目前为止, 藜科是否应作为独立的科还存在争议。此外, 广义苋科内部各亚科之间的系统关系也尚未厘清。对广义苋科所有13个亚科代表类群进行取样(共59种), 基于8个叶绿体序列片段重建其系统发育关系, 并结合分子钟估算, 对该科及其主要分支的起源与分化时间进行推测。结果表明, 广义苋科与狭义苋科都是很好的单系, 但藜科并非单系, 因此不支持藜科在科级水平的地位, 支持广义苋科的观点。除了多节草亚科(Polycnemoideae)之外, 其它亚科的系统位置均得到很好的分辨。分子钟估算结果表明, 广义苋科于白垩纪晚期约69.9 Ma分化出该科的2个主要分支, 且该科在白垩纪-古近纪边界附近时期(约66.0 Ma)可能发生过快速辐射分化事件。     

基于Cytb基因序列探讨蝽亚科11种昆虫的系统发育关系

对蝽亚科6属11种昆虫线粒体DNA细胞色素b基因部分序列进行PCR扩增和序列测定。比较其同源性,统计密码子使用频率并应用生物学软件构建分子系统树。在获得的432bp序列中,碱基T,C,A和G的平均含量分别是38．1,18．2,31．9和11．8％,表现出强烈的AT偏向性;就每个氨基酸密码子来看,第3位点的A＋T含量较高,达到85．5％。该序列片段中共有162个核甘酸位点发生变异（约占37．5％）,种间序列差异范围为0．9％～19．4％,平均为16．6％,变异较大。以筛豆龟蝽Megaeopta cribraria为外群,通过多种方法构建的系统发育树拓扑结构一致,这6属11种昆虫大致形成4个分支：珀蝽属、碧蝽属、菜蝽属3属的关系最接近,形成一个分支;真蝽属的3种聚为1支,与第1支形成姊妹群;曼蝽属的2种形成1支;麻皮蝽位于系统树的基部,为分化较早的1支,是蝽亚科中较为原始的类群。     

Phylogenetic relationships among Oryza species revealed by AFLP markers

 The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species, five related genera, and three outgroup taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta ^* O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms. Received: 1 July 1998 / Accepted: 2 November 1998     

Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes

The A-genome group in Oryza consists of eight diploid species and is distributed world-wide. Here we reconstructed the phylogeny among the A-genome species based on sequences of nuclear genes and MITE (miniature inverted-repeat transposable elements) insertions. Thirty-seven accessions representing two cultivated and six wild species from the A-genome group were sampled. Introns of four nuclear single-copy genes on different chromosomes were sequenced and analysed by both maximum parsimony (MP) and Bayesian inference methods. All the species except for Oryza rufipogon and Oryza nivara formed a monophyletic group and the Australian endemic Oryza meridionalis was the earliest divergent lineage. Two subspecies of Oryza sativa (ssp. indica and ssp. japonica) formed two separate monophyletic groups, suggestive of their polyphyletic origin. Based on molecular clock approach, we estimated that the divergence of the A-genome group occurred c. 2.0 million years ago (mya) while the two subspecies (indica and japonica) separated c. 0.4 mya. Intron sequences of nuclear genes provide sufficient resolution and are informative for phylogenetic inference at lower taxonomic levels.     

药用野生稻复合体ITS1和ITS2序列变异及其系统进化分析

通过PCR扩增并测序分析稻属药用野生稻复合体5个野生稻种基因组完整的ITS区及5.8S区,并与栽培稻ITS序列进行比较,构建分子系统进化树,探讨了稻属药用野生稻复合体内不同种间的亲缘关系和系统进化.结果表明,ITS1和ITS2均有较高的G/C含量,ITS1序列的长度多态性相对较高,ITS2序列的碱基突变频率较高.药用野生稻和高秆野生稻亲缘关系很近,而与栽培稻亲缘关系较远;短药野生稻、斑点野生稻、澳洲野生稻与药用野生稻亲缘关系渐近.处于进化的过渡阶段.     

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceol     

Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences

Internal transcribed spacer (ITS-1) sequences from 97 accessions representing 23 species of Lactuca and related genera were determined and used to evaluate species relationships of Lactuca sensu lato (s.l.). The ITS-1 phylogenies, calculated using PAUP and PHYLIP, correspond better to the classification of Feráková than to other classifications evaluated, although the inclusion of sect. Lactuca subsect. Cyanicae is not supported. Therefore, exclusion of subsect. Cyanicae from Lactuca sensu Feráková is proposed. The amended genus contains the entire gene pool (sensu Harlan and De Wet) of cultivated lettuce (Lactuca sativa). The position of the species in the amended classification corresponds to their position in the lettuce gene pool. In the ITS-1 phylogenies, a clade with L. sativa, L. serriola, L. dregeana, L. altaica, and L. aculeata represents the primary gene pool. L. virosa and L. saligna, branching off closest to this clade, encompass the secondary gene pool. L. virosa is possibly of hybrid origin. The primary and secondary gene pool species are classified in sect. Lactuca subsect. Lactuca. The species L. quercina, L. viminea, L. sibirica, and L. tatarica, branching off next, represent the tertiary gene pool. They are classified in Lactuca sect. Lactucopsis, sect. Phaenixopus, and sect. Mulgedium, respectively. L. perennis and L. tenerrima, classified in sect. Lactuca subsect. Cyanicae, form clades with species from related genera and are not part of the lettuce gene pool.     

Phylogenetic relationships among Hystrix species and related species based on expressed sequence tag-polymerase chain reaction

Twelve species, including three Hystrix species, five Leymus species, Hordeum bogdanii, Pseudoroegneria spicata, Psathyrostachys huashanica, and Roegneria ciliaris, were used for expressed sequence tag-polymerase chain reaction (EST-PCR) assay. A total of 125 products were amplified by 72 sets of EST-PCR markers developed in barley, among which 106 (84.8%) products were found to be polymorphic. Each EST-PCR marker produced 0–6 polymorphic bands, with an average of 1.47. The relationship between H. duthiei s...     

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.     

从12S rRNA基因序列推测鹭科13种鸟类的系统发生关系

对鹭科12个种的线粒体12S rRNA基因全长约975bp的序列进行了测定,并从GenBank获得黄顶夜鹭12S rRNA基因全序列。比对后的序列长993bp,含363变异位点,288个多态位点,187个简约信息位点。使用邻接法和最大简约法重建的分子系统树将13种鹭聚为2支：第一支包括白鹭、中白鹭、大白鹭、池鹭、牛背鹭、苍鹭、草鹭、夜鹭、黄顶夜鹭,第二支由黄苇渴Gan、黑苇Gan、栗苇Gan、大麻Gan组成。结果提示将鹭科分为鹭亚科和Gan亚科的传统观点是合理的,不支持Payne将鹭科分为日鹭亚科(Ardeinae)、夜鹭亚科(Nycticracinae)、Gan亚科(Botaurinae)和虎鹭亚科(Tigrisomatinae)的观点。进一步的分析表明：白鹭在系统演化中要早于大白鹭和中白鹭分支出来,大白鹭和中白鹭与苍鹭、草鹭和牛背鹭间的亲缘关系较近,而与白鹭较远,支持Sibley(1990)将大白鹭和中白鹭作为独立的大白鹭属(Casmerodius)和中白鹭属(Mesophoyx)的建议;黑Gan、栗苇Gan与黄苇Gan在系统发生中构成一单系群,提示将黑Gan置于苇Gan属(Ixobrychus)是合适的[动物学报49(2)：205—210,2003]。     

Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1

The family Cyprinidae is widely distributed in East Asia, and has the important phylogenetic signifi- cance in the fish evolution. In this study, the 5′ end partial sequences (containing exon 1, exon 2 and indel 1) of S6K1 gene were obtained from 30 representative species in Cyprinidae and outgroup using PCR amplification and sequencing. The phylogenetic relationships of Cyprinidae were reconstructed with neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian meth- ods. Myxocyprinus asiaticus (Catostomidae) was assigned to the outgroup taxon. Similar phylogenetic relationships within the family Cyprinidae were achieved with the four analyses. Leuciscini and Barbini were monophyletic lineages respectively with the high nodal supports. Leuciscini comprises Hy- pophthalmichthyinae, Xenocyprinae, Cultrinae, Gobioninae, Acheilognathinae and East Asian species of Leuciscinae and Danioninae. Monophyly of East Asian clade was supported with high nodal support. Barbini comprises Schizothoracinae, Barbinae, Cyprininae and Labeoninae. The monophyletic lineage consisting of Danio rerio, D. myersi, and Rasbora trilineata was basal in the tree. In addition, the large fragment indels in intron 1 were analyzed to improve the understanding of Cyprinidae relationships. The results showed that the large fragment indels were correlated with the relations among species. Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size.