基于叶绿体四个DNA片段联合分析探讨山茶属长柄山茶组、金花茶组和超长柄茶组的系统位置与亲缘关系

为探讨山茶属茶亚属(Camellia subgen.Thea)中长柄山茶组(sect.Longipedicellata)、金花茶组(sect.Chrysantha)和超长柄茶组(sect.Longissima)的系统位置和亲缘关系,本研究选取了该属4个亚属11组28个种及2个外类群的材料,对这些材料的叶绿体4个DNA片段(rp/16、psbA-trnH、trnL-F和rp/32-trnL)进行了测序,运用邻接法(neighbor-joining)、最大简约法(maximum-parsimony)和贝叶斯推断(Bayesian inference)对获得的序列进行了联合矩阵分析.并构建基因树.基因树的拓扑结构显示:1)金花茶组包括3个平行的支系,并且长柄山茶组的模式种长柄山茶(Camellia longipedicellata)嵌于其中一个支系,因而金花茶组可能是一个并系或多系类群;2)长柄山茶与越南分布的金花茶组种类在分子系统树上构成一个单系支,暗示了长柄山茶组和金花茶组之间可能具有紧密的亲缘关系;3)超长柄茶组不是一个单系类群,该组的河口超长柄茶(C.hekouensis)位于系统树的基部,与山茶属其余种构成姐妹群.由于缺乏更广泛取样的分析,超长柄茶在山茶属中的系统位置仍然不明确,超长柄茶组与长柄山茶组的亲缘关系问题也没有得到解决.     

山茶属油茶组、短柱茶组和红山茶组植物叶的红外光谱分析及其分类学意义

利用傅立叶红外光谱仪和OMNI采样器直接、迅速、准确地测定山茶属Camellia4组63种2变种植物叶片的红外光谱,结果表明：各分类群（种）的红外光谱具有高度特异性,其红外光谱图的变化可以作为山茶属植物属下的分类依据之一。这也暗示了利用标准红外光谱图库,可以区分和鉴定出山茶属植物的种类。经主成分分析后的红外光谱数据构建的树型聚类图与先前的形态分类结果大体一致,能将油茶组sect.Oleifera和短柱茶组sect.Paracamellia植物明显区分,并且各组中亲缘关系较近的种聚在一起。因此支持它们作为两个独立的组处理。但是,红山茶组sect.Camellia内的滇山茶亚组subsect.Lucidissima和光果红山茶亚组subsect.Reticulata植物在聚类图上很难区分,建议将这两个亚组植物进行归并。最后讨论了张宏达和闵天禄系统中存在分歧的油茶组、短柱茶组和红山茶组内的种间分类关系。     

基于叶绿体四个DNA 片段联合分析探讨山茶属长柄山茶组、金花茶组和超长柄茶组的系统位置与亲缘关系

为探讨山茶属茶亚属 (Camellia subgenThea) 中长柄山茶组 (sectLongipedicellata)、金花茶组 (sectChrysantha)和超长柄茶组 (sectLongissima) 的系统位置和亲缘关系,本研究选取了该属4个亚属11组28个种及2个外类群的材料,对这些材料的叶绿体4个DNA片段 (rpl16、psbA trnH、trnL F和rpl32 trnL) 进行了测序,运用邻接法 (neighbor joining)、最大简约法 (maximum parsimony) 和贝叶斯推断 (Bayesian inference) 对获得的序列进行了联合矩阵分析,并构建基因树。基因树的拓扑结构显示：1) 金花茶组包括3个平行的支系,并且长柄山茶组的模式种长柄山茶 (Camellia longipedicellata) 嵌于其中一个支系,因而金花茶组可能是一个并系或多系类群;2) 长柄山茶与越南分布的金花茶组种类在分子系统树上构成一个单系支,暗示了长柄山茶组和金花茶组之间可能具有紧密的亲缘关系;3) 超长柄茶组不是一个单系类群,该组的河口超长柄茶 (C. hekouensis) 位于系统树的基部,与山茶属其余种构成姐妹群。由于缺乏更广泛取样的分析,超长柄茶在山茶属中的系统位置仍然不明确,超长柄茶组与长柄山茶组的亲缘关系问题也没有得到解决。     

基于matR基因序列分析的山茶科系统关系

通过线粒体matR基因序列分析探讨了山茶科的分类学范围和系统演化关系。结果显示,传统山茶科的两个核心——山茶亚科（Theoideae或Camellioideae）和厚皮香亚科（Ternstroemioideae）不构成姐妹群关系,山茶亚科是一个支持率很高的单系类群,厚皮香亚科没有形成单系;山茶亚科下可区分出3个明显的分支,基部的分支由紫茎属（Stewartia）和舟柄茶属（Hartia）组成,木荷属（Schima）、美洲荷属（Franklirda）和美国大头茶属（Gordonia）构成第2个分支,该分支与由山茶属（Camellia）、核果茶属（Pyrenaria）、多瓣核果茶属（Parapyrenaria）、石笔木属（Tutcheria）、大头荣属（Polyspora）和圆籽荷属（Aptersperma）组成的第3个分支互为姐妹群。研究结果很好地支持了Prince和Parks等学者提出的的狭义山茶科（仅含山茶亚科）和狭义大头茶属的概念以及科下3个族（紫茎族Stewartieae、大头茶族Gordonieae和山茶族Theeae）的划分。但本研究更为清晰地揭示了科下3个族间的系统关系,即紫茎族是最基部的分支,山茶族与大头茶族间有更近的亲缘关系。同时,本文认为,厚皮香（亚）科是否为单系类群值得进一步研究。     

后蕊苣苔属分类

本文根据雄蕊、花冠及柱头的形态特征将后蕊苣苔属的9种植物划分为4组,并讨论了这4群的亲缘关系及地理分布.作者同意B.L.Burtt的看法,即汕头后蕊苣苔组可能源于粗筒苣苔属,而后蕊苣苔组等其它3个组可能源于马铃苣苔属。     

20种山茶科植物的叶表皮微形态研究

为解决一些山茶科(Theaceae)的分类学问题,该研究在光学显微镜下对山茶科2亚科6属共20种植物的13种叶表皮微形态特征进行了观察,并利用聚类分析和主成分分析对这些特征进行分析,为山茶科的科学分类提供参考资料。结果表明:(1)山茶科20种植物的13种叶表皮微形态特征能够区分种间差异和分类等级,显示了比较全面的分类价值。(2)基于微形态特征的聚类分析和主成分分析结果显示,20个种分为2个大类群以及10个分支,很好地区分了山茶亚科(Theoideae)与厚皮香亚科(Ternstroemoideae),并将大部分分类地位相近的物种归类到一起,较好地反映了物种之间的亲缘关系。(3)该研究结果支持将小黄花茶组(Sect.Luteoflora)作为独立的一个组;支持将重庆山茶(Camellia chungkingensis Chang)从瘤果茶组(Sect.Tuberculata Chang Tax.)中分离;支持将山茶亚科与厚皮香亚科划分为两个较大类群,认为将厚皮香亚科并入五列木科(Pentaphylacaceae)的观点还有待更多实验证据的支持。     

基于淫羊藿属(Epimedium L.)核型似近系数的聚类分析及其系统演化意义

为揭示淫羊藿属(Epimedium L.)植物染色体组遗传与进化,阐明该属植物系统亲缘关系和现代地理分布格局形成。该文对淫羊藿属植物51个分类群(43种、1亚种、6变种和1个栽培品种)和2种温哥华属(Vancouveria Morren et Decne.)植物的根尖进行了有丝分裂中期染色体核型分析,并运用核型似近系数聚类分析方法对这53个分类群植物的核型进行了聚类研究。结果表明:所有种类的染色体数均为12,二倍体(2n=2x=12),第1对同源染色体均为随体染色体,核型均为Stebbins的2A或1A型。可见,淫羊藿属植物染色体组在遗传进化中确实较为保守,种间核型非常相似。核型似近系数聚类分析为淫羊藿属植物系统进化研究提供了一些明显的线索。分析结果完全支持该属属下两个亚属(Subgen.Rhizophyllum和Subgen.Epimedium)的划分。亚属Epimedium的核型似近系数聚类结果显示,该类群物种间的系统亲缘关系与地理分布密切相关。核型似近系数分析结果还发现,来自东亚地区的淫羊藿属植物染色体组具有明显的变异,显示了更高的遗传多样性。基于上述研究结果,推断了淫羊藿属植物现代地理分布格局的形成过程。该研究结果可为淫羊藿属植物的资源利用、系统分类和遗传演化等领域的研究提供参考。     

山茶科系统发育诠释——Ⅲ.关于金花茶组及山茶属演化若干问题

作者通过比较认为山茶属金花茶组的模式和古茶组的模式不是同一分类单位,因而取消金花茶组是不恰当的。金花茶组是一个自然的集合体。作者详细地分析了山茶属内演化的四个阶段:第一阶段表现为苞被不分化、大型、宿存、子房5室、心皮部分分离;第二阶段演化出苞被宿存和苞被脱落两个类群,前者较为原始的代表是离蕊茶织和短蕊茶组,较为进化的代表是管蕊茶组;后者较为原始的代表是半宿萼茶组、瘤果茶组、糙果茶组,较为进化的代表是油茶组、短柱茶组、红山茶组;第三阶段是苞被分化为小苞片和萼片的类群,金花茶组和长柄茶组是较为原始而茶组、超长柄茶组则是较为进化的代表;第四阶段的连蕊茶组和毛蕊茶组苞萼小型化且宿存,的代表,雌、雄蕊均高度连合,子房室不完全发育 它们只能由第三阶段具有多数小苞片的原始类群发展出来,认为把山茶属划分为四个亚属的系统是合理的。 作者还认为,花的颜色以及其他相似性状的集合是划分山茶属次级分类单位的重要依据;分类系统的自然性和实用性相结合是分类学家始终应该追随的目标,混淆不同差异的做法是不可取的。最后,作者认为山茶属没有真正的顶生花。     

中国紫金牛属的分支分类学研究

基于60个形态学性状,对中国广义报春花科（Primulaceae s.l.）紫金牛属（Ardisia）90个分类群的系统发育关系运用分支分析方法进行了分析。采用最简约性分析得到了100个同等简约树。50%多数规则一致树的分支结构与以前建立的紫金牛亚属划分系统基本一致。外类群酸藤子属、铁仔属、密花树属聚在分支树的最基部,紫金牛属为一单系类群。形态分支树的一致性指数和保持性指数和各分支内部支持率均较低,只在种与变种或亚种之间获得较高的支持率。高木亚属、腋序亚属、短序亚属、顶序亚属处于分支树较为基部的位置,推测这四个亚属的类群在紫金牛属中较为原始;圆齿亚属和锯齿亚属共同组成一大支,二者亲缘关系紧密,推测这两个亚属为该属中最为进化的类群。结合形态学对属内系统发育关系进行了讨论和推测了一些性状的演化趋势,以期为分类修订提供依据。     

蒿属与邻近属的谱系分支分析

本文首次报道“蒿属与邻近属的谱系分支分析”,结果如下:在蒿自然群中,蒿属和绢蒿属及线叶菊属和栉叶蒿属各为一对姐妹群,后一对姐妹群还与毛蒿自然群有较近的亲缘关系;紊蒿属和百花蒿属在进化过程中,作为两个独立的属,很早就与蒿自然群其它属分化出。在蒿属各组中,腺毛蒿组和白苞蒿组为一对姐妹群,并与艾组构成姐妹关系;龙蒿亚属三个组(龙蒿组、牡蒿组和球蒿组)的亲缘关系很接近,且与友蒿组有较近的亲缘关系。 研究的结果支持林有润的蒿属与蒿自然群的演化假说和紊蒿作为一个独立的属的观点以及将中国蒿属分为蒿亚属和龙蒿亚属以及七个组的观点。根据谱系分支分析的结果以及形态上的特征,建议在蒿属下建立一新亚属,灰蒿亚属。     

中国茶藨子属的研究

通过对国产茶藨子属的形态、分类和地理分布的研究,笔者支持把该属置于虎耳草科的观点,不赞成把它分离作为独立的科。另外,认为Rehder系统中所划分的4个亚属较合理,故予以采纳,但笔者对其中的亚属、组和系的划分、各分类类目的内容、系统排列的顺序等诸方面都作了较大修订。从系统发育的观点出发,对亚属的排列次序则和Rehder系统有很大不同,而对组和系的范围及其系统位置也作了较大改动。中国茶藨子属植物初步确定为59种30变种,隶属于4亚属10组15系(包括5新系)。依据对茶藨子属分布区的分析,首次提出了东亚区是茶藨子属植物的现代分布中心,在东亚区中,中国-喜马拉雅森林植物亚区中的横断山脉地区和中国-日本森林植物亚区的西部是茶藨子属发生和发展的关键地区。     

A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles

Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para- or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification. Why? The Global Carex Group (GCG) here takes the position that the historical and continued use of subgenera and sections serves to (i) organize our understanding of lineages in Carex, (ii) create an identification mechanism to break the ~2000 species of Carex into manageable groups and stimulate its study, and (iii) provide a framework to recognize morphologically diagnosable lineages within Carex. Unfortunately, the current understanding of phylogenetic relationships in Carex is not yet sufficient for a global reclassification of the genus within a Linnean infrageneric (sectional) framework. Rather than leaving Carex classification in its current state, which is misleading and confusing, we here take the intermediate steps of implementing the recently revised subgeneric classification and using a combination of informally named clades and formally named sections to reflect the current state of our knowledge. This hybrid classification framework is presented in an order corresponding to a linear arrangement of the clades on a ladderized phylogeny, largely based on the recent phylogenies published by the GCG. It organizes Carex into six subgenera, which are, in turn, subdivided into 62 formally named Linnean sections plus 49 informal groups. This framework will serve as a roadmap for research on Carex phylogeny, enabling further development of a complete reclassification by presenting relevant morphological and geographical information on clades where possible and standardizing the use of formal sectional names.     

五味子属（五味子科）分类系统的初步修订

通过对前人提出的五味子属（五味子科）分类系统的点评,根据五味子属植物的33个形态性状及其性状分析,经过分支分析,提出一个新的五味子属分类系统：将五味子属分为五味子亚属和团蕊五味子亚属;将五味子亚属分为多蕊五味子组、少蕊五味子组、中华五味子组和五味子组。编排了分亚属、组和种的检索表,对每个种上分类等级均列出其模式、异名和代表种。     

Phylogenetic relationships among Bactrocera species (Diptera: Tephritidae) inferred from mitochondrial DNA sequences

Several members of the dipteran family Tephritdae are serious pests because females lay eggs in ripening fruit. The genus Bactrocera is one of the largest within the family with over 500 described species arranged in 28 subgenera. The phylogenetic relationships among the various species and subgenera, and the monophyly of specific groups have not been examined using a rigorous phylogenetic analysis. Therefore, phylogenetic relationships among 24 Bactrocera species belonging to 9 subgenera were inferred from DNA sequence of portions of the mitochondrial 16S rRNA, cytochrome oxidase II, tRNA(Lys), and tRNA(Asp) genes. Two morphological characters that traditionally have been used to define the four groups within the subgenus Bactrocera were evaluated in a phylogenetic context by mapping the character states onto the parsimony tree. In addition, the evolutionary trend in male-lure response was evaluated in a phylogenetic context. Maximum parsimony analyses suggested the following relationships: (1) the genus Bactrocera is monophyletic, (2) the subgenus B. (Zeugodacus) is paraphyletic, (3) the subgenus B. (Daculus) is a sister group to subgenus B. (Bactrocera), and (4) the subgenus B. (Bactrocera) is monophyletic. The mapping analyses suggested that the morphological characters exhibit a simple evolutionary transition from one character state to another. Male-lure response was identified as being a labile behavior that has been lost on multiple occasions. Cue-lure response was plesiomorphic to methyl-eugenol response, and the latter has evolved independently within the Bactrocera and Zeugodacus groups of subgenera. The implications of our results for devising a coherent, consolidated classification for Bactrocera is discussed.     

An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent “series”. Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five “series”, 25 sections and one “series” are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.     

Phylogenetic relationships among Passiflora species based on the glutamine synthetase nuclear gene expressed in chloroplast (ncpGS)

This paper presents the first molecular phylogeny of the genus Passiflora encompassing almost all sections of this large genus. The nuclear-encoded chloroplast-expressed glutamine synthetase gene (ncpGS) was used to examine the relationships among Passiflora species (passionflowers), which was then compared with the new classification proposed by Feuillet and MacDougal. The resulting Bayesian, likelihood, and parsimony trees are congruent and well supported. The 90 Passiflora species examined apparently split into eight main subgenera: Plectostemma, Granadilla, Astrophea, Deidamioides, Polyanthea, Dysosmia, Tetrapathea, and Tryphostemmatoides. These results are in overall agreement with the Feuillet and MacDougal's classification but here we propose that three additional subgenera, Polyanthea, Dysosmia, and Tetrapathea, should be maintained. We observe a striking overall correlation between the phylogenetic position of the different species and their chromosome number. The first clade contains the arborescent species of the subgenus Astrophea, with n=12. The second clade, subgenus Plectostemma, includes species from four subgenera of Killip's classification with n=6 chromosomes. The last clade, subgenus Granadilla, includes species of seven old subgenera with n=9. Subgenus Dysosmia, with a variable chromosome number of n=9-11, is considered here as a separate subgenus closely related to the subgenus Granadilla.     

Evolution of Mexican Bursera (Burseraceae) inferred from ITS,ETS, and 5S nuclear ribosomal DNA sequences

I reconstructed a phylogeny of 66 species and varieties of Bursera and 9 outgroup species using sequences of the internal transcribed spacer region (ITS), the 5S non-transcribed region (5S-NTS), and the external transcribed region (ETS) of nuclear ribosomal DNA. This study extends a previously proposed parsimony-based phylogenetic study that used the ITS sequences of 57 Bursera species and five outgroups. Parsimony and maximum likelihood methods were used to infer the phylogeny in this new study. Analyses of the combined data sets largely confirmed the phylogenetic relationships proposed by the previous molecular study but generated a considerably more robust topology. The new phylogenies corroborate the monophyly of the genus, and its division into the two monophyletic subgenera or sections, Bursera and Bullockia. The current analyses also identify four main groups of species in section Bursera, and two in section Bullockia, confirming some of the previously proposed groups based on fruit, flower, and leaf morphology. One previously problematic species B. sarcopoda, which has sometimes been placed in Commiphora, is shown to belong in Bursera. Another controversial species, Commiphora leptophloeos, which was thought to belong to Bursera, falls within Commiphora.     

RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs

The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by Ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic‐alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.     

The effect of phylogeny on interspecific body shape variation in darters (Pisces: Percidae)

We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of individual species and subspecies revealed qualitative similarities within most traditionally recognized taxonomic groups (genera and subgenera). Canonical variates analysis and a UPGMA cluster analysis were conducted to explore further the relationships among body shapes of species; both analyses revealed patterns of variation consistent with the interpretation that shape is associated with taxonomic affinities. Normalized Mantel statistics revealed a significant positive association between body shape differences and phylogenetic interrelatedness for each of four recent phylogenetic hypotheses, providing evidence of a phylogenetic effect. This result is somewhat surprising, however, given the largely incompatible nature of these four phylogenies. We provide evidence that this result may be due to (1) the inclusion of multiple sets of closely related species to represent the traditionally recognized genera and subgenera within each phylogeny and/or (2) the inclusion of several species with relatively divergent shapes and their particular positions within the phylogenies relative to one another or to the other species of darters.     

Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data

A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria . Aragoa is sister to genus Plantago . Plantago subgenus Littorella is sister to the other subgenera of Plantago . The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans . Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni , endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 323–338.