竹亚科系统学和生物地理学研究进展及存在的问题

对近年来在竹亚科作为一个单系类群的界定、其系统位置的确定、内部系统演化趋势以及地理分布和起源方面研究所取得的进展进行了评述。竹亚科作为一个单系类群仅包括了木本的竹族（Bambuseae)和一个草本的莪利竹族（Olyreae),其中莪利竹族分布在新几内亚的伊里安竹（Buergersiochloa)处于Olyreae最基部。禾本科12个亚科中除了3个亚科为基部类群以外,其余9个亚科分成PACCAD（包括黍亚科,狭义的芦竹亚科,广义的虎尾草亚科,假淡竹叶亚科,三芒草亚科和扁芒草亚科）和BOP单系分支（包括竹亚科,稻亚科和早熟禾亚科）。在BOP支中,竹亚科与早熟禾亚科相近缘,共同组成稻亚科的姐妹群。竹亚科分成草本和木本两个单系类群,木本竹子又分成热带和温带支系,热带支系进一步分成新世界热带和旧世界热带两个单系类群。从现有的化石证据和基部类群的地理分布推断,竹亚科很可能起源于晚白垩纪的冈瓦纳古陆。最后,本文就竹亚科研究尚存在的问题做了初步探讨。     

国产画眉草亚族叶表皮微形态特征及其在属间关系上的意义

通过国产画眉草亚族叶片表皮的解剖观察,结合外部形态,对该亚族内6个属的属间关系进行了分析。结果表明：羽穗草属应是国产画眉草亚族中最原始的类群,最高级的类群仍数细画眉草属,而其余4属即画眉草属、弯穗草属、尖稃草属和镰稃草属的演化水平居于两者之间;画眉草属和弯穗草属可能直接起源于原始的羽穗草属,而较高级的尖稃草属和镰稃草属又可能直接起源于较原始的画眉草属,并在镰稃草属的基础上进而派生了最进化的细画眉草属。整个研究结果既弥补了前人演化理论的不足,又为今后族进化的全面探讨提供了参考。     

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。     

质体系统发育基因组解析旋花科系统发育关系

旋花科是一个世界广布的类群,具有丰富的形态特征和重要的经济价值。然而,目前该科主要分支或族间的系统发育关系问题一直未解决。为解析旋花科内系统发育关系,该研究代表性选取旋花科内8个族40个物种,基于质体全基因组数据,使用最大似然法和贝叶斯推论进行系统发育分析。结果表明:(1)旋花科质体基因组均为四分体结构,质体基因组大小为113 273～164 112 bp,蛋白质编码基因数目为66～79个。(2)基于五种DNA矩阵(即WCG、CDS、LSC、IR、SSC)的系统发育分析结果显示,WCG矩阵和CDS矩阵的拓扑结构基本一致,仅少数分支的支持率略有差异; LSC矩阵和WCG矩阵的拓扑结构差异在于菟丝子族、马蹄金族和盐帚花族的系统位置; AU检验和SH检验结果显示,WCG矩阵和SSC矩阵与IR矩阵的拓扑结构有显著冲突。(3)所有系统发育分析结果均显示,菟丝子属和马蹄金族都包括在旋花亚科内,应处理为族等级。(4)基于WCG矩阵和CDS矩阵较好地解决了旋花科8个族之间的系统发育关系,即心被藤族和丁公藤族聚为一支,最先从旋花亚科分化出来,随后是菟丝子族,剩下的5个族分成2个分支。(5)系统发育基因组分析证实,由于鱼黄草族特别是鱼黄草属是一个多系类群,因此需重新修订该族的分类地位和鱼黄草属的划分。     

缘蝽科族级单元系统发育关系支序分析(半翅目:异翅亚目:缘蝽总科)

在已有比较形态学研究基础上,本文选择了15个特征方面（外生殖器为主）的74个新征,以支序分析方法探讨了缘蝽科族（或亚科）的系统发育关系。结果表明棒缘蝽亚科、希缘蝽族、沟缘蝽族较为原始,与其余类群差异较大,缘蝽科的范围值得进一步研究;除Chariesterini外的缘蝽亚科是高等的缘蝽类群;Chariesterini似应从缘蝽亚科中独立出来;狭义巨缘蝽族以及萧的鼻缘蝽族、梭缘蝽族、昧缘蝽族、曼缘蝽族成立;拟黛缘蝽属、副黛缘蝽属、华黛缘蝽属、异黛缘蝽属应从”黛缘蝽族”中分别独立出来成立新族,即拟黛缘蝽族、副黛缘蝽族、华黛缘蝽族和异黛缘蝽族,以使原有的黛缘蝽族成为自然类群。     

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。     

基于线粒体COⅠ基因的凤蝶亚科部分物种系统发育关系

通过对凤蝶亚科Papilioninae11属27种的线粒体细胞色素c氧化酶Ⅰ基因(COⅠ)序列测定,以阿波罗绢蝶Parnassius apollo为外群,分别采用邻接法(NJ)、最大简约法(MP)和最大似然法(ML)构建凤蝶亚科的系统发育树,初步探讨了其系统发育关系。结果显示,凤蝶亚科11属27个物种分为4个主要的分支,分别是裳凤蝶族Troidini、凤蝶族Papilionini、燕凤蝶族Lampropterini和喙凤蝶族Teinopalpini,与传统分类学观点一致。其中,燕凤蝶族构成凤蝶亚科系统发育树基部的一个独立分支,且为单系发生。凤蝶属Papilio中美凤蝶亚属Menelaides和翠凤蝶亚属Princeps首先相聚,华凤蝶亚属Sinoprinceps和凤蝶亚属Papilio亲缘关系较近,随后两分支再聚为一支,构成凤蝶属。本研究结果从分子水平验证了凤蝶亚科传统的形态分类地位,并为澄清凤蝶亚科物种间系统发育关系提供了基础资料。     

基于28S rRNA D2序列的内茧蜂亚科的分子系统发育

首次利用同源28S rRNA D2基因序列对内茧蜂亚科Rogadinae （昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）进行了分子系统学研究。本研究从95%～100%乙醇浸渍保存的标本中提取基因组DNA并扩增了10种内群种类和5种外群种类的28S rDNA D2片段并测序（GenBank序列号AY167645-AY167659）,利用BLAST搜索相关的同源序列, 采用了GenBank中13个种类的28S rRNA D2同源序列,然后据此进行分子分析。利用3个外群（共8个种类）和3种建树方法 (距离邻近法distance based neighbor joining, NJ; 最大俭约法maximum parsimony, MP; 和最大似然法maximum likelihood, ML)分析了内茧蜂亚科内的分子系统发育关系。结果表明,由分子数据产生的不同的分子系统树均显示内茧蜂亚科是一个单系群。内茧蜂亚科内依据形态和生物学特征的分群（族和亚族）及其系统发育关系得到部分支持。NJ、MP和ML分析结果均表明内茧蜂族Rogadini不是一个单系,而是一个并系,其余3族则得到不同程度的支持。内茧蜂族可分成2个分支：“脊茧蜂属Aleiodes+弓脉茧蜂属Arcaleiodes”和“沟内茧蜂属Canalirogas+锥齿茧蜂属Conspinaria+刺茧蜂属Spinaria+内茧蜂属Rogas”,二者不是姐妹群。脊茧蜂属Aleiodes和弓脉茧蜂属Arcaleiodes始终是姐妹群。脊茧蜂属Aleiodes是一个单系,并可分成2个姐妹分支,这与依据形态和生物学特征的亚属分群相一致。弓脉茧蜂属Arcaleiodes Chen et He,1991是一个独立的属。分支“沟内茧蜂属Canalirogas+锥齿茧蜂属Conspinaria+刺茧蜂属Spinaria+内茧蜂属Rogas”的单系性仅得到部分分子数据的支持;因形态特异（腹部成甲壳状）而列为亚族级的刺茧蜂属Spinaria,分子分析没有证实这一点。横纹茧蜂族Clinocentrini是个单系,并在内茧蜂亚科的系统发育中处于基部（原始）的位置。我们研究结果还表明,阔跗茧蜂属Yelicones和潜蛾茧蜂属Stiropius相对应的阔跗茧蜂族Yeliconini和潜蛾茧蜂族Stiropiini为2个独立的分支, 与形态和生物学的结果一致,但它们在内茧蜂亚科的系统发育的位置不明,有待今后进一步研究。     

缘蝽科的比较形态学研究Ⅰ（异翅亚目：缘蝽总科）

本研究叙述了缘蝽科的基本特征以及缘蝽科中２２个族或亚科级单元的比较形态学特征,特别是外生殖器的特征描述及其图解多为首次报道。认为瘤缘蝽族、喙缘蝽族、竹缘蝽族、沟缘蝽亚科、达缘蝽族、同缘蝽族、特缘蝽族及美洲各族（或亚科）为单系群;梭缘蝽族（包括唯一属梭缘蝽属）的族级地位成立;缘蝽族各属关系复杂;黛缘蝽族是一个复系类群,各属关系复杂,在头部、阳茎和雄虫生殖腔等方面的构造已呈明显差异,此族似不成立;岗缘蝽族应是一单系群,但Ｐｌｉｎａｃｈｔｕｓｂａｓａｌｉｓ似应独立成属并移出岗缘蝽族;曼缘蝽族、昧缘蝽族及鼻缘蝽族［仅１属１种,该属另外１种ＳｉｎｏｔｎｇｕｓｒｕｂｒｏｍａｃｕｌｕｓＨｓｉａｏ被移到类缘蝽属中,即Ａｎａｃａｎｔｈｏｃｏｒｉｓｒｕｂｒｏｍａｃｕｌｕｓ（Ｈｓｉａｏ）（ｎ．ｃｏｍｂ,新组合）为单属族,它们的系统学地位有待进一步研究;希缘蝽族（或亚科）身体构造很特异,是较原始的缘蝽类群;棒缘蝽亚科亦为较原始的类群,其中棒缘蝽属群各属组成一单系群,证明Ｓｔａｌ（１８７３）将它们成立棒缘蝽族合理;其余棒缘蝽亚科各属虽在某些外部形态上表现出一定的亲缘关系,但属间特征交叉,且与棒缘蝽族有许多共同特征,若归为一族,则造成     

基于2个核糖体DNA序列的国产白酒草属、小舌菊属和歧伞菊属（菊科紫菀族）分子系统学研究

国产白酒草亚族（菊科紫菀族）由白酒草属（Conyza）、小舌菊属（Microglossa）和歧伞菊属（Thespis）3个小属组成,且国产白酒草亚族各属间及其与非洲白酒草属植物之间的分子系统发育关系尚无报道,故本研究利用核糖体DNA ITS和ETS序列并采用最大简约法和贝叶斯分析法,重建了国产白酒草亚族的分子系统发育树。结果表明,国产4种白酒草属植物、歧伞菊和非洲白酒草属植物组成一支,而劲直白酒草的两变种和小舌菊嵌入田基黄亚族分支;小舌菊与Psiadia pascalii近缘。基于这些结果,我们认为：（1）劲直白酒草和Conyza incisa应处理为田基黄亚族的一个独立的属;（2）国产4种白酒草属植物和歧伞菊以及大多数非洲白酒草属植物属于Eschenbachia属,而且Eschenbachia属代表一个新的亚族,歧伞菊可处理为Eschenbachia属的一个组。Eschenbachia属可能从非洲经数次长距离传播到达我国南部;（3）Welwitschiella 和小舌菊属应保持属的地位,Psiadia pascalii、Conyza scabrida和C. pyrrhopappa可并入小舌菊属。     

Caryopsis morphology of the Chloridoideae (Gramineae) and its systematic implications

Macro- and micromorphological analysis of the caryopses of 58 taxa belonging to 45 genera of Chloridoideae allows the recognition of three caryopsis types according to differences in ventral face and hilum morphology. First is the convex ventral face, corresponding with a leaf-shaped hilum, observed in the tribe Pappophoreae. Second is the flat ventral face, corresponding with a rudimentary, needle-shaped or oblong hilum, observed in the tribes Eragrostideae and Leptureae. The third type, observed in the tribe Cynodonteae, is the concave ventral face, corresponding with a grooved or triangular hilum. The ventral face and hilum, together with other useful caryopsis characters, including six different shapes, seven types of spermoderm sculpture and three types of stylopodium, may be used as diagnostic characteristics of genera, and even species, in Chloridoideae. A key to identify the different species of 45 genera is provided.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 57–72.     

Phylogenetic structure in the grass family (Poaceae) as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among representatives of all subfamilies of the grass family (Poaceae), using Joinvillea (Joinvilleaceae) as the outgroup, placed most genera into two major clades. The first of these groups corresponds to a broadly circumscribed subfamily Pooideae that includes all sampled representatives of Ampelodesmeae, Aveneae, Brachypodieae, Bromeae, Diarrheneae, Meliceae, Poeae, Stipeae, and Triticeae. The second major clade includes all sampled representatives of four subfamilies (Panicoideae [tribes Andropogoneae and Paniceae], Arundinoideae [Arundineae], Chloridoideae [Eragrostideae], and Centothecoideae [Centotheceae]). Within this group (the “PACC” clade), the Panicoideae are resolved as monophyletic and as the sister group of the clade that comprises the other three subfamilies. Within the latter group, Danthonia (Arundinoideae) and Eragroslis (Chloridoideae) are resolved as a stable monophyletic group that excludes Phragmites (Arundinoideae); this structure is inconsistent with the Arundinoideae being monophyletic as currently circumscribed. The PACC clade is placed within a more inclusive though unstable clade that includes the woody Bambusoideae (Bambuseae) plus several disparate tribes of herbaceous grasses of uncertain affinity that are often recognized as herbaceous Bambusoideae (Brachyelytreae, Nardeae, Olyreae, Oryzeae, and Phareae). Among eight most-parsimonious trees resolved by the analysis, four include a monophyletic Bambusoideae sensu lato (comprising Bambuseae and all five of these herbaceous tribes) as the sister group of the PACC clade; in the other four trees these bambusoid elements are not resolved as monophyletic, and the PACC clade is nested among these tribes. These results are consistent with those of previous analyses that resolve a basal or near-basal branch within the family between Pooideae and all other grasses. However, resolution by the present analysis of the PACC clade, which includes Centothecoideae, Chloridoideae, and Panicoideae, but excludes Bambusoideae, is inconsistent with the results of previous analyses that place Bambusoideae and Panicoideae in a monophyletic group that excludes Centothecoideae and Chloridoideae.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

PROLAMIN AND IMMUNOLOGICAL STUDIES IN THE POACEAE. III. SUBFAMILY CHLORIDOIDEAE

Prolamin size variation and structural similarities were used as molecular characters to address questions pertaining to tribal structure and phylogenetic origin of the Chloridoideae. Prolamin polypeptides were resolved by SDS-PAGE (sodium dodecyl sulphate polyacrylamide gel electrophoresis), and the immunological cross-reactivities were measured by ELISA (enzyme-linked immunosorbent assay) and immunoblotting. Thirty-three species were examined from 24 genera belonging to six chloridoid tribes and three outgroup subfamilies (Arundinoideae, Panicoideae, and Pooideae). The study supports the inclusion of the Cynodonteae, Eragrosteae, and Sporoboleae under one tribe. Members of the Pappophoreae and Spartineae appeared as distinct lineages. The results suggest a strong evolutionary relationship between the Chloridoideae and Arundinoideae.     

Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges

We aim to present phylogenetic major groups within the subfamily Cyperoideae (Cyperaceae) on the basis of three molecular data sets; nuclear ribosomal internal transcribed spacer and 5.8S ribosomal RNA region, the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene, and trnL intron and trnL-F intergenic spacer. Three molecular data and two combined data sets were used to obtain robust and detailed phylogenetic trees by using maximum parsimony and Bayesian inference, respectively. We analyzed 81 genera and 426 species of Cyperaceae, including Korean species. We suggest one early diverged group (EDGs), and two major clades (FAEC and SDC) within the subfamily Cyperoideae. And the clade EDGs comprises six tribes (Schoeneae, Bisboeckelereae, Sclerieae, Cryptangieae, Trilepideae, and Rhynchosporeae) at the basal nodes of Cyperoideae. The FAEC clade (posterior probability [PP]/bootstrap value [BS] = 1.00/85) comprises four tribes (Fuireneae, Abildgaardieae, Eleocharideae, Cypereae), and the SDC clade (PP/BS = 1.00/86) comprises three tribes (Scirpeae, Dulichieae, Cariceae). These three clades used for phylogenetic groups in our study will be useful for establishing the major lineage of the sedge family. The phylogeny of Korean sedges was also investigated within the whole phylogeny of Cyperaceae. The 20 genera of Korean sedges were placed in 10 tribes forming 14 clades.     

A molecular phylogeny and classification of Verbenaceae

? Premise of the study: Verbenaceae consist of trees, shrubs, lianas, and herbs distributed primarily in Latin America, where they occur in a wide array of ecosystems. A second center of diversity exists in Africa. Competing morphology-based classifications that rely on different traits conflict in significant ways. A broad phylogenetic study was undertaken to assess those classifications and to examine the historical geography of the family. ? Methods: Analysis of seven chloroplast DNA regions for 109 species, representing all genera except one monotypic genus, provide inference into evolutionary relationships in Verbenaceae. ? Key results: The phylogeny shows that none of the traditional classifications reflect phylogenetic relationships very well. Eight clades are recognized as tribes (Casselieae, Citharexyleae, Duranteae, Lantaneae, Neospartoneae trib. nov., Petreeae, Priveae, and Verbeneae). Two genera, Dipyrena and Rhaphithamnus, remain unplaced in these larger clades. Petreeae, which consist of Neotropical lianas, are sister to the rest of the family. Lantaneae and Verbeneae together form a derived clade that comprises approximately two-thirds of the species in Verbenaceae. ? Conclusions: We present a new tribal classification, including one new tribe, Neospartoneae trib. nov., to accommodate three small genera of Argentine species (Diostea, Neosparton, and Lampaya). Phylogenetic inference suggests a South American origin for Verbenaceae, with approximately six colonization events having given rise to the Old World species.     

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.     

A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: Incongruence with available tribal classifications

The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters.     

Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences

The Malpighiaceae are a family of ～1250 species of predominantly New World tropical flowering plants. Infrafamilial classification has long been based on fruit characters. Phylogenetic analyses of chloroplast DNA nucleotide sequences were analyzed to help resolve the phylogeny of Malpighiaceae. A total of 79 species, representing 58 of the 65 currently recognized genera, were studied. The 3' region of the gene ndhF was sequenced for 77 species and the noncoding intergenic spacer region trnL-F was sequenced for 65 species; both sequences were obtained for the outgroup, Humiria (Humiriaceae). Phylogenetic relationships inferred from these data sets are largely congruent with one another and with results from combined analyses. The family is divided into two major clades, recognized here as the subfamilies Byrsonimoideae (New World only) and Malpighioideae (New World and Old World). Niedenzu's tribes are all polyphyletic, suggesting extensive convergence on similar fruit types; only de Jussieu's tribe Gaudichaudieae and Anderson's tribes Acmanthereae and Galphimieae are monophyletic. Fleshy fruits evolved three times in the family and bristly fruits at least three times. Among the wing-fruited vines, which constitute more than half the diversity in the family, genera with dorsal-winged samaras are fairly well resolved, while the resolution of taxa with lateral-winged samaras is poor. The trees suggest a shift from radially symmetrical pollen arrangement to globally symmetrical pollen at the base of one of the clades within the Malpighioideae. The Old World taxa fall into at least six and as many as nine clades.