Molecular phylogeny and species identification of pufferfish of the genus Takifugu (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships and species identification of pufferfishes of the genus Takifugu were examined by use of randomly amplified polymorphic DNA (RAPD) and sequencing of the amplified partial mitochondrial 16S ribosomal RNA genes. Amplifications with 200 ten-base primers under predetermined optimal reaction conditions yielded 1962 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances between 5 species of Takifugu and Lagocephalus spadiceus as the outgroup were calculated from the presence or absence of the amplified fragments. Approximately 572 bp of the 16S ribosonial RNA gene was amplified, using universal primers, and used to determine the genetic distance values. Topological phylogenic trees for the 5 species of Takifugu and outgroup were generated from neighbor-joining analysis based on the data set of RAPD analysis and sequences of mitochondrial 16S rDNA. The genetic distance between Takifugu rubripes and Takifugu pseudommus was almost the same as that between individuals within cacti species, but much smaller than that between T. rubripes, T. pseudommus, and the other species. The molecular data gathered from both analysis of mitochondria and nuclear DNA strongly indicated that T. rubripes and T. pseudommus should be regarded as the same species. A fragment of approximately 900 bp was amplified from the genome of all 26 T. pseudommus individuals examined and 4 individuals of intermediate varieties between T. rubripes and T. pseudommus. Of the 32 T. rubripes individuals, only 3 had the amplified fragment. These results suggest that this fragment may be useful in distinguishing between T. rubripes and T. pseudommus.

Morphology and Molecular Phylogeny of Trimyema koreanum n. sp., a Ciliate from the Hypersaline Water of a Solar Saltern

A new ciliate, Trimyema koreanum n. sp., isolated from hypersaline water (salinity of 293 parts per thousand) from a solar saltern in Korea, was investigated using live observation, protargol impregnation, and gene sequencing. Trimyema koreanum is about 30 x 13 mu m in vivo, has usually 23 longitudinal ciliary rows forming two distinct ciliary girdles visible both in vivo and in protargol impregnation. A third indistinct ciliary girdle as well as a girdle of mucocysts is distinguishable only in impregnated cells. We suggest T. koreanum as a new species, differing from the most similar species, T. marinum, by the presence of two distinct ciliary girdles (T. marinum usually has six ciliary girdles clearly visible in living cells and three anterior spirals that encircle the cell completely). Although the number of known 18S rRNA sequences in the genus Trimyema was limited, the Trimyema group including T. koreanum forms a strong clade. The phylogenetic position confirms that the isolate belongs to the genus Trimyema and is different from previously sequenced species. Trimyema koreanum is able to consume both prokaryotes and small eukaryotes (specifically, the alga Dunaliella sp.).

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species (n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis, and hence should be transferred to the genus Schizopygopsis. Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected. (c) 2007 The Authors Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Molecular phylogeny of some genera of Pamphagidae (Acridoidea, Orthoptera) from China based on mitochondrial 16S rDNA sequences

Based on the mitochondrial 16S ribosomal DNA partial sequences (473 bp) of 9 species of Pamphagidae (Acridoidea, Orthoptera) from China and of 4 species of Pamphagidae and 2 species of Pyrgomorphidae and Acrididae (as outgroups) retrieved from GenBank, we constructed the molecular phylogeny using the Neighbor Joining (NJ) and Minimum Evolution ( ME) methods based on the nucleotide Kimura 2-parameter model. The results of our study shown that: 1) the ranges of the 16S rDNA nucleotide divergence between two species of a genus were 0.21%, among genera of a subfamily were 0.42-3.38%, and among subfamilies of Pamphagidae were 1.90-8.88%, respectively. The phylogenetic tree shows that: 1) all Pamphagidae taxa form a monophyletic clade, and are well separated from the outgroup; 2) the African taxa Porthetinae (Lobosceliana brevicornis) and Akicerinae (Batrachotetrix sp.) are distinctly separated from the Chinese taxa Prionotropisinae; 3) Haplotropis bruneriana and Glauia terrea of Pamphaginae are nested in the middle of the tree, but their phylogenetic status is uncertain in this study; 4) 8 genera of Asiotmethis, Beybienkia, Mongolotmethis, Sinotmethis, Rhinotmethis, Filchnerella, Eotmethis and Pseudotmethis from China are all grouped into the subfamily Prionotropisinae, but their phylogenetic relationships are not clearly resolved.

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences

Background and Aims Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau.Methods The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained.Key Results Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years.Conclusions Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.

Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae)

All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identification of specific progenitors remains difficult for some endemics, especially some endemic genera. Nannoglottis, with about eight species endemic to this region, is one such genus. Past taxonomic treatments have suggested its relationships with four different tribes of Asteraceae. We intend to identify the closest relatives of Nannoglottis by evaluating the level of monophyly, tribal delimitation, and systematic position of the genus by using molecular data from ndhF gene, trnL-F, and ITS region sequences. We find that all sampled species of Nannoglottis are a well-defined monophyly. This supports all recent taxonomic treatments of Nannoglottis, in which all sampled species were placed in one broadly re-circumscribed genus. Nannoglottis is most closely related to the Astereae, but stands as an isolated genus as the first diverging lineage of the tribe, without close relatives. A tentative relationship was suggested for Nannoglottis and the next lineage of the tribe was based on the ITS topology, the "basal group," which consists of seven genera from the Southern Hemisphere. Such a relationship is supported by some commonly shared plesiomorphic morphological characters. Despite the very early divergence of Nannoglottis in the Astereae, the tribe must be regarded to have its origin in Southern Hemisphere rather than in Asia, because based on all morphological, molecular, biogeographical, and fossil data, the Asteraceae and its major lineages (tribes) are supposed to have originated in the former area. Long-distance dispersal using Southeast Asia as a steppingstone from Southern Hemisphere to the Qinghai-Tibet Plateau is the most likely explanation for this unusual biogeographic link of Nannoglottis. The 23-32-million-year divergence time between Nannoglottis and the other Astereae estimated by DNA sequences predated the formation of the plateau. This estimation is further favored by the fossil record of the Asteraceae and the possible time of origin of the Astereae. Nannoglottis seems to have reached the Qinghai-Tibet area in the Oligocene-Eocene and then re-diversified with the uplift of the plateau. The molecular infragenetic phylogeny of the genus identifies two distinct clades, which reject the earlier infrageneric classification based on the arrangement of the involucral bracts and the length of the ligules, but agree well with the habits and ecological preferences of its current species. The "alpine shrub" vs. "coniferous forest" divergence within Nannoglottis was estimated at about 3.4 million years ago when the plateau began its first large-scale uplifting and the coniferous vegetation began to appear. Most of the current species at the "coniferous forest" clade of the genus are estimated to have originated from 1.02 to 1.94 million years ago, when the second and third uprisings of the plateau occurred, the climate oscillated and the habitats were strongly changed. The assumed evolution, speciation diversity, and radiation of Nannoglottis based on molecular phylogeny and divergence times agree well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau. (C) 2002 Elsevier Science (USA). All rights reserved.

A preliminary analysis of the phylogeny of the Swertiinae (Gentianaceae) based on ITS data

To better understand the floral diversity and the phylogeny of the Swertiinae (Gentianaceae), the internal transcribed spacer (ITS) region of nrDNA for 17 species and one outgroup was sequenced. Our data suggest that corolla type, gland shape, and corolla appendage are poorly correlated with the ITS phylogeny. The genus Swertia s.l. and the rotate group previously recognized based on the corolla types and gland shapes are polyphyletic. Four genera with simple protruding glands and three taxa with corolla appendages are not clustered as the monophyletic groups. Four separate clades, corresponding to the four sections, were identified in Swertia s.1. Lomatogoniopsis with the simple protruding gland type of the tubular group closely related to Lomatogonium of the rotate group. The deeply lobing corolla and concave foveae may be ancestral in the Swertiinae, while the tubular corolla and the protruding glands may have undergone convergent evolution.

Variation in mitochondrial DNA and phylogeny of six species of pikas (Ochotona)

Phylogenetic relationships of six species of Ochotona were investigated using mitochondrial DNA (mtDNA) restriction-site analysis. The phylogenetic tree constructed using PAUP was based on 62 phylogenetically informative sites with O. erythrotis designated as an outgroup. Two clades were evident. One contained O. curzoniae, O. huangensis, and O. thibetana. in the second, O. daurica was a sister taxon of O. cansus. The five species appear to come from different maternal lineages. The branching structure of the tree and sequence divergence confirm that huangensis and cansus are distinct species, and that mol-osa is a synonym of O. cansus rather than O. thibetana. Divergence time, estimated from genetic distances, indicates that the ancestors of the two maternal lineages diverged ca. 6.5 x 10(6) years ago. O. curzoniae diverged from O. huangensis, and O. daurica diverged from O. cansus, at about the same time (ca. 3.4 x 10(6) years ago). These data suggest a period of rapid radiation of the genus Ochotona in China, perhaps during the late Pliocene. These calculations correspond roughly to tectonic events and environmental changes in China throughout this period, and appear to be substantiated by the fossil record.

杉科植物的系统发育、 分类和地理分布

本文对杉科植物的分类系统作了回顾。以形态学为依据，参考其他学科的研究成果，用分支分析和表征分析两种方法探讨了杉科植物的系统演化关系．提出了新的分类系统。对杉科植物的系统分类作了修订．通过对各属现代分布和地史分布的研究，结合古地理和古气候资料，讨论了杉科植物的分布中心、起源时间、起源地、散布途径及现代分布格局的成因．主要结论如下： 1．属间关系：柳杉属是现存杉科植物中最原始的类群．水松属和落羽杉属关系密切，二者与柳杉属近缘．巨杉属和北美红杉属关系密切，是中级进化水平的类群．水杉属的系统位置比较孤立，与巨杉属和北美红杉属的关缘关系相对较近．杉木属、密叶杉属和台湾杉属关系密切，是杉科植物中的高级进化类群，其中台湾杉属最为进化． 2．系统排列：支持金松科的成立．将杉科分成5族，即柳杉族（仅含柳杉属）、落羽杉族（含水松属、落羽杉属）、北美红杉族（含巨杉属、北美红杉属）、水杉族（仅含水杉属）和杉木族（含杉木属、密叶杉属及台湾杉属）． 3．分类：经修订，杉科植物共9属12种4变种．将德昌杉木、米德杉木和厚皮杉木归并，作为杉木的变种，支持柳杉作为日本柳杉的变种、台湾杉木作为杉木的变种、秃杉和台湾杉归并的观点。 4．地理分布：我国长江、秦岭以南至华南一带是杉科的现代分布中心，我国华北北部及东北、朝鲜、日本和前苏联西伯利亚东南部等地可能为起源中心和早期分化中心，起源时间可追溯至早侏罗纪或晚三叠纪．杉科的现存各属均为古老的孑遗类群．

中国苏铁属系统学研究

本文系统地总结了分布于我国的苏铁属13种植物的形态和地理分布，并在此基础上进行了解剖，微形态和生化分析。此外，还用表征分类的方法探讨了属内亲缘关系。结合古植物和古地理的知识对性状演化趋势和现代分布格局的成因进行了讨论。本文主要结论如下： 1．从种子蛋白电泳结果表明，所有现存苏铁类植物在39.8kd- 49.5kd之间均有—连续分布的混合多肽，为苏铁类所特有。杂种后代在种子蛋白电泳结果上可以表现出来。种子蛋白多肽分布在苏铁属内差异非常小，在属间差异明显，根据属间多肽距离确定苏铁属的分化较早，系统位置比较孤立。 2．形态特征表征分类结果表明攀枝花苏铁、台东苏铁、苏铁和篦齿苏铁应分在一组Sect.Asiotientales。组Sect.lndosinensis中的广东苏铁与、海南苏铁的亲缘关系较近。通过对叶表皮的观察，发现苏铁屑内植物有两种气孔类型：一种是以C.revoluta为代表的具气孔外拱盖的I型气孔，II型气孔无气孔外拱盖，为属内多数植物所具有;叶解剖的结果表明叉叶苏铁和多歧苏铁小叶中具树脂道，叶表皮和叶解剖的结果都支持台东苏铁成立。 3.攀枝花苏铁与把关河苏铁应为同一种，贵州苏铁与四川苏铁很相似，初步处理为一种，采用C.szechuanensis为学名。 4．苏铁类性状演化不均衡，染色体进化与形态进化不同步。结合化石证据确定，具掌状大孢子叶、二叉分枝脉的叉叶苏铁是现存苏铁属内最原始的类群. 5．苏铁属花粉均为远极球形单沟或舟形单沟，外壁表面纹饰为小的凹穴，种间共性明显，只在大小和形状上有微小差别。

异叶苣苔属系统学和进化研究——兼论尖舌苣苔族的系统发育

异叶苣苔属(Whytockia)隶属于苦苣苔科(Gesneriaceae)、尖舌苣苔族(Klugieae)．70年代以来，该属作为Klugieae中最原始的类群才逐渐被人们所认识，并被认为是解决Klugieae系统发育问题的关键类群，但到目前为止，对该属变异式样及系统发育的认识仍然极其有限．鉴于上述原因，本文结合蜡叶标本和大量的野外观察和采集，从形态学、维管束的结构和分化，形态发生和细胞学等方面，进行异叶苣苔属的系统学和进化研究，并兼论尖舌苣苔族的系统发育． 1．通过对异叶苣苔属大量性状的仔细观察和比较，本文选择了34个性状，并分析了他们的变异式样及其形成原因，为进一步的系统学研究提供依据． 2．地上茎的形态发生研究揭示出异叶苣苔属植物的顶芽完全受到抑制，位于小型叶腋的侧芽萌发，从而替代顶芽生长，地上茎的不分枝是位于大型叶腋的腋芽受到抑制所致，该研究纠正了前人的观察错误． 3．花序及花的形态发生过程表明，异叶苣苔属的花序呈对花从花序轴内侧二列式连续发生，没有任何分枝和附属物．花各部分的发生顺序基本上呈向心式，但在花冠和雄蕊原基之间则为离心式发生．花萼和花冠原基的发生及发育顺序均呈下降式，从而使花萼和花冠在芽中呈下降覆瓦状排列，退化雄蕊是由发育停滞所致．雌蕊的两个心皮在形态发生过程中由离生到合生，该属具中轴胎座的二室子房起源于两个离生心皮的近轴面内卷式愈合，柱头从离生到合生决定于个体发育中愈合部向上推进的程度． 4．为了澄清性状演化极性这一关键问题、本文作了花部器官解剖以及心皮维管束结构及分化过程的研究，结果表明，该属花梗和花萼中均具有分泌道和雄蕊束从中柱独立分出，同独叶苣苔属(Monophyllaea)十分相似：花盘低且薄并且没有维管束，以及子房壁维管束具有不同来源而区别于尖舌苣苔族(Klugieae)中的其它类群．异叶苣苔属的心皮结合程度和胎座形态可分为三种类型，即A型：心皮结合部的中轴区膨大，但四个瓣片的上部分离、B型：除中轴区膨大外，四个瓣片也成对愈合，胎座呈锚形、C型：中轴区不膨大，四个瓣片完全分离，子房上部一室．前者保留了较多的叶性，可能是该属乃至尖舌苣苔族中最原始心皮及胎座形态．后二者代表着两个相反的演化趋势． 5．本文首次报道了异叶苣苔属的染色体数目和核型，染色体数目均为2n＝18，x＝9．核型分别是2A或3A．核型的演化趋势，即从对称到不对称和随体的丢失同外部形态的变异密切相关。 6．深入地比较和分析了异叶苣苔属和其他类群的关系以及性状的演化趋势，并运用分支分析方法，重建属的系统发育． 7．生态、地理分布和演化的研究表明：异叶苣苔属的多样化中心分别是云南东南部和滇、贵、川交界区域，起源于第三纪或更早期的古热带湿润性森林植物区系，起源地可能是两个现代多样化中心所连接的整个区域，即：滇东南至滇贵川交界区域． 8．本文对异叶苣苔属进行全面的分类学修订，包括7个种，其中一个新种，新组合1个种和一个变种、根据该属的系统发育式样，在属下新设两个组．系统排列如下： 异叶苣苔属Whytockia W. W. Smith 组1：异叶苣苔组Sect. Whytockia Y. Z. Wang sect. nov. 1．河口异叶苣苔W. hekouensis Y. Z. Wang 2．毕节异叶苣苔W. bijieensis Y. Z. Wang, sp. nov. 3．异叶苣苔W. chiritiflora (Oliv.) W.W. Smith 4．峨眉异叶苣苔W. wilsonii (A. Weber) Y. Z. Wang, stat. nov. 5．紫红异叶苣苔W. purpurascens Y. Z. Wang 组2：台湾异叶苣苔组Sect. Synstigma Y. Z. Wang, sect. nov. 6．白花异叶苣苔W. tsiangiana (Hand.-Mazz) A. Weber 7．台湾异叶苣苔W. sasakii (Hayata)B．L．Burtt. 9．在异叶苣苔属系统学和进化研究的基础上，结合前人工作，本文进一步探讨尖舌苣苔族的系统发育．大量的证据充分显示出异叶苣苔属和圆果苣苔属分别是Klugieae最原始的类群，该族中的尖舌苣苔属(Rhynchoglossum)，盾座苣苔属(Epithema)和独叶苣苔属(Mono phyllaea)，可能是从Whytockia植物的早期类群直接演化而来，十字苣苔属(Stauranthera)和Loxonia也可能直接或间接来自Gyrogyne植物的早期类群．尖舌苣苔族植物可能起源于亚洲大陆或更准确地说，中国西南部地区，在随后的演化过程中，经过分化、迁移，逐渐形成广布于南亚、东南亚及太平洋岛屿至西非、中美洲的现代地理分布式样。

石荠苎属的系统学与进化

石荠苎属(Mosla (Benth.) Buch.-Hamilt. ex Maxim.)是唇形科的一个小属，仅分布于东亚，该属复杂的变异式样一直困扰着系统学家．本论文是对该属进行三年物种生物学研究的结果．本研究从居群生物学出发，在广泛的野外调查后选取了47个居群进行取样和观察，在控制环境因素的实验设计条件下，测量了31个居群53个形态性状并分析了其变异规律;在扫描电镜下观察了含外类群在内的6属38个居群的花粉和小坚果表面微形态：对27个居群做了细胞学研究：对22个居群15个酶系统做了等位酶分析，获得了28个位点的资料;进行了35个组合的796次人工杂交．综合上述各方面资料的分析结果，对石荠苎属的形态变异与进化、居群分化、生殖隔离、物种形成、类群划分，以及起源和扩展作了详细的分析和讨论． 形态特征的数量遗传学分析表明，叶片大小和形状、苞片形态、花序（果序）和花萼（果期花萼）的复杂变异式样是造成分类混乱的主要原因．叶片大小和形状在小鱼仙草(M. dianthera)中呈现幅度很宽的连续变异，极端情况常分别被描述为不同的种，如M．remottllora和M．grosseserrata．少数突变体以及种间偶尔产生的杂交个体在苞片和花序形态上表现异常，都曾引起分类的混乱．本研究已经澄清M. bracteata和M. tamdaoensis是突变体，而M. exfoliata和M. longispica则是种间杂种．M.fomosana花萼上唇裂片长度的变异是导致分类困难的另一个原因，是小鱼仙草花萼上唇中裂片变异的极端类型。 通过比较分析揭示了石荠苎属中苞片形状、花序结构、花朵大小、花萼形态、小坚果和花粉粒表面纹饰以及染色体的变异和演化趋势，苞片由发达的叶状类型向披针形方向演化;花序由花朵疏离的松散状向紧缩的头状类型演化;花萼由近辐射对称，五个裂片近等长向二唇形演化;花冠由发达、鲜艳向退化方向演化：小坚果由具旋涡状深雕纹向具网纹类型演化;花粉粒由无明显突起向有明显条文或块状突起的类型演化;核型由不对称性小向不对称性增强发展;繁育系统由以异交为主向以自交为主演化，并且带动一系列花部形态的相关变异． 等位酶分析结果表明，石荠苎属种内的进化以遗传变异的积累和繁育系统的转变造成的居群间分化为主要特征．杭州石荠苎各居群的平均遗传距离为0.026，聚类分析结果发现7个居群明显分化为两支，居群3704，4704和3712为一支，其他居群为一支，等位酶资料获得的结果也得到形态和生殖特征的支持．3704、4704和3712在毛被、花朵大小、小坚果大小和颜色在均与其他居群有差异，繁育系统上，这三个居群表现出更明显的异交特性．小鱼仙草居群之间遗传分化甚至大于少数亲缘种之间的遗传分化，平均遗传距离达到0.034，但杂交实验发现，居群之间并不存在生殖隔离，不同的居群之间在叶片大小、叶形、苞片长短和花萼上唇中裂片的长短也有所不同．杭州石荠苎和小鱼仙草种内居群之间的形态和等位酶分化说明居群之问正处于分化和物种形成的早期阶段，生殖隔离还没有建立。 突变（包括染色体结构变异）的积累和繁育系统的转变是石荠苎属物种形成的基础，苏州石荠苎和石荠苎的分化是由于染色体结构变异的积累，具体表现在核型不对称性上的差异，造成生殖隔离．另一些比较明显的物种形成机制为：染色体多倍化，形成M.pauciflora;染色体结构变异，如随体染色体的臂间易位，产生M.cavaleriei;繁育系统由异交转变为自交产生M．chinensis．另外，在物种形成过程中，花期和生态位分化等促进了生殖隔离的完善． 石荠苎属形态上界限清楚，而且存在生殖隔离的种有八个，它们是小花荠苎(M.cavaleriei Levl.);石香薷 (M. chinensis Maxim.);小鱼仙草 (M. dianthera (Buch.-Hamilt. ex Roxb.) Maxim.);杭州石荠苎(M．hangchouensis Matsuda);日本石荠苎(M. japonica (Benth.) Maxim.);疏花荠苎(M. pauciflora (C. Y. Wu) C. Y. Wu et H. W. Li);石荠苎(M. punctulata (J.F. Gmelin) Nakai)和苏州石荠苎(M. soochouensis Matsuda). 石荠苎属的近缘属是香薷属(Elsholtzia)、香简草属(Keiskea)和紫苏属(Perilla)。石荠苎属与近缘属的分化大约在260万年之前，因为那时石荠苎属的祖先就发生了分化，形成以杭州石荠苎一一石香薷的祖先和以小花荠苎一一小鱼仙草的祖先为代表的两条进化主线，从香薷属和香简草属的现代分布式样-以及石荠苎属的分布特点推断，华东地区可能是石荠苎属的起源和演化的舞台，华东地区具有最大的种类多样性、变异性、特有性和多度．