苔藓植物一些东亚特有属的分子系统学研究

苔藓是高等植物（有胚植物或陆地植物）中最原始的一类，但种类却丰富多样，其形态和生长环境的多样化程度高于蕨类和裸子植物，且对极端环境的忍耐力更强，分布范围也更广。“特有”是一个地理概念，它是相对广布而言，当一个类群的分布范围有一定的限制时即为特有现象。“东亚特有”是指分布范围主要局限于中国，朝鲜，日本和蒙古等，向北可及俄罗斯远东地区，少数可分布至中国南部相邻地区的植物类群。东亚地区主要以温带植物区系为主，但也包含一些热带植物区系成分，还因为第四纪以来受冰川活动影响较少，因此植物种类非常丰富。东亚地区也是苔藓植物的多样性中心之一，这里有较多的特有成分。在我国总共分布有苔藓植物东亚特有属35属，其中苔类5属，藓类30属。长期以来，特有成分始终引起人们的极大关注，不仅是因为其在植物地理学上的重要性，还因为特有类群中包含了孓遗类群，往往系统位置比较关键，此外，大部分特有类群对人为干扰比较敏感，对其保护就愈加重要，因为它在这个地区的消失就意味着一个类群的灭绝。 我国对苔藓植物东亚特有类群已有较好的认识，在前人知识积累的基础之上，我们期望通过分子系统学的方法，开展对东亚特有苔藓属的研究，逐步揭开特有属植物的神秘面纱，最终在系统树上找到它们各自应该属于自己的位置。 在本次研究中，我们总共得到十一个苔藓植物东亚特有属的新鲜材料。在实验室中我们对这十一个特有属叶绿体和核的六个基因（叶绿体atpB, rbcL, cp-SSU, cp-LSU 和核18S，26S rDNA）进行了测序，并在此基础之上，构建了来自苔藓植物106个属上述六个基因的联合矩阵，并对它们进行了系统学分析。本文所选十一个特有属中除三个苔类属和一个线齿藓类的属之外，其它七个特有属都属于侧蒴藓类。根据近几年的研究结果，侧蒴藓类中灰藓目被认为是起源自一次快速辐射演化，灰藓目各科之间的关系以及各科的范围都很难确定。即便本实验测序一万多bp，这一支之内的关系仍不能解决。 在以上结果的基础上，本文对线齿藓类的树发藓属（Microdendron）进行了较为详细的研究，我们用最大简约法分析了金发藓目15属，33种的18S, rbcL和trnL-F序列的联合矩阵。对树发藓属的微形态进行了电镜扫描。形态和分子数据的分析结果表明，这个特有属在属级水平是不成立的，它仅是小金发藓属的一个种。此结果支持将这个东亚特有属降为种的等级。此外，本文还对囊绒苔属（Trichocoleopsis）和新绒苔属（Neotrichocolea）的系统位置做了比较详细的研究。我们分别分析了一个苔类植物57属的四基因（cp-SSU, cp-LSU, atpB and rbcL）矩阵和一个苔类植物24属的九基因（cp-SSU, cp-LSU, atpB, psbA, rps4, rbcL, 18S, 26S and nad5）联合矩阵，结果显示囊绒苔属和新绒苔属互为姐妹群关系，而毛叶苔属（Ptilidium）又是它们二者的姐妹群。研究结果支持了囊绒苔属和新绒苔属组成新绒苔科（Neotrichocoleaceae），而不同于前人的观点：将上述两属放置于毛叶苔科（Ptilidiaceae）、绒苔科（Trichocoleaceae）或多囊苔科（Lepidolaenaceae）。另外值得注意的是这两个特有属和毛叶苔属组成的一支位于叶苔类（Leafy liverwort）中“Leafy I”和“Leafy II”两大支之间，但这一支确切的系统位置没有解决，仍有待于进一步研究。 除此之外，本文还利用GenBank中的数据对东亚特有属日鳞苔属（Nipponolejeunea）和耳坠苔属（Ascidiota）（未获得实验材料）进行了初步的系统学分析。结果表明传统上放在细鳞苔科的日鳞苔属与毛耳苔科的毛耳苔属（Jubula）为姐妹群关系，建议将日鳞苔属置于毛耳苔科;耳坠苔属是光萼苔科的成员，属的分类等级是合理的。 最后本文利用罚分似然法，选取多个化石作为标定点，对来自苔藓植物主要类群及其它陆地植物共115个类群5个基因（atpB, rbcL, cp-SSU, cp-LSU, 18S）的矩阵进行了分子钟的分析，初步估算11个东亚特有属的分化时间。

Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces : Cypriniformes) inferred from cytochrome b sequences

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8.89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4.78 mya from the Chinese group. The northern-southern clades of S. nigripinnis began to diverge c. 2.12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0.34 mya. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.

土圞儿属和旋花豆属的系统学研究

土圞儿属（含8种）和旋花豆属（含2种）隶属于豆科、菜豆族、刺桐亚族。土圞儿属呈东亚-北美间断分布，旋花豆属分布于喜玛拉雅地区。传统上，这两个属被认为系统关系非常近。目前对于土圞儿属中种的划分和分类问题缺乏世界范围内的深入研究，因此该属应予以修订。另外，土圞儿属内种间和土圞儿属与旋花豆属间的系统关系也需要进一步研究。本文对这两个属进行了世界范围内的分类学修订。同时，基于形态学、解剖学、孢粉学特征和分子系统学方面的研究，对土圞儿属内部和这两个属之间的系统发育关系进行了探讨。结果如下： 1. 形态学 在标本室研究和野外考查的基础上，对土圞儿属和旋花豆属植物形态性状的变异式样及其分类学意义进行了分析，发现块茎的形态、小叶的大小和形态、花序的类型和花冠的形态等特征在种内稳定，是比较可靠的分类学性状。通过对花序的研究，认为花序的类型可能反映了土圞儿属内各种之间的演化关系，推测肉色土圞儿可能是土圞儿属中较为进化的种类，而云南土圞儿和纤细土圞儿则可能较为原始。 2. 叶表皮特征 首次在光学显微镜和扫描电子显微镜下，对土圞儿属和旋花豆属全部8种植物的叶表皮进行了观察。发现这两个属叶表皮的性状，特别是表皮细胞的形状、垂周壁的式样和蜡质纹饰的特征，对于理解土圞儿属内和这两个属之间的系统关系有重要意义。叶表皮的特征支持以下结论：纤细土圞儿是一个独立的种，而不是云南土圞儿之下的一个变种;对于土圞儿属进行亚属的划分是不合理的。 3. 孢粉学 在光学显微镜和扫描电子显微镜下，对7种土圞儿属和旋花豆属植物的花粉进行了观察。这两个属的花粉均为三孔沟，三角球形或球形。土圞儿属的花粉可划分为两种类型：肉色土圞儿的花粉外壁为典型的网状纹饰;其他的种花粉外壁较光滑，具颗粒状或短条纹状纹饰。肉色土圞儿花粉外壁纹饰的类型可能反映了其在Apios属中较进化的位置。旋花豆属的花粉特征和肉色土圞儿相似，这也许说明了两者之间的亲缘关系较近。 4. 分子系统学 通过对土圞儿属和旋花豆属6种植物的两个DNA片段ITS和H3D进行简约性分析，构建了这两个属之间的系统关系树。结果如下：土圞儿属和旋花豆属是亲缘关系较近的姐妹群;土圞儿属自身组成一个单系群，是一个自然的类群;北美的土圞儿聚成一支，隐藏在东亚的种里。分子证据和花序类型、花粉形态等重要的形态学证据相吻合。基于上述证据，我们对土圞儿属东亚-北美间断分布的格局及其可能的成因进行了初步探讨。 5. 分类修订 对土圞儿属和旋花豆属进行了分类修订，考证了关于这两个属曾发表过的所有的名称。确认了土圞儿属应包含6种，旋花豆属有2种。排除了5个不包括在土圞儿属内的种名。此外，本文还给出了这两个属各个种的地理分布图、分种检索表、形态描述和插图。

Description of a new genus and two new species of labeonine fishes from South China (Teleostei : Cyprinidae)

A new genus and two new species are described from the Pearl River drainage in Guangxi Province, South China. Hongshuia, new genus, can be distinguished from all other Asian genera of the Labeonini by having a lower lip with its median lobe modified into a round, fleshy plate peripherally greatly protruded so as to form a ring-like fold that is posteromedially continuous with the mental region, and centrally sunken so as to form a round, flat, fleshy pad. This genus is distinct from all other Asian labeonine genera of the Garrina except for one newly described species of Parasinilabeo ( P. longibarbus), Pseudocrossocheilus, and Sinocrossocheilus, in the presence of well-developed maxillary barbels. Hongshuia differs from the above three genera in the lower lip morphology, and further from both Pseudocrossocheilus and Qianlabeo in the number of pharyngeal tooth rows and from Sinocrossocheilus in the colour pattern. Two new species, H. banmo and H. paoli, differ in the distribution density and degree of development of papillae on the rostral fold, depth of indentations on the distal edge of the rostral fold, presence or absence of papillae on the lower lip, size and shape of tubercles on the tip of the snout and anterior portion of the lachrymal, length, position and colour pattern of the dorsal fin, and snout length.

Phylogenetic origins of the Himalayan endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae : Cardueae) based on three DNA regions

Background and Aims It is an enduring question as to the mechanisms leading to the high diversity and the processes producing endemics with unusual morphologies in the Himalayan alpine region. In the present study, the phylogenetic relationships and origins of three such endemic genera were analysed, Dolomiaea, Diplazoptilon and Xanthopappus, all in the tribe Cardueae of Asteraceae.Methods The nuclear rDNA internal transcribed spacer (ITS) and plastid trnL-F and psbA-trnH regions of these three genera were sequenced. The same regions for other related genera in Cardueae were also sequenced or downloaded from GenBank. Phylogenetic trees were constructed from individual and combined data sets of the three types of sequences using maximum parsimony, maximum likelihood and Bayesian analyses.Key Results The phylogenetic tree obtained allowed earlier hypotheses concerning the relationships of these three endemic genera based on gross morphology to be rejected. Frolovia and Saussurea costus were deeply nested within Dolomiaea, and the strong statistical support for the Dolomiaea-Frolovia clade suggested that circumscription of Dolomiaea should be more broadly redefined. Diplazoptilon was resolved as sister to Himalaiella, and these two together are sister to Lipschitziella. The clade comprising these three genera is sister to Jurinea, and together these four genera are sister to the Dolomiaea-Frolovia clade. Xanthopappus, previously hypothesized to be closely related to Carduus, was found to be nested within a well-supported but not fully resolved Onopordum group with Alfredia, Ancathia, Lamyropappus, Olgaea, Synurus and Syreitschikovia, rather than the Cardinis group. The crude dating based on ITS sequence divergence revealed that the divergence time of Dolomiaea-Frolovia from its sister group probably occurred 13.6-12.2 million years ago (Ma), and the divergence times of the other two genera, Xanthopappus and Diplazoptilon, from their close relatives around 5.7-4.7 Ma and 2.0-1.6 Ma, respectively.Conclusions The findings provide an improved understanding of the intergeneric relationships in Cardueae. The crude calibration of lineages indicates that the uplifts of the Qiinghai -Tibetan Plateau since the Miocene might have served as a continuous stimulus for the production of these morphologically aberrant endemic elements of the Himalayan flora.

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.

鳞毛蕨科、叉蕨科和藤蕨科的分子系统学研究

利用叶绿体rbcL和atpB基因对鳞毛蕨科、叉蕨科和藤蕨科进行了系统发育重建。对鳞毛蕨科的范畴和科下划分进行了重点研究，同时基于叶绿体rps4-trnS和trnL-F序列对该科三个东亚特有属（玉龙蕨属、柳叶蕨属和鞭叶蕨属）的分类等级进行了研究，基于rbcL、atpB和accD基因重新讨论了拟贯众属的系统位置。主要内容包括： 1.鳞毛蕨科的界定及三个东亚特有属的系统位置 利用rbcL和atpB基因，探讨了鳞毛蕨类及其近缘类群的系统发育关系。取样包括了鳞毛蕨类所有主要的分类群，尤其是增加了中国和东亚地区的类群代表。两个基因片段的联合分析较好地解决了鳞毛蕨类及其近缘类群的系统发育关系。研究结果显示广义鳞毛蕨科是个多系类群，传统上置于鳞毛蕨科中的蹄盖蕨类athyrioid、球子蕨类onocleoid和叉蕨类植物tectarioid均应该从鳞毛蕨科分出而独立成科。我们的研究结果支持Smith et al.（2006）对鳞毛蕨科的重新界定，但被作者暂时置于鳞毛蕨科的三个属：大膜盖蕨属Leucostegia、肿足蕨属Hypodematium和Didymochlaena应该从鳞毛蕨科分立出去;红腺蕨属Diacalpe、毛枝蕨属Leptorumohra和黔蕨属Phanerophlebiopsis应该作为鳞毛蕨科的成员，同时被Smith et al.（2006）保留在叉蕨科的黄腺羽蕨属Pleocnemia也应该作为鳞毛蕨科成员。鳞毛蕨科下分为四个主要的分支：鳞毛蕨支dryopteroids、耳蕨支polystichoids、肋毛蕨支ctenitoids和舌蕨支elaphoglossoids。鳞毛蕨支和耳蕨支互为姐妹群，舌蕨支是其他三个分支的姐妹群。 玉龙蕨属Sorolepidium、柳叶蕨属Cyrtogonellum和鞭叶蕨属Cyrtomidictyum是鳞毛蕨科中的三个东亚特有属，这三个特有属的分类等级和系统位置在不同的分类系统中存在争议。本文对rbcL基因进行分析并结合孢子扫描电镜观察，不支持玉龙蕨属成为一个独立的属，而应该作为耳蕨属的异名。利用rbcL、atpB、trnL-F和rps4-trnS四个DNA片段对柳叶蕨属和鞭叶蕨属进行的系统学分析，支持鞭叶蕨属作为一个独立的属，并且位于整个耳蕨类植物的基部位置。柳叶蕨属同耳蕨属近缘，尤其是同耳蕨属的细裂耳蕨组Sphaenopolystichum、半开羽耳蕨组Haplopolystichum和戟叶耳蕨组Crucifilix关系较近。但是柳叶蕨属的分类等级以及与耳蕨属的属间界限尚需要进一步研究。 2.叉蕨科的分子系统学研究 对rbcL和atpB两个基因片段的单独和联合分析均表明，秦仁昌定义的叉蕨科Tectariaceae不是一个自然的单系类群。在系统发育树上，肋毛蕨属Ctenitis、轴鳞蕨属Dryopsis、节毛蕨属Lastreopsis和黄腺羽蕨属Pleocnemia与鳞毛蕨科聚在一起构成一个强支持的分支。当把上述四个属排除以后，叉蕨属Tectaria、轴鳞蕨属Ctenitopsis、地耳蕨属Quercifilix、牙蕨属Pteridrys和沙皮蕨属Hemigramma形成一个单系类群，并得到很好的支持，该单系类群同条蕨科、骨碎补科和水龙骨科形成姐妹群关系。该单系类群同目前Smith et al.（2006）对叉蕨科的定义一致。在rbcL基因单独分析中，爬树蕨属Arthropteris同叉蕨属－沙皮蕨属聚在一起，但支持率较低。 3.藤蕨科的分子系统学研究及拟贯众属的系统位置 根据对薄囊蕨类114个分类群的rbcL基因和30个代表类群的rbcL、atpB和accD基因的系统发育分析，发现传统的藤蕨科Lomariopsidaceae不是单系类群，除了藤蕨属和Thysanosoria仍然为藤蕨科成员外，藤蕨科的主要成员（实蕨属Bolbitis、网藤蕨属Lomagramma、舌蕨属Elaphoglossum和Teratophyllum）同鳞毛蕨科植物聚在一起，因此应该被归并到鳞毛蕨科。根据Smith et al.（2006）对藤蕨科的最新定义，藤蕨科包括藤蕨属Lomariopsis、肾蕨属Nephrolepis等在内的4个属。但是本文的研究不支持把肾蕨属作为藤蕨科成员，而应该作为一个独立的分类单元，即成立肾蕨科更为合适。根据我们的分析，拟贯众属Cyclopeltis既不是鳞毛蕨科也不是叉蕨科成员，而与藤蕨属Lomariopsis聚成一个强支持的姐妹群。叶片奇数一回羽状、侧生羽片以关节着生于叶轴，叶脉游离等形态特征支持两者的近缘关系。

Mitochondrial cytochrome b gene sequence diversity in the Korean hare, Lepus coreanus Thomas (Mammalia, Lagomorpha)

Partial sequences of the mitochondrial cytochrome b gene of the Korean hare (Lepus coreanus) were analyzed to determine the degree of genetic diversity. Nine haPlotyes were observed, and the maximum Tamura-Nei nucleotide distance among them was 2.8%, indicating that genetic diversity of L. coreanus is moderate. In order to clarify the Korean hare's taxonomic status and relationship with the Manchurian hare (L. mandshuricus) and the Chinese hare (L. sinensis), these nine haplotypes of the Korean hare were compared with 13 haplotypes from five other species of eastern Asian Lepus including L. mandshwicus and L. sinensis. The Korean hare was distinct in its cytochrome b gene, and it is confirmed that L. coreanus is a valid species, as noted by Jones and Johnson (1965, Univ. Kansas Publ. (Mus. Nat. Hist.) 16:357). Further analyses of mtDNA cytochrome b gene with additional specimens of L. coreanus from North Korea and other species of Lepus from eastern Asia are needed to clarify the taxonomic status of the divergent mtDNA clades of L. mandshuricus and L. sinensis.

Revision of the labeonine genus Sinocrossocheilus (Teleostei : Cyprinidae) from South China

Sinocrossocheilus was recently diagnosed by Su et al. (2003) as consisting of nine species, i.e. S. bamaensis, S. guizhouensis, S. liuchengensis, S. longibullus, S. tridentis, S. microstomatus, S. nigrovittatus, S. labiatus, and S. papillolabrus. It is actually a catch-all genus that is composed of some species misidentified from Pseudocrossocheilus and Hongshuia. Sinocrossocheilus is here redefined based mainly on the details of the lower lip morphology; it is easily separated from all other Asian Labeonini genera in possessing a lower lip with its median lobe modified into a densely papillated, greatly protruded, crescentic fold and a papillose, slightly protruded, triangular fleshy pad which is posteriorly continuous with the mental region. Two species are recognized in this genus: S. guizhouensis and S. labiatus. Detailed redescriptions are given for the two species. All remaining species do not fit with the new definition of Sinocrossocheilus; six species, i.e. S. papillolabrus, S. nigrovittatus, S. bamaensis, S. longibullus, S. liuchengensis, and S. tridentis, should be moved to Pseudocrossocheilus and S. microstomatus to Hongshuia.