Phylogenetic Relationships of Amaryllidaceae Based on matK Sequence Data

matK gene, which is located in the chloroplast genome and evolves more quickly than the rbcL gene. A total of 31 species representing 31 of the 59 genera in the family were examined in this study. We also used 21 species from another ten families of Asparagales, four species from three families of Liliales and Acorus as outgroups. We obtained partial sequences of matK with lengths of 1,109–1,148 bp, corresponding to positions 230 to 1,343 of the Oryza sativa matK gene. The pairwise percentage sequence divergence ranged from 0 to 19.1% for all the species examined except Acorus, and 0 to 4.6% within Amaryllidaceae. Two methods of phylogenetic analysis, the Maximum Parsimony and Neighbor-Joining methods, were used. The trees obtained from these two analyses were fundamentally consistent. In both trees, the Amaryllidaceae sensu Dahlgren et al. formed a well-supported monophyletic clade with 100% bootstrap support. Amaryllidaceae were included in the Asparagales; however, its phylogenetic position within the Asparagales was not clearly resolved. Judging from the NJ tree, Agapanthus might be a sister group of the Amaryllidaceae, although bootstrap support for this was low. Character-state mapping was used to infer a center of origin and the biogeographic history of Amaryllidaceae. The result supports the hypothesis that the family evolved in Africa and subsequently spread to other continents, further suggesting that South America is the center of secondary diversification. Received 6 January 1999/ Accepted in revised form 8 April 1999     

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matK基因的松属白皮松组分子系统发育分析

基于matK基因对松属(Pinus L.)白皮松组(sect.Parrya Myre)进行了分子系统发育分析.白皮松组为一个并系类群,因为白松组的成员与该组(包括越南的扁叶松(P.krempfii Lecomte))的亚洲成员形成一个强烈支持的分支(靴带值92%).在这个分支中,白松组的3个代表种形成一个稳定的单系,而白皮松组的亚洲成员之间系统发育关系不明确.扁叶松和西藏白皮松(P. gerardiana Wall.ex D.Don)聚在一起,但只有61%的支持率.虽然在以前4个cpDNA基因序列分析时五针白皮松(P.squamata X.W.Li)与白皮松(P.bungeana Zucc.ex Loud.)和西藏白皮松形成一个单系,但在本文的分析中三者的关系不明确.在邻接树和多数一致简约树上,北美的白皮松组成员形成一个支持率低的分支.北美的subsect.Balfourianae Engelm.亚组(包括P.aristata Engelm.)是一个单系,但支持率较低.美洲另外两个亚组subsect.Cembroides Englem.和subsect.Rzedowskianae Carv.的组间和组内关系不确定,它们在严格一致简约树上形成一个多歧分支.     

Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well-supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus-Alangium, (2) nyssoids (Nyssa-Davidia-Camptotheca)- mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae-Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL-matK trees indicate that matK has a much higher A-T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0 :7.5). Among- lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.     

基于matK基因的松属白皮松组分子系统发育分析(英文)

基于matK基因对松属(Pinus L.)白皮松组(sect.Parrya Myre)进行了分子系统发育分析。白皮松组为一个并系类群,因为白松组的成员与该组(包括越南的扁叶松(P.krempfii Lecomte))的亚洲成员形成一个强烈支持的分支(靴带值92％)。在这个分支中,白松组的3个代表种形成一个稳定的单系,而白皮松组的亚洲成员之间系统发育关系不明确。扁叶松和西藏白皮松(P.gerardiana Wall.ex D.Don)聚在一起,但只有61％的支持率。虽然在以前4个cpDNA基因序列分析时五针白皮松(P.squamata X.W.Li)与白皮松(P.bungeana Zucc.ex Loud.)和西藏白皮松形成一个单系,但在本文的分析中三者的关系不明确。在邻接树和多数一致简约树上,北美的白皮松组成员形成一个支持率低的分支。北美的subsect.Balfourianae Engelm.亚组(包括P.aristata Engelm.)是一个单系,但支持率较低。美洲另外两个亚组subsect.Cembroides Englem.和subsect.Rzedowskianae Carv.的组间和组内关系不确定,它们在严格一致简约树上形成一个多歧分支。     

Phylogenetic relationships of the Magnoliaceae inferred from cpDNA matK sequences

The coding region of the matK gene was sequenced to infer the phylogeny of the family Magnoliaceae. Phylogenetic analyses of 21 matK sequences representing ten genera of Magnoliaceae and three outgroups suggest relationships among both subfamilies and genera. Monophyly of the subfamily Liriodendroideae (the genus Liriodendron) and the subfamily Magnolioideae is strongly supported, respectively. Within the subfamily Magnolioideae, three clades are formed: (1) the genus Magnlietia, (2) the subgenus Magnolia, and (3) the subgenus Yulania, with the genera Michelia, Paramichelia, Tsoongiodendron, Alcimandra, Kmeria, Parakmeria and Manglietiastrum. However, the genus Magnolia is shown to be a polyphyletic group, and the genus Michelia a paraphyletic group. Relatively low sequence divergences are detected among genera of the the subfamily Magnolioideae, ranging from 0.14% to 1.70%, especially in the tribe Micheliinae (0.14–0.98%). Molecular evidence from matK sequence data suggests that the phylogenetic positions and the delimitation of the eight genera Magnolia, Michelia, Tsoongiodendron, Paramichelia, Alcimandra, Kmeria, Parakmeria and Manglietiastrum need to be reconsidered. Received: 2 January 2000 / Accepted: 12 February 2000     

Molecular Phylogeny of Nicotiana (Solanaceae) Based on the Nucleotide Sequence of the matK Gene

Abstract: Intrageneric relationships in the genus Nicotiana were investigated by comparison of DNA sequences of the matK gene of the chloroplast genome. A total of 40 taxa were examined in this study, representing 39 of the approximately 70 wild species of this genus. We obtained the full sequences of the 1530 bp matK ORFs; no variations in length due to insertions or deletions were found. The phylogenetic trees obtained from maximum parsimony (MP) and neighbour-joining (NJ) methods were fundamentally consistent. The genus Nicotiana formed a clade in these trees. The traditional classification of this genus was mostly in agreement with the molecular phylogeny. However, all three subgenera and some sections did not form a monophyletic group. Character-state mappings were used to infer a centre of origin, biogeographic history, and transition of chromosome number. The results support the previous hypothesis that this genus originated in South America and subsequently spread to other continents. The suggestion that the ancestral basic chromosome number is x = 12 and that polyploidy and aneuploidy have occurred independently several times during the evolution of Nicotiana species is also discussed.     

Molecular Systematics of Trilliaceae I. Phylogenetic Analyses of Trillium Using matK Gene Sequences

matK was conducted using 41 Trillium taxa and two out-group taxa (Veratrum maackii and Helonias bullata). A total of 1608 base pairs were analyzed and compared., and then there were 61 variable (36 informative) sites among Trillium species. Fifteen insertion/deletion events (indels) of six or fifteen base pairs were also detected. Phylogenetic analyses of the sequence data revealed that the subgenus Phyllantherum (sessile-flowered species) forms a distinct monophyletic group, whereas the subgenus Trillium (pedicellate-flowered species) does not form a monophyletic group, and is composed of three distinct groups and three basally located species in the tree: (1) the Erectum group, (2) the Grandiflorum group, and (3) the Pusillum group and (4) the three species, including T. govanianum, T. undulatum, and T. rivale. T .rivale appears to be the most basally diverged and a very specialized taxon among the ingroup members. Our matK data indicated that the closest relative of the subgenus Phyllantherum is the Grandiflorum group. The results are concordant with the results of the RFLP analysis of cpDNA and also more or less with those of the cladistic analysis of morphological characters. Received 11 September 1998/ Accepted in revised form 25 December 1998     

Infrafamilial Phylogeny of the Aquatic Angiosperm Podostemaceae Inferred from the Nucleotide Sequences of the matK Gene

Abstract: The infrafamilial relationships of Podostemaceae were deduced from nucleotide sequences of the chloroplast matK gene. The matK phylogenetic analyses show that Podostemaceae are composed of two major clades that correspond to the subfamily Tristichoideae sensu stricto and Weddellina and the subfamily Podostemoideae. Weddellina, which has long been recognized as a member of the Tristichoideae, is sister to the Podostemoideae, supporting the classification that recognized a third subfamily Weddellinoideae. Malaccotristicha malayana and Terniopsis sessilis form a basal clade in Tristichoideae sensu stricto. Tristichoideae show a high morphological diversity and, surprisingly, a close relationship exists between Dalzellia zeylanica and Indotristicha ramosissima, which remarkably differ in their body plans. A few genera defined by particular characters, such as Synstylis and Torrenticola, merge into clades of other larger genera. The Podostemoideae taxa studied are composed of two American clades, an Asian-Australian clade and a Madagascan clade, and may suggest that the subfamily perhaps originated in America and migrated to the Old World.     

Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences

Nucleotide sequences from four chloroplast genes, the matK, chlL, intergenic spacer (IGS) region between trnL and trnF, and an intron of trnL, were determined from all species of Taxodiaceae and five species of Cupressaceae sensu stricto (s.s.). Phylogenetic trees were constructed using the maximum parsimony and the neighbor-joining methods with Cunninghamia as an outgroup. These analyses provided greater resolution of relationships among genera and higher bootstrap supports for clades compared to previous analyses. Results indicate that Taiwania diverged first, and then Athrotaxis diverged from the remaining genera. Metasequoia, Sequoia, and Sequoiadendron form a clade. Taxodium and Glyptostrobus form a clade, which is the sister to Cryptomeria. Cupressaceae s.s. are derived from within Taxodiaceae, being the most closely related to the Cryptomeria/Taxodium/Glyptostrobus clade. These relationships are consistent with previous morphological groupings and the analyses of molecular data. In addition, we found acceleration of evolutionary rates in Cupressaceae s.s. Possible causes for the acceleration are discussed.     

线蛱蝶亚科蝶类部分类群线粒体COI基因的分子系统发生分析

以线粒体细胞色素氧化酶I（COI）基因作分子标记,对线蛱蝶亚科蝴蝶进行序列测定．序列分析的结果表明．经比对和处理后的序列总长度是645bp,其中有199个变异位点,147个简约信息位点;所编码的氨基酸序列中有18个变异位点,7个信息位点．A＋T平均含量为69．6％,G＋C平均含量为30．4％,碱基组成出现AT偏斜．以蛱蝶亚科及秀蛱蝶亚科物种为外类群,用NJ、MP及贝叶斯法重建了该亚科的系统发生树,探讨了它们主要类群间的系统发生关系．分子系统树显示,线蛱蝶亚科由以下3大支系：环蛱蝶族＋翠蛱蝶族、线蛱蝶族、丽蛱蝶族构成;其中,环蛱蝶族为单系群（NJ树也支持线蛱蝶族的单系性）;翠蛱蝶族与环蛱蝶族亲缘关系较近：丽蛱蝶族可能是该亚科较早分化出的一支．     

Phylogenetic systematics of the tribe Millettieae (Leguminosae) based on chloroplast trnK/matK sequences and its implications for evolutionary patterns in Papilionoideae

Phylogenetic relationships in the tribe Millettieae and allies in the subfamily Papilionoideae (Leguminosae) were reconstructed from chloroplast trnK/matK sequences. Sixty-two accessions representing 57 traditionally recognized genera of Papilionoideae were sampled, including 27 samples from Millettieae. Phylogenies were constructed using maximum parsimony and are well resolved and supported by high bootstrap values. A well-supported "core Millettieae" clade is recognized, comprising the four large genera Millettia, Lonchocarpus, Derris, and Tephrosia. Several other small genera of Millettieae are not in the core Millettieae clade. Platycyamus is grouped with Phaseoleae (in part). Ostryocarpus, Austrosteenisia, and Dalbergiella are neither in the core Millettieae or Phaseoleae clade. These taxa, along with core Millettieae and Phaseoleae, form a monophyletic sister group to Indigofereae. Cyclolobium and Poecilanthe are close to Brongniartieae. Callerya and Wisteria belong to a large clade that includes all the legumes that lack the inverted repeat in their chloroplast genome, which confirms previous rbcL and phytochrome gene family phylogenies. The evolutionary history of four characters was examined in Millettieae and allies: the presence of canavanine, inflorescence types, the dehiscence of pods, and the presence of winged pods. trnK/matK sequence analysis suggests that the presence of a pseudoraceme or pseudopanicle and the accumulation of nonprotein amino acids are phylogenetically informative for Millettieae and allies with only a few exceptions.     

Phylogenetic relationships in Saxifragaceae sensu lato: A comparison of topologies based on 18S rDNA and rbcL sequences

Relationships among the morphologically diverse members of Saxifragaceae sensu lato were inferred using 130 18S rDNA sequences. Phylogenetic analyses were conducted using representatives of all 17 subfamilies of Saxifragaceae sensu lato, as well as numerous additional taxa traditionally assigned to subclasses Magnoliidae, Caryophyllidae, Hamamelidae, Dilleniidae, Rosidae, and Asteridae. This analysis indicates that Saxifragaceae should be narrowly defined (Saxifragaceae sensu stricto) to consist of ~30 herbaceous genera. Furthermore, Saxifragaceae s. s. are part of a well-supported clade (referred to herein as Saxifragales) that also comprises lteoideae, Pterostemonoideae, Ribesioideae, Penthoroideae, and Tetracarpaeoideae, all traditional subfamilies of Saxifragaceae sensu lato, as well as Crassulaceae and Haloragaceae (both of subclass Rosidae). Paeoniaceae (Dilleniideae), and Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae (all of Hamamelidae). The remaining subfamilies of Saxifragaceae sensu lato fall outside this clade. Francoa (Francooideae) and Bauera (Baueroideae) are allied, respectively, with the rosid families Greyiaceae and Cunoniaceae. Brexia (Brexioideae), Parnassia (Parnassioideae), and Lepuropetolon (Lepuropetaloideae) appear in a clade with Celastraceae. Representatives of Phyllonomoideae, Eremosynoideae, Hydrangeoideae, Escallonioideae, Montinioideae, and Vahlioideae are related to taxa belonging to an expanded asterid clade (Asteridae sensu lato). The relationships suggested by analysis of 18S rDNA sequences are highly concordant with those suggested by analysis of rbcL sequences. Furthermore, these relationships are also supported in large part by other lines of evidence, including embryology. serology, and iridoid chemistry.     

基于线粒体Cytb基因序列探讨中国斑翅蝗科部分种类的系统发育关系

基于斑翅蝗科14种的线粒体Cytb基因462 bp序列,使用MEGA2和PAUP4.0b软件包进行分析,显示Cytb基因序列具有明显的高A、T偏向性和距离依赖的TS/TV值.采用邻接法(NJ)、最大似然法(MP)和极似然法(ML)分别构建斑翅蝗科4亚科8属的系统发育树,不同算法构建的系统发育树均支持分为四大分支(亚科):A(绿纹蝗属)、B(束颈蝗属)、C((飞蝗属+车蝗属)+小车蝗属)、D((痂蝗属+异痂蝗属)+皱膝蝗属);红胫小车蝗和黄胫小车蝗作为两个种比较合适;痂蝗亚科和异痂蝗亚科应该合并为一个亚科;飞蝗亚科与斑翅蝗亚科的分类关系尚未解决,需要进一步的研究进行分析验证.     

Cladistic analysis of the Lythraceae sensu lato based on morphological characters

GRAHAM, S. A., CRISCI, J. V. & HOCH, P. C, 1993. Cladistic analysis of the Lythraceae sensu lato based on morphological characters. The Lythraceae s. I. comprise 31 mostly highly distinctive genera distributed worldwide. Cladistic analyses of the family were undertaken using 26 characters from anatomy, floral morphology, pollen, and seed morphology. Of four outgroup hypotheses, the Onagraceae offered the best heuristic assessment, generating 3746 trees with a tree length of 83 and consistency index and (C.I.) of 0.41. A strict consensus tree from the 3746 trees produced a basal monophyletic group of five genera (Sonneratia, Duabanga, Punka, Lagerstroemia, Lawsonia) characterized by anthotelic (determinate) inflorescences and wet stigmas, and a second clade with blastotelic (indeterminate) inflorescences, dry stigmas, and reduced carpel number. Successive weighting with Onagraceae as outgroup generated five most parsimonious trees with a tree length of 164 and C.I. of 0.75. Internal branches are weakly supported by only seven non-homoplasious characters. Significant results of the analysis include: (1) recognition of the two major clades and a total of seven monophyletic groups within the family; (2) the paraphyly of subfamily Lythroideae (Lythraceae s. s .); and (3) indication that genera endemic to the New World have been derived from more than one ancient Old World evolutionary line. The current taxonomic classification of the family is not closely correlated with results of the cladistic analysis.     

40种蕨类植物matK基因的系统分类及分子进化研究

采用“放松分子钟”模型、氨基酸位点正选择模型和分子内共进化网络估算方法,对蕨类植物Ⅱ型内含子成熟酶蛋白K(Maturase K,MATK)编码基因matK的进化趋势进行研究。结果显示:matK基因在蕨类植物系统学研究中具有一定的应用价值,与rbcL基因和psaA基因联合后能显著提升系统发育树的可信度;蕨类植物MATK蛋白中存在少数曾经历正选择的位点;MATK蛋白内部有多对氨基酸位点共同构成共进化网络。在被子植物兴起环境改变后,MATK蛋白部分位点发生适应性进化,通过位点间共进化网络协同作用方式提升蕨类植物对新光合环境的适应能力。     

木兰族和含笑族的系统学关系——基于叶绿体matK基因序列分析

采用PCR直接测序法,对木兰属国产组(各1种)和含笑属各组(各1种)的叶绿体DNA,matK基因序列进行测定分析,结果表明：木兰属和含笑属不能明显区分开,故不支持以顶生花和腋生花来划分木兰族和含笑族。     

A Molecular Phylogenetic Investigation of Bakuella,Anteholosticha, and Caudiholosticha (Protista,Ciliophora, Hypotrichia) Based on Three‐Gene Sequences

Traditionally classifications of the Urostyloida have been mainly based on morphology and morphogenesis. Recent molecular phylogenetic analyses have been largely based on single‐gene data for a limited number of taxa. Consequently, incongruence has arisen between the morphological/morphogenetic and the molecular data. In this study, the three phylogenetic markers (SSU rDNA, ITS1‐5.8S‐ITS2 region, and LSU‐rDNA) of three urostyloid genera represented by four species (Bakuella granulifera, Anteholosticha monilata, Caudiholosticha sylvatica, and C. tetracirra) were sequenced to investigate their phylogeny. The results show that: (1) all three genera should be regarded as the members of the order Urostyloida within the subclass Hypotrichia, as indicated by morphological characters; (2) phylogenetic analyses and sequence similarities both indicate that neither Anteholosticha nor Caudiholosticha are monophyletic and the systematic assignment of both genera awaits further evaluation; and (3) Bakuella has a closer relationship with Urostyla than with bakuellids (e.g. Apobakuella and Metaurostylopsis), suggesting Bakuella may belong to the family Urostylidae rather than the family Bakuellidae.