Phylogenetic Analyses of Aurantioideae (Rutaceae) Based on Non-Coding Plastid DNA Sequences and Phytochemical Features

Abstract: Sequences of the plastid DNA atp B/ rbc L intergenic spacer and rps16 intron from 23 genera and 47 species of Rutaceae were used to resolve phylogenetic relationships in subfamily Aurantioideae. According to these, the subfamily is monophyletic, but its classical subdivision into tribes Clauseneae and Citreae is only justified if the genus Murraya s.s. (exclusive of the species segregated as Bergera , e.g., Murraya koenigii and M. siamensis ) and Merrillia are transferred to Citreae s.l. This conclusion is also well supported by phytochemistry, demonstrating accumulation of carbazoles in Bergera and Clausena , and of 8-prenylated coumarins and polyoxygenated flavonoids in Murraya s.s. and Merrillia. Formation of both carbazoles, as well as 8-prenylated coumarins, and polyoxygenated flavonoids in Micromelum suggests relationships between Clauseneae s.s. and Citreae s.l. The monophyly of several larger genera in both tribes is supported by relatively high bootstrap percentages and specific chemical profiles for e.g., Clausena, Micromelum, Glycosmis and Atalantia. In contrast, molecular, chemical, and other data show that none of the subtribes recognized within Aurantioideae reflect phylogenetic relationships. Only the clades with Clausena + Bergera, Murraya s.s. + Merrillia, and Citrus + Clymenia + Eremocitrus + Fortunella + Poncirus ("true Citrus fruit trees") are well supported by such data. Among the outgroup genera, Zanthoxylum (Rutoideae) and Toddalia (Toddalioideae) are much closer to each other than to Ruta (Rutoideae).     

Pollen morphology of the subfamily Aurantioideae (Rutaceae)

The Aurantioideae is one of seven subfamilies of the Rutaceae consisting of two tribes, the Clauseneae, containing five genera, and the Citreae, with 28 genera. Each tribe contains three subtribes. The pollen morphology of the subfamily Aurantioideae is described and illustrated for the first time based on light and scanning electron microscopy. Five pollen types have been recognised in the subfamily, based mainly on aperture number and exine ornamentation. The pollen grains show a high degree of intergeneric variation. Pollen grains of Clauseneae are 3-colporate, microstriate or microstriato-reticulate, whereas pollen grains of Citreae are almost always 4/5 colporate with exines varying from microperforate to coarsely reticulate. Congruence between pollen types and the currently accepted classification is discussed, as well as the systematic implications of pollen morphology for the subfamily.     

真正柑橘果树类植物基于AFLP分子标记的分类与进化研究

用AFLP分子标记技术对芸香科Rutaceae柑橘亚科Aurantioideae真正柑橘果树类(the True Citrus Fruit Trees Group) 6属植物的59个生物类型以及九里香Murraya exotica L.、蚝壳刺Severinia buxifolia Tenore和酒饼簕Atalantia buxifolia Oliv.进行了分析。从64对引物组合中筛选出15对分辨率好的引物对全部材料进行了扩增, 共获得312条带, 其中多态型带305条, 多态位点达97.8%。利用PAUP软件构建了全部材料基于AFLP数据的UPGMA距离树。结果表明, AFLP证据支持基于形态特征建立的真正柑橘果树群以及群内各属的划分, 只是金柑属Fortunella Swingle作为一个独立的分支嵌于柑橘属Citrus L.内。对于柑橘属, 我们的分子证据支持Swingle关于亚属的划分以及Scora等关于C. medica、C. grandis和C. reticulata是真正柑橘亚属subgen. Eucitrus三个基本种的观点。AFLP分子证据显示宜昌橙C. ichangensis Swingle位于真正柑橘亚属中, 与香橙C. junos Sieb. ex Tanaka的亲缘关系最近, 而与大翼橙亚属subgen. Papeda中马蜂柑C. hystrix DC.相隔甚远。另外, 莽山野橘C. mangshanensis S. W. He &; G. F. Liu在系统树上居于宽皮柑橘类的基部。最后, 对真正柑橘果树群6属植物间以及柑橘属各主要类型(种)的进化关系进行了详细的讨论。     

Taxonomic and phylogenetic relationships among the genera of the True Citrus Fruit Trees Group (Aurantioideae,Rutaceae) based on AFLP markers

Fifty-nine genotypes representing six genera of the True Citrus Fruit Trees Group (Aurantioideae, Rutaceae) were analyzed using AFLP technique to study their taxonomic and phylogenetic relationships. Fifteen primer combinations (out of 64 screened) were selected based on the polymorphism and quality of the bands produced by the primer and used in the present study. A total of 312 bands were obtained, of which 305 (97.8%) were polymorphic. The UPGMA tree of all genotypes was constructed based on the AFLP data using PAUP* beta version 4.0b8 software. Our AFLP molecular tree clearly confirms that the True Citrus Fruit Trees Group is monophyletic and supports the division of the group into genera mainly based on morphological characters, except that the genus Fortunella was nested within the genus Citrus cluster (as a monophyletic sub-branch). The subdivision of the genus Citrus into subgen. Papeda and subgen. Eucitrus as suggested by W. T. Swingle based on morphological characters and the point of view that C. medica, C. grandis and C. reticulata are the three basic species of the subgen. Eucitrus were also supported by our molecular data. In addition, contrary to the expectation based on morphological data, however, our molecular data demonstrated that C. ichangensis is more closely related to C. junos of the subgen. Eucitrus than to the C. hystrix of the subgen. Papeda. Furthermore, our study provided the first evidence that C. mangshanensis is basal to all the loose-skin citrus types. Finally, the taxonomic and phylogenetic relationships among the six genera and the important genotypes of the genus Citrus were dis-cussed in detail.     

Phylogenetic relationships of the Aurantioideae inferred from chloroplast DNA sequence data

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because of the lack of a phylogenetic framework. The rps16 and trnL-trnF sequences of the chloroplast were analyzed phylogenetically to construct an evolutionary history and evaluate the most recent classification system of Swingle and Reece (The Citrus Industry, volume 1 [1967]). Taxa representing tribes Citreae and Clauseneae and five of the six subtribes were sampled. Conflicts in the positions of some taxa between the rps16 and trnL-trnF trees are poorly supported. In all analyses, the Aurantioideae are monophyletic. The strict consensus tree of the combined analysis indicates that the two tribes along with the subtribes sampled are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece. The tribes and subtribes are in need of revision.     

Phylogenetic relationships of the Aurantioideae (Rutaceae) based on the nuclear ribosomal DNA ITS region and three noncoding chloroplast DNA regions, atpB-rbcL spacer, rps16, and trnL-trnF

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because a phylogenetic framework has been lacking. In order to construct an evolutionary history and evaluate the most recent classification system [Swingle and Reece 1967. The botany of Citrus and its wild relatives, in: The Citrus Industry, vol. 1, History, World Distribution, Botany, and Varieties. University of California, Berkeley, pp. 190-430], one nuclear and three noncoding chloroplast genes were sequenced and analyzed phylogenetically along with selected non-molecular characters. Taxa representing tribes Citreae and Clauseneae and their six subtribes were sampled. In all analyses Aurantioideae is monophyletic. The majority-rule consensus tree from the combined analysis indicates that the two tribes are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece (1967). The tribes and subtribes are in need of revision.     

Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences

We used nucleotide sequences from the internal transcribed spacers and 5.8S gene of nuclear ribosomal DNA to test competing phylogenetic and biogeographic hypotheses in Gleditsia. Eleven of 13 Gleditsia species were sampled, along with two species of its sister genus, Gymnocladus. Analyses of ITS data and of a combined data set that included sequences of ITS and two chloroplast genes supported several conclusions that were interpreted in light of fossil data and current legume phylogeny. Gleditsia and Gymnocladus appear to have originated in eastern Asia during the Eocene. Eastern North American species of both genera most likely evolved from ancestors that migrated across the Bering land bridge, but the eastern Asian/eastern North American disjunction appears to be much older in Gymnocladus than in Gleditsia. Gleditsia amorphoides, from temperate South America, is sister to the rest of the genus, suggesting early long-distance dispersal from Asia. The remainder of Gleditsia is divided into three unresolved clades, possibly indicating a split early in the evolution of the genus. Two of those clades contain only Asian species, and one contains Asian and North American species. The North American species, Gleditsia triacanthos and Gleditsia aquatica, are polymorphic and paraphyletic with respect to their ITS and cpDNA sequences, which suggests recent diversification.     

Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data

Nucleotide sequences of the chloroplast-encoded rbcL gene were used to examine phylogenetic relationships of the genus Salix together with other allied genera of the family Salicaceae. Phylogenetic analyses of rbcL sequences strongly suggest the monophyly of three commonly recognized genera (Chosenia, Salix, and Toisusu). Two monophyletic groups are recognized within the larger monophyletic group. They do not correspond with any infrageneric taxa proposed so far. With regard to character evolution, it is thought that the reduction of stamen number from more than two stamens to two might occur in at least three lineages and that fused bud scales evolved several times and/or the reverse evolution occurred from fused to free. Some types of pollen surfaces are considered to have evolved independently.     

Phylogenetic relationships of Ruteae (Rutaceae): new evidence from the chloroplast genome and comparisons with non-molecular data

Phylogenetic analyses of three cpDNA markers (matK, rpl16, and trnL–trnF) were performed to evaluate previous treatments of Ruteae based on morphology and phytochemistry that contradicted each other, especially regarding the taxonomic status of Haplophyllum and Dictamnus. Trees derived from morphological, phytochemical, and molecular datasets of Ruteae were then compared to look for possible patterns of agreement among them. Furthermore, non-molecular characters were mapped on the molecular phylogeny to identify uniquely derived states and patterns of homoplasy in the morphological and phytochemical datasets. The phylogenetic analyses determined that Haplophyllum and Ruta form reciprocally exclusive monophyletic groups and that Dictamnus is not closely related to the other genera of Ruteae. The different types of datasets were partly incongruent with each other. The discordant phylogenetic patterns between the phytochemical and molecular trees might be best explained in terms of convergence in secondary chemical compounds. Finally, only a few non-molecular synapomorphies provided support for the clades of the molecular tree, while most of the morphological characters traditionally used for taxonomic purposes were found to be homoplasious. Within the context of the phylogenetic relationships supported by molecular data, Ruta, the type genus for the family, can only be diagnosed by using a combination of plesiomorphic, homoplasious, and autapomorphic morphological character states.     

Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis

 Relationships among 88 accessions representing 45 Citrus species, three man-made hybrids, and six related genera were examined for restriction fragment length polymorphisms (RFLP). Thirty-two Citrus and three Microcitrus accessions were also examined by random amplified polymorphic DNA (RAPD) analysis. A measure of relative heterozygosity was estimated based on the mean of the number of fragments per individual per probe-enzyme combination (PEC) divided by total number of fragments per PEC for all non-hybrid Citrus individuals. The presence in a Citrus species of a rare band found also in a related genus was taken as an indication of possible introgression, while the presence of several fragments unique to 1 species was used to indicate non-involvement of that species in hybridization events. Most species that have been described in the literature as hybrids had high heterozygosity indices and no unique fragments. Distance matrices and dendrograms were generated using simple matching coefficient and neighbor-joining cluster analysis. RFLP and RAPD data gave approximately the same results. These data showed C. maxima was affiliated with the papedas C. hongheensis and C. latipes. C. medica clustered with C. indica when only non-hybrid taxa were examined, or among limes, lemons, and relatives when all species were considered. Mandarins did not show strongly supported groupings among themselves, nor with other species. These data showed that several accessions were probably assigned to the wrong species. Received: 30 September 1997 / Accepted: 29 October 1997     

Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes

Glassfrogs (family Centrolenidae) represent an exceptionally diverse group among Neotropical anurans, but their evolutionary relationships never have been assessed from a molecular perspective. Mitochondrial and nuclear markers were used to develop a novel hypothesis of centrolenid phylogeny. Ingroup sampling included 100 terminals, with 78 (53%) of the named species in the family, representing most of the phenotypic diversity described for the group. Thirty-five species representing taxa traditionally associated with glassfrogs were used as outgroups. Gene sampling consisted of complete or partial sequences of three mitochondrial (12S, 16S, ND1) and three nuclear markers (c-myc exon 2, RAG1, POMC) for a total of 4362 bp. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and combined datasets. The separate analysis of mitochondrial and nuclear datasets allowed us to clarify the relationships within glassfrogs; also, we corroborate the sister-group relationship between Allophryne ruthveni and glassfrogs. The new phylogeny differs significantly from all previous morphology-based hypotheses of relationships, and shows that hypotheses based on few traits are likely to misrepresent evolutionary history. Traits previously hypothesized as unambiguous synapomorphies are shown to be homoplastic, and all genera in the current taxonomy (Centrolene, Cochranella, Hyalinobatrachium, Nymphargus) are found to be poly- or paraphyletic. The new topology implies a South American origin of glassfrogs and reveals allopatric speciation as the most important speciation mechanism. The phylogeny profoundly affects the traditional interpretations of glassfrog taxonomy, character evolution, and biogeography—topics that now require more extensive evaluation in future studies.     

Phylogenetic Relationships and Evolution of the Androecia in Ruteae (Rutaceae)

Ruta, which belongs to tribe Ruteae, is the type genus of the subfamily Rutoideae and the family Rutaceae. Molecular systematic studies have shown that the genera in Ruteae are closer related to Aurantioideae than to most other genera of Rutoideae, some of the genera traditionally placed in Ruteae have been shown to be nested within the Aurantioideae clade, but the diagnostic characters for determining new patterns in the relationship are poor. In this study, we investigated the floral development of Boenninghausenia in Ruteae (sensu stricto), Haplophyllum in the basal position of Aurantioideae and Murraya in traditional Aurantioideae using scanning electron microscopy. The androecium of Boenninghausenia is obdiplostemony. As androecia in other genera within Ruteae (s.s.) are also obdiplostemonous, reconstruction of the ancestral state indicates that obdiplostemony is an ancestral character in this clade. Because the androecia of Haplophyllum and Murraya are also obdiplostemonous, obdiplostemony is also an ancestral character in Aurantioideae clade. The ancestral state reconstruction indicates this character can serve as a synapomorphy of the Ruteae-Aurantioideae clade. The results of our work also shed light on the evolution of the androecium in Rutaceae, as the obdiplostemony of this group is clearly derived from haplostemony in the ancestral genera in Rutaceae and has develop into polyandry by increasing antepetalous stamens.     

基于ITS序列探讨杜鹃花属马银花组的系统发育

以杜鹃花属叶状苞亚属Rhododendron　subg. Therorhodion (Maxim.) Gray 的叶状苞杜鹃R. redowskianum Maxim.为外类群,使用PAUP4.0b8软件对马银花亚属sub g. Azaleastrum Planch.的马银花组sect. Azaleastrum (Planch.) Maxim. 7种1 变种和长蕊杜鹃组sect. Choniastrum Planch. 2种及2个相关的单型亚属（异蕊杜鹃 亚属subg. Mumeazalea Max     

Phylogenetic relationships among Heliconiinae genera based on morphology (Lepidoptera: Nymphalidae)

Abstract.  Phylogenetic relationships among Heliconiinae genera are proposed based on early-stage and adult morphology. Parsimony analyses of forty-nine species in twenty-nine genera indicate that Heliconiinae can be divided into four main groups: (1) Pardopsis , Acraea and Actinote ; (2) Cethosia plus Neotropical genera; (3) Oriental genera and (4) fritillaries. Analyses of adult characters suggested that Oriental genera form a monophyletic group, whereas those of adult plus early-stage characters artificially split this group into three separate lineages. Our character set does not contain enough phylogenetic information to resolve relationships among fritillary genera with confidence, and further studies of this group are needed. The classification of the Heliconiinae is revised based on our results.     

Phylogenetic relationships of Rhododendroideae (Ericaceae)

The Rhododendroideae are usually recognized as a subfamily within Ericaceae. This group has been considered primitive (i.e., occupying the ancestral or basal position relative to all other Ericaceae) due to the occurrence of separate petals in several taxa, deciduous corollas, and septicidally dehiscent capsules. Previous molecular studies using rbcL and nr18s sequences have indicated that Rhododendroideae may be paraphyletic and cladistically derived (i.e., the relative position in the geneology of Ericaceae is not basal). The matK sequences of 42 taxa from traditional Rhododendroideae and potentially related clades were obtained via standard gene amplication and double-stranded dideoxy sequencing. Phylogenetic analyses of these sequences using Actinidia chinensis as the outgroup indicate that the Rhododendroideae are paraphyletic. Trees obtained in the analyses indicate an expanded rhododendroid clade that includes four major subclades - empetroid, rhodo, ericoid, and phyllodocoid. The ericoid clade is sister to the phyllodocoid clade and the empetroid clade is sister to the rhodo clade. Relationships within the clades are generally well resolved except within the rhodo clade where matK data indicate that Rhododendron is probably paraphyletic. Daboecia and Calluna are included within the ericoid clade; Erica is paraphyletic. Cassiope lies outside the rhododendroid clade. The relationships indicated by the matK data suggest that sympetalous flowers are likely plesiomorphic within rhododendroids.     

Phylogenetic relationships of galeaspids (Agnatha)

We present the first parsimony analysis of the agnathan subclass Galeaspida based on the analysis of 53 morphological characters. Three most parsimonious cladograms (126 steps in length; CI = 0.508; RI = 0.801) were discovered. An amended classification of the Galeaspida is proposed corresponding to the present analysis. Our results suggest that hanyangaspids, xiushuiaspids and day on-gaspids from the Llandovery-Wenlock of Silurian are basal galeaspids. Within the remaining galeaspids, three major monophyletic groups (the Eugaleaspidiformes, the Polybranchiaspidiformes and the Huananaspidiformes) are well supported. It is shown that the dorsal fenestrae of the headshield evolved twice within the Galeaspida, one in the polybranchiaspidiform lineage, and the other in the huananaspidiform lineage (nested within the Huananaspidae). The chronological distribution of galeaspids highlights two radiations of the group, one for basal galeaspids and eugaleaspids in the Telychian (Llandovery) of Silurian, and the other for polybranchiaspidiforms and huananaspidiforms in the Lochkovian of Early Devonian. Selected from Vertebrata PalAsiatica, 2006, 44 (1): 1–27