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 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.     

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 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).     

Heterochromatin banding patterns in Rutaceae-Aurantioideae--a case of parallel chromosomal evolution

The heterochromatin banding patterns in the karyotypes of 17 species belonging to 15 genera of Rutaceae subfamily Aurantioideae (= Citroideae) were analyzed with the fluorochromes chromomycin (CMA) and 4'-6-diamidino-2-phenylindole-2HCl (DAPI). All species were diploids, except one tetraploid (Clausena excavata) and two hexaploids [Glycosmis parviflora agg. (aggregate) and G. pentaphylla agg.]. There are only CMA/DAPI bands, including those associated with the nucleolus. Using recent cpDNA (chloroplast DNA) sequence data as a phylogenetic background, it becomes evident that generally more basal genera with rather plesiomorphic traits in their morphology, anatomy, and phytochemistry exhibit very small amounts of heterochromatin (e.g., Glycosmis, Severinia, Swinglea), whereas relatively advanced genera from different clades with more apomorphic characters display numerous large CMA bands (e.g., Merrillia, Feroniella, Fortunella). Heterochromatin increase (from 0.7 to 13.7%) is interpreted as apomorphic. The bands are mostly located in the larger chromosomes and at telomeric regions of larger arms. However, one of the largest chromosome pair has been conserved throughout the subfamily with only very little heterochromatin. The heterochromatin-rich patterns observed in different clades of Aurantioideae appear quite similar, suggesting a kind of parallel chromosomal evolution. In respect to the current classification of the subfamily, it is proposed to divide Murraya s.l. (sensu lato) into Bergera and Murraya s.s. (sensu stricto) and to place the former near Clausena into Clauseneae s.s. and the latter together with Merrillia into Citreae s.l. The subtribes recognized within Clauseneae s.s. and Citreae s.l. appear heterogeneous and should be abandoned. On the other hand, the monophyletic nature of the core group of Citrinae, i.e., the Citrus clade with Eremocitrus, Microcitrus, Clymenia, Poncirus, Fortunella, and Citrus, is well supported.     

The age and biogeography of Citrus and the orange subfamily (Rutaceae: Aurantioideae) in Australasia and New Caledonia

The geological history of Australasia, New Caledonia, and Southeast Asia, has been complex, resulting in competing biogeographic hypotheses for taxa found here. Alternative hypotheses-Gondwanan vicariance, rafting terranes, long-distance dispersal-may be distinguished by different predicted divergence times between disjunct sister taxa. Taxa within Rutaceae subfamily Aurantioideae are ideal for testing these hypotheses because of their distributions. Therefore, the ages of Rutaceae and Aurantioideae were estimated using molecular dating. One data set comprised 51 sequences of rbcL and atpB with sampling across rosids and three fossil calibrations: crown Fabales+Fagales+Rosales (>94 Ma), Fabaceae (>51 Ma) and stem Ailanthus, Simaroubaceae (>52 Ma). Another data set comprised 81 Aurantioideae using >8 kb of chloroplast sequence and secondary calibration. Confidence in estimated divergence times was explored by varying the root age, dating method (strict, local, and relaxed clocks), and inclusion of internal calibrations. We conclude that the Rutaceae crown diverged in the Eocene (36.4-56.8 Ma, mean 47.6), whereas the Aurantioideae crown originated in the early Miocene (12.1-28.2 Ma, mean 19.8). This young age suggests that Gondwanan vicariance does not explain the distributions of extant Aurantioideae. Taxa found in New Caledonia may have arrived by separate transoceanic dispersal events.     

Leave it to the leaves: a molecular phylogenetic study of Malaxideae (Epidendroideae, Orchidaceae)

Nuclear ITS and plastid matK sequences were collected for 71 taxa of Malaxideae (Orchidaceae). Resulting cladograms are highly resolved and well supported by jackknife analyses. These indicate that the traditional classification system of the tribe using characters primarily related to floral morphology does not reflect the evolutionary history of these taxa. Rather, the tribe is split into two major clades: one of terrestrial species and another of epiphytes. Within the epiphytic clade, taxa with laterally compressed leaves (Oberonia) are monophyletic, whereas the remaining taxa (Liparis pro parte) have elongate conduplicate leaves and form a paraphyletic grade of at least two additional monophyletic lineages. Within the terrestrial clade, taxa with plicate leaves (Liparis p.p. and Malaxis p.p.) clearly separate from taxa with conduplicate leaves (Liparis p.p. and Malaxis p.p.). Although further taxon sampling should take place before nomenclature is changed, it seems evident that Malaxideae will need to be divided into at least seven genera. Furthermore, the transition from epiphytic to terrestrial habit is documented to have occurred only once in Malaxideae, and the value of vegetative over reproductive features in classifying some groups of orchids is again demonstrated.     

Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea)

A comprehensive tribal‐level classification for the world’s subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions (cytochrome oxidase subunit I‐subunit II, elongation factor‐1α and wingless). Monophyly of the family is strongly supported, as are some of the traditionally recognized subfamilies, with the following relationships: (Coeliadinae + (“Pyrginae” + (Heteropterinae + (Trapezitinae + Hesperiinae)))). The subfamily Pyrginae of contemporary authors was recovered as a paraphyletic grade of taxa. The formerly recognized subfamily Pyrrhopyginae, although monophyletic, is downgraded to a tribe of the “Pyrginae”. The former subfamily Megathyminae is an infra‐tribal group of the Hesperiinae. The Australian endemic Euschemon rafflesia is a hesperiid, possibly related to “Pyrginae” (Eudamini). Most of the traditionally recognized groups and subgroups of genera currently employed to partition the subfamilies of the Hesperiidae are not monophyletic. We recognize eight pyrgine and six hesperiine tribes, including the new tribe Moncini. © The Willi Hennig Society 2008.     

Phylogenetic relationships of Moxostoma and Scartomyzon (Catostomidae) based on mitochondrial cytochrome b sequence data

A recent phylogenetic study based on morphological, biochemical and early life history characters resurrected the genus Scartomyzon (jumprock suckers, c . eight−10 species) from Moxostoma (redhorse suckers, c . 10–11 species) and advanced the understanding of relationships among species in these two genera, and the genealogical affinities of these genera with other evolutionary lineages within the tribe Moxostomatini in the subfamily Catostominae. To further examine phylogenetic relationships among moxostomatin suckers, the complete mitochondrial (mt) cytochrome b gene was sequenced from all species within this tribe and representative outgroup taxa from the Catostomini and other catostomid subfamilies. Phylogenetic analysis of gene sequences yielded two monophyletic clades within Catostominae: Catostomus + Deltistes + Xyrauchen + Erimyzon + Minytrema and Moxostoma + Scartomyzon + Hypentelium + Thoburnia . Within the Moxostomatini, Thoburnia was either unresolved or polyphyletic; Thoburnia atripinnis was sister to a monophyletic Hypentelium . In turn, this clade was sister to a monophyletic clade containing Scartomyzon and Moxostoma . Scartomyzon was never resolved as monophyletic, but was always recovered as a polyphyletic group embedded within Moxostoma , rendering the latter genus paraphyletic if ' Scartomyzon ' continues to be recognized. Relationships among lineages within the Moxostoma and' Scartomyzon 'clade were resolved as a polytomy. To better reflect phylogenetic relationships resolved in this analysis, the following changes to the classification of the tribe Moxostomatini are proposed: subsumption of' Scartomyzon 'into Moxostoma ; restriction of the tribe Moxostomatini to Moxostoma ; resurrect the tribe Erimyzonini, containing Erimyzon and Minytrema , classified as incertae sedis within Catostominae; retain the tribe Thoburniini.     

Phylogenetic placement of Psilopeganum,a rare monotypic genus of Rutaceae (the citrus family) endemic to China

Psilopeganum (Rutaceae) is a rare monotypic genus endemic to the vicinity of the Yangtze River valley in Chongqing, Hubei, Sichuan and Guizhou provinces in China. It differs from most Rutaceae taxa by its herbaceous habit and has been treated as a member of the tribe Ruteae. Our study is the first attempt to place Psilopeganumin a phylogenetic context and our results show that the genus belongs to a clade with Boenninghausenia, Ruta and Thamnosma, which are part of Ruteae. Within this group, the position of Psilopeganum remains unclear because the Boenninghausenia-Thamnosma clade, Psilopeganum and Ruta form a trichotomy in most analyses. The ITS dataset placed Psilopeganum as sister to the Mediterranean and Canarian genus Ruta, which is corroborated by morphological similarities. Our studies support that Ruteae is paraphyletic with respect to Aurantioideae and that Dictamnus does not belong to Ruteae. The Indian, Sri Lankan, and Malagasy genusChloroxylon is sister to the Boenninghausenia-Psilopeganum-Ruta-Thamnosma clade, despite its traditional placement in the subfamily Flindersioideae. The placement of Chloroxylon is consistent with an origin of the group of Chloroxylon, Boenninghausenia, Psilopeganum, Ruta and Thamnosma in southern Asia. The rapid uplifts of the Himalayas could account for one or two vicariance events splitting the lineages of the Boenninghausenia-Psilopeganum-Ruta-Thamnosma clade, and may explain the short branch length and low support for the relationships among Psilopeganum, Ruta, and the Boenninghausenia-Thamnosma clade.     

DISTRIBUTION OF ENZYMATIC BROWNING OF YOUNG SHOOT HOMOGENATES IN THE AURANTIOIDEAE

Distribution of polyphenol oxidase-catalyzed browning of young shoot homogenates was studied in 428 accessions of the orange subfamily Aurantioideae. Browning and nonbrowning phenotypes were found in both tribes, namely Clauseneae and Citreae. The browning taxa had sufficient polyphenol oxidase activity and a presently unknown phenolic substrate, while the nonbrowning taxa were devoid of both. A third group of taxa contained the substrate only and they too were designated as browning since their homogenates turned brown when the enzyme from a known source was added. The color of homogenates was taxon-specific in most browning and nonbrowning taxa. Within the genus Citrus, 4 out of the 16 species recognized by Swingle were browning and 2 were nonbrowning. Exceptions noted within either group of taxa were presumably hybrids or mutants. The significance of enzymatic browning as an additional taxonomic criterion in studying species relationships and as a genetic marker in identificaton of hybrid taxa was discussed.     

真正柑桔果树群植物的分支学研究

本文用相容性分析方法(Compatability snalysis)分析了真正柑桔果树群(芸香科Rutaceae-柑桔亚科Aurantioideae-柑桔族(Citreae)-柑桔亚族(Citrinae)植物内各属间的分支学关系。给出了建立在7个相容性性状组成的最大族所决定的分支图。性状极性的确定使用了外群法。结果表明,柑桔属(Citrus L.)和多蕊桔属(Clymenia Swing)构成一个单系类群,他们的姐妹群是金柑属(Fortunella Swing.)。被认为起源于中国的3个属,柑桔属(Citrus)、金柑属(Fortunella)和积属(Poncirus Raf.)并未构成一个单系类群。本文还利用分支关系分析和讨论了真正柑桔果树群的种系发生关系。     

First phylogeny of predatory flower flies (Diptera, Syrphidae, Syrphinae) using mitochondrial COI and nuclear 28S rRNA genes: conflict and congruence with the current tribal classification

The family Syrphidae (Diptera) is traditionally divided into three subfamilies. The aim of this study was to address the monophyly of the tribes within the subfamily Syrphinae (virtually all with predaceous habits), as well as the phylogenetic placement of particular genera using molecular characters. Sequence data from the mitochondrial protein-coding gene cytochrome c oxidase subunit I ( COI ) and the nuclear 28S ribosomal RNA gene of 98 Syrphinae taxa were analyzed using optimization alignment to explore phylogenetic relationships among included taxa. Volucella pellucens was used as outgroup, and representatives of the tribe Pipizini (Eristalinae), with similar larval feeding mode, were also included. Congruence of our results with current tribal classification of Syrphinae is discussed. Our results include the tribe Toxomerini resolved as monophyletic but placed in a clade with genera Ocyptamus and Eosalpingogaster . Some genera traditionally placed into Syrphini were resolved outside of this tribe, as the sister groups to other tribes or genera. The tribe Bacchini was resolved into several different clades. We recovered Paragini as a monophyletic group, and sister group of the genus Allobaccha . The present results highlight the need of a reclassification of Syrphinae.
© The Willi Hennig Society 2008.     

BIOLOGICAL AND HISTORICAL FACTORS INFLUENCING GENETIC DIVERSITY IN THE SCUTELLARIA ANGUSTIFOLIA COMPLEX (LABIATAE)

Studies of genetic diversity at isozyme loci were used to examine the phylogenetic distribution of several frequently reported population-genetic parameters in a putatively monophyletic group of plant species, the Scutellaria angustifolia complex. The influence of taxon-specific differences in habitat preference, breeding system, degree of endemism, and phylogenetic relatedness was examined. Many characters of reproductive morphology traditionally used in phylogenetic inference vary with breeding system. To the extent that reproductive systems are conservative markers of phylogenetic relationships, one would expect the distribution of genetic variation to be similar in closely related taxa. Results showed that closely related taxa may exhibit very different genetic-diversity statistics and that distantly related taxa may exhibit very similar genetic-diversity statistics. This suggests that complex patterns of evolution of breeding systems and morphological characters have occurred in the ten taxa included in the Scutellaria angustifolia complex. Similarity in habitat is not associated with similarity in genetic diversity in this group of species.     

Phylogenetic relationships within the tribe Janieae (Corallinales,Rhodophyta) based on molecular and morphological data: a reappraisal of Jania1

Generic boundaries among the genera Cheilosporum, Haliptilon, and Jania—currently referred to the tribe Janieae (Corallinaceae, Corallinales, Rhodophyta)—were reassessed. Phylogenetic relationships among 42 corallinoidean taxa were determined based on 26 anatomical characters and nuclear SSU rDNA sequence data for 11 species (with two duplicate plants) referred to the tribe Corallineae and 15 species referred to the tribe Janieae (two species of Cheilosporum, seven of Haliptilon, and six of Jania, with five duplicate plants). Results from our approach were consistent with the hypothesis that the tribe Janieae is monophyletic. Our data indicate, however, that Jania and Haliptilon as currently delimited are not monophyletic, and that Cheilosporum should not be recognized as an independent genus within the Janieae. Our data resolved two well‐supported biogeographic clades for the included Janieae, an Indian‐Pacific clade and a temperate North Atlantic clade. Among anatomical characters, reproductive structures reflected the evolution of the Janieae. Based on our results, three genera, Cheilosporum, Haliptilon, and Jania, should be merged into a single genus, with Jania having nomenclatural priority. We therefore propose new combinations where necessary of some species previously included in Cheilosporum and Haliptilon.     

Distribution of Rutaceae-specific Repeated Sequences Isolated from Citrus Genomes

Three clones of dispersed repetitive sequences (MCS-26a, JA-5and JB-7) were isolated from a library of PCR products amplifiedfrom Citrus DNA using primers complementary to the minisatellitecore sequences. Distribution of these repetitive sequences inthe genomic DNA was highly variable among members of the Rutaceaefamily studied here. MCS-26a was specifically amplified in thesubfamily Aurantioideae, but not in other subfamilies of theRutaceae. Different levels of JA-5 amplification were observedamong genera in the subfamily Aurantioideae. JB-7 was widelydetected throughout the Rutaceae. These data suggest that thethree repeated sequences analysed in this study were amplifiedat different stages in the evolution of Rutaceae and that theyare useful for systematic studies of the Rutaceae. In addition,the repetitive sequences displayed a high level of restrictionfragment length polymorphism (RFLP) among Citrus species andtheir relatives, suggesting that they serve as hot spots forchanges in the genome after amplification. Copyright 2001 Annalsof Botany Company Citrus, Rutaceae, repeated sequences, DNA fingerprinting, RFLP     

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.     

Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data

Phylogenetic analysis of phytochrome (PHY) genes reveals the identity and relationships of four PHY loci among papilionoid Leguminosae. A phylogenetic analysis of loci combined according to species suggests that most of the tribe Millettieae belongs to one of two monophyletic clades: the Derris–Lonchocarpus or the Tephrosia clade. Together these two form a monophyletic group that is sister to a lineage represented by Millettia grandis of Millettia sect. Compresso-gemmatae. Collectively, this large monophyletic group is referred to as the Millettieae-core group, which based on our sampling, includes species of Millettieae that do not accumulate the nonprotein amino acid canavanine and that mostly have pseudoracemose or pseudopaniculate inflorescences. This new phylogenetic framework assists in targeting additional taxa for future sampling. For example, the “American Derris” (Deguelia), which accumulate canavanine, might not be members of the Millettieae core group. Afgekia is also predicted not to be a member because it accumulates canavanine and has an inflorescence of terminal racemes. PHY gene analysis specifically reveals that certain genera traditionally classified in Millettieae are actually distantly related to the Millettieae core group, such as Austrosteensia, Callerya, Craibia, Cyclolobium, Fordia, Platycyamus, Poecilanthe, and Wisteria.