Phylogenetic reticulation in subtribe Helianthinae

Incongruence between phylogenetic estimates based on nuclear and chloroplast DNA (cpDNA) markers was used to infer that there have been at least two instances of chloroplast transfer, presumably through wide hybridization, in subtribe Helianthinae. One instance involved Simsia dombeyana, which exhibited a cpDNA restriction site phenotype that was markedly divergent from all of the other species of the genus that were surveyed but that matched the restriction site pattern previously reported for South American species of Viguiera. In contrast, analysis of sequence data from the nuclear ribosomal DNA internal transcribed spacer (ITS) region showed Simsia to be entirely monophyletic and placed samples of S. dombeyana as the sister group to the relatively derived S. foetida, a result concordant with morphological information. A sample of a South American species of Viguiera was placed by ITS sequence data as the sister group to a member of V. subg. Amphilepis, which was consistent with cpDNA restriction site data. Samples of Tithonia formed a single monophyletic clade based on ITS sequence data, whereas they were split between two divergent clades based on cpDNA restriction site analysis. The results suggested that cpDNA transfer has occurred between taxa diverged to the level of morphologically distinct genera, and highlight the need for careful and complete assessment of molecular data as a source of phylogenetic information.     

Evidence from chloroplast DNA restriction site analysis on the relationships of Scalesia (Asteraceae: Heliantheae)

Chloroplast DNA restriction site variation provided data with which to compare the Galápagos Island endemic Scalesia to potential sister groups within subtribe Helianthinae. Pappobolus is suggested by these data to be the most likely sister group to Scalesia. It is an Andean endemic genus that includes the South American species once regarded as a subgenus of Helianthus and later assigned to Helianthopsis. Two other groups considered as potential sister groups based on their geographic distribution in South America were not placed near Scalesia in the most parsimonious tree. Viguiera sect. Diplostichis appears to be relatively basal within subtribe Helianthinae, and the South American species of Viguiera, although previously classified in more than one subgenus, appear to form a single, monophyletic group that is not the sister group to Scalesia. The minimum of ten restriction site differences between Scalesia and Pappobolus of approximately 525 sites surveyed yielded an estimated sequence divergence of 0.19%, and an estimated time of divergence of approximately 1.9–6.2 million years.     

A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae) II. Derived lineages

Sequence data for internal transcribed spacer (ITS) and partial external transcribed spacer (ETS) regions were combined in a phylogenetic analysis with previously obtained plastid DNA restriction site data to provide a comprehensive molecular phylogenetic hypothesis for derived members of subtribe Helianthinae. Analyses of the two molecular datasets provided conflicting evidence on relationships among some groups, supporting the hypothesis that hybridization has played a significant role in the divergence of the subtribe. A revised generic‐level classification is presented that divides the approximately 350 species of the subtribe among 21 genera. The paraphyletic Viguiera is narrowed to embrace only the type species, V. dentata. Four newly described genera, Dendroviguiera, Gonzalezia, Heiseria and Sidneya, are composed of species formerly included in Viguiera. Aldama is expanded to include 118 species extending from southwestern North America and Mexico to South America. This requires 116 new combinations, including 58 that were recently transferred into Rhysolepis, which is a synonym of Aldama, based on molecular phylogenetic results. One species of Viguiera is transferred to Tithonia, and two combinations in Hymenostephium are validated. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 311–331.     

Phylogenetic analysis of Helianthus (Asteraceae) based on chloroplast DNA restriction site data

 Chloroplast DNA (cpDNA) restriction site data were used to analyze phylogenetic relationships within Helianthus. Data from new samples were consistent with previous results and showed the genus to be a well-defined (11 site changes) lineage within subtribe Helianthinae. The affinities of 2 species, Viguiera similis and V. phenax (V. ludens) that have sometimes been included in Helianthus were shown to lie outside the genus. The two species of Phoebanthus, however, formed a phylogenetic ingroup to the perennial Helianthus. Within the genus, cpDNA data indicated that there are four distinct phylogenetic lineages. Two of the lineages each contained a single, annual species (H. agrestis and H. porteri, respectively). The remaining annual species collectively formed a third lineage (sect. Helianthus). The fourth lineage contained all of the perennial species, including those of Phoebanthus. Within the perennial lineage, there was little variation in restriction site characters. The 3 species of series Pumili formed a paraphyletic group at the base of the perennial lineage, and the 3 species of series Ciliares formed a group that was supported by a single restriction site character. Received: 2 September 1996 / Accepted: 25 October 1996     

RESTRICTION FRAGMENT ANALYSIS OF CHLOROPLAST DNA AND THE SYSTEMATICS OF VIGUIERA AND RELATED GENERA (ASTERACEAE: HELIANTHEAE)

Phylogenetic relationships among 31 species representing variously Helianthus, Helianthopsis, Heliomeris, Simsia, Viguiera, and Tithonia were assessed by chloroplast DNA restriction site mapping. A total of 147 mutations including 92 informative ones was detected using 16 restriction enzymes, with an estimated sequence divergence within the group of 1.4%. Parsimony analysis produced a single most parsimonious tree with a length of 161 steps and a consistency index of 0.91. Statistically significant clades, as assessed by the bootstrap method, correspond to a number of taxa recognized previously, including Helianthus (3 species), Helianthopsis (5 species), and several groups within Viguiera, including sect. Maculatae (4 species), the Baja California group (6 species), sect. Paradosa (2 species) and V. dentata (3 samples). However, species of Viguiera collectively form a highly paraphyletic group relative to species of other genera. Helianthus and Helianthopsis were separated into different clades, supporting their recent segregation. Placement of H. porteri in Helianthus rather than Heliomeris was confirmed; the single sample of the latter genus was most similar to the Baja California group of Viguiera. An expected relationship between Simsia (2 species) and one member of Viguiera ser. Grammatoglossae was confirmed (although not with two other putatively related members of Viguiera) and an unexpected relationship between Simsia and Tithonia was suggested. The presence of Mexican taxa as the more basal groups in the tree points toward a possible Mexican origin for Viguiera and related genera. A molecular clock hypothesis is rejected in many pairwise comparisons involving woody taxa with herbaceous ones, although it could not be rejected in most pairwise comparisons involving taxa of similar habit.     

SYSTEMATIC IMPLICATIONS OF CHLOROPLAST DNA VARIATION IN THE SUBTRIBE MICROSERIDINAE (ASTERACEAE: LACTUCEAE)

Phylogenetic relationships among six of the seven currently recognized genera of the subtribe Microseridinae were examined using comparative restriction site mapping of the chloroplast genome. Complete cleavage maps of 17 enzymes were constructed for 35 of the 46 species in the subtribe and six representative outgroup species from four other subtribes of the Lactuceae. A total of 373 restriction site mutations was detected, 180 of which were phylogenetically informative. The chloroplast DNA mutations were used to generate phylogenetic trees using Dollo, Wagner, and weighted parsimony, and the resulting monophyletic groups were evaluated by the bootstrap method. The results indicate that the Microseridinae is paraphyletic because Stephanomeria is nested within the six core genera of the subtribe. Five of the genera of the Microseridinae are monophyletic, whereas Microseris is paraphyletic because one of its species, M. lindleyi, is more closely related to Agoseris and Nothocalais. The distant relationship of M. lindleyi to the rest of the species of Microseris is enigmatic, especially in view of its known involvement in the origin of two allotetraploid species, M. decipiens and M. heterocarpa. The taxonomic implications of these results lead to a revised classification of Microseris in which the genus Uropappus is revived to accommodate M. lindleyi, and a new genus, Stebbinsoseris, is described to include the allotetraploids. The cpDNA phylogeny is used to evaluate the patterns of character evolution within the Microseridinae, as well as to test previous hypotheses that differences in generation time result in unequal rates of chloroplast DNA evolution.     

Chloroplast DNA diversity in the genusRubus (Rosaceae) revealed by Southern hybridization

The variability in chloroplast DNA type of 20Rubus genotypes was examined by Southern hybridization. DNA extracted from theRubus accessions was digested with two restriction enzymes (EcoRI and EcoRV) and heterologous chloroplast DNA sequences from barley and pea were used as probes to detectRubus chloroplast DNA sequences on Southern blots ofRubus total DNA. Restriction fragment length polymorphism was detected and a total of 92 restriction fragments were generated by the probe/enzyme combinations examined. Cladistic principles based on the parsimony assumption were used to assemble a phylogenetic tree based on chloroplast restriction fragment length data. The phylogenetic tree grouped the taxonomically defined species and is in general agreement with information based on morphological criteria. However, the Japanese red raspberryR. illecebrosus was shown to have diverged considerably in terms of evolutionary time from other species in subg.Idaeobatus. Furthermore, the molecular approach provides a quantitative estimate of the relationship between species that is difficult to obtain from morphological data. In order to complement the chloroplast DNA information a ribosomal DNA probe was also included in the analysis and provided further information on the phylogenetic relationships withinRubus.     

Kauriphanes n. gen., a new genus of braconid parasitoid wasp (Hymenoptera: Braconidae: Doryctinae) from New Zealand

A new genus belonging to the braconid wasp subfamily Doryctinae, Kauriphanes n. gen. (type species K. khalaimi n. sp.), is described from New Zealand. This genus is placed within the doryctine subtribe Caenophanina. The extent of this subtribe is discussed and the phylogenetic relationships of three of its genera were investigated using one mitochondrial and one nuclear DNA sequence markers. Similar to previous studies, the Bayesian analyses performed significantly support a clade with the included members of Caenophanina as a sister group of a clade with the examined species of Spathiini sensu stricto. The placement of the Caenophanini within Doryctini, however, is left pendant to further exhaustive phylogenetic studies. A key to genera and subgenera belonging to Caenophanina is given.     

EVOLUTION OF POPULUS NIGRA (SECT. AIGEIROS):INTROGRESSIVE HYBRIDIZATION AND THE CHLOROPLAST CONTRIBUTION OF POPULUS ALBA (SECT. POPULUS)

Restriction site variation in chloroplast DNA and nuclear ribosomal DNA was examined in 16 accessions from the Salicaceae comprising ten species of Populus and one outgroup species of Salix. Forty-nine restriction site mutations in the chloroplast DNAs were used to generate one most parsimonious phylogenetic tree. This tree indicates that all varieties of P. nigra (black poplars of sect. Aigeiros) have a chloroplast genome, maternally inherited, derived from the clade including the white poplars (P. alba and segregate species of sect. Populus) and divergent from the American cottonwoods of their own section. Twenty-one restriction site mutations in the nuclear ribosomal DNAs generated a single most parsimonious phylogenetic tree that indicates that the nuclear genome ofP. nigra is distinct from both the white poplars and American cottonwoods. The incongruity of these independent molecular phylogenies provides evidence for an unusual origin of the black poplars. Populus alba or its immediate ancestor acted as the maternal parent in a hybridization event with the paternal lineage of P. nigra. Subsequent backcrosses to the paternal species gave rise to the extant P. nigra with a chloroplast genome of P. alba and the nuclear genome of the paternal species. These hybridization and introgression events must have pre-dated the divergence of the black poplar varieties. The biphyletic nature of the P. nigra genomes suggests that dependency on one class of molecular or morphological markers or the merging of the two kinds of data sets to derive accurate estimates of true phylogenies could be misleading in plants.     

PCR产物的RFLP分析在黄芪亚族（豆科）系统学研究中的应用初探

用聚合酶链式反应（ＰＣＲ）将豆科黄芪亚族７属９种及甘草亚族１属１种植物叶绿体基因组中ｎｄｈＦ和ｐｓｂＡ基因中一段约３．１ｋｂ的ＤＮＡ扩增出来,并摸索出一最佳的ＰＣＲ条件,使得此条带得以特异性扩增,可直接用于限制性内切酶水解。通过对此扩增片段的限制性片段长度多态性（ＲＦＬＰ）的初步分析,认为利用ＰＣＲ扩增出的ＤＮＡ进行ＲＦＬＰ分析来探讨植物的系统进化问题在中国现行条件下大有潜力,其方法简单易行,结果     

Chloroplast DNA restriction fragment length polymorphisms (RFLPs) in Musa species

Summary Taxonomic and phylogenetic determinations within the genus Musa are established using a numerical, morphology-based scoring system. However, within this system, the classification and relationships of some types are disputed. The application of chloroplast DNA (cpDNA) restriction fragment length polymorphism (RFLP) analysis to Musa taxonomy provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Whole-cell DNA was extracted from lyophilized Musa leaf-blade tissue and digested with various restriction enzymes, Southern blotted onto nylon membranes, and probed using radioactively labeled heterologous orchid cpDNA fragments. Phylogenies were inferred from cpDNA RFLP patterns using PAUP software. The relationships between most species examined were as expected; however, some species (M. beccarii and M. basjoo) did not conform to the conventional morphology-based phylogeny.     

THE TAXONOMIC SIGNIFICANCE OF ANTHOCHLORS IN THE SUBTRIBE COREOPSIDINAE (COMPOSITAE,HELIANTHEAE)

Anthochlors (chalcones and aurones) are found in a number of plant families including the Compositae. Within this family they were once thought to occur only in the subtribe Coreopsidinae of the tribe Heliantheae. More recent studies show them to occur also in the tribes Cardueae, Eupatorieae, Helineae, Inuleae, and Lactuceae. This has suggested that anthochlors are no longer good taxonomic markers for the Coreopsidinae. A survey of 69 of approximately 210 genera of the Heliantheae shows anthochlors present only in the Coreopsidinae except for Helianthus, Simsia, Tithonia, and Viguiera, closely related genera of the subtribe Helianthinae. Of the 32 genera of the Coreopsidinae recently recognized, 30 were surveyed from available material and all contain anthochlors except Guardiola and Venegasia. The results indicate that, despite some variation, anthochlors are still good taxonomic markers for the Coreopsidinae. This represents the only case within the family in which a particular type of flavonoid is taxonomically diagnostic at the subtribal level.     

Phylogenetic and genetic studies in Papaver section Oxytona: cytogenetics,isozyme analysis and chloroplast DNA variation

Summary Chromosome behaviour at meiosis, isozyme studies and analysis of the chloroplast DNA restriction fragments were used to assess the phylogenetic relations among the three Papaver species of the section Oxytona. The multivalents observed in diplotene — diakinesis stages of meiosis of the hexaploid P. pseudo-orientale and its tetraploid hybrid with P. bracteatum indicate the autopolyploid nature of this section. Further evidence supporting this conclusion was obtained from isozyme analysis. The same number of isozymes was expressed in all the species regardless of their ploidy level. Inheritance studies conducted with Pgi, Dia and Acp allozymes demonstrated, for the first time, the transfer and expression of genetic material among these species. The differences found in the chloroplast DNA restriction fragments of the Oxytona species and of P. somniferum indicate intensive evolution of the chloroplast DNA in the genus Papaver. The similarity of the chloroplast DNA restriction patterns and of the isozymes in P. orientale and P. pseudo-orientale suggested that P. orientale was the female parent in the cross generating P. pseudo-orientale and that the latter species is of recent origin.Contribution no. 2199 —E, 1987 series from the Agricultural Research Organization, The Volcani center, Bet Dagan 50 250, Israel     

A revised classification of subtribe Helianthinae (Asteraceae: Heliantheae). I. Basal lineages

Results for nuclear ITS sequences were combined with previously obtained data from cpDNA restriction site studies to provide a comprehensive molecular phylogeny for subtribe Helianthinae. Results from the two molecular data sets were mostly congruent for basally diverging branches of the subtribe. Based on the results, combined with morphological observations, the basally diverging branches are placed in six genera, including one newly described. Bahiopsis is resurrected to accommodate species previously placed in Viguiera subgenus Bahiopsis . Calanticaria is newly proposed for the five species of Viguiera ser. Brevifolieae . Heliomeris is retained for the group sometimes included within Viguiera as sect. Heliomeris . Hymenostephium is revived and enlarged to include a number of species of similar habit and involucre, including members of Viguiera sect. Diplostichis , Haploca-lymma and Garcilassa . Although cpDNA results place the morphologically distinctive Sclerocarpus within the clade including species of Hymenostephium , the ITS data were consistent with morphology in suggesting it to be a distinctive lineage.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 65–76.     

A Preliminary Study on the Use of RFLP Analysis of the PCR Amplified Products in the ystematic Investigation of the Subtribe Astragalinae (Fabaceae)

The analysis of variation at the molecular level has been proven extremely useful in the reconstruction of plant phylogenetic relationships. A DNA fragment of 3100-base pairs (bp) in the chloroplast genes ndhF and psbA has been amplified from 9 species of 7 genera in the subtribe Astragalinae and 1 species in the subtribe Glycyrrhizinae. A proper procedure for specifically PCR-amplifing the 3.1 kb fragment was presented. By this procedure, the PCR products could be digested directly after amplification. The restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified products indicated that it had potential systematic significances in the phylogenetic studies of the subtribe Astragalinae. This approach could also reduce time, expense and the amount of DNA required, and furthermore, obtain reliable results.     

Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): insights from plastid matK and nuclear ribosomal ITS sequences

We conducted phylogenetic analyses using two DNA sequence data sets derived from matK, the maturase-coding gene located in an intron of the plastid gene trnK, and the internal transcribed spacer region of 18S–26S nuclear ribosomal DNA to examine relationships in subtribe Aeridinae (Orchidaceae). Specifically, we investigated (1) phylogenetic relationships among genera in the subtribe, (2) the congruence between previous classifications of the subtribe and the phylogenetic relationships inferred from the molecular data, and (3) evolutionary trends of taxonomically important characters of the subtribe, such as pollinia, a spurred lip, and a column foot. In all, 75 species representing 62 genera in subtribe Aeridinae were examined. Our analyses provided the following insights: (1) monophyly of subtribe Aeridinae was tentatively supported in which 14 subclades reflecting phylogenetic relationships can be recognized, (2) results are inconsistent with previous classifications of the subtribe, and (3) repeated evolution of previously emphasized characters such as pollinia number and apertures, length of spur, and column foot was confirmed. It was found that the inconsistencies are mainly caused by homoplasy of these characters. At the genus level, Phalaenopsis, Cleisostoma, and Sarcochilus are shown to be non-monophyletic.     

First molecular phylogenetic insights into the evolution of Eriocaulon (Eriocaulaceae,Poales)

Eriocaulon is a genus of c. 470 aquatic and wetland species of the monocot plant family Eriocaulaceae. It is widely distributed in Africa, Asia and America, with centres of species richness in the tropics. Most species of Eriocaulon grow in wetlands although some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. In a previous molecular phylogenetic hypothesis, Eriocaulon was recovered as sister of the African endemic genus Mesanthemum. Several regional infrageneric classifications have been proposed for Eriocaulon. This study aims to critically assess the existing infrageneric classifications through phylogenetic reconstruction of infrageneric relationships, based on DNA sequence data of four chloroplast markers and one nuclear marker. There is little congruence between our molecular results and previous morphology-based infrageneric classifications. However, some similarities can be found, including Fyson’s sect. Leucantherae and Zhang’s sect. Apoda. Further phylogenetic studies, particularly focusing on less well sampled regions such as the Neotropics, will help provide a more global overview of the relationships in Eriocaulon and may enable suggesting the first global infrageneric classification.

     

The phylogeny of Lens (Leguminosae): new insight from ITS sequence analysis

 Lens includes L. culinaris subsp. culinaris (the cultivated lentil) and several wild species distributed from the Mediterranean region to western Asia. We compared sequence variation in the ITS region among species of Lens in an effort to end persisting uncertainty regarding the phylogeny of the genus. The parsimony analysis revealed a single minimum-length tree with a topology congruent with patterns derived by previous studies of nuclear and chloroplast DNA RFLPs. The basal and highly divergent status of the L. nigricans clade is depicted, and the progenitor-derivative relationship between L. culinaris subsp. orientalis and L. culinaris subsp. culinaris is reaffirmed. Resolution in the tree was improved by combining the ITS data set with a pre-existing set of chloroplast DNA restriction site data obtained from the same group of samples. Received May 8, 2000 Accepted October 26, 2001     

The Hawaiian Archipelago is a stepping stone for dispersal in the Pacific: an example from the plant genus Melicope (Rutaceae)

Aim Pacific biogeographical patterns in the widespread plant genus Melicope J.R. Forst. & G. Forst. (Rutaceae) were examined by generating phylogenetic hypotheses based on chloroplast and nuclear ribosomal sequence data. The aims of the study were to identify the number of colonization events of Melicope to the Hawaiian Islands and to reveal the relationship of Hawaiian Melicope to the Hawaiian endemic genus Platydesma H. Mann. The ultimate goal was to determine if the Hawaiian Islands served as a source area for the colonization of Polynesia. Location Nineteen accessions were sampled in this study, namely eight Melicope species from the Hawaiian Islands, four from the Marquesas Islands, one species each from Tahiti, Australia and Lord Howe Island, two Australian outgroups and two species of the Hawaiian endemic genus Platydesma. To place our results in a broader context, 19 sequences obtained from GenBank were included in an additional analysis, including samples from Australia, Papua New Guinea, New Zealand, Southeast Polynesia and Asia. Methods DNA sequences were generated across 19 accessions for one nuclear ribosomal and three chloroplast gene regions. Maximum parsimony analyses were conducted on separate and combined data sets, and a maximum likelihood analysis was conducted on the combined nuclear ribosomal and chloroplast data set. A broader nuclear ribosomal maximum parsimony analysis using sequences obtained from GenBank was also performed. Geographic areas were mapped onto the combined chloroplast and nuclear ribosomal tree, as well as onto the broader tree, using the parsimony criterion to determine the dispersal patterns. Results Phylogenetic analyses revealed that Platydesma is nested within Melicope and is sister to the Hawaiian members of Melicope. The Hawaiian Melicope + Platydesma lineage was a result of a single colonization event, probably from the Austral region. Finally, Marquesan Melicope descended from at least one, and possibly two, colonization events from the Hawaiian Islands. Main conclusions These data demonstrate a shifting paradigm of Pacific oceanic island biogeography, in which the patterns of long‐distance dispersal and colonization in the Pacific are more dynamic than previously thought, and suggest that the Hawaiian Islands may act as a stepping stone for dispersal throughout the Pacific.