Revisiting the phylogeny of Dipsacales: New insights from phylogenomic analyses of complete plastomic sequences

Phylogenetic relationships in Dipsacales have long been a major challenge. Although considerable progress has been made during the past two decades, questions remain; the uncertain systematic positions of Heptacodium, Triplostegia, and Zabelia, in particular, impede our understanding of Dipsacales evolution. Here we use 75 complete plastomic sequences to reconstruct the phylogeny of Dipsacales, of which 28 were newly generated. Two primary clades were recovered that form the phylogenetic backbone of Dipsacales. Seven of the primary clades correspond to the recognized families Adoxaceae, Caprifoliaceae s. str., Diervillaceae, Dipsacaceae, Linnaeaceae, Morinaceae, and Valerianaceae, and one corresponds to Zabelia, which was found to be the closest relative of Morinaceae in all analyses. Additionally, our results, with greatly increased confidence in most branches, show that Heptacodium and Triplostegia are members of Caprifoliaceae s. str. and Dipsacaceae, respectively. The results of our study indicate that the complete plastomic sequences provide a fully‐resolved and well‐supported representation of the phylogenetic relationships within Dipsacales.     

Phylogenetic relationships of the disputed genus Triplostegia based on trnL-F sequences

The phylogenetie relationships of Triplostegia Wall. ex DC., comprising two species of perennial herbs from southeastern Asia, have long been in dispute. This genus was placed in either Dipsacaceae or Valerianaceae or in a family of its own, Triplostegiaceae. In this paper, the chloroplast DNA (cpDNA) trn L-F regions of 21 species in the Dipsacales s. l. (including Valerianaceae, Dipsacaceae, Triplostegia, Morina, Caprifoliaceae s. l. and Adoxaceae) and an outgroup Panax schin-seng Nees. were amplified and sequenced. The phylogenetic relationships among these 22 species were constructed based on trn L-F sequences. The results demonstrated that Valerianaceae, Dipsacaceae, Triplostegia, Morina and four genera from the Caprifoliaceae s. l. form a monophyletic group with a strong support (100% bootstrap). Triplostegia, a sister group to Dipsacaceae, is close enough to be placed in the Dipsacaceae as a subfamily. The traditional Caprifoliaceae s.l. are polyphyletic, and relationships of Morina among the groups within Dipsacales s. l. are uncertain. Key words Triplostegia; Caprifoliaceae s. l.; Morina; Dipsacales s. l.; trnL-F sequences; Sys-tematic position     

从叶绿体DNA trnL-F序列论双参属的归属问题

双参属Triplostegia Wall．ex DC．由分布于东南亚地区的2个种组成,为多年生草本植物。它的归属一直存在争议,有时置于川续断科Dipsacaceae或败酱科Valerianaceae,有时单立一科,即双参科Triplostegiaceae。本研究对广义川续断目Dipsacales s．l．的21种植物(分别来自于败酱科、川续断科、双参属、刺参属Morina、广义忍冬科Caprifoliaceae s. l．、五福花科 Adoxaceae)和外类群人参Panax schin-seng Nees．的叶绿体 DNA trnL-F区进行了测序,并建立系统发育树状图。结果显示,败酱科、川续断科、双参属、刺参属和广义忍冬科的4个属(双盾木属Dipelta、虫胃实属Kolkwitzia、六道木属Abelia和北极花属Linnaea)形成 了一个单系群并得到了很强的支持(100％ bootstrap);双参属与川续断科有更近的关系,建议作为一个亚科置于川续断科;广义忍冬科为一多系类群;而刺参属与其他广义川续断目类群之间的关系尚不能确定。     

Pollen Morphology of Caprifoliaceae from China and Its Taxonomic Signi-ficance

The pollen morphology of 54 samples representing 12 genera and 31 species was investigated with the aid of scanning electron microscope. Observed were pollen grains of Sambucus, Viburnum, Lonicera, Leycesteria, Heptacodium, Linnaea, Abelia, Dipelta, Kolkwitzia, Symphoricarpos, Triosteum, Weigela. Based on the shape, size, position and number of aperture, exine sculpture, three types are recognized: 1. Pollen grains subprolate, less frequently prolate, rather small, 3-colporate, exine reticulate, as in Sambucus, Viburnum. 2. Mostly spheroidal, subolate, bigger than the former, also 3-colporate, exine spinulose as in Lonicera, Leycesteria, Heptacodium, Triosteum, Linnaea, Abelia, Dipelta, Kolkwitzia, Symphoriocarpos, Weigela. 3. Spheriodal, more or less flattend, exine scabrous as in Abelia section Zabelia and Lonicera section Isoxylosteum. 1. The systematic position of Caprifoliaceae: It has been generally treated as a member of the order Rubiales together with Rubiaceae, Valeriaceae and Dipsacaceae on floral characters. In respect to serological character, it has a close relationship with Cornaceae, and was placed in Araliales. The above stated 2nd and 3rd types of pollen grains are similar to those of Patrinia (Valerianaceae), Scabiosa (Adoxaceae), Cornus (Cornaceae), and the pollen grains of the 1st type are similar to those of Styraceae, Genetianaceae and Araliaceae. Taking the information so far available into consideration, the authors agree to the Cronquists treatment retaining Caprifoliaceae in the order Dipsacales together with Adoxaceae, Valerianaceae and Dipsacaceae. 2. The division of tribes: Formerly Sambuceae included the genera Sambucus and Viburnum. Fritsch (1891) segregated Viburnum from Sambuceae and suggested a new tribe Viburneae including Triosteum. There is distinct difference in palynological features between these two genera. The exine sculpture of Viburnum is reticulate, but that of Triosteum is spinulose. It is reasonable to separate another new tribe, Triosteae, from Viburneae. 3. The pollen morphorlogy of several Chinese endemic genera, such as Heptacodium, Dipelta, Kolkwitzia resembles that of Lonicera, Leycesteria, Linnaea, Symphoricarpos, Abelia, Triosteum. This evidence supports the foregoing treatment including them in Caprifoliaceae. 4. Two different exine sculptures are shown in sections of the genera Abelia and Lonicera. In Abelia the exine of the section Euabelia is spinulose, but that of the section Zabelia is scabrous. Likewise, in Lonicera, the exine of the section Isoxylosteum is scabrous, while that of other sections such as Nintooa, Isika, Lonicera, subgenus Caprifolium, is spinulose. It shows that pollen morphology is one of diagnostic characters for section division.     

川续断目的花粉演化

以APGⅢ定义的川续断目(Dipsacales)忍冬科(Caprifoliaceae)和五福花科(Adoxaceae)为研究对象,基于已有的川续断目分子系统树和花粉形态数据,分析了忍冬科25属和五福花科5属的花粉形态多样性,采用简约法(Fitch Parsimony)推测花粉祖征和演化式样,寻找共衍征和分类性状.选择花粉萌发孔数目、萌发孔类型、花粉形状、大小和外壁纹饰五个关键性状推断了其演化式样.研究表明:三孔沟、近球形、较小花粉、网状纹饰是川续断目花粉祖征.长球型、中等和较大花粉,以及刺状纹饰是忍冬科的共衍征,支持忍冬科和科下分支为单系群.忍冬科花粉刺状纹饰和五福花科花粉网状纹饰明显将两个科区分开来.通过追溯性状演化分析,支持将七子花属(Heptacodium)置于忍冬族(Caprifolieae),以及Zabelia置于刺续断科的观点.     

Dating the Dipsacales: comparing models, genes, and evolutionary implications

Dipsacales is an asterid angiosperm clade of ca. 1100 species, with most of its lineages occupying temperate regions of the Northern Hemisphere. A recent phylogenetic analysis based on 7593 nucleotides of chloroplast DNA recovered a well-resolved and strongly supported phylogenetic hypothesis, which we use here to estimate divergence times within the group. A molecular clock is strongly rejected, regardless of data partition. We used recently proposed methods that relax the assumption of rate constancy among lineages (local clocks, nonparametric rate smoothing, penalized likelihood, and Bayesian relaxed clock) to estimate the ages of major lineages. Age estimates for Dipsacales varied widely among markers and codon positions, and depended on the fossils used for calibration and method of analysis. Some methods yielded dates for the Dipsacales diversification that appear to be too old (prior to the presumed 125 my [million years] age of eudicots), and others suggested ages that are too young based on well-documented Dipsacales fossils. Concordant penalized likelihood and Bayesian studies imply that Dipsacales originated in the Cretaceous, as did its two major lineages, Adoxaceae and Caprifoliaceae. However, diversification of crown Adoxaceae and Caprifoliaceae mainly occurred in the Tertiary, with the origin of major lineages within these clades mainly occurring during the Eocene. Another round of diversification appears to have occurred in the Miocene. Several radiations, such as Valerianaceae in South America and Dipsacaceae around the Mediterranean, are even more recent. This study demonstrates the wide range of divergence times that can be obtained using different methods and data sets, and cautions against reliance on age estimates based on only a single gene or methodology. Despite this variance, significant conclusions can be made about the timing of Dipsacales evolution.     

Preliminary phylogeny of Valerianaceae (Dipsacales) inferred from nuclear and chloroplast DNA sequence data

Valerianaceae is a relatively small (ca. 350 species), but morphologically diverse angiosperm clade. Sequence data from the entire ndhF gene, the trnL-F intergenic spacer region, the trnL intron, the matK region, the rbcL-atpB intergenic spacer region and internal transcribed spacer (ITS) region of nuclear ribosomal DNA were collected for 21 taxa within Dipsacaceae and Valerianaceae (1 and 20, respectively). These data were included in several phylogenetic analyses with previously published sequences from Dipsacales. Results from these analyses (maximum parsimony, maximum likelihood, and Bayesian analysis) are in strong agreement with many of the conclusions from previous studies, most importantly: (1) Valerianaceae is sister to Dipsacaceae; (2) Triplostegia is more closely related to species of Dipsacaceae than to Valerianaceae; and (3) Valeriana appears not to be monophyletic, with Valeriana celtica falling outside the remainder of the species of Valeriana sampled here (with very strong support). With the exception of V. celtica, these data support two major clades within Valeriana; one that is exclusively New World and another that is distributed in both the Old and New World. Although the species of Valerianaceae and its sister group Dipsacaceae plus Triplostegia, are widely distributed in the Northern Hemisphere, and the data imply that Valerianaceae diversified initially in Asia (the Himalayan Patrinia and Nardostachys falling at the base of the clade), the center of modern species diversity for the group is in the Andes of South America with as many as 175 species restricted to that region. Although the exclusively South American taxa form a clade in the chloroplast and combined ITS and chloroplast analyses, support values tend to be low. Future studies will need to include additional data, in the form of both characters and taxa, before any strong conclusions about the character evolution, diversification, and biogeography of the South American valerians can be made.     

Molecular Phylogeny and Species Speciation of Adoxaceae. s. s

It remains unclear about the speciation and phylogeny of Adoxaceae s. s ., a small family with 3 genera and 4 species . In this paper , ITS ( nuclear DNA internal transcribed spacer) regions of Adoxa orientalis and Sambucus adnata were firstly sequenced . Phylogenetic trees were constructed for all species of Adoxaceae (four species ) , Sambucus, Viburnum and four genera of Caprifoliaceae . The divergences among four species of this family were further calculated based on the calibration of the fossil records of the Caprifoliaceae and the general evolutionary rate of herbs for ITS . The phylogenetic analyses did not support the previous assumptions on the phylogeny and species divergence of Adoxaceae s. s . based on the morphological evidence : Tetradoxa is not the firstly diverged and it clustered with two species of Adoxa as a monophylogenetic group , paralleling to the other lineage comprising of monotypic Sinadoxa . The allopatric speciation at the diploid level might have contributed to the differentiation among Sinadoxa corydalifolia, Tetradoxa omeiensis and Adoxa moschatellina and the polyploidy to the origin of A. orientalis . The crude timing based on ITS sequence differentiation suggested a recent divergence among all four species probably between the late Miocene and the Tertiary and this speciation process might be closely correlated with habitat fragmentation and change due to the extensive uplifts of the Qinghai-Tibetan Plateau and climatic oscillation during the glacial and interglacial ages occurred at this stage .     

狭义五福花科的分子系统学和物种分化

狭义五福花科(Adoxaceae.s.s)仅含3属4种,但该科的物种分化、系统发育和分类一直存在争议。本文通过测定东方五福花和血满草的ITS(核糖体DNA内转录间隔区)序列,构建了包括狭义五福花科(4种)、广义忍冬科接骨木属、荚属以及其余4属植物在内的系统发育树。研究结果不支持狭义五福花科内根据形态学证据做出的系统发育假设四福花不是该科中最早分化出来的种;该物种与五福花属的两个物种形成一个单系群,与另一分支华福花属相对应。该科中3个物种,四福花、五福花和华福花之间的分化主要是在二倍体水平上的异域分化,而东方五福花则是通过多倍化形成的。粗略的时间估算表明这些物种之间的分化较晚,可能在第三纪末至第四纪早中期,与青池高原近期强烈隆升以及冰期气候反复变化形成的环境变迁密切相关。     

A search for the phylogenetic position of the seven-son flower (Heptacodium, Dipsacales): Combining molecular and morphological evidence

A first report on the problematic phylogenetic position ofHeptacodium (2 spp.; China) using molecular data from chloroplast DNA is presented. Amplification of ORF2280 homolog region was executed in a number of representative taxa in order to determine ifHeptacodium shows similar structural rearrangements as other Dipsacales. DNA sequences ofndhF were generated to clarify the phylogenetic position ofHeptacodium among Caprifoliaceae (s.l.). Six outgroup taxa and fifteen representatives of Dipsacales were sampled and more than 2100 basepairs ofndhF sequence were used in a cladistic analysis. Parsimony analysis produced two shortest trees and showedHeptacodium as sister to all members of Caprifoliaceae (s.str.), although weakly supported. Additionally, trees were constructed withndhF data supplemented with availablerbcL sequences and a morphological data set. Results of all analyses support an unresolved basal position forHeptacodium among Caprifoliaceae (s.l.), which in part explains the difficulty experienced previously in classifying the genus.     

Occurrence of plastids in the sperm cells of Caprifoliaceae: biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance

It is widely held that organelles inherit from the maternal lineage. However, the plastid genome in quite a few angiosperms appears to be biparentally transmitted. It is unclear how and why biparental inheritance of the genome became activated. Here, we detected widespread occurrence of plastids in the sperm cells (a cellular prerequisite for biparental inheritance) of traditional Caprifoliaceae. Of the 12 genera sampled, the sperm cells of Abelia, Dipelta, Heptacodium, Kolkwitzia, Leycesteria, Linnaea, Lonicera, Symphoricarpos, Triosteum and Weigela possessed inheritable plastids. The other genera, Sambucus and Viburnum, lacked plastids in sperm cells. Interestingly, such exclusion of plastids in the sperm cells of some Caprifoliaceae appeared to be associated with the divergence of Dipsacales phylogeny. Closer examination of Weigela florida revealed that both plastids and plastid DNA were highly duplicated in the generative cells. This implies that the appearance of plastids in sperm cells involved cellular mechanisms. Because such mechanisms must enhance the strength of plastid transmission through the paternal lineage and appear ubiquitous in species exhibiting biparental or potential biparental plastid inheritance, we presume that biparental plastid genetics may be a derived trait in angiosperms. This is consistent with our extended phylogenetic analysis using species with recently discovered modes of potential plastid inheritance. The results show that basal and early angiosperms have maternal plastid transmission, whereas all potential biparental transmission occurs at terminal branches of the tree. Thus, unlike previous studies, we suggest that biparental plastid inheritance in angiosperms was unilaterally converted from the maternal transmission mode during late angiosperm evolution.     

Molecular phylogeny of selected Old World Astragalus (Fabaceae): incongruence among chloroplast trnL-F, ndhF and nuclear ribosomal DNA ITS sequences

This study reports maximum parsimony and Bayesian phylogenetic analyses of selected Old World Astragalus using two chloroplast fragments including trnL-F and ndhF and the nuclear ribosomal internal transcribed spacer (nrDNA ITS). A total of 52 taxa including 34 euploid Old World and New World Astragalus , one aneuploid species from the Neo-Astragalus clade as a representative and 14 other Astragalean taxa, plus Cheseneya astragalina and two species of Caragana as outgroups were analyzed for both trnL-F and nrDNA ITS regions. ndhF was analyzed in 30 taxa and the same number for the combination of these three datasets were examined. In general, the trnL-F dataset and the ndhF and nrDNA ITS datasets generated more or less the same clades within Astragalus . However, in the trnL-F and ndhF phylogenies, Astragalus species are not gathered in a single clade, the so-called Astragalus s.s., as indicated by the nrDNA ITS tree. Visual inspection of these three phylogenies revealed that they were inconsistent regarding the position and relationships of Astragalus hemsleyi , A. ophiocarpus , A. annularis–A. epiglottis / Astragalus pelecinus, A. echinatus and A. arizonicus . Incongruence length difference test suggested that the trnL-F , ndhF and nrDNA ITS datasets were incongruent. In spite of this, phylogenetic analyses of the combined datasets as one unit or as three partitions generated trees that were topologically similar as a mix of the cpDNA and the nrDNA ITS trees. However, the combined dataset provided more resolved and statistically supported clades. The recently described A. memoriosus appeared closely related to A. stocksii (both from sect. Caraganella ) based on both trnL-F and nrDNA ITS sequences.     

The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences

A phylogenetic study of Asteridae sensu lato was conducted based on chloroplast ndhF gene sequences for 116 ingroup and 13 outgroup species. Prior molecular studies based on rbcL sequences identified terminal groups corresponding to families, but were unable to resolve relationships among them. These results are largely consistent with earlier rbcL studies, but provide much greater resolution and stronger bootstrap support throughout the tree. The parsimony analysis found eight equally parsimonious trees, all of which recognize four major clades with the following relationship: (Cornales (Ericales (Euasterids I, Euasterids II))). Euasterids I includes (Garryales ((Solanales, Boraginaceae) (Gentianales, Lamiales))), although with weak support for relationships among the named clades. Euasterids II includes (Aquifoliales (Asterales (Apiales, Dipsacales))) with strong support for these relationships. Relationships within Ericales are weakly supported and merit further attention.     

Higher level phylogeny and evolutionary trends in Campanulaceae subfam. Lobelioideae: molecular signal overshadows morphology

Relationships within the subfamily Lobelioideae in Campanulaceae are inferred from DNA sequence variation in the rbcL and ndhF genes, and the trnL-F region including the trnL intron and the trnL-F intergenic spacer. Results derived from Bayesian and parsimony analyses provide evidence for the long-suspected paraphyly of the genus Lobelia, comprising over 400 species as presently circumscribed. The perennial dwarf herbs belonging to the Andean genus Lysipomia are sister to a group comprising the Neotropical shrubs Burmeistera, Centropogon, and Siphocampylus. Giant lobelioids from the Hawaiian Islands, Brazil, Africa, and Sri Lanka form a strongly supported group. Character optimizations on the phylogenetic tree reveal that shifts in fruit types and lignification have occurred much more commonly than generally assumed. The main clades in the subfamily are outlined, which largely contradict previous classifications based on morphology.     

Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes

Phylogenetic interrelationships in the enlarged order Ericales were investigated by jackknife analysis of a combination of DNA sequences from the plastid genes rbcL, ndhF, atpB, and the mitochondrial genes atp1 and matR. Several well-supported groups were identified, but neither a combination of all gene sequences nor any one alone fully resolved the relationships between all major clades in Ericales. All investigated families except Theaceae were found to be monophyletic. Four families, Marcgraviaceae, Balsaminaceae, Pellicieraceae, and Tetrameristaceae form a monophyletic group that is the sister of the remaining families. On the next higher level, Fouquieriaceae and Polemoniaceae form a clade that is sister to the majority of families that form a group with eight supported clades between which the interrelationships are unresolved: Theaceae-Ternstroemioideae with Ficalhoa, Sladenia, and Pentaphylacaceae; Theaceae-Theoideae; Ebenaceae and Lissocarpaceae; Symplocaceae; Maesaceae, Theophrastaceae, Primulaceae, and Myrsinaceae; Styracaceae and Diapensiaceae; Lecythidaceae and Sapotaceae; Actinidiaceae, Roridulaceae, Sarraceniaceae, Clethraceae, Cyrillaceae, and Ericaceae.     

A supermatrix approach provides a comprehensive genus-level phylogeny for Gentianales

Gentianales consist of Apocynaceae, Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae, of which the majority are woody plants in tropical and subtropical areas. Despite extensive efforts in reconstructing the phylogeny of Gentianales based on molecular data, some interfamily and intrafamily relationships remain uncertain. We reconstructed the genus-level phylogeny of Gentianales based on the supermatrix of eight plastid markers (rbcL, matK, atpB, ndhF, rpl16, rps16, thetrnL-trnF region, and atpB-rbcL spacer) and one mitochondrial gene (matR) using maximum likelihood. The major clades and their relationships retrieved in the present study concur with those of previous studies. All of the five families of Gentianales are monophyletic with strong support. We resolved Rubiaceae as sister to the remaining families in Gentianales and showed support for the sister relationship between Loganiaceae and Apocynaceae. Our results provide new insights into relationships among intrafamilial clades. For example, within Rubiaceae we found that Craterispermeae were sister to Morindeae + (Palicoureeae + Psychotrieae) and that Theligoneae were sister to Putorieae. Within Gentianaceae, our phylogeny revealed that Gentianeae were sister to Helieae and Potalieae, and subtribe Lisianthiinae were sister to Potaliinae and Faroinae. Within Loganiaceae, we found Neuburgia as sister to Spigelieae. Within Apocynaceae, our results supported Amsonieae as sister to Melodineae, and Hunterieae as sister to a clade comprising Plumerieae + (Carisseae + APSA). We also confirmed the monophyly of Perplocoideae and the relationships among Baisseeae + (Secamonoideae + Asclepiadoideae).     

Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences

Phylogenetic relationships within Malvaceae s.l., a clade that includes the traditional families Bombacaceae, Malvaceae s.str., Sterculiaceae, and Tiliaceae, have become greatly clarified thanks to recent molecular systematic research. In this paper, we use DNA sequences of four plastid regions (atpB, matK, ndhF, and rbcL) to study relationships within Malvadendrina, one of the two major clades of Malvaceae s.l. The four data sets were generally in agreement, but five terminal taxa manifested highly unexpected affinities in the rbcL partition, and the non-coding sequences of the trnK intron were found to provide limited phylogenetic information for resolving relationships at the base of Malvadendrina. The remaining data strongly support the existence of six major clades within Malvadendrina: Brownlowioideae, Dombeyoideae, Helicteroideae, Malvatheca (comprising Bombacoideae and Malvoideae), Sterculioideae, and Tilioideae. These data also resolve the placement of two problematic taxa: Nesogordonia (in Dombeyoideae) and Mortoniodendron (in Tilioideae). The relationships among the six clades are not definitively resolved, but the best-supported topology has Dombeyoideae as sister to the remainder of Malvadendrina (posterior probability PP=80%) and Sterculioideae as sister to Malvatheca (PP=86%). This early branching position of Dombeyoideae is supported by similarities in floral characters between members of that clade and outgroup taxa in Byttnerioideae. Similarly, the sister-group relationship of Sterculioideae and Malvatheca receives support from androecial characteristics, like subsessile or sessile anthers and an absence of staminodes, shared by these two clades.