Phylogeny and evolution of the Betulaceae as inferred from DNA sequences,morphology, and paleobotany

Phylogeny of the Betulaceae is assessed on the basis of rbcL, ITS, and morphological data. Based upon 26 rbcL sequences representing most “higher” hamamelid families, the Betulaceae are monophyletic, with Casuarinaceae as its sister group, regardless of whether the outgroup is Cunoniaceae, Cercidiphyllaceae, Hamamelidaceae, or Nothofagus. Within the Betulaceae, two sister clades are evident, corresponding to the subfamilies Betuloideae and Coryloideae. However, with only 13 phylogenetically informative sites, the rbcL sequences provide limited intra-subfamilial resolution. Internal transcribed spacer (ITS) sequences provided 96 phylogenetically informative sites from 491 aligned sites resulting in a single most parsimonious tree of 374 steps (consistency index = 0.791) with two major lineages corresponding to the two traditional subfamilies: Betuloideae (Alnus, Betula) and Coryloideae (Corylus, Ostryopsis, Carpinus, Ostrya). This arrangement is mostly consistent with those from rbcL and morphology and is greatly reinforced by analyses with the three data sets combined. In the Coryloideae, the Ostryopsis–Carpinus–Ostrya clade is well supported, with Corylus as its sister group. The sister-group relationship between Ostryopsis and the Carpinus–Ostrya clade is well supported by ITS, rbcL, and morphological data. Phylogenetic relationships among the extant genera deduced by these analyses are compatible with inferences from ecological evolution and the extensive fossil record.     

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.     

Harvesting Betulaceae sequences from GenBank to generate a new chronogram for the family

Betulaceae, with 120–150 species in six genera, are a family of Fagales that occurs mainly in the Northern Hemisphere. Previous studies of the evolution of Alnus, Betula, Carpinus, Corylus, Ostrya and Ostryopsis have relied on a relatively small number of sequence data and molecular clocks with fixed‐point calibrations. We exploited GenBank to construct Betulaceae matrices of up to 900 sequence accessions and 9300 nucleotides of nuclear and plastid DNA; we also computed species consensus sequences to build 46‐ and 29‐species matrices that strike a balance between species sampling and nucleotide sampling. Trees were rooted on Ticodendraceae and Casuarinaceae, and divergence times were inferred under relaxed and strict molecular clocks, using alternative fossil constraints. The data support the traditional two subfamilies, Betuloideae (Alnus, Betula) and Coryloideae, and show that Ostryopsis is sister to Ostrya/Carpinus. The fossil record and molecular clocks calibrated with alternating fossils indicate that the stem lineage of Betulaceae dates back to the Upper Cretaceous, the two subfamilies to the Palaeocene and the most recent common ancestors of each of the living genera to the mid‐ to late Miocene. A substitution rate shift in Coryloideae between 25 and 15 Mya preceded the mid‐Miocene climatic optimum and may be linked to temperate niches that became available following the mid‐Miocene. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 465–477.     

Phylogeny and biogeography of Sassafras (Lauraceae) disjunct between eastern Asia and eastern North America

Sassafras (Lauraceae) consists of three species disjunct between eastern Asia (S. tzumu and S. randaiense) and eastern North America (S. albidum). Phylogenetic analysis based on sequences of nuclear ribosomal ITS and three chloroplast non-coding regions (rpl16, trnL-F, and psbA-trnH) showed that Sassafras is monophyletic and that the eastern North American S. albidum is sister to the clade of its two eastern Asian counterparts. Their intercontinental divergence was estimated to be 13.80 ± 2.29−16.69 ± 2.52 million years ago (mya) using the penalized likelihood method with the ITS and three chloroplast markers. Biogeographic analyses combined with fossil evidence suggest that Sassafras has a relict distribution in the Northern Hemisphere without a Gondwanan link. The divergence time of the two eastern Asian species (the continental Chinese Sassafras tzumu and S. randaiense endemic to Taiwan) is estimated to be 0.61 ± 0.75−2.23 ± 0.76 mya. Sassafras randaiense from Taiwan was most likely derived from an ancestor from continental China.     

Sequences of low-copy nuclear gene support the monophyly of Ostrya and paraphyly of Carpinus (Betulaceae)

Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has remained controversial. In this study, sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera. Ostrya species form a robust clade, supporting the monophyly of the genus. The clade, however, is located between Carpinus cordata and the remaining species of Carpinus, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Carpinus. Within Carpinus, section Distegocarpus is polyphyletic, whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.     

低拷贝核基因序列支持桦木科铁木属为单系鹅耳枥属为并系

Coryloideae consists offour generaCorylus,Ostryopsis,Carpinus,and Ostrya.While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya,the monophyly of the two genera has remained controversial.In this study,sequences of the nuclear nitrate reductase(Nia)were used to test the naturalness of the two genera.Ostrya species form a robust clade,supporting the monophyly of the genus.The clade,however,is located between Carpinus cordata and the remaining species of Carpinus,indicating that Carpinus iS paraphyletic.and Ostrya has evolved from witllin Carpinus.Within Carpinus,section Distegocarpus is polyphyletic,whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.     

Historical biogeography and phylogenetic relationships of the genus Chamaecyparis (Cupressaceae) inferred from chloroplast DNA polymorphism

The genus Chamaecyparis comprises five species and one variety native to Taiwan, Japan, Canada, and USA, which demonstrates a classical eastern Asian, western North American, and eastern North American disjunct distributional pattern. The phylogenetic relationships of the species of Chamaecyparis were inferred by comparing 1130 bp of the combined data set of chloroplast trnV intron and petG-trnP intergenic spacer. The phylogenetic tree shows that Chamaecyparis nootkatensis (Cupressus nootkatensis or Xanthocyparis nootkatensis) is clearly diverged from other Chamaecyparis species. For Chamaecyparis species, C. thyoides is sister to C. formosensis and C. pisifera and these together form a monophyletic group. C. lawsoniana is sister to C. obtusa and C. taiwanensis; and these form another monophyletic group. Homogeneity in evolutionary rates was found among species in these two monophyletic groups. Results indicate the divergent evolution of C. taiwanensis and C. formosensis and molecular evidence in this investigation supports C. taiwanensis as a variety of C. obtusa. Utility of cpDNA intergenic spacer petG-trnP in Chamaecyparis is also discussed. Several biogeographical implications were inferred: (1) at least two divergence events have produced the eastern Asian, and both western and eastern North American disjunct distribution in Chamaecyparis; (2) intercontinental sister species pairs are found in Chamaecyparis; (3) cpDNA divergence between two intercontinental sister pairs of C. thyoides and C. pisifera, and C. lawsoniana and C. obtusa is 2.8% and 1.1%, which suggest an estimated divergence time of 14 and 5.5 million years ago during middle and late Miocene, respectively; (4) cpDNA divergence of two Asian Chamaecyparis groups between C. obtusa and C. taiwanensis, and between C. pisifera and C. formosensis is 0.25% and 0.57%, which suggest an estimated divergence time of 1.3 and 2.9 million years ago during Pleistocene and late Pliocene, respectively; these estimated divergence times suggest a relatively recent migration of Chamaecyparis to Taiwan from the Japanese Archipelago; (5) that climatic deterioration caused the disappearance of Chamaecyparis in continental Asia is probable.     

The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribeSonchinae (Asteraceae:Lactuceae)

The systematic utility of sequences from a non-coding region of chloroplast DNA (cpDNA) betweenpsbA andtrnH^(GUG) was examined by assessing phylogenetic relationships in subtribeSonchinae (Asteraceae:Lactuceae). Primers constructed against highly conserved regions of tRNA genes were used for PCR amplification and sequencing. ThepsbA-trnH intergenic spacer contains several insertions and deletions (indels) inSonchinae with the length varying from 385 to 450 bp. Sequence divergence ranges from 0.00% to 7.54% withinSonchinae, with an average of 2.4%. Average sequence divergence inSonchus subg.Sonchus is 2.0%, while the mean for subg.Dendrosonchus and its close relatives in Macaronesia (the woodySonchus alliance) is 1.0%. Our results suggest that this region does not evolve rapidly enough to resolve relationships among closely related genera or insular endemics in theAsteraceae. The phylogenetic utility ofpsbA-trnH sequences of the non-coding cpDNA was compared to sequences from the ITS region of nuclear ribosomal DNA. The results suggest that ITS sequences evolve nearly four times faster thanpsbA-trnH intergenic spacer sequences. Furthermore, the ITS sequences provide more variable and phylogenetically informative sites and generate more highly resolved trees with more strongly supported clades, and thus are more suitable for phylogenetic comparisons at lower taxonomic levels than thepsbA-trnH intergenic chloroplast sequences.     

Phylogenetics of Quiinaceae (Malpighiales): evidence from trnL-trnF sequence data and morphology

We present the first parsimony analyses of the Neotropical family Quiinaceae using nucleotide sequence data from the non-coding trnL intron and trnL-trnF intergenic spacer of the plastid genome, analysed separately as well as in combination with morphology. Both molecules and combined data recover Quiinaceae as a well-supported monophyletic group. Quiinaceae form a polytomy together with their potential sister groups, the monophyletic Ochnaceae s.str. and the monotypic Medusagynaceae from the Seychelles in the Indian Ocean. Froesia is resolved as sister to the rest of the family. Other members of the family, Lacunaria, Quiina, and Touroulia, are all recovered as monophyletic despite the inclusion of strikingly distinctive representatives (L. oppositifolia and Q. pteridophylla). Relationships among the last three genera, however, are yet uncertain. Optimising characters of breeding system onto the molecular phylogeny reveals that bisexual flowers (Froesia) are the ancestral state in Quiinaceae, whereas androdioecy (Quiina, Touroulia) and dioecy (Lacunaria) are derived breeding systems.     

Phylogenetic relationship of Clauseneae (Rutaceae) inferred from plastid and nuclear DNA data and taxonomic implication for some major taxa

Using sequences of the nuclear ribosomal ITS region as well as the chloroplast DNA trnL‐trnF and atpB‐rbcL regions, this study aims to provide further insight into the phylogenetic relationships within Clauseneae and its relationship to Citreae (Rutaceae). Using maximum likelihood (ML) and Bayesian inference (BI), we reconstructed the phylogeny of Clauseneae based on trnL‐F, atpB‐rbcL and ITS sequences. Our data matrix contained 91 accessions, representing 72 species and varieties from 31 genera and two outgroups, including new and extensive sampling of species and varieties representing four genera in the tribe Clauseneae. In the subfamily Aurantioideae, six major clades were resolved with strong support: 1) Micromelum clade: Micromelum; 2) Glycosmis clade: Glycosmis; 3) Bergera clade: Murraya sect. Bergera; 4) Clausena clade: Clausena; 5) Murraya clade: Murraya sect. Murraya + Merrillia; 6) Citreae clade: Citreae. Micromelum, Glycosmis, Clausena and Merrillia were confirmed as monophyletic. In contrast, Murraya s.l. was reconstructed as polyphyletic. Murraya sect. Bergera clustered with Clausena while Murraya sect. Murraya and Merrillia together formed a clade that is sister to the tribe Citreae. All members from Citreae were clustered into a natural group. The genus Micromelum was found to be primitive in this subfamily and more close to Glycosmis. Based on the phylogeny and morphological characters, we discuss the taxonomy of some members of Clauseneae and conclude that the current tribal and generic classification need further revision.     

基于5个基因片段的野胡麻属系统位置研究

对单种属野胡麻属(原隶属于广义玄参科)及其可能近缘类群广泛取样,选择合适外类群,通过对4个叶绿体基因联合数据(trnL-F、rps16、rbcL、rps2)、核基因ITS片段、叶绿体基因与核基因ITS片段联合数据,进行最大简约法和贝叶斯法分析,探讨野胡麻属在科级系统位置及其与近缘类群系统发育关系。结果表明,所有系统树都支持野胡麻属先和肉果草属构成姐妹群关系,叶绿体基因联合系统树支持率分别为97%[Bootstrap(BS)]和100%[Posterior probability(PP)];ITS系统树支持率分别为99%(BS)和100%(PP);叶绿体基因和ITS联合系统树支持率均为100%(BS和PP)。野胡麻属、肉果草属与通泉草属一起构成一单系群,叶绿体基因联合系统树、ITS系统树、叶绿体基因和ITS联合系统树的支持率均为100%(BS和PP)。形态学证据也支持野胡麻属、肉果草属和通泉草属这3个属的近缘关系。本研究结果支持单种属野胡麻属隶属于透骨草科的通泉草亚科,与肉果草属亲缘关系最近,这两个属进而与通泉草属近缘,可能隶属于通泉草属内,与岩白翠亲缘关系较近,也可能与通泉草属互为姐妹群关系。     

The position ofCastrilanthemum Vogt & Oberprieler and the phylogeny of Mediterranean Anthemideae (Compositae) as inferred from nrDNA ITS and cpDNAtrnL/trnF IGS sequence variation

Sequences of the nrDNA internal transcribed spacer (ITS) region and the cpDNAtrnL/trnF intergenic spacer (IGS) region were analysed for 41 Mediterranean and Eurasian representatives of the Anthemideae (Compositae) to ascertain the systematic position of the unispecific genusCastrilanthemum Vogt & Oberprieler and to study the phylogeny of the Anthemideae in the Mediterranean region. Both markers consistently point to the close relationship ofCastrilanthemum with the W Mediterranean generaLeucanthemopsis (Giroux) Heywood andProlongoa Boiss., forming a strongly supported monophyletic group (theLeucanthemopsis-group which also comprises the unispecific genusHymenostemma (Kunze) Willk.). Results also demonstrate that subtribes Achilleinae, Leucantheminae, and Matricariinae sensu Bremer & Humphries are non-monophyletic. Besides results from sequence variation, a marked 5bp-deletion intrnL/trnF IGS divides all these subtribes into more basal subgroups which are related to each other and to the large Eurasian generaTanacetum L. andAnthemis L., and a monophyletic group of closely related and more advanced subgroups which also contain the monophyletic Chrysantheminae sensu Bremer & Humphries. For this second group a W Mediterranean centre of diversification is suggested, however, its sister-group relationships within the basal grade of generic groups remain unclear.     

Phylogenetic analysis of Asian<Emphasis Type="Italic"> Symplocos</Emphasis> (Symplocaceae) based on nuclear and chloroplast DNA sequences

Thirty species and one variety of Symplocos (Symplocaceae), including all taxa distributed in Japan, were phylogenetically analyzed with DNA sequence data. The evolution of morphological characters is discussed on the basis of the phylogenetic relationships obtained. All species were Asian, except one, S. austromexicana, from Mexico. The nuclear ribosomal internal transcribed spacer (ITS) region and two intergenic spacer regions, between trnL and trnF, and between trnH and psbA of chloroplast DNA were used. The topologies of trees obtained from ITS and the chloroplast intergenic spacers are largely congruent. S. sonoharae, the representative of the subgenus Symplocos in Asia, was sister to all other species. The position of the American species, S. austromexicana, which also belongs to the subgenus Symplocos, was not well resolved. The phylogenetic tree based on combined sequence data largely supports the monophyletic origin of the infrageneric sections proposed earlier. However, the phylogenetic relationship between them is not well resolved, probably due to rapid diversification. The section Palura, a deciduous group, is well defined in the DNA analysis, suggesting its independent status in the genus Symplocos. In spite of their morphological divergence, the three endemic species of the Bonin Islands are monophyletic. The occurrence of curved seeds seems to be homoplastic, scattered over the phylogenetic tree without showing a particular infrageneric relationship.     

薯蓣属根状茎组基于3个cpDNA序列的分子系统研究

Seventeen species, one subspecies and one variety of Dioscorea sect. Stenophora Uline were investigated for their phylogenetic relationships based on a sequence analysis of chloroplast matK and rbcL genes and trnL-F intergenic spacer by maximum parsimony and maximum likelihood methods. The results showed that (a) sect. Stenophora was a strongly supported monophyletic group; (b) D. rockii, D. membranacea, D. banzhuana, and D. simulans formed a moderately supported monophyletic group, and D. prazeri was weakly supported to be sister to this group; (c) D. althaeoides and D. nipponica ssp. nipponica formed a moderately supported clade, and D. nipponica ssp. rosthornii was not a member of this clade; (d) D. zingiberensis and D. sinoparviflora showed a moderate to strong sister relationship; and (e) D. collettii var. hypoglauca and D. collettii var. collettii were sister to each other, but with only weak support.     

Phylogenetic relationships within Pappophoreae s.l. (Poaceae: Chloridoideae): Additional evidence based on ITS and trnL-F sequence data

Historically, Pappophoreae included the genera Cottea, Enneapogon, Kaokochloa, Pappophorum and Schmidtia. Some authors consider this tribe as a well-supported monophyletic group; while other evidences reveals Pappophoreae as polyphyletic, with Pappophorum separated from the rest of the tribe. When the latter happens, it can form a clade with Tridens flavus. Molecular phylogenetic analyses of the subfamily Chloridoideae have included few species of Pappophoreae; therefore, further research involving more representatives of this tribe is needed. With the aim of providing new evidence to help clarify the phylogenetic position of Pappophorum and its relationships with other genera of the tribe and the subfamily Chloridoideae, eight new sequences of ITS and trnL-F regions of Pappophoreae species were generated. These sequences were analyzed together with other available sequence data obtained from GenBank, using maximum parsimony and Bayesian inference, for individual (trnL-F or ITS) or combined trnL-F/ITS data sets. All analyses reveal that Pappophoreae is polyphyletic, with Pappophorum separated from the rest of the tribe forming a well-supported clade sister to Tridens flavus.     

Pollination by fungus gnats (Diptera: Mycetophilidae) and self-recognition sites in Tolmiea menziesii (Saxifragaceae)

Coleeae (Bignoniaceae) are a tribe almost entirely restricted to Madagascar. Coleeae have previously been placed in neotropical Crescentieae due to species with indehiscent fruits, a character otherwise unusual in Bignoniaceae. A phylogeny based on three chloroplast regions (ndhF, trnT-L spacer, trnL-F spacer) identifies a monophyletic Coleeae that is endemic to Madagascar and surrounding islands of the Indian Ocean (Seychelles, Comores and Mascarenes). African Kigelia is not a member of Coleeae, rather it is more closely related to a subset of African and Southeast Asian species of Tecomeae. The molecular phylogeny indicates that indehiscent fruit have arisen repeatedly in Bignoniaceae: in Coleeae, Kigelia and Crescentieae. The characteristic fleshy fruits of species of Coleeae likely arose autochthonously in Madagascar. Within Coleeae Colea and Ophiocolea are sisters, Phyllarthron is sister to Colea + Ophiocolea, and Rhodocolea is sister to the rest of the tribe.     

Molecular markers in Viola L. subsect. Viola: Application and taxonomic implications for the identification of dubious herbarium specimens

Abstract

The authors report the use of nuclear [internal transcribed spacer (ITS) sequences 1 and 2] and chloroplast DNA (trnS-trnG intergenic spacer sequences) in Viola subsect. Viola for separate tracking of maternal lineages and detecting dubious herbarium specimens. A phylogenetic investigation carried out on ITS data after removal of all material with possible hybrid origin showed that V. hirta is a monophyletic unit, whereas V. odorata includes at least V. collina and V. jaubertiana, as well as three sequences of V. alba subsp. dehnhardtii from literature. In some, among the sampled individuals, the morphological attribution to one species is contradicted by nuclear DNA, which indicated a wide distance from other non-specific individuals from different locations and closer proximity to a different species. Chloroplast DNA data for the same individuals, on the contrary concurred with morphological evidence. These findings confirm document univocal correlation between our chosen chloroplast sequences and the studied taxa at species or subspecies level; these sequences have the appropriate variability range to be employed for detection of the maternal lineage of unknown Viola samples.     

Phylogenetic Framework for Trema (Celtidaceae)

We used ITS and trnL sequence data, analyzed separately and combined by MP, to explore species relationships and concepts in Trema (Celtidaceae), a pantropical genus of pioneer trees. Whether Trema is monophyletic or includes Parasponia is still unresolved. Three clades within Trema received moderate to high support, one from the New World and two from the Old World, but their relationships were not resolved. In the New World, specimens of T. micrantha formed two groups consistent with endocarp morphology. Group I, with smaller brown endocarps, is a highly supported clade sister to T. lamarckiana. Group II, with larger black endocarps, is poorly resolved with several subclades, including the highly supported T. integerrima clade. Both Old World clades contain Asian and African species, with three or more species in each region. Trema orientalis is not monophyletic: specimens from Africa formed a highly supported clade sister to T. africana, while those from Asia were sister to T. aspera from Australia.     

The architecture of the chloroplast psbA-trnH non-coding region in angiosperms

The psbA-trnH intergenic region is among the most variable regions in the angiosperm chloroplast genome. It is a popular tool for plant population genetics and species level phylogenetics and has been proposed as suitable for DNA barcoding studies. This region contains two parts differing in their evolutionary conservation: 1) the psbA 3′UTR (untranslated region) and 2) the psbA-trnH intergenic non-transcribed spacer. We compared the sequence and RNA secondary structure of the psbA 3′ UTR across angiosperms and found consensus motifs corresponding to the stem portions of the RNA stem-loop structures and a consensus TTAGTGTATA box. The psbA-trnH spacer exhibited patterns that can be explained by the independent evolution of large inversions in the psbA 3′UTR and mutational hot spots in the remaining portion of the psbA-trnH spacer. We conclude that a comparison of chloroplast UTRs across angiosperms offer clues to the identity of putative regulatory elements and information about selective constraints imposed on the chloroplast non-coding regions.     

Phylogenetic relationships of Italian Bellevalia species (Asparagaceae), inferred from morphology,karyology and molecular systematics

The seven Bellevalia species and subspecies known from Italy, representing about 10% of the genus and three out of six sections, were studied. An integrated morphological, karyological and molecular approach was used to infer phylogenetic and systematic relationships among them. B. romana (the generitype) is the most distinctive species on karyotype asymmetry grounds. B. boissieri and B.dubia, usually considered as subspecies of one species (the latter endemic to Sicily), deserve specific status based on biparental nrDNA markers (internal transcribed spacer, ITS), since they do not form a single clade. The allotetraploid endemic B. pelagica, morphologically similar to B. romana, is sister to the latter under parsimony, both in morphological and ITS trees; it is also related with B. dubia, based on karyotype asymmetry and a uniparental cpDNA marker (trnL^(UAA)–trnF^(GAA) IGS (intergenic spacer)). A second allotetraploid endemic, B. webbiana, is closely related, on morphological, karyological and molecular grounds, with B. boissieri and B. ciliata, and also with B. trifoliata, three species that might all involved in its origin. B. sect. Conicae Feinbr. and sect. Nutantes Feinbr. are here typified, the former (type: B. ciliata) is most likely a synonym of the latter (type: B. trifoliata).