Search

A molecular phylogenetic investigation was undertaken for 30 species belonging to 15 genera of the palm family Arecaceae in Bangladesh to infer evolutionary relationships and molecular dating utilizing plastid-based matK and rbcL genes through multifacetedalgorithm driven approaches with Neighbor-Joining, Maximum-Likelihood, and Bayesian Inference methods. The study revealed that matK has better species discrimination efficiency than rbcL gene due to its highly variable nature. Transition/transversion bias test corroborated this finding as matK showed higher bias (2.632) than rbcL (2.235). Nucleotide substitution patterns were visualized via HYPERMUT program, which unveiled higher variability in matK and lower variability in rbcL alignment. Phylogenetic trees constructed with matK revealed monophyletic nature of origin for all the three subfamilies, viz. Arecoideae, Coryphoideae and Calamoideae, while rbcL trees exhibited polyphyly for Coryphoideae and monophyly for Arecoideae and Calamoideae. All the nine tribes belonging to three subfamilies demonstrated monophyletic nature in matK trees. Bootstrap support and Bayesian posterior probability were found to be higher in matK topologies than that of rbcL. The molecular clock test unraveled an equal evolutionary rate for matK and unequal rate for rbcL sequences. Molecular dating approach unveiled Calamoideae to be the most ancient subfamily (65.75 MYA) among the three subfamilies that originated during the Late Cretaceous period in the Mesozoic era, whereas Coryphoideae and Arecoideae were found to have originated in the Cenozoic era. [ABSTRACT FROM AUTHOR]

Backgroud: Twelve taxa of herbaceous Paeonia species were recorded in Türkiye. All definitions were performed morphologically and/or anatomically and there is no study based on DNA barcode sequences. Three barcode regions were sequenced to determine the phylogenetic relationships of Turkish Paeonia taxa. The chemical comparison of roots was also investigated. Methods and results: The taxons were collected between May and June 2021 from nine cities. Leaf materials were used for DNA isolation and ITS, matK and rbcL regions were amplified and sequenced. There was no difference among taxa in terms of rbcL sequences. But the ITS and matK regions distinguished 12 taxa and structured them in two groups. ITS region distinguished P. peregrina, P. arietina, and P. tenuifolia from other taxa, while matK region distinguished P. arietina and P. witmanniana from other taxa. Both barcode sequences actually showed that the registration of P. mascula subsp. arasicola was actually 100% similar to P. arietina. ITS was the most polymorphic region (n = 54) followed by matK (n = 9). These sequences could successfully discriminate Paoenia species from each other and diploid P. tenuifolia. The methanolic root (100 gr) extracts were examined for total phenolic and flavonoid content, and antioxidant activities. Significant variation was found for polyphenolic content, and antioxidant properties (TPC from 204.23 to 2343.89 mg, TFC from 7.73 to 66.16 mg, and FRAP from 523.81 to 4338.62 mg). SC50 values of ABTS and DPPH were ranged from 115.08 to 1115.52 μg/ml and 73.83 to 963.59 μg/ml, respectively. Conclusion: It was concluded that 11 of 12 taxa had differences in terms of ITS and matK sequences and these region must be used for the correct identification of Turkish Paeonia. [ABSTRACT FROM AUTHOR]

Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only polyploid that has recently spread in different eco-geographical regions across the world. Understanding what confers such ecological advantages to this species, compared to its diploid and polyploid congeners, first requires clarification of the ecogeographical and evolutionary context of its formation. To achieve this, the geographical distributions of all Ulex spp. were estimated from species occurrence records, and phylogenetic analyses including all Ulex spp. were performed based on four nuclear (ITS and ETS nrDNA) and plastid (rps12 intron and trnK - matK) regions. The resulting trees were dated using a secondary calibration. Patterns of DNA sequence variation and dated phylogenetic trees were then interpreted in light of previous knowledge of chromosome numbers in Ulex to infer past events of polyploid speciation in the genus. We show that: (1) most current Ulex spp. radiated in the Iberian Peninsula during the past 1–2 Myr; (2) the history of Ulex was punctuated by multiple whole-genome duplication events; and (3) U. europaeus subsp. europaeus is the only gorse taxon that was formed by hybridization of two well-differentiated lineages (which separated c. 5 Mya) with wide climatic ranges (currently represented by Ulex minor and Ulex europaeus subsp. latebracteatus), possibly contributing to the invasive nature and wider climatic range of U. europaeus subsp. europaeus. These findings provide a much-needed evolutionary framework in which to explore the adaptive consequences of genome mergers and duplication in Ulex. [ABSTRACT FROM AUTHOR]

A new orchid species, Liparis macrosepala, is illustrated and described from Yunnan Province, China, based on morphological and molecular analyses. This plant is characterised by the ovoid-fusiform, slightly compressed pseudobulbs with 4 or 5 leaves with slightly crisped margins on their apical half, dorsal sepal heart-shaped, lip with a bituberculate basal callus and a thickened folded lateral lobe on each side, centrally with one cavity with slightly raised margins, the column with a single pair of broadly triangular, obtuse wings. Maximum Likelihood and Bayesian Inference analyses of combined nrITS and plastid matK DNA sequences place this species in section Cestichis. [ABSTRACT FROM AUTHOR]

Camellia is the largest and most important genus in the family Theaceae, with many species being of great economic, ornamental and ecological value. However, the phylogenetic resolution of these species has been difficult due to interspecific hybridization and polyploidy. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. In this study, four chloroplast genomic regions (matK, rbcL, ycf1, trnL-F) were used as markers among 161 species representing all four subgenera within this genus to investigate the phylogeny and interspecies relationship of the genus Camellia. The results showed that the 161 species of the genus Camellia could be grouped into 13 clades (A-M). Clades A and B mainly consisted of sect. Camellia. Clades C and I were made up of sect. Theopsis and sect. Eriandria. Clades D and J were composed of species from sect. Thea. Clade F consisted of the sect. Paracamellia species, whilst Clades G and M included sect. Furfuracea species. Clade H contained sect. Tuberculata and most species of sect. Pseudocamellia, whereas Clades K and L comprised the sect. Chrysantha species. These results supported that 161 Camellia species form paraphyletic groups, rather than a monophyletic group. And they demonstrated that the taxonomic position of related species could be resolved to some extent via sequencing markers in organelle genome, thus providing valuable cytoplasmic genetic information or maternal genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of various Camellia species. [ABSTRACT FROM AUTHOR]

The jewel orchids (Goodyerinae), named after their often colourful leaves, have a pantropical distribution with a clear Asian centre of diversity. However, the Nearctic and Neotropical America together form a second centre of diversity, with one-third of known species of Goodyerinae. Previously, only a few American samples have been included in phylogenetic studies, and their putatively Asian origins and American divergence times were poorly known. To elucidate these topics, we inferred phylogenetic trees, performed molecular dating and reconstructed biogeographic history using nuclear ribosomal ITS and plastid matK sequences for 34 species of Goodyerinae from the New World and 76 previously published accessions of Cranichideae. Our well-supported phylogenetic topology suggests two independent dispersal events to the New World from the Indomalesian region during the Miocene. The first inferred dispersal of a Neotropical clade diverged c. 11 Mya from their most recent common ancestor (MRCA), comprising three highly supported subclades that do not match the limits of Aspidogyne , Kreodanthus and Microchilus as previously circumscribed. The second dispersal involved a largely Nearctic clade of Goodyera s.l. diverging c. 8.4 Mya from the MRCA and exhibiting a complex biogeographic history with subsequent dispersals between the Nearctic and Indomalesia. The occurrence of these species in gallery forests putatively prevented vicariance events imposed by the expansion of the Chacoan region as previously detected for epiphytic Orchidaceae. Eighty-nine nomenclatural combinations and three new names in Microchilus are proposed. [ABSTRACT FROM AUTHOR]

Reconstructing the phylogenetic history of species in large taxonomic groups remains a challenge despite ever increasing access to molecular data. In subfamily Cercidoideae (Leguminosae), the large pantropical Bauhinia s.l. (~380 spp.) is never supported as monophyletic, but the generic boundaries and the number of genera that should be recognised remains a challenging taxonomic and phylogenetic question. Here we reconstruct the phylogeny of Bauhinia s.l. and related genera in the subfamily using sequences obtained from five loci (matK, trnL‐F, Leafy, and two previously undetected duplicate copies of Legcyc), which we analyse individually and in a concatenated matrix (excluding Leafy). The individual and concatenated analyses generally support two distinct lineages in Bauhinia s.l.: (1) the Bauhinia clade, containing Bauhinia s.str., Brenierea, and Piliostigma; and (2) the Phanera clade, containing Barklya, Cheniella, Gigasiphon, Lasiobema, Lysiphyllum, Phanera s.str., Schnella, and Tylosema. Based on our analyses, we recognise 14 genera in Cercidoideae. We resurrect the genus Tournaya from Gigasiphon, and synonymise the Asian segregate genus Lasiobema back into Phanera s.str. Our analyses reveal a clear gene duplication event in CYCLOIDEA that is shared by all Cercidoideae excluding the sister lineage to the subfamily, Cercis, supporting recent hypotheses for a whole genome duplication in all Cercidoideae except this genus. [ABSTRACT FROM AUTHOR]

In this study, we tried to figure out phylogenetic relationships and taxonomical positions of closely related Muscari species. Four different cpDNA regions including both coding and non-coding ones, namely, matK, trnT(UGU)-trnL(UAA) intergenic spacer (IGS), trnL(UAA) intron and trnL(UAA)-F(GAA) IGS, were employed to determine the exact circumscription of three subgenera, Muscari, Leopoldia and Botryanthus. Seventy Muscari accessions representing 31 Muscari species and different number of previously published sequences retrieved from NCBI database were analyzed. The concatenated and matK data alone were observed to be informative while none of the used non-coding regions was suitable to determine phylogeny of Muscari. Concatenated alignment gave almost the same tree topology with matK sequence. Muscari azureum and M. coeleste phylogenetically separated from all other species of Botryanthus and four main clades were observed in both of the trees even though three subgenera are accepted by Flora of Turkey. After discussing the phylogenetic positions and morphological characters in detail, moving of these two species from Botryanthus to Pseudomuscari subgenus was suggested. Thus, this study proposes that the number of Muscari subgenera should be increased from three to four in Flora of Turkey. The position of M. mirum was also remarkable; it always located distantly to its relatives of Leopoldia. Although this species may also be distinguished based on morphological features such as quite shorter plant length, one or sometimes two relatively wider leaves, and a larger fruit, it needs further studies to resolve its position reliably. Interesting positions of other species were also discussed in detail based on morphological characters in the text. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships within the monocot order Poales have been well studied, but several unrelated questions remain. These include the relationships among the basal families in the order, family delimitations within the restiid clade, and the search for nuclear single-copy gene loci to test the relationships based on chloroplast loci. To this end two nuclear loci (PhyB, Topo6) were explored both at the ordinal level, and within the Bromeliaceae and the restiid clade. First, a plastid reference tree was inferred based on matK, using 140 taxa covering all APG IV families of Poales, and analyzed using parsimony, maximum likelihood and Bayesian methods. The trees inferred from matK closely approach the published phylogeny based on whole-plastome sequencing. Of the two nuclear loci, Topo6 supported a congruent, but much less resolved phylogeny. By contrast, PhyB indicated different phylogenetic relationships, with, inter alia, Mayacaceae and Typhaceae sister to Poaceae, and Flagellariaceae in a basally branching position within the Poales. Within the restiid clade the differences between the three markers appear less serious. The Anarthria clade is first diverging in all analyses, followed by Restionoideae, Sporadanthoideae, Centrolepidoideae and Leptocarpoideae in the matK and Topo6 data, but in the PhyB data Centrolepidoideae diverges next, followed by a paraphyletic Restionoideae with a clade consisting of the monophyletic Sporadanthoideae and Leptocarpoideae nested within them. The Bromeliaceae phylogeny obtained from Topo6 is insufficiently sampled to make reliable statements, but indicates a good starting point for further investigations. We find that matK is remarkably good at retrieving the chloroplast phylogeny, that Topo6, despite low resolution, is suitable to test the generality of the plastid phylogeny as a taxic phylogeny, that PhyB might be too complex to be really useful at the level of families within an order, that the inclusion of the centrolepids in Restionaceae might be valid, but that there is no phylogenetic support for or against including the Anarthria clade in Restionaceae. The basal arrangement of families in the Poales (Bromeliaceae, Typhaceae, Rapateaceae) remains unresolved. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships among nine Turkish Orchis species were inferred from variation in the internal transcribed spacer and maturase Kinase regions. Foreign sequences were also retrieved from NCBI to increase interspecific sampling. The topology of ITS tree was broadly congruent to that of matK tree. The trees showed two major clades; the first one included species from Orchis and Neotinea subgenera and the second included species of Anacamptis subgenus. Phylogenetic separation of some species found in Neotinea and Anacamptis subgenera were previously reported, and the current study also indicated that moving these species into Neotinea and Anacamptis genera could be reasonable. [ABSTRACT FROM AUTHOR]

In this study, the species identifications of seven Ephedra plants, including three medicinal plants from the Pharmacopoeia of the People’s Republic of China, were conducted using phylogenetic analyses, and the method’s validity was verified. The phylogenetic trees constructed from the maturase-coding gene (matK) and internal transcribed spacer 1 (ITS1) sequences showed that the former could be used for identifying five Ephedra plants, Ephedra intermedia, E. equisetina, E. antisyphilitica, E. major, and E. aphylla, but it had less power to discriminate E. sinica and E. przewalskii, while the latter could distinguish five Ephedra plants, E. przewalskii, E. equisetina, E. antisyphilitica, E. major, and E. aphylla, but it had less power to discriminate E. sinica and E. intermedia. However, when the two genes were combined, the seven species could be completely distinguished from each other, especially the medicinal plants from the others, which is significant in developing their pharmaceutical uses and in performing quality control assessments of herbal medicines. The method presented here could be applied to the analysis of processed Ephedra plants and to the identification of the botanical origins of crude drugs. Additionally, we discovered that E. equisetina and E. major were probably closely related to each other, and that E. sinica, E. intermedia, and E. przewalskii also had a close genetic relationship.

Plastid DNA markers sequencing and DNA fingerprinting approaches were used and compared for resolving molecular phylogeny of closely related, previously unexplored Amorphophallus species of India. The utility of individual plastid markers namely rbcL, matK, trnH- psbA, trnLC- trnLD, their combined dataset and two fingerprinting techniques viz. RAPD and ISSR were tested for their efficacy to resolves Amorphophallus species into three sections specific clades namely Rhaphiophallus, Conophallus and Amorphophallus. In the present study, sequences of these four plastid DNA regions as well as RAPD and ISSR profiles of 16 Amorphophallus species together with six varieties of two species were generated and analyzed. Maximum likelihood and Bayesian Inference based construction of phylogenetic trees indicated that among the four plastid DNA regions tested individually and their combined dataset, rbcL was found best suited for resolving closely related Amorphophallus species into section specific clades. When analyzed individually, rbcL exhibited better discrimination ability than matK, trnH- psbA, trnLC- trnLD and combination of all four tested plastid markers. Among two fingerprinting techniques used, the resolution of Amorphophallus species using RAPD was better than ISSR and combination of RAPD +ISSR and in congruence with resolution based on rbcL. [ABSTRACT FROM AUTHOR]

The phylogenetic status of the genus Atraphaxis and its relationship with woody Polygonum species is examined based on nrDNA ITS and two chloroplast regions ( matK and rpl32- trnL). Morphological and palynological studies for the selected taxa are also performed. Our results revealed that several woody Polygonum species (namely P. spinosum, P. aridum, P. dumosum, P. salicornioides, P. khajeh- jamali and P. botuliforme) endemic to Iran formed a distinct clade, and are nested within Atraphaxis. Atraphaxis ovczinnikovii, (= P. ovczinnikovii), was the first diverging lineage as sister to an assemblage of these taxa and the bulk of Atraphaxis species. Three other woody Polygonum species (P. afghanicum, P. paronychioides and P. thymifolium) were nested within herbaceous Polygonum species. Ochrea and pollen characteristics corroborated the phylogenetic results as well. Based on molecular and morphological evidence, we transferred the aforementioned six Polygonum species into Atraphaxis. The newly delimited genus Atraphaxis is comprised of three lineages, corresponding to three new sections: Atraphaxis, Polygonoides and Ovczinnikovia. The different position of A. botuliformis (= P. botuliforme) in nrDNA ITS and combined chloroplast DNA analyses indicated that it had possibly experienced the hybrid or introgression for a long time. Taxonomic descriptions for Atraphaxis and its sections as well as the diagnostic key to sections and species occurring in Iran, are presented. [ABSTRACT FROM AUTHOR]

Background and Aims Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. Methods A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. Key Results The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. Conclusions This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris. [ABSTRACT FROM PUBLISHER]

Previous molecular phylogenetic studies of Fabaceae indicated that species of Wisteria, an intercontinental disjunct genus between eastern Asia and eastern North America, formed a clade derived from within Callerya. However, interspecific relationships were not well resolved or supported. In this study, we used sequences of the nuclear ribosomal DNA internal transcribed spacer region and the chloroplast gene matK to examine interspecific relationships and explore implications of the phylogeny for the systematics and biogeography of Wisteria. Our results showed that Wisteria with deciduous leaves and racemose inflorescences formed a strongly supported clade derived from within the paraphyletic Callerya. Afgekia was also found to be included within Callerya. Therefore, our data support the merger of Afgekia, Callerya, and Wisteria. The phylogenetic pattern suggested that the deciduousness in Wisteria may be a derived trait likely in response to temperate climate, and the racemose inflorescences in the Afgekia- Callerya- Wisteria clade may have evolved from panicles. Our study also provided strong support for the sister relationship of the North American and eastern Asian species of Wisteria. In the Asian clade, Wisteria brachybotrys Siebold & Zucc. of Japan was sister to the clade containing W. floribunda (Willd.) DC of Japan and Korea, and W. sinensis (Sims) Sweet of China. However, our data offered weak support for the sister relationship of W. floribunda and W. sinensis. Our divergence time and biogeographic analyses suggested that the eastern Asian-North American disjunction in Wisteria may have occurred through a dispersal event in the middle Miocene (13.4 Mya) from the Old World to the New World across the Bering land bridge followed by vicariance in the late Miocene (6.8 Mya). This study added another example to the 'out of Asia' migration for the eastern Asian-eastern North American disjunction. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships of Dioscorea, including sections Botryosicyos, Combilium, Enantiophyllum, Lasiophyton, Opsophyton, Shannicorea and Stenophora, are reconstructed with chloroplast trnL-F, matK, rbcL and atpB-rbcL sequence data, covering a total of 72 accessions including 48 ingroup species and five outgroup species from East and Southeast Asia. The seven Asian sections do reflect the genetic relationships among the species that they include. In summary, D. sect. Combilium and sect. Shannicorea are recognized as closely related sections with moderate support. The results also support Burkills treatment of subsect. Euopsophyton (D. bulbifera) as sect. Opsophyton and subsect. Macrourae (D. sansibarensis) as sect. Macroura. In addition, there is a well-supported sister relationship between D. sect. Lasiophyton and sect. Botryosicyos. The level of morphological characters and molecular divergence within D. sect. Enantiophyllum is low, but the members of this group could still be distinguished from each other. [ABSTRACT FROM AUTHOR]

Abstract: Habenaria is a large genus of terrestrial orchids distributed throughout the tropical and subtropical regions of the world. The integrity and monophyly of this genus have been under discussion for many years, and at one time or another, several genera have been either included in a broadly defined Habenaria or segregated from it. In this study, the phylogenetic relationships of the Neotropical members of the genus and selected groups of African Habenaria were investigated using DNA sequences from the nuclear internal transcribed spacer (ITS) region and the plastid matK gene sampled from 151 taxa of Habenaria from the Neotropics (ca. 51% of the total) as well as 20 species of Habenaria and Bonatea from the Old World. Bayesian and parsimony trees were congruent with each other, and in all analyses, the Neotropical species formed a highly supported group. African species of Habenaria in sections Dolichostachyae, Podandria, Diphyllae, Ceratopetalae and Bilabrellae, and the Neotropical clade formed a highly supported “core Habenaria clade”, which includes the type species of the genus from the New World. The topology of the trees indicates an African origin for the Neotropical clade and the low sequence divergence among the Neotropical species suggests a recent radiation of the genus in the New World. Species of Bonatea and Habenaria sections Chlorinae and Multipartitae formed a well-supported clade that was sister to the “core Habenaria clade”. The Neotropical clade consists of at least 21 well-supported subgroups, but all Neotropical sections of the current sectional classification are paraphyletic or polyphyletic and will need extensive revision and recircumscription. Most of the Neotropical subgroups formed morphologically uniform assemblage of species, but some cases of morphological divergence within subgroups and convergence between subgroups indicated that morphology alone can be misleading for inferring relationships within the genus. The genera Bertauxia, Kusibabella and Habenella, segregated from New World Habenaria, are not monophyletic and a revision of the sectional classification rather than a generic division seems most appropriate. Our results do not support an extensive generic fragmentation of Habenaria as previously suggested and will provide a framework for revising the infrageneric classification and investigating the patterns of morphological evolution and geographical distribution of the genus in the New World. [Copyright &y& Elsevier]

Euphorbia subg. Euphorbia is the largest and most diverse of four recently recognized subgenera within Euphorbia and is distributed across the tropics and subtropics. Relationships within this group have been difficult to discern due mainly to homoplasious morphological characters and inadequate taxon sampling in previous phylogenetic studies. Here we present a phylogenetic analysis of E. subg. Euphorbia, using one nuclear and two plastid regions, for the most complete sampling of molecular sequence data to date. We assign 661 species to the subgenus and show that it is comprised of four highly supported clades, including a single New World clade and multiple independent lineages on Madagascar. Using this phylogenetic frame-work we discuss patterns of homoplasy in morphological evolution and general patterns of biogeography. Finally, we present a new sectional classification of E. subg. Euphorbia comprising 21 sections, nine of them newly described here. [ABSTRACT FROM AUTHOR]

Asphodelaceae subfam. Alooideae (Asparagales) currently comprises five genera, four of which are endemic to southern Africa. Despite their importance in commercial horticulture the evolutionary relationships among the genera are still incompletely understood. This study examines phylogenetic relationships in the subfamily using an expanded molecular sequence dataset from three plastid regions (matK, rbcLa, trnH-psbA) and the first subunit of the nuclear ribosomal internal transcribed spacer (ITS1). Sequence data were analysed using maximum parsimony and Bayesian statistics, and selected morphological traits were mapped onto the molecular phylogeny. Haworthia is confirmed as being polyphyletic, comprising three main clades that largely correlate with current subgeneric circumscriptions. Astroloba and Gasteria are evidently each monophyletic and sister respectively to Astroloba and H. subg. Robustipedunculares. Chortolirion is shown to be deeply nested within Aloe and is formally included in that genus. Aloe itself is clearly polyphyletic, with the dwarf species A. aristata allied to Haworthia subg. Robustipedunculares. The taxonomic implications of these findings are examined but branch support at critical lower nodes is insufficient at this stage to justify implementing major taxonomic changes. [ABSTRACT FROM AUTHOR]

The river-weed family Podostemaceae ( c. 300 species in c. 54 genera) shows a number of morphological innovations to be adapted to its unusual aquatic habitat, and its unique or rare bauplan features have been reflected in the traditional (i.e. non-molecular) classification recognizing numerous monotypic or oligospecific genera. The infrasubfamilial relationships of many genera remained unclear. The present study used molecular phylogenetic analysis of matK sequences for 657 samples ( c. 132 species/ c. 43 genera). The family was traditionally divided into three subfamilies (Podostemoideae, Tristichoideae and Weddellinoideae). American Podostemoideae were shown to be polyphyletic and divided into four clades, i.e. Ceratolacis, Diamantina, Podostemum and all other genera. Among the podostemoid clades, Diamantina was the first branching clade and a clade comprising Mourera and the Apinagia subclade was then sister to the remainder of the New World and Old World Podostemoideae with low statistic supports. The Old World Podostemoideae comprised four monophyletic clades, i.e. two African clades, one Madagascan clade and one Asian clade, although the relationships among these clades and American Ceratolacis and Podostemum were poorly resolved. African Podostemoideae were polyphyletic, with Saxicolella pro parte being weakly supported as sister to the remaining Old World Podostemoideae plus Ceratolacis and Podostemum. In contrast to the American and African clades, monophyly of four Asian subclades was well supported. Plants of Tristicha (Tristichoideae) and of Weddellina (Weddellinoideae), which are currently treated as monospecific, had great matK differentiation equivalent to at least interspecific variation. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 461-492. [ABSTRACT FROM AUTHOR]

The genetic diversity and evolutionary divergence in Liquidambar species and Liquidambar orientalis varieties were compared with respect to the matK gene. A total of 66 genotypes from 18 different populations were sampled in southwestern Turkey. The matK region, which is about 1,512 bp in length, was sequenced and studied. L. orientalis, L. styraciflua, and L. formosana had similar magnitude of nucleotide diversity, while L. styraciflua and L. acalycina possessed higher evolutionary divergence. The highest evolutionary divergence was found between L. styraciflua and eastern Asian Liquidambar species (0.0102). However, the evolutionary divergence between L. orientalis and other species was of a similar magnitude. The maximum-parsimony phylogenetic tree showed that L. styraciflua and L. orientalis formed a closer clade while East Asian species were in a separate clade. This suggests that the North Atlantic Land Bridge through southern Greenland may have facilitated continuous distribution of Liquidambar species from southeastern Europe to eastern North America in early Tertiary period. The maximum-parsimony tree with only 18 Oriental sweetgum populations indicated that there were two main clusters: one with mainly L. orientalis var. integriloba and the other with var. orientalis and undetermined populations. High nucleotide diversity (0.0028) and divergence (0.00072) were found in L. orientalis var. integriloba populations and Muğla-1 geographical region. This region could be considered as the major refugium and genetic diversity center for the species. The low genetic diversity and divergence at intraspecies level suggest that L. orientalis populations in Turkey share an ancestral polymorphism from which two varieties may have evolved. [ABSTRACT FROM AUTHOR]

Phylogenetic analyses of the subtribe Hyptidinae (Lamiaceae) based on nuclear ITS and ETS, and plastid trnL-F, trnS-G, trnD-T, and matK are presented. The analysis of the ITS dataset included 218 specimens representing 180 species of Hyptidinae. This analysis was used to select a smaller representative sample of 69 species of Hyptidinae for further analysis based on all above regions. The monophyly of Hyptidinae and almost all genera is well-supported, with noticeable paraphyly of Hyptis which is ancestor ofall remaining genera of Hyptidinae. Eriope is monophyletic with the exclusion of E. simplex, while Hypenia represents a monophyletic group excluding H. vitifolia. Hyptis eximia was shown to be associated with Hyptidendron, and Peltodon is embedded within the Hyplis s.str. dade. Internal relationships within Hyptis s.str. were not completely resolved; a preliminary discussion on the taxonomy treatment of the complex and the subdivision of Hyptis are presented. [ABSTRACT FROM AUTHOR]

The tribe Forsythieae comprises 2 genera ( Forsythia and Abeliophyllum) and 14 species distributed mostly in the Far East. Although Forsythieae is considered monophyletic, with many symplesiomorphic characters, the phylogenetic status of Abeliophyllum remains controversial. We assessed the phylogenetic relationships of Forsythieae, based on a 3.3-kb plastid fragment ( trnL- F region and matK gene) and nuclear internal transcribed spacer ( ITS) region DNA sequences. We obtained a highly resolved and strongly supported topology with possible outgroups. The topology of the combined tree was congruent with those of the ITS region and matK gene. Maximum parsimony, maximum likelihood, and Bayesian inference tree analyses for the combined data also yielded identical relationships. Combined sequence data strongly supported the monophyly of Forsythieae and the close relationship between Fontanesia and Jasminum. Oleaceae, not Fontanesia, was found to be a sister group to Forsythieae. Moreover, the genus Abeliophyllum was distinctly independent of Forsythia. Three Forsythia lineages were suggested: (a) ONJ ( ovata- nakaii- japonica clade), (b) VGE ( viridissima- giraldiana- europaea), and (c) KISS ( koreana- intermedia- saxatilis- suspensa). Our results indicated that F. × intermedia is not a hybrid between F. suspensa and F. viridissima, but further studies are needed to determine its taxonomic identity. Furthermore, the diverse fruit shapes in Oleaceae are assumed to be the result of parallelism or convergence. [ABSTRACT FROM AUTHOR]

The phylogeny of Pooideae, one of the largest subfamilies of grasses, has been intensively studied during the past years. To investigate the early evolutionary splits in Pooideae we used a broad sample of genera with uncertain placement, some of which have not been studied in molecular phylogenetics before, complemented by representatives from other lineages of this subfamily. Morphological, cytogenetic and biogeographical analyses were added to the molecular sequence work on chloroplast matK-3'trnK and nuclear ITS. According to chloroplast DNA data, a new and well-supported lineage was identified among the early branches. It consisted of Phaenosperma and a larger group of genera encompassing Anisopogon, Danthoniastrum, Duthiea, Metcalfia, Pseudodanthonia (inclusion resting on ITS and morphology), Sinochasea and Stephanachne. Based on structural characters we suggest to keep Phaenosperma under the monotypic tribe Phaenospermateae and to accommodate the other genera under a new tribe Duthieeae, which is morphologically well-defined by synapomorphic spikelet features. Megalachne and Podophorus were not part of the early diverging Pooideae lineages but belong to the Aveneae/Poeae complex. Morphological characteristics of Duthieeae are discussed with respect especially to Stipeae and reveal consistent differences between both tribes. The genera of Duthieeae and the major lineages of Stipeae are keyed. A cytogenetic survey of exemplary taxa corroborates high chromosome base numbers as prevailing within the early diverging lineages of Pooideae, but chromosome sizes are more highly varied than previously reported. Ecogeographical analyses point to warm and humid conditions as the ancestral bioclimatic niche of Phaenosperma and Duthieeae, whereas adaptation to cold and drought occurred only in a part of Duthieeae but was obviously less successful than in the widespread and much more species-rich tribe Stipeae. The distribution of Duthieeae with species-poor or monotypic genera in mountains of the northern hemisphere and Anisopogon as an outlier in Australia suggests relict character. [ABSTRACT FROM AUTHOR]

Abstract: The evolution of the eastern Asian and eastern North American disjunction of the witch-hazel genus Hamamelis L. (Hamamelidaceae) was examined through phylogenetic and biogeographic analyses. Phylogenetic relationships of all Hamamelis species were reconstructed using parsimony and Bayesian analyses of sequence data from six plastid (trnL-F, psaA-ycf3, rps16, matK, atpB-rbcL, and psbA-trnH) and two nuclear (ITS and ETS) DNA regions. The phylogeny was then used to infer the biogeographic origin and subsequent diversification using both event-based (DIVA) and maximum likelihood (LAGRANGE) methods incorporating fossil data. The times of divergence within Hamamelis were estimated with the Bayesian approach using the program BEAST. A very low level of molecular variation was detected in both the plastid and the nuclear DNA regions within Hamamelis. The combined analyses resulted in a phylogeny of the genus with higher resolution and support values. Hamamelis was supported to be monophyletic with H. mollis from eastern China diverged first in the genus. All North American species formed a clade and was sister to the eastern Asian H. japonica. Within the North American clade, H. mexicana was sister to H. vernalis, and the recently described species H. ovalis was found to be closely related to the widespread species H. virginiana. The stem age of Hamamelis was estimated to be at the Eocene (51.2mya, with 95% HDP: 49.0–54.6mya), and the crown age of the genus was dated to be at the late Miocene (9.7mya, with 95% HDP: 3.6–18.1mya, or 10.6mya, with 95% HDP: 4.2–19.6mya). The disjunction between the eastern Asian and the eastern North American species was dated to be 7.1mya (95% HDP: 3.1–13.6mya) or 7.7mya (95% HDP: 3.4–13.6mya). Biogeographic analyses incorporating fossils resulted in more equally possible solutions at the stem lineage of Hamamelis than those including extant species only. Eastern Asia is inferred to be the most-likely area for the origin of Hamamelis. The current disjunction was due to the extinction in western North America and Europe from Eocene to late Miocene, and later migration from eastern Asia into North America. The Bering land bridge was hypothesized to have played an important role in the evolution of this disjunction. The current species diversity of the genus was the result of relatively recent diversification events during the late Miocene rather than long accumulation of lineages from the early Tertiary. [Copyright &y& Elsevier]

Abstract: Because the classification of Nymphaea in India has been reported to be confusing, molecular taxonomic revision of four Indian representatives of the genus namely N. nouchali, N. pubescens, N. rubra and N. tetragona based on ITS, trnK intron and matK gene is presented and discussed. Molecular evidence provided here is in disagreement about the taxonomic identity of one specimen of N. nouchali and indicated a probable misidentification of N. tetragona. Interestingly, sequence analysis revealed lack of or low sequence divergence between N. pubescens and N. rubra. Phylogenetic relationship among members of Nymphaea subg. Lotos, represented by all known species viz. N. lotus, N. petersiana, N. pubescens and N. rubra was also conducted. Maximum parsimony analysis of the combined data matrix depicted two clades with N. petersiana and N. lotus forming one, N. pubescens and N. rubra representing the other. Bayesian inference showed N. petersiana as first branching, followed by N. lotus with N. pubescens and N. rubra emerging as a separate clade. The results indicated no close association between N. petersiana and N. nouchali, thereby, contradicting the morphology-based treatment of placing N. petersiana in synonymy under N. capensis and N. nouchali, respectively. [Copyright &y& Elsevier]

Leontopodium is a genus of approximately 30 species with a conspicuous Asian-European disjunct distribution. In this study samples from the Himalayan/Tibetan centre of diversity of the genus, as well as from Europe, were analysed to infer a phylogeny of the genus using sequences of nuclear ribosomal (ITS and ETS) and plastid (matK and trnL/F) DNA. The Southeast Tibetan monotypic Sinoleontopodium [Leontopodium lingianum (Y.L.Chen) Dickoré, comb. nov.] falls into Leontopodium. Monophyly of Leontopodium, including Sinoleontopodium, is supported. Due to low rates of sequence divergence, intrageneric relationships in general are weakly supported, a pattern frequently observed in plant groups centred in the Tibetan Plateau. Three phylogenetic groups can be identified, however, and these are also supported by morphology. The low levels of nucleotide divergence suggest a young age for the group, which has been influenced by the turbulent geological history of the Tibetan Plateau. Leontopodium is a characteristic Sino- Himalayan element that appears to have found its way into the mountains of Europe in geologically recent times. The two European taxa, Leontopodium alpinum and L. nivale, form a genetically distinct group, which, considering the wide geographic disjunction, shows surprisingly little divergence from its Asian relatives. [ABSTRACT FROM AUTHOR]

The article presents a study which explores the genetic relationship between the species of the angiosperm genus Myriophyllum (Haloragaceae), water milfoils. The study examined the phylogenetic structures of 43 sample species taken from several continents including Australia, Europe and Asia. Results show that there are multiple cryptic species in Australian species and suggests realignments within the subgeneric classification such as the recombination of monotypic genus Meziella.

DNA barcoding ("barcoding") has been proposed as a rapid and practical molecular method to identify species via diagnostic variation in short orthologous DNA sequences from one or a few universal genomic regions. It seeks to address in a rapid and simple way the "taxonomic impediment" of a greater need for taxonomic identifications than can be supplied by taxonomists. Using a complicated plant group, Solanum sect. Petota (wild potatoes), I tested barcoding with the most variable and frequently suggested plant barcoding regions: the internal nontranscribed spacer of nuclear ribosomal DNA (ITS) and the plastid markers trnH-psbA intergenic spacer and matK. These DNA regions fail to provide species-specific markers in sect. Petota because the ITS has too much intraspecific variation and the plastid markers lack sufficient polymorphism. The complications seen in wild potatoes are common in many plant groups, but they have not been assessed with barcoding. Barcoding is a retroactive procedure that relies on well-defined species to function, is based solely on a limited number of DNA sequences that are often inappropriate at the species level, has been poorly tested with geographically well-dispersed replicate samples from difficult taxonomic groups, and discounts substantial practical and theoretical problems in defining species. [ABSTRACT FROM AUTHOR]

Karyotype structures revealed by in situ hybridization with ribosomal and satellite DNAs and fluorochrome staining of AT- or GC-rich regions are reported for 23 diploid to tetraploid taxa of Aveneae genera Arrhenatherum, Avena, Helictotrichon, and Pseudarrhenatherum. Chromosomal features are compared with a molecular phylogeny generated on nuclear ribosomal (ITS, 5S) and chloroplast (matK) DNA sequences. Ancestral chromosomal character states are (1) two satellite chromosomes per set of x = 7, (2) 5S rDNA localized in nonsatellite chromosomes, (3) large chromosomes with (4) rather equal lengths of their respective chromosome arms, (5) sets with strong variance of chromosome lengths, (6) absence or small amounts of heterochromatin, and (7) absence or no detectable amplification of the satellite DNAs tested. Overall, most karyotype characteristics are species specific, but common patterns were found for the species of two large subgenera of Helictotrichon. Pseudarrhenatherum, although nested in the molecular phylogeny within Helictotrichon subgenus Helictotrichon, deviates strongly in karyotype characters such as Arrhenatherum as sister of Avena. The karyotype of Helictotrichon jahandiezii, sister to the clade of Helictotrichon subgenera Helictotrichon, Avena, and Arrhenatherum, strongly resembles that of Avena macrostachya. Karyotype features suggest that perennial A. macrostachya and H. jahandiezii are close to the C-genome species of annual Avena, whereas the Avena A genome resembles that of Arrhenatherum. [ABSTRACT FROM AUTHOR]

Abstract: The oil-secreting orchids of southern Africa belong to the sub-tribe Coryciinae within Diseae. A phylogeny of Diseae is inferred using sequence data from all genera in the tribe, with an emphasis on resolving generic classifications within Coryciinae. Nuclear (ITS) and plastid (trnLF and matK) gene region sequences were analysed for 79 ingroup taxa and three outgroup taxa. Coryciinae is confirmed to be diphyletic, with Disperis and Coryciinae sensu stricto (s.s.) forming separate monophyletic clades. The current genera Corycium and Pterygodium are not monophyletic according to our analysis and we propose a subdivision of Coryciinae s.s. into 10 monophyletic clades including three monotypic groups. Previous generic classifications of Coryciinae s.s. have been hampered by convergent evolution of floral parts, a consequence of few pollinator species and limited pollinia attachment sites in the oil-bee pollination system common to this group. [Copyright &y& Elsevier]

Abstract: Molecular phylogenetic studies of Haemodoraceae in the Greater Cape and Southwest Australian Floristic Region (SWAFR) using trnL, trnL-F and matK sequence data affirm the presence of old and young rapidly radiated lineages in both regions. Commencement of tribal and generic divergence in the subfamilies occured in the Eocene in the two regions, but subsequent patterns of radiation differ slightly. The hypothesis of rapid recent speciation in these regions from the late Pliocene as the major explanation for endemic species richness is still repeated by several contemporary authors despite increasing molecular phylogenetic evidence to the contrary. Our estimates of the age of lineages in Haemodoraceae show significant lineage turnover occurring over the last 15 million years, since the mid-Miocene, with divergence of the major clades beginning in the Eocene. The search for independent evidence to date speciation episodes reliably and investigation of molecular analyses across a broad spectrum of these clades must be pursued to advance ideas rigorously concerning origins of species richness. These regions continue to confound attempts to develop theory concerning origins of global species richness, with consequent implications for conservation biology. [Copyright &y& Elsevier]

Abstract: The matK gene has been among the most useful loci for resolving plant phylogenetic relationships at different evolutionary time-scales, but much less is known about the phylogenetic utility of the flanking trnK intron, especially for deep level phylogenetics. We compared the relative performance of matK and trnK intron regions for resolving the relationships of the early diverging eudicots (angiosperms). The two regions display similar nucleotide compositions and distributions of rate variation among sites. The trnK intron sequences also provide similar levels of phylogenetic information per-site as matK. Combining the trnK intron sequences with matK increases overall bootstrap support for the early diverging eudicots compared to analyses of matK alone. MP, ML and Bayesian analyses provide strong support for eudicots, the sister group relationship of Ranunculales to remaining eudicots, and a Buxales+Trochodendraceae+core eudicots clade. matK and the trnK intron support conflicting positions for Buxales and Trochodendrales in relation to the core eudicots. [Copyright &y& Elsevier]

A phylogenetic analysis of Violaceae is presented using sequences from rbcL, atpB, matK and 18S rDNA from 39 species and 19 genera. The combined analysis of four molecular markers resulted in only one most parsimonious tree, and 33 of all 38 nodes within Violaceae are supported by a bootstrap proportion of more than 50%. Fusispermum is in a basal-most position and Rinorea, Decorsella, Rinoreocarpus and the other Violaceae are successively diverged. The monogeneric subfamily Fusispermoideae is supported, and it shares a number of plesiomorphies with Passifloraceae (a convolute petal aestivation, actinomorphic flowers and connate filaments). The other monogeneric subfamily Leonioideae is sunken within the subfamily Violoideae and is sister to Gloeospermum, sharing some seed morphological characteristics. The present molecular phylogenetic analysis suggests that the convolute, apotact and quincuncial petal aestivation is successively derived within the family. The evolutionary trends of the other morphological characteristics, such as a filament connation, the number of carpels and floral symmetry, are discussed. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships, morphology, and distribution of the enigmatic species Andrachne cuneifolia of problematic generic affiliation were examined. Nuclear internal transcribed spacer (ITS) and plastid matK sequences were analysed with a matrix of matK and ITS DNA sequences for Phyllanthus and Andrachne species. According to this analysis, this taxon belongs in the genus Phyllanthus, subgenus Xylophylla. Comparison of morphological characters also supports the placement of this species in Phyllanthus subgenus Xylophylla. The correct name is Phyllanthus cuneifolius (Britton) Croizat. A full description, illustration, conservation rating, and distribution map are provided. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 519–525. [ABSTRACT FROM AUTHOR]

Abstract: Phylogenetic relationships for Hieracium subgen. Pilosella were inferred from chloroplast (trnT–trnL, matK) and nuclear (ITS) sequence data. Chloroplast markers revealed the existence of two divergent haplotype groups within the subgenus that did not correspond to presumed relationships. Furthermore, chloroplast haplotypes of the genera Hispidella and Andryala nested each within one of these groups. In contrast, ITS data were generally in accord with morphology and other evidence and were therefore assumed to reflect the true phylogeny. They revealed a sister relationship between Pilosella and Hispidella and a joint clade of Hieracium subgenera Hieracium and Chionoracium (Stenotheca) while genus Andryala represented a third major lineage of the final ingroup cluster. Detailed analysis of trnT–trnL character state evolution along the ITS tree suggested two intergeneric hybridization events between ancestral lineages that resulted in cytoplasmic transfer (from Hieracium/Chionoracium to Pilosella, and from the introgressed Pilosella lineage to Andryala). These chloroplast capture events, the first of which involved a now extinct haplotype, are the most likely explanation for the observed incongruencies between plastid and nuclear DNA markers. [Copyright &y& Elsevier]

Phylogenetic relationships within Clematis, including Naravelia, Archiclematis and Clematopsis, were analysed using nucleotide sequences of chloroplast DNA [(1) matK and trnK introns; (2) atpB- rbcL spacer; (3) rpoB-trnC spacer; (4) psbA-trnH-trnQ spacer; (5) rbcL-accD spacer] and the nuclear ITS regions. The phylogenetic trees resulting from these analyses suggested nine major clades. The genera Archiclematis, Naravelia and Clematopsis were found to be nested within the genus Clematis, and should be included within it. Within the genus Clematis, the traditional subgenus Viorna was found to be monophyletic. The remaining subgenera ( Flammula, Clematis and Campanella) and sections Flammula, Clematis and Cheiropsis, however, were found to be paraphyletic or polyphyletic. Recircumscription of several groups in Clematis was suggested. Enormous morphological diversification and very few nucleotide substitutions within Clematis indicate the recent radiation of the genus. Clematidinae shares a gene order with Anemoninae between the starting point of large single copy region and trnQ of chloroplast DNA, although Hepatica, a genus in Anemoninae, shows a different order in the region near trnH. [ABSTRACT FROM AUTHOR]

The plastid matK gene, trnL/F spacer, and nuclear rDNA ITS were sequenced for 36 species of Leontodon and 29 taxa of related genera of tribe Lactuceae. Phylogenetic relationships inferred from the independent and combined data are largely congruent and reveal that Leontodon sensu lato (s.l.) as presently defined is diphyletic: L. subgenus Leontodon forms a clade with Helminthotheca, Picris and Hypochaeris as sister genera, whereas L. subgenus Oporinia appears as a separate clade with strong bootstrap support and is thus better treated as a separate genus. Previous sectional classifications of Leontodon s.l. are considered in the light of DNA and additional morphological and karyological data. Support is presented for a core group of Hypochaeridinae sensu stricto (s.s.) with the two clades of Leontodon s.I., Helminthotheca, Picris, and Hypochaeris, whereas Urospermum, Hyoseris, Aposeris, and Rhagadiolus appear to be positioned more distantly. [ABSTRACT FROM AUTHOR]

The article focuses on the molecular phylogeny of Aristolochia sensu lato based on sequences of rbcL, matK and phyA genes with special citation to differentiation of chromosome numbers. The genus Aristolochia sensu lato contains over 400 species from warm temperate to tropical regions globally. Its taxonomic treatment have been controversial. It was proposed that the genus should be divided into four genera in two subtribes.

Phylogenetic information is useful for the exploitation of ornamental germplasm in introducing novel resources or selecting closely related species for the introgression of horticultural interesting traits. However, in traditional plant systematics, limited numbers of morphological parameters have been evaluated as key characters, and hence, have often caused confusion in classification and induced many conflicts among taxonomists. On the other hand, recently developing molecular phylogeny provides more accurate and stable information for the relationship within each taxon level. In this article, we show some examples to apply molecular phylogenetic data on exploitation of ornamental germplasm in introducing novel resources with genus Rhododendron (Ericaceae) and on selection of closely related species for the introgression of horticulturally interesting traits with genus Dendrobium (Orchidaceae). doi:10.1300/J411v17n01_03 [ABSTRACT FROM PUBLISHER]

Members of tribe Vandeae (Orizhidaceae) form a large, pantropical clade of horticulturally important epiphytes. Monopodial leafless members of Vandeae have undergone extreme reduction in habit and represent a novel adaptation to the canopy environment in tropical Africa, Asia, and America. To study the evolution of monopodial leaflessness, molecular and structural evidence was used to generate phylogenetic hypotheses for Vandeae. Molecular analyses used sequence data from ITS nrDNA, trnL-F plastid DNA, and matK plastid DNA. Maximum parsimony analyses of these three DNA regions each supported two subtribes within monopodial Vandeae: Aeridinae and a combined Angraecinae + Aerangidinae. Adding structural characters to sequence data resulted in trees with more homoplasy, but gave fewer trees each with more well-supported clades than either data set alone. Two techniques for examining character evolution were compared: (l) mapping vegetative characters onto a molecular topology and (2) tracing vegetative characters onto a combined structural and molecular topology. In both cases, structural synapomorphies supporting monopodial Vandeae were nearly identical. A change in leaf morphology (usually reduced to a nonphotosynthetic scale), monopodial growth habit, and aeration complexes for gas exchange in photosynthetic roots seem to be the most important characters in making the evolutionary transition to leaflessness. [ABSTRACT FROM AUTHOR]

Abstract: The order Nymphaeales is a group of water-living flowering plants. This group is taxonomically small but has great significance in understanding the early evolution of angiosperms. Classification of this order varies from recognition of two to four families. We reconstructed the phylogenetic relationships of six genera of Nymphaeales (Barclaya, Brasenia, Cabomba, Nuphar, Nymphaea, Victoria). The ITS2-4 DNA region of these species was amplified, sequenced and used for phylogenetic analysis. As a result, two clades were resolved: Barclaya + Cabomba and Nuphar + Nymphaea + Victoria. Given that the length of the region analyzed was less than a kilobase, a decision was made to include other genes into the analysis to further verify the results of tree estimations. Thus, we combined ITS2-4 sequences with those of rbcL, matK and 18S rRNA genes. In the latter case, the genera of Nymphaeales form two well-supported clades, however, Barclaya joined the Nymphaea clade. These results support the taxonomic system of Nymphaeales which consists of the two families: Cabombaceae (with the genera Cabomba and Brasenia) and Nymphaeaceae (with the genera Barclaya, Euryale, Nuphar, Nymphaea, Ondinea and Victoria). [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]

Two new species of Heloniopsis (Melanthiaceae) endemic to Korea are described: H. tubiflora and H. koreana. Heloniopsis tubiflora is similar to H. orientalis, but the former has flowers at anthesis arranged obliquely downward (to pendulous) and has a basally tubular perianth, usually recurved apically (rarely straight) and bluish-purple to purple (but usually whitish near the apex when mature). Heloniopsis koreana differs from H. orientalis in having leaves that are usually spathulate, rarely oblanceolate, with minutely undulate margin, and with tepals slightly saccate to non-saccate at the base. Through comparison of herbarium specimens, we con- elude that all plants in Korea comprise these two new endemic species. Based on the molecular phylogeny resulting from combined analyses of trnK 5′ intron and matK DNA sequence data, Heloniopsis comprises three lineages: (1) five species in Japan and Taiwan; (2) H. koreana; and (3) H. tubiflora. [ABSTRACT FROM AUTHOR]

The phylogenetic relationships of the genus Saussurea DC. and Hemistepta lyrata Bunge were analyzed using the nuclear ribosomal ITS and chloroplast matK gene. Phylogenetic analyses revealed that Saussurea ceratocarpa Decne. of subg. Jurinocera (Baill.) Lipsch. and the species assigned to sect. Elatae Hook.f. of subg. Saussurea were separated from all other members of the genus Saussurea. The species of subgen. Jurinocera and subgen. Saussurea sect. Elatae form a monophyletic unit along with a group including genus Jurinea Cass. The species of subg. Jurinocera and sect. Elatae share 4–5-gonal cypselas and apical pericarpal crowns bearing sharp horns or sharp teeth. The Saussurea s.s. group is comprised of representatives of six sections of the subg. Saussurea and morphologically distinctive subgenera [Amphilaena (Stschegl.) Lipsch., Eriocoryne (DC.) Hook.f., and Theodorea (Cass.) Lipsch.]. Two frigid-adapted forms, the “snowball plants” of subg. Eriocoryne and the "glasshouse plants" of subg. Amphilaena, were confirmed as members of Saussurea s.s. Hemistepta lyrata and Saussurea s.s. show a close sister relationship, which is supported by the pappus dimorphism involving free, short, scabrid outer bristles or tiny outer scales and basally connate in a ring, with much longer, plumose inner bristles. [ABSTRACT FROM AUTHOR]

The systematic position of Parashorea chinensis (Dipterocarpaceae) was investigated by using maximum parsimony analysis of nucleotide sequences of marK, trnL intron, and trnL-trnF intergenic spacer region of chloroplast DNA. Previous studies have placed the taxon in Parashorea or Shorea. Analyses indicate that P. chinensis belongs within Parashorea (80% bootstrap) rather than within Shorea. Furthermore, P. chinensis Wang Hsie and P. chinensis Wang Hsie var. tcwangsiensis Lin Chi are further confirmed to be the same taxon. [ABSTRACT FROM AUTHOR]

Using matK and rbcL sequences (3,269 bp in total) from 113 genera of 45 families, we conducted a combined analysis to contribute to the understanding of major evolutionary relationships in the monocotyledons. Trees resulting from the parsimony analysis are similar to those generated by earlier single or multiple gene analyses, but their strict consensus tree provides much better resolution of relationships among major clades. We find that Acorus (Acorales) is a sister group to the rest of the monocots, which receives 100% bootstrap support. A clade comprising Alismatales is diverged as the next branch, followed successively by Petrosaviaceae, the Dioscoreales--Pandanales clade, Liliales, Asparagales and commelinoids. All of these clades are strongly supported (with more than 90% boot-strap support). The sister-group relationship is also strongly supported between Alismatales and the remaining mono-cots (except for Acorus) (100%), between Petrosaviaceae and the remaining monocots (except for Acorus and Alismatales) (100%), between the clade comprising Dioscoreales and Pandanales and the clade comprising Liliales, Asparagales and commelinoids (87%), and between Liliales and the Asparagales--commelinoids clade (89%). Only the sister-group relationship between Aspar-agales and commelinoids is weakly supported (68%). Results also support the inclusion of Petrosaviaceae in its own order Petrosaviales, Nartheciaceae in Dioscoreales and Hanguanaceae in Commelinales. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of the ‘core’ Laureae (Litsea complex) was conducted using the chloroplast gene matK and nuclear ribosomal DNA ITS sequences to investigate generic relationships and boundaries within the complex. Despite low genetic divergence for matK, rooting of the tree with Sassafras resulted in Iteadaphne as the basal member of the complex and five resolved clades: a Neolitsea clade and then Laurus, Parasassafras, Litsea and Lindera clades in a large polytomy with unresolved Lindera sections plus Umbellularia. A combined analysis of the data (identical to the ITS results) provided a more resolved phylogeny of the Laureae, with four major lineages: the Laurus, Litsea, Lindera and Actinodaphne II clades. These clades also appear to reflect the importance of inflorescence structure and ontogeny within the Laureae, as well as data from cuticular micromorphology, but there was no support for traditional generic characters such as 2- versus 4- celled anthers. As a result, genera such as Actinodaphne, Litsea, Neolitsea and Lindera were polyphyletic in all analyses. Parasassafras was related to Sinosassafras by the matK data, but distant from it in the ITS and combined analyses. [ABSTRACT FROM AUTHOR]

FLORICAULA/LEAFY (FLO/LFY) is a single-copy nuclear-encoded homeotic gene containing two introns. We have investigated the utility of the second intron of FLO/LFY (FLint2) as a tool for phylogeny reconstruction at lower taxonomic levels. As an example, the phylogeny of 46 Amorphophallus, two Pseudodracontium, and four outgroup species is reconstructed using maximum parsimony and maximum likelihood analyses of FLint2 sequences. We designed new primers based on conserved sequences of the second and third exon for use in a range of Aroid taxa to amplify and sequence the second intron. In Amorphophallus FLint2 proved to be rather short (143–222 bp), highly variable and unsaturated. In all but two species a single amplification product was found. Results from phylogenetic analysis of FLint2 are largely congruent with results using the chloroplast regions rbcL, matK, and trnL, and compare favorably in percentage of informative characters, overall homoplasy levels, number of well-supported clades in consensus trees and resolution of ingroup relationships within Amorphophallus. When amplification products are not too large, alignment is relatively straightforward, and sequences are used in combination with other fast evolving markers, the Flint2 intron may be a valuable new tool for phylogenetic studies at lower taxonomic levels. [Copyright &y& Elsevier]