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

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

Molecular phylogenetics of Meliaceae (Sapindales) based on nuclear and plastid DNA sequences

Phylogenetic analyses of Meliaceae, including representatives of all four currently recognized subfamilies and all but two tribes (32 genera and 35 species, respectively), were carried out using DNA sequence data from three regions: plastid genes rbcL, matK (partial), and nuclear 26S rDNA (partial). Individual and combined phylogenetic analyses were performed for the rbcL, matK, and 26S rDNA data sets. Although the percentage of informative characters is highest in the segment of matK sequenced, rbcL provides the greatest number of informative characters of the three regions, resulting in the best resolved trees. Results of parsimony analyses support the recognition of only two subfamilies (Melioideae and Swietenioideae), which are sister groups. Melieae are the only tribe recognized previously that are strongly supported as monophyletic. The members of the two small monogeneric subfamilies, Quivisianthe and Capuronianthus, fall within Melioideae and Swietenioideae, respectively, supporting their taxonomic inclusion in these groups. Furthermore, the data indicate a close relationship between Aglaieae and Guareeae and a possible monophyletic origin of Cedreleae of Swietenioideae. For Trichilieae (Melioideae) and Swietenieae (Swietenioideae) lack of monophyly is indicated.     

Molecular phylogenetics of Fouquieriaceae: evidence from nuclear rDNA ITS studies

Molecular sequence data from the 18S-26S rDNA internal transcribed spacer (ITS) region support the monophyly of Fouquieria sensu lato (Fouquieriaceae) and the three subgenera (subg. Fouquieria, subg. Bronnia, subg. Idria) previously recognized within it. Resolution within subg. Fouquieria differs somewhat between parsimony and maximum likelihood (ML) trees. Section Fouquieria and sect. Ocotilla within subg. Fouquieria are not well supported as monophyletic groups. Uncertainty regarding placement of the root within Fouquieriaceae makes discussion of character evolution within the family difficult. Three root positions are consistent with rate-constant evolution of ITS sequences: (1) along the branch to subg. Idria, (2) along the branch to subg. Bronnia, and (3) along the branch to subg. Fouquieria. The first root position listed is equivalent to an outgroup rooting. The third root position listed is equivalent to a midpoint rooting. Of the three root positions above, only the third is along a branch that may be sufficiently long to act as a long-branch attractor. The first two root positions would result in character reconstruction suggesting that succulent growth forms and white floral pigmentation are ancestral within the family, with shifts to woody growth forms and to red floral pigmentation. The third root position results in equivocal reconstruction of the ancestral growth form, equivocal reconstruction of ancestral floral pigmentation in parsimony trees, and a suggestion of white floral pigmentation as ancestral in ML trees. Two previous hypotheses of polyploid origins are compatible with the molecular data presented here: (1) origin of the tetraploid F. diguetii from F. macdougalii, and (2) allopolyploid origin of the hexaploid F. burragei from the tetraploid F. diguetii and a diploid species similar to F. splendens. Direct descent of the hexaploid F. columnaris from the subg. Bronnia lineage is not supported by our data. An amphiploid origin of F. columnaris involving a member of the subg. Bronnia lineage and an extinct taxon outside subg. Bronnia, however, cannot be ruled out.     

Molecular phylogenetics of Paphiopedilum (Cypripedioideae; Orchidaceae) based on nuclear ribosomal ITS and plastid sequences

Phylogenetic relationships in the genus Paphiopedilum were studied using nuclear ribosomal internal transcribed spacer (ITS) and plastid sequence data. The results confirm that the genus Paphiopedilum is monophyletic, and the division of the genus into three subgenera Parvisepalum, Brachypetalum and Paphiopedilum is well supported. Four sections of subgenus Paphiopedilum (Pardalopetalum, Cochlopetalum, Paphiopedilum and Barbata) are recovered as in a recent infrageneric treatment, with strong support. Section Coryopedilum is also recovered, with low bootstrap but high posterior probability values for support of monophyly. Relationships in section Barbata remain unresolved, and short branch lengths and the narrow geographical distribution of many species in the section suggest that it possibly underwent rapid radiation. Mapping chromosome and genome size data (including some new genome size measurements) onto the phylogenetic framework shows that there is no clear trend in increase in chromosome number in the genus. However, the diploid chromosome number of 2n = 26 in subgenera Parvisepalum and Brachypetalum suggests that this is the ancestral condition, and higher chromosome numbers in sections Cochlopetalum and Barbata suggest that centric fission has possibly occurred in parallel in these sections. The trend for genome size evolution is also unclear, although species in section Barbata have larger genome sizes than those in other sections. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 176–196.     

Molecular systematics of Malpighiaceae: evidence from plastid rbcL and matK sequences

Phylogenetic analyses of DNA nucleotide sequences from the plastid genes rbcL and matK were employed to investigate intergeneric relationships within Malpighiaceae. Cladistic relationships generated from the independent data matrices for the family are generally in agreement with those from the combined matrix. At the base of Malpighiaceae are several clades mostly representing genera from a paraphyletic subfamily Byrsonimoideae. Intergeneric relationships among these byrsonimoid malpighs are well supported by the bootstrap, and the tribe Galphimeae is monophyletic. There is also a well-supported clade of genera corresponding to tribes Banisterieae plus Gaudichaudieae present in all trees, and many of the relationships among these banisterioid malpighs are well supported by the bootstrap. However, tribes Hiraeae and Tricomarieae (the hiraeoid malpighs) are paraphyletic and largely unresolved. Species of Mascagnia are distributed throughout these hiraeoid clades, confirming the suspected polyphyly of this large genus. Optimization of selected morphological characters on these trees demonstrates clear phylogenetic trends such as the evolution of globally symmetrical from radially symmetrical pollen, increased modification and sterilization of stamens, and switch from base chromosome number n = 6 to n = 10.     

基于13 个内含子的序列探讨鲸目的系统发育关系

本文基于实验室筛选得到的13 对内含子标记,在鲸偶蹄目的15 个物种中进行有效扩增,并重建了这15
个物种的系统发育关系。结果表明,抹香鲸总科(Physeteroidea) 位于齿鲸亚目(Odontoceti)的基部,从而支
持了传统的齿鲸亚目的单系性。在海豚总科(Delphinoidea)内部,贝斯分析结果支持了鼠海豚科(Phocoenidae)
和一角鲸科(Monodontidae)的姐妹群关系,而后再与海豚科(Delphinidae)相聚。系统发育分析同时还
强烈支持了海豚科的四个属(Sousa,Tursiops,Stenella,Delphinus)组成一个单系的“复合体”。另外,我们的分
析结果并不支持瓶鼻海豚属(Tursiops)和原海豚属(Stenella)的单系性。基于松散分子钟的分歧时间估算与以
往文献中的结果没有明显差异。这些研究结果提示,核基因内含子序列有希望解决一些长期存在的鲸类系统发
育问题。     

Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences

Background

Previous phylogenetics studies of Asparagales, although extensive and generally well supported, have left several sets of taxa unclearly placed and have not addressed all relationships within certain clades thoroughly (some clades were relatively sparsely sampled). One of the most important of these is sampling within and placement of Nolinoideae (Ruscaceae s.l.) of Asparagaceae sensu Angiosperm Phylogeny Group (APG) III, which subfamily includes taxa previously referred to Convallariaceae, Dracaenaaceae, Eriospermaceae, Nolinaceae and Ruscaceae.

Methods

A phylogenetic analysis of a combined data set for 126 taxa of Ruscaceae s.l. and related groups in Asparagales based on three nuclear and plastid DNA coding genes, 18S rDNA (1796 bp), rbcL (1338 bp) and matK (1668 bp), representing a total of approx. 4·8 kb is presented. Parsimony and Bayesian inference analyses were conducted to elucidate relationships of Ruscaceae s.l. and related groups, and parsimony bootstrap analysis was performed to assess support of clades.

Key Results

The combination of the three genes results in the most highly resolved and strongly supported topology yet obtained for Asparagales including Ruscaceae s.l. Asparagales relationships are nearly congruent with previous combined gene analyses, which were reflected in the APG III classification. Parsimony and Bayesian analyses yield identical relationships except for some slight variation among the core asparagoid families, which nevertheless form a strongly supported group in both types of analyses. In core asparagoids, five major clades are identified: (1) Alliaceae s.l. (sensu APG III, Amarylidaceae–Agapanthaceae–Alliaceae); (2) Asparagaceae–Laxmanniaceae–Ruscaceae s.l.; (3) Themidaceae; (4) Hyacinthaceae; (5) Anemarrhenaceae–Behniaceae–Herreriaceae–Agavaceae (clades 2–5 collectively Asparagaceae s.l. sensu APG III). The position of Aphyllanthes is labile, but it is sister to Themidaceae in the combined maximum-parsimony tree and sister to Anemarrhenaceae in the Bayesian analysis. The highly supported clade of Xanthorrhoeaceae s.l. (sensu APG III, including Asphodelaceae and Hemerocallidaceae) is sister to the core asparagoids. Ruscaceae s.l. are a well-supported group. Asparagaceae s.s. are sister to Ruscaceae s.l., even though the clade of the two families is weakly supported; Laxmanniaceae are strongly supported as sister to Ruscaceae s.l. and Asparagaceae. Ruscaceae s.l. include six principal clades that often reflect previously named groups: (1) tribe Polygonateae (excluding Disporopsis); (2) tribe Ophiopogoneae; (3) tribe Convallarieae (excluding Theropogon); (4) Ruscaceae s.s. + Dracaenaceae + Theropogon + Disporopsis + Comospermum; (5) Nolinaceae, (6) Eriospermum.

Conclusions

The analyses here were largely conducted with new data collected for the same loci as in previous studies, but in this case from different species/DNA accessions and greater sampling in many cases than in previously published analyses; nonetheless, the results largely mirror those of previously conducted studies. This demonstrates the robustness of these results and answers questions often raised about reproducibility of DNA results, given the often sparse sampling of taxa in some studies, particularly the earliest ones. The results also provide a clear set of patterns on which to base a new classification of the subfamilies of Asparagaceae s.l., particularly Ruscaceae s.l. (= Nolinoideae of Asparagaceae s.l.), and examine other putatively important characters of Asparagales.     

Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences

To study the inter- and infrafamilial phylogenetic relationships in the order Caryophyllales sensu lato (s.l.), ～930 base pairs of the matK plastid gene have been sequenced and analyzed for 127 taxa. In addition, these sequences have been combined with the rbcL plastid gene for 53 taxa and with the rbcL and atpB plastid genes as well as the nuclear 18S rDNA for 26 taxa to provide increased support for deeper branches. The red pigments of Corbichonia, Lophiocarpus, and Sarcobatus have been tested and shown to belong to the betacyanin class of compounds. Most taxa of the order are clearly grouped into two main clades (i.e., "core" and "noncore" Caryophyllales) which are, in turn, divided into well-defined subunits. Phytolaccaceae and Molluginaceae are polyphyletic, and Portulacaceae are paraphyletic, whereas Agdestidaceae, Barbeuiaceae, Petiveriaceae, and Sarcobataceae should be given familial recognition. Two additional lineages are potentially appropriate to be elevated to the family level in the future: the genera Lophiocarpus and Corbichonia form a well-supported clade on the basis of molecular and chemical evidence, and Limeum appears to be separated from other Molluginaceae based on both molecular and ultrastructural data.     

Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences

We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.     

Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid DNA sequences

To evaluate the monophyly of subtribe Pleurothallidinae (Epidendreae: Orchidaceae) and the component genera and to reveal evolutionary relationships and trends, we sequenced the nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2) and 5.8S gene for 185 taxa. In addition, to improve the overall assessments along the spine of the topology, we added plastid sequences from matK, the trnL intron, and the trnL-F intergenic spacer for a representative subset of those taxa in the ITS study. All results were highly congruent, and so we then combined the sequence data from all three data sets in a separate analysis of 58 representative taxa. There is strong support in most analyses for the monophyly of Pleurothallidinae and in some for inclusion of Dilomilis and Neocognauxia of Laeliinae. Although most genera in the nine clades identified in the analyses are monophyletic, all data sets are highly congruent in revealing the polyphyly of Pleurothallis and its constitutent subgenera as presently understood. The high degree of homoplasy in morphological characters, especially floral characters, limits their usefulness in phylogenetic reconstruction of the subtribe.     

Molecular phylogenetics of Prescottiinae s.l. and their close allies (Orchidaceae, Cranichideae) inferred from plastid and nuclear ribosomal DNA sequences

The Andes are a cradle of orchid evolution, but most phylogenetic studies of Orchidaceae in this biodiversity hotspot have dealt with epiphytic epidendroid lineages. Here we present a study on neotropical, terrestrial, orchidoid taxa of Prescottiinae s.l. (8 genera, ～100 species), which are adapted to some of the highest elevation habitats on earth that support orchids. They are currently included within an expanded concept of Cranichidinae in the tribe Cranichideae, but DNA sequence data show that neither Prescottiinae s.l. nor Cranichidinae s.s. are monophyletic. Prescottiinae s.l. consist of two strongly supported lineages: the Altensteinia and Prescottia clades, which have closer affinities to Spiranthinae than to Cranichidinae. The Prescottia clade comprises two well-supported subclades, one including most sampled species of Prescottia and a second one with Pseudocranichis thysanochila sister to Prescottia tubulosa. As a group, they are sister to Spiranthinae. Sister to this pair is the Altensteinia clade comprised of six genera, whose intergeneric relationships are well resolved. Finally, Cranichidinae s.s. is sister to all three of these clades. Morphological and ecological features distinguishing the major groups are discussed, as are potential synapomorphies to define them. The reconstructed phylogeny indicates that the classification of Cranichideae needs to be reexamined.     

Molecular systematics and biogeography of Wisteria inferred from nucleotide sequences of nuclear and plastid genes

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 ofAfgekia, 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 ofW. 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.     

Molecular phylogeny of Chinese Rubia (Rubiaceae: Rubieae) inferred from nuclear and plastid DNA sequences

Rubia L. is the type genus of the coffee family Rubiaceae and the third largest genus in the tribe Rubieae, comprising ca. 80 species restricted to the Old World. China is an important diversity center for Rubia, where approximately half of its species occur. However, its internal phylogenetic relationships are still poorly understood. The objective of the present study is to contribute to the phylogenetic relationships within Rubia, using the nuclear internal transcribed spacer and six plastid markers and focusing on species from China. Twenty-seven species of Rubia were sampled to infer their phylogeny using Maximum parsimony, Maximum likelihood, and Bayesian analyses. The monophyly of Rubia is supported, provided that R. rezniczenkoana Litv. is excluded from Rubia and transferred to Galium as a new combination: G. rezniczenkoanum (Litv.) L. E Yang & Z. L. Nie. Within Rubia, two clades are clearly supported. They correspond to the traditional sect. Rubias.l. (A) and sect. Oligoneura Pojark. (B), and are morphologically mainly separable by their pinnate (A) versus palmate (B) leaf venation. Plesiomorphic features are the pinnate leaf veining in sect. Rubia s.l. and the occurrence of some species with opposite leaves and true stipules in sect. Oligoneura. In sect. Oligoneura one can assume an evolution from species with opposite leaves and true stipules (as in the R. siamensis Craib group) to those with whorls of two leaves and two leaf-like stipules (as in ser. Chinenses and the R. mandersii Collett & Hemsl. group) and finally with whorls of 6 or even more elements (as in ser. Cordifoliae). The correlation between clades recognized by DNA analyses and available differential morphological features is partly only loose, particularly in the group of R. cordifolia with 2×, 4×, and 6× cytotypes. This may be due to rapid evolutionary divergence and/or hybridization and allopolyploidy.     

Molecular phylogenetics of tribe Poranthereae (Phyllanthaceae; Euphorbiaceae sensu lato)

Novel insights into the evolutionary history of a taxonomically complex tropical plant group were gained in this study using DNA sequence data. A molecular phylogenetic analysis of the newly circumscribed and expanded tribe Poranthereae (Phyllanthaceae) is presented. Sampling included 97 accessions for 63 of c. 120 species. Largely congruent results have been obtained from nuclear ribosomal ITS and plastid matK sequences. These analyses support the recognition of Andrachne and Leptopus as distinct genera. The deceptively similar Andrachne section Phyllanthopsis, Andrachne ovalis, and Leptopus decaisnei are separate lineages to be segregated. Zimmermannia and Zimmermanniopsis are embedded in Meineckia; Oreoporanthera is embedded in Poranthera; and Archileptopus is embedded in Leptopus. Andrachne section Pseudophyllanthus is polyphyletic, the two Madagascan endemics emerging as a sister clade to Meineckia. The noncontiguous distributions of Andrachne sensu lato and Leptopus sensu lato were found to be the result of separate evolutionary histories of morphologically similar clades, whereas Andrachne sensu stricto and Meineckia remain geographically disjunct. Actephila and Leptopus are sisters with a sympatric distribution in humid Asia. Presence of petals appears to be plesiomorphic for the tribe. Petals are reduced in Actephila and Oreoporanthera and lost in the Meineckia clade.     

Molecular phylogenetics of Hypoxidaceae--evidence from plastid DNA data and inferences on morphology and biogeography

Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G--only rarely used in monocot research--contributed a substantial number of potentially parsimony informative characters. Hypoxidaceae consist of three well-supported major clades, but their interrelationships remain unresolved. Our data indicate that in the Pauridia clade one long-distance dispersal event occurred from southern Africa to Australia. Long-distance dispersal scenarios may also be likely for the current distribution of Hypoxis, which occurs on four continents. In the Curculigo clade, the present distribution of Curculigo s.s. on four continents could support a Gondwanan origin, but the level of divergence is too low for this hypothesis to be likely. The main clades correspond well with some floral characters, habit and palynological data, whereas chromosomal data exhibit plasticity and probably result from polyploidization and subsequent dysploidy and/or aneuploidy. Evolutionary flexibility is also suggested by the number of reported pollination syndromes: melittophily, myophily, sapromyophily, and cantharophily. Based on our phylogenetic results, we suggest cautious nomenclatural reorganization to generate monophyly at the generic level.     

Molecular phylogenetics of Linaceae with complete generic sampling and data from two plastid genes

The phylogeny of Linaceae is examined, with sampling from the 13 commonly recognized genera of the family and sequence data from the plastid genes matK and rbcL. Representatives of 24 additional families of the order Malpighiales are included in the analyses, with members of Celastrales, Fabales, Fagales, Oxalidales and Rosales used as outgroups. Linaceae and both subfamilies, the temperate Linoideae and the tropical Hugonioideae, are found to be monophyletic in likelihood‐ and parsimony‐based analyses, although the monophyly of Hugonioideae is not well supported. Average divergence time estimates using rbcL indicate that the subfamilies diverged from each other during the Palaeocene, approximately 60 million years ago. No sister group to Linaceae is consistently identified in these analyses, and relationships among families of Malpighiales are not well resolved. In accord with previous estimates of Linoideae phylogeny, Linum is shown to be nonmonophyletic, with several segregate genera nested within it, but the relationships of the south‐east Asian genera, Anisadenia, Reinwardtia and Tirpitzia, remain uncertain. In Hugonioideae, Indorouchera and Philbornea are found to be closely related to members of Hugonia section Durandea. Relationships of the neotropical genera Hebepetalum and Roucheria to the palaeotropical hugonioids are not consistently resolved. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 64–83.