Coding of insertion-deletion events of the chloroplastic intergene atp beta-rbcL for the phylogeny of the Valerianeae tribe (Valerianaceae)

A preliminary analysis of the sequence alignment of the chloroplast intergene atp beta-rbcL in tribe Valerianeae reveals that insertion-deletion evolutionary events ('indels'), combined with nucleotide substitutions, have occurred in large zones in some of the studied taxa. Due to the frequent occurrence and large size of indels within this tribe, intergene length varies from 531 to 788 base pairs within the studied species. This situation poses gap coding problems that we had to tackle before phylogenetic analysis. Four methods of gap coding were used: elimination of gapped sites ('complete omission'), 'missing data', 'fifth base' and Barriel's coding method, which translates indels into new multistate characters in the data matrix. After application of these four methods of data treatment, phylogenetic analyses (maximum parsimony) did not lead to very different results. Three robust clades emerged in each case, corresponding to the Centranthinae subtribe (genus Centranthus), the Fediinae subtribe (genera Fedia and Valerianella), and the American species of Valeriana. The theoretical basis and biological significance of these four methods are discussed in order to apply the best ones in future studies.     

A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for 26 species representing 11 genera of the tribe Oryzeae and three outgroup species. The sequenced fragments varied from 1522 base pairs (bp) to 1534 bp in length with 15.4% variable and 7.9% phylogenetically informative sites when the outgroups were excluded. The aligned sequences were analyzed by maximum parsimony and neighbor-joining methods. Analyses of the sequence data indicated that species of Oryzeae form a strongly supported monophyletic group, concordant with previous morphological and anatomical evidence. The tribe Oryzeae can be divided into two monophyletic lineages, corresponding to the traditionally recognized subtribes Oryzinae and Zizaniinae. The first subtribe consists of Oryza and Leersia, while the subtribe Zizaniinae includes the remaining genera. The matK sequence data did not support the close affinities of the monoecious genera in Oryzeae, implying the possibility of multiple origins of the floral structures in the tribe. It is noteworthy that Porteresia coarctata is closely related to Oryza species, suggesting that it should be treated as a member in the genus Oryza rather than a separate monotypic genus.     

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.     

Phylogeny of amorpheae (fabaceae: papilionoideae)

The legume tribe Amorpheae comprises eight genera and 240 species with variable floral form. In this study, we inferred a phylogeny for Amorpheae using DNA sequence data from the plastid trnK intron, including matK, and the nuclear ribosomal ITS1, 5.8S, and ITS2. Our data resulted in a well-resolved phylogeny in which the tribe is divided into the daleoids (Dalea, Marina, and Psorothamnus), characterized by generally papilionaceous corollas, and the amorphoids (Amorpha, Apoplanesia, Errazurizia, Eysenhardtia, and Parryella), characterized by non-papilionaceous flowers. We found evidence for the paraphyly of Psorothamnus and for the monophyly of Dalea once D. filiciformis is transferred to monophyletic Marina. Errazurizia rotundata is more closely related to Amorpha than to the other errazurizias, and Eysenhardtia is supported to be monophyletic. The monotypic Parryella and Apoplanesia are placed within the amorphoids. Among Papilionoideae, trnK/matK sequence data provide strong evidence for the monophyly of Amorpheae and place Amorpheae as sister to the recently discovered dalbergioid clade.     

Molecular Phylogeny of Nicotiana (Solanaceae) Based on the Nucleotide Sequence of the matK Gene

Abstract: Intrageneric relationships in the genus Nicotiana were investigated by comparison of DNA sequences of the matK gene of the chloroplast genome. A total of 40 taxa were examined in this study, representing 39 of the approximately 70 wild species of this genus. We obtained the full sequences of the 1530 bp matK ORFs; no variations in length due to insertions or deletions were found. The phylogenetic trees obtained from maximum parsimony (MP) and neighbour-joining (NJ) methods were fundamentally consistent. The genus Nicotiana formed a clade in these trees. The traditional classification of this genus was mostly in agreement with the molecular phylogeny. However, all three subgenera and some sections did not form a monophyletic group. Character-state mappings were used to infer a centre of origin, biogeographic history, and transition of chromosome number. The results support the previous hypothesis that this genus originated in South America and subsequently spread to other continents. The suggestion that the ancestral basic chromosome number is x = 12 and that polyploidy and aneuploidy have occurred independently several times during the evolution of Nicotiana species is also discussed.     

First insights into fern matK phylogeny

MatK, the only maturase gene in the land plant plastid genome, is a very popular phylogenetic marker that has been extensively applied in reconstructing angiosperm phylogeny. However, the use of matK in fern phylogeny is largely unknown, due to difficulties with amplification: ferns have lost the flanking trnK exons, typically the region used for designing stable priming sites. We developed primers that are either universal or lineage-specific that successfully amplify matK across all fern families. To evaluate whether matK is as powerful a phylogenetic marker in ferns as in angiosperms, we compared its sequence characteristics and phylogenetic performance to those of rbcL and atpA. Among these three genes, matK has the highest variability and substitution evenness, yet shows the least homoplasy. Most importantly, applying matK in fern phylogenetics better resolved relationships among families, especially within eupolypods I and II. Here we demonstrate the power of matK for fern phylogenetic reconstruction, as well as provide primers and extensive sequence data that will greatly facilitate future evolutionary studies of ferns.     

基于ITS和matK序列的獐牙菜亚族 (龙胆科龙胆族)分子系统学

为探讨獐牙菜亚族（subtribe Swertiinae）各属之间和一些属内的系统关系,本研究选取了该亚族14属68种1变种,采用最大简约法（maximum parsimony）和贝叶斯法（Bayesian inference）对样品核基因ITS和叶绿体基因matK的两个片段进行独立和联合分析。结果显示：Bartonia位于亚族的最基部;喉毛花属（Comastoma）、肋柱花属（Lomatogonium）和假龙胆属（Gentianella）都非单系,处于同一个较为进化的分支中;獐牙菜属折皱组（Swertia sect. Rugosa）和獐牙菜组（S. sect. Swertia）亲缘关系最近,宽丝组（S. sect. Platynema）和藏獐牙菜组（S. sect. Kingdon Wardia）亲缘关系最近;口药花属（Jaeschkea）与獐牙菜属多枝组（S. sect. Ophelia）的大籽獐牙菜（Smacrosperma）亲缘关系最近。同时讨论了獐牙菜亚族形态分类与分子数据不一致的原因。     

Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae)

Corallorhizinae are a small group of Old and New World temperate orchids of which a core monophyletic group comprises Govenia, Cremastra, Aplectrum, Oreorchis and the leafless Corallorhiza, and which according to phylogenetic analysis of nuclear ITS and plastid matK sequences, are related in this way: (Govenia (Cremastra (Aplectrum (Oreorchis (Corallorhiza))))). This hypothesis is consistent with the progressive deletion of the trnK intron and matK ORF. Frameshift-resulting indels yield a predicted loss of translation for the critical "domain X" region of matK and are evidence that matK is a probable pseudogene in Aplectrum, Oreorchis, and Corallorhiza. Within Corallorhiza, a previous hypothesis based on plastid DNA restriction site analysis is confirmed, with the thickened-labellum C. striata group being sister to the thin-labellum remainder of the genus, within which the circumboreal C. trifida is sister to the remainder, which then comprise two further sister groups: C. maculata + C. bulbosa + C. mertensiana and C. odontorhiza + C. wisteriana. A close relationship between C. striata and the recently described Appalachian C. bentleyi is shown; in particular, C. bentleyi is more closely allied to a southern Mexican population of C. striata than it is to northern North American C. striata populations, suggesting that two lineages, each with Mexican and northern North American populations, exist within the C. striata group.     

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

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

Molecular 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.     

The phylogeny of Patrinieae sensu Graebner (Valerianaceae) revisited: additional evidence from ndhF sequence data

 DNA sequences of both 5′ and 3′ regions of the plastid ndhF gene were generated in order to study the position of Patrinia and Nardostachys, to check the potential paraphyletic nature of Patrinieae, and to evaluate the possible link between the tribe and Linnaeaceae. Parsimony analysis showed very strong support for Patrinia as sister to all members of Valerianaceae (including Nardostachys) and indicated the paraphyletic nature of the tribe Patrinieae. Additionally, trees were constructed from available rbcL data separately and supplemented with ndhF sequences. Topologies of these combined cladograms are in agreement with the ndhF phylogeny, suggesting that the traditionally circumscribed Patrinieae can no longer be recognized but must be considered as part of a basal grade in Valerianaceae. Parsimony analysis based on a morphological data set supported a monophyletic Patrinieae; combination with the molecular data showed a paraphyletic Patrinieae. Furthermore, the possible link between Patrinieae and Linnaeaceae is evaluated. Received July 12, 2001 Accepted February 25, 2002     

Molecular phylogeny of the Caryophyllaceae (Caryophyllales) inferred from chloroplast matK and nuclear rDNA ITS sequences

Caryophyllaceae is a principally holarctic family including around 2200 species often classified into the three subfamilies Alsinoideae, Caryophylloideae, and Paronychioideae. Complex and possibly homoplasious morphological characters within the family make taxa difficult to delimit and diagnose. To explore part of the morphological evolution within the family, we investigated the phylogeny of the Caryophyllaceae by means of analyzing plastid and nuclear sequence data with parsimony and Bayesian methods. We describe a mode of tracing a stable phylogenetic signal in ITS sequences, and a significant common signal is shared with the plastid data. Parsimony and Bayesian analyses yield some differences in tree resolution. None of the subfamilies appear monophyletic, but the monophyly of the Caryophylloideae is not contradicted. Alsinoideae are paraphyletic, with Arenaria subg. Eremogone and Minuartia subg. Spergella more closely related to the Caryophylloideae. There is strong support for the inclusion of Spergula-Spergularia in an Alsinoideae-Caryophylloideae clade. Putative synapomorphies for these groupings are twice as many stamens as number of sepals and a caryophyllad-type of embryogeny. Paronychioideae form a basal grade, where tribe Corrigioleae are sister to the rest of the family. Free styles and capsules with simple teeth are possibly plesiomorphic for the family.     

Pollinators underestimated: a molecular phylogeny reveals widespread floral convergence in oil-secreting orchids (sub-tribe Coryciinae) of the Cape of South Africa

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.     

Phylogenetic systematics of the colorful, cyanide-producing millipedes of Appalachia (Polydesmida, Xystodesmidae, Apheloriini) using a total evidence Bayesian approach

Here, we provide an exemplar-approach phylogeny of the xystodesmid millipede tribe Apheloriini with a focus on genus-group relationships-particularly of the genus Brachoria. Exemplars for the phylogenetic analysis were chosen to represent the maximum breadth of morphological diversity within all nominal genera in the tribe Apheloriini, and to broadly sample the genus Brachoria. In addition, three closely related tribes were used (Rhysodesmini, Nannariini, and Pachydesmini). Morphological and DNA sequence data were scored for Bayesian inference of phylogeny. Phylogenetic analysis resulted in polyphyletic genera Brachoria and Sigmoria, a monophyletic Apheloriini, and a "southern clade" that contains most of the tribal species diversity. We used this phylogeny to track morphological character histories and reconstruct ancestral states using stochastic character mapping. Based on the findings from the character mapping study, the diagnostic feature of the genus Brachoria, the cingulum, evolved independently in two lineages. We compared our phylogeny against prior classifications using Bayes factor hypothesis-testing and found that our phylogenetic hypothesis is inconsistent with the previous hypotheses underlying the most recent classification. With our preferred total-evidence phylogeny as a framework for taxonomic modifications, we describe a new genus, Appalachioria; supply phylogenetic diagnoses of monophyletic taxa; and provide a phylogeny-based classification for the tribe Apheloriini.     

Critical Reexamination of Palynological Characters Used to Delimit Asclepiadaceae in Comparison to the Molecular Phylogeny Obtained from PlastidmatK Sequences

The family Asclepiadaceae (Dicotyledones) was created by Brown in 1810 by splitting in two the family Apocynaceae of Jussieu established in 1789. The morphological characters used to make this distinction were mainly palynological, such as presence of tetrads or pollinia and number and orientation of pollinia. Those characters, still used in higher taxonomic delimitation (families, subfamilies, and tribes), are here critically reexamined and compared to a molecular phylogeny obtained with one of the more variable plastid genes (matK) of 46 species in the order Gentianales. In this molecular phylogeny, Asclepiadaceae form a monophyletic group derived from within Apocynaceae. Each of the subfamilies of Asclepiadaceae is monophyletic and based on reliable palynological characters, but palynological characters are not useful to delimit tribes of the subfamily Asclepiadoideae. Based on the molecular data, these tribes have undergone parallelisms in several reproductive traits.     

Phylogeny of Eastern North American Coreopsis (Asteraceae-Coreopsideae): insights from nuclear and plastid sequences, and comments on character evolution

A molecular phylogenetic study of eastern North American Coreopsis and representatives of other genera of tribe Coreopsideae was conducted using combined sequences from nuclear ITS and two plastid regions (matK, rpl16). A total of 25-30 species has been recognized in five sections of Coreopsis in eastern North America. Based on morphological characters, these taxa have generally been considered a monophyletic group. Our well-resolved phylogeny supports the monophyly of sections that have been recognized in Coreopsis, but the sections collectively do not comprise a monophyletic group because species of north temperate Bidens occur within one of the two major Coreopsis clades. The most notable departure of present results from prior views of relationships among sections is the lack of a sister group relationship between sections Calliopsis and Eublepharis; the shared presence of four-lobed disk floret corollas had been used to support a close relationship between these two sections. Relationships within sections show both similarities and differences with the results of previous studies based primarily on morphological characters. Mapping of morphological characters used taxonomically in Coreopsis and related genera onto the phylogeny indicates that the evolution of these characters has been complex, and this compromises their value for defining monophyletic groups. Examples include the annual habit, alternate leaves, winged fruits, red or brown basal spots on the yellow ligules, and four-lobed disk floret corollas.