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Understanding the relationships within the Caryophyllaceae has been difficult, in part because of arbitrarily and poorly defined genera and difficulty in determining phylogenetically useful morphological characters. This study represents the most complete phylogenetic analysis of the family to date, with particular focus on the genera and relationships within the large subfamily Alsinoideae, using molecular characters to examine the monophyly of taxa and the validity of the current taxonomy as well as to resolve the obscure origins of divergent taxa such as the endemic HawaiianSchiedea. Maximum parsimony and maximum likelihood analyses of three chloroplast gene regions (matK,trnL‐F, andrps16) from 81 newly sampled and 65 GenBank specimens reveal that several tribes and genera, especially within the Alsinoideae, are not monophyletic. Large genera such asArenariaandMinuartiaare polyphyletic, as are several smaller genera. The phylogenies reveal that the closest relatives toSchiedeaare a pair of widespread, largely Arctic taxa,Honckenya peploidesandWilhelmsia physodes. More importantly, the three traditional subfamilies (Alsinoideae, Caryophylloideae, and Paronychioideae) are not reflective of natural groups; we propose abandoning this classification in favor of a new system that recognizes major lineages of the molecular phylogeny at the tribal level. A new tribe, Eremogoneae Rabeler & W.L. Wagner, is described here.

Phylogenetic relationships within Miconia and other genera in the Neotropical tribe Miconieae were investigated using a maximum parsimony analysis of nuclear internal transcribed spacer and ndhF nucleotide sequences. Included were all sections in Miconia (212 species, ∼20% of the genus) and 12 of the 15 remaining genera assigned to the tribe (an additional 239 species). Given the tribe's reputation for problematic generic distinctions, it was not surprising that most traditionally recognized taxonomic groups-both genera and sections-were shown to be polyphyletic or paraphyletic. Nevertheless, Miconia is composed of several distinct monophyletic groups, with a large majority of the species belonging to only four clades. Some of these groups represent parts of sections proposed in the last revision of the genus, but most of the diversification seems to have occurred in geographical areas that are more restricted than would have been predicted by the distribution of these sections. Moreover, parallel evolutionary trends are seen in anther form, i.e., shifts from elongate to shorter anthers and from minute-pored to large-pored or slitlike dehiscent anthers. These changes may relate to pollinator shifts, especially from buzz pollination to nonvibrational pollination. Thus, the major evolutionary diversifications within the tribe have been obscured by convergence in stamen morphology, leading to many arbitrary generic and sectional circumscriptions.

Few studies have addressed the evolutionary relationships within Polygonaceae from a global perspective. The convoluted taxonomic history of Polygonaceae is a major barrier to understanding evolution in this group, and only portions of it have been included in systematic treatments. Phylogenetic studies have been limited in both taxon sampling and amount of data. Our objective is to identify clades within Polygonaceae and to provide a global estimate of phylogenetic relationships in this morphologically diverse and geographically widespread group. We include a total of 75 species representing approximately 40 of the 55 named genera in the family. We use three chloroplast regions (rbcL,matK, andndhF) and the ribosomal internal transcribed spacer to understand the phylogenetic relationships in Polygonaceae. Maximum parsimony and maximum likelihood are used to analyze the data.Symmeriais the sister group to remaining Polygonaceae sampled, and there is strong support for this placement.Afrobrunnichiabranches next but has only moderate support. Two large clades comprise Polygonaceae, generally corresponding to those found in previous molecular analyses. Circumscription of most of the currently recognized subgroups within Polygonaceae did not agree with clades identified in the total data analyses, with the exception of Rumiceae Dum.

A first comprehensive phylogenetic analysis of tribe Salsoleae s.l. (Salsoloideae: Chenopodiaceae) is presented based on maximum parsimony and maximum likelihood analysis of nuclear ribosomal internal transcribed spacer and chloroplastpsbB‐psbHDNA sequences. Our data strongly support (1) the sister relationship of Camphorosmeae to the Salsoleae s.l.; (2) splitting of Salsoleae s.l. into two monophyletic tribes, Salsoleae s.s. and Caroxyloneae tribus nova; (3) the current status of most monotypic or oligotypic genera in Salsoleae; and (4) polyphyly of the Botschantzev and Freitag (among others) circumscriptions ofSalsola, which falls into 10 (on average) monophyletic genera/lineages. Three well‐supported genera are described as new (Pyankovia,Kaviria, andTurania), and four previously described genera are resurrected (Caroxylon,Climacoptera,Kali, andXylosalsola).Salsolas.s. include a group of central and southwest Asian and north African species that consists ofSalsolasect.Salsolas.s.,Salsolasect.Caroxylonsubsect.Coccosalsola,Salsolasect.Obpyrifolia,Fadenia,Hypocylix,Seidlitzia, andDarniella. All species of tribe Caroxyloneae investigated so far have C4photosynthesis of the NAD‐malic enzyme subtype, while the majority of the species of Salsoleae s.s. are known to be of the NADP‐malic enzyme subtype.

Nucleotide sequences of seven chloroplast (atpBandrbcL, SSU and LSU rDNAs), mitochondrial (atp1, LSU rDNA), and nuclear (18S rDNA) genes from 192 land plants and their algal relatives were analyzed using maximum likelihood and maximum parsimony methods. Liverworts, mosses, hornworts, lycophytes, monilophytes (ferns), seed plants, and angiosperms all represent strongly supported monophyletic groups. Three bryophyte lineages form a paraphyletic group to vascular plants, with liverworts representing the sister to all other land plants and hornworts being sister to vascular plants. Lycophytes are sister to all other vascular plants, which are divided into two clades, one being monilophytes, which includeEquisetum, Psilotaceae‐Ophioglossaceae, Marattiaceae, and leptosporangiate ferns, and the other being seed plants. Relationships among the monilophyte lineages remain unresolved. Within seed plants, extant gymnosperms form a moderately supported clade in which Gnetales are related to conifers. This clade is sister to angiosperms. Most of the relationships among all major lineages of nonflowering land plants are supported by bootstrap values of 75% or higher, except those among basal monilophyte lineages and among some gymnosperm lineages, probably because of extinctions. The closest algal relative of land plants is Characeae, and this relationship is well supported. Several methodological issues on reconstructing large, deep phylogenies are also discussed.

The phylogenetic relationships of 51 isolates representing 27 species of Phytophthora were assessed by sequence alignment of 568 bp of the mitochondrially encoded cytochrome oxidase II gene. A total of 1299 bp of the cytochrome oxidase I gene also were examined for a subset of 13 species. The cox II gene trees constructed by a heuristic search, based on maximum parsimony for a bootstrap 50% majority-rule consensus tree, revealed 18 species grouping into seven clades and nine species unaffiliated with a specific clade. The phylogenetic relationships among species observed on cox II gene trees did not exhibit consistent similarities in groupings for morphology, pathogenicity, host range or temperature optima. The topology of cox I gene trees, constructed by a heuristic search based on maximum parsimony for a bootstrap 50% majority-rule consensus tree for 13 species of Phytophthora, revealed 10 species grouping into three clades and three species unaffiliated with a specific clade. The groupings in general agreed with what was observed in the cox II tree. Species relationships observed for the cox II gene tree were in agreement with those based on ITS regions, with several notable exceptions. Some of these differences were noted in species in which the same isolates were used for both ITS and cox II analysis, suggesting either a differential rate of evolutionary divergence for these two regions or incorrect assumptions about alignment of ITS sequences. Analysis of combined data sets of ITS and cox II sequences generated a tree that did not differ substantially from analysis of ITS data alone, however, the results of a partition homogeneity test suggest that combining data sets may not be valid.

Soybean sudden-death syndrome has become a serious constraint to commercial production of this crop in North and South America during the past decade. To assess whether the primary etiological agent is panmictic in both hemispheres, morphological and molecular phylogenetic analyses were conducted on strains selected to represent the known pathogenic and genetic diversity of this pathogen. Maximum-parsimony analysis of DNA sequences from the nuclear ribosomal intergenic spacer region and the single copy nuclear gene translation elongation factor 1-α, together with detailed morphological comparisons of conidial features, indicate that SDS of soybean in North and South America is caused by two phylogenetically and morphologically distinct species. Fusarium virguliforme sp. nov., formally known as F. solani f. sp. glycines, is described and illustrated for the SDS pathogen in North America, and F. tucumaniae sp. nov. is proposed for the South American pathogen. The molecular phylogenetic results challenge the forma specialis naming system because pathogenicity to soybean might have evolved convergently in F. tucumaniae and F. virguliforme. Phylogenetic evidence indicates the two SDS pathogens do not share a most recent common ancestor, since F. tucumaniae was resolved as a sister to a pathogen of Phaseolus vulgaris, F. phaseoli comb. nov. All three pathogens appear to have evolutionary origins in the southern hemisphere since they are deeply nested within a South American clade of the F. solani species complex.

In order to investigate phylogenetic relationships of the Peronosporomycetes (Oomycetes), nuclear large subunit ribosomal DNA sequences containing the D1 and D2 region were analyzed of 92 species belonging to the orders Peronosporales, Pythiales, Leptomitales, Rhipidiales, Saprolegniales and Sclerosporales. The data were analyzed applying methods of neighbor-joining as well as maximum parsimony, both statistically supported using the bootstrap method. The results confirm the major division between the Pythiales and Peronosporales on the one hand and the Saprolegniales, Leptomitales, and Rhipidiales on the other. The Sclerosporales were shown to be polyphyletic; while Sclerosporaceae are nested within the Peronosporaceae, the Verrucalvaceae are merged within the Saprolegniales. Within the Peronosporomycetidae, Pythiales as well as Peronosporales as currently defined are polyphyletic. The well supported Albugo clade appears to be the most basal lineage, followed by a Pythium-Lagenidium clade. The third, highly supported clade comprises the Peronosporaceae together with Sclerospora, Phytophthora, and Peronophythora. Peronophythora is placed within Phytophthora, indicating that both genera should be merged. Bremiella seems to be polyphyletic within the genus Plasmopara, suggesting a transfer to Plasmopara. The species of Peronospora do not appear as a monophyletic group. Peronospora species growing on Brassicaceae form a highly supported clade.

This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea's efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as \"source\" of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation. We focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a \"Hennigian forest\"). The binary representations of the genomic (DNA) data have been made by script . The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data. The binary matrix may be easily re-written as a set of rooted trees ( relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, can help to identify clades the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data. Our proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual \"data\" also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the \"direct\" alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major differences between our recent proposal and the 3TA, as originally designed and implemented: (1) the 3TA deals with the three-taxon statements or minimal relationships. According to the logic of 3TA, the set of the minimal trees must be established as a binary matrix and used as an input for the parsimony program. In this paper, we operate directly with maximal relationships written just as trees, not as binary matrices, while also using the Average Consensus method instead of the MP analysis. The solely 'reversal'-based groups can always be found by our method without the separate scoring of the putative reversals before analyses.

Numerous TCP genes (transcription factors with a TCP domain) occur in legumes. Genes of this class in Arabidopsis (TCP1) and snapdragon (Antirrhinum majus; CYCLOIDEA) have been shown to be asymmetrically expressed in developing floral primordia, and in snapdragon, they are required for floral zygomorphy (bilaterally symmetrical flowers). These genes are therefore particularly interesting in Leguminosae, a family that is thought to have evolved zygomorphy independently from other zygomorphic angiosperm lineages. Using a phylogenomic approach, we show that homologs of TCP1/CYCLOIDEA occur in legumes and may be divided into two main classes (LEGCYC group I and II), apparently the result of an early duplication, and each class is characterized by a typical amino acid signature in the TCP domain. Furthermore, group I genes in legumes may be divided into two subclasses (LEGCYC IA and IB), apparently the result of a duplication near the base of the papilionoid legumes or below. Most papilionoid legumes investigated have all three genes present (LEGCYC IA, IB, and II), inviting further work to investigate possible functional difference between the three types. However, within these three major gene groups, the precise relationships of the paralogs between species are difficult to determine probably because of a complex history of duplication and loss with lineage sorting or heterotachy (within-site rate variation) due to functional differentiation. The results illustrate both the potential and the difficulties of orthology determination in variable gene families, on which the phylogenomic approach to formulating hypotheses of function depends.