FURTHER STUDIES OF PRESUMEDLY PRIMITIVE GREEN ALGAE,INCLUDING THE DESCRIPTION OF PEDINOPHYCEAE CLASS. NOV. AND RESULTOR GEN. NOV.1

The tiny jumping flagellate originally described as Pedinomonas mikron Throndsen was isolated into pure culture from Australian waters and its ultrastructure critically examined. Pedinomonas mikron differs in behavior and in features of the flagellar apparatus from P. minor, the type species from freshwater, and is referred to the new genus Resultor. The two genera are closely related and form the new class Pedinophyceae, which is characterized by features of the flagellar apparatus, mitosis, and cytokinesis. The flagella show the 11/5 orientation otherwise characteristic of Ulvophyceae and Pleurastrophyceae, but they are arranged end to end as in the Chlorophyceae. The flagellar root system is asymmetric and includes a rhizoplast that emerges from the base of one flagellum but subsequently associates with a microtubular root from the second basal body. Mitosis studied previously by Pickett-Heaps and Ott in Pedinomonas is closed, unlike in other green algae, and the spindle is persistent. No phycoplast or phragmoplast is formed during cytokinesis. The eyespot of the Pedinophyceae is located at the opposite end of the cell from the flagella and adjacent to the pyrenoid, as in the most primitive members of the Prasinophyceae. Members of the Pedinophyceae lack prasinoxanthin and Mg 2,4D, characteristic of certain other primitive green algae. The primitive green algae include the classes Prasinophyceae and Pedinophyceae. Micromonadophyceae Mattox et Stewart is considered a synonym of Prasinophyceae. Two new orders are established, Pedinomonadales, containing all known members of the Pedinophyceae, and Scourfieldiales, with the single family Scourfieldiaceae fam. nov. and the single genus Scourfieldia.     

Molecular phylogeny in the Lardizabalaceae

Eleven species belonging to seven genera in the Lardizabalaceae were analyzed in terms of restriction fragment length polymorphism (RFLP) of chloroplast DNA and the sequence of the chloroplast gene,rbcL, of Lardizabalaceae and its related families. Phylogenetic trees inferred from parsimony, neighbor joining and maximum likelihood methods based on RFLP data showed that two South American genera,Boquila andLardizabala, and three East Asian genera,Akebia, Holboellia andStauntonia are closely related to each other, respectively. On the other hand, the parsimony, neighbor joining and maximum likelihood trees constructed using sequence data of therbcL gene showed thatAkebia, Stauntonia, Boquila andLardizabala clustered as(((Akebia, Stauntonia), Boquila), Lardizabala). This difference may be attributable to fewer informative sites inrbcL genes than in RFLP in this family.Decaisnea diverges at the very base of the Lardizabalaceae.     

EVOLUTIONARY ANALYSIS OF THE LARGE SUBUNIT OF CARBOXYLASE (rbcL) NUCLEOTIDE SEQUENCE AMONG THE GRASSES (GRAMINEAE)

The full nucleotide sequences of the chloroplast encoded large subunit of ribulose-1,5-bisphosphate carboxylase (rbcL) are available for nine grass species and partial sequence data for one species. Relative rate tests of the “molecular clock” hypothesis suggest that rbcL evolved more rapidly in the lineage leading to Zea than in those leading to the other species. The estimated overall substitution rate for rbcL among these grasses is about 5 times 10^?10 substitutions per site per year, or about one-half the synonymous rate. The nine full sequences were analyzed by the UPGMA, Wagner parsimony, maximum likelihood, and Fitch-Margoliash methods. The latter three methods produced trees with the same topology. This topology largely agrees with current taxonomic evidence regarding the relationships among these grasses. UPGMA produced a topology that conflicts more substantially with available taxonomic evidence. Statistical comparison of the three alternative topologies for the subfamilies Panicoideae, Pooideae and Bambusoideae failed to support one of these topologies over the others, reflecting the taxonomic ambiguities surrounding the relationships among these taxa. Phylogenetic analyses based on the partial sequences of all 10 species gave conflicting results with regard to the relationship between Hordeum and Triticum, both members of the tribe Triticeae. This indicates that rbcL sequences contain too little information to resolve relationships among genera within this tribe. Overall, the results suggest that rbcL sequence data can provide some new information concerning grass phylogeny, but that the amount of available data from this gene is too small to differentiate statistically among alternative topologies for the grasses. Conflicting results from parsimony, maximum likelihood, and Fitch-Margoliash methods proved useful in exploring the validity of assumptions underlying these methods.     

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid,nuclear gene and spacer sequences

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretum and Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretum is strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminalia as it forms a polytomy with Anogeissus. This clade is sister to Conocarpus. Electronic Publication     

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.     

An ultrastructural study of Marsupiomonas pelliculata gen. et sp. nov., a new member of the Pedinophyceae

A new species, Marsupiomonas pelliculata gen. et sp. nov. (Pedinophyceae), is described. A single flagellum emerges from a deep pit with a distinctive thickened margin. The flagellum has rigid fibrillar hairs which are probably formed in the perinuclear space. A short second flagellar basal body lies within the cell close to the basal body of the emergent flagellum and the flagellar root system consists of striated and microtubular roots. There is a distinctive theca covering all but the anterior end of the cell and also a single large bright green chloroplast with an immersed pyrenoid surrounded by a starch shell. The wide salinity tolerance of the species is discussed in relation to its distribution in estuarine and salt marsh habitats. The salient features of the new species—the insertion of the emergent flagellum into a deep pit and the possession of a theca—are also seen in Pedinomonas tenuis, and it is suggested that P. tenuis could be transferred to the new genus Marsupiomonas. The class Pedinophyceae now includes three genera (Pedinomonas, Resultor and Marsupiomonas) and the distinguishing features are discussed.     

Phylogenetic Relationships of Amaryllidaceae Based on matK Sequence Data

matK gene, which is located in the chloroplast genome and evolves more quickly than the rbcL gene. A total of 31 species representing 31 of the 59 genera in the family were examined in this study. We also used 21 species from another ten families of Asparagales, four species from three families of Liliales and Acorus as outgroups. We obtained partial sequences of matK with lengths of 1,109–1,148 bp, corresponding to positions 230 to 1,343 of the Oryza sativa matK gene. The pairwise percentage sequence divergence ranged from 0 to 19.1% for all the species examined except Acorus, and 0 to 4.6% within Amaryllidaceae. Two methods of phylogenetic analysis, the Maximum Parsimony and Neighbor-Joining methods, were used. The trees obtained from these two analyses were fundamentally consistent. In both trees, the Amaryllidaceae sensu Dahlgren et al. formed a well-supported monophyletic clade with 100% bootstrap support. Amaryllidaceae were included in the Asparagales; however, its phylogenetic position within the Asparagales was not clearly resolved. Judging from the NJ tree, Agapanthus might be a sister group of the Amaryllidaceae, although bootstrap support for this was low. Character-state mapping was used to infer a center of origin and the biogeographic history of Amaryllidaceae. The result supports the hypothesis that the family evolved in Africa and subsequently spread to other continents, further suggesting that South America is the center of secondary diversification. Received 6 January 1999/ Accepted in revised form 8 April 1999     

Phylogenetic analyses of 18s rdna sequences reveal a new coccoid lineage of the prasinophyceae (Chlorophyta)

Phylogenetic analyses of 18S rDNA sequences from 25 prasinophytes, including 10 coccoid isolates, reveals that coccoid organisms are found in at least three prasinophyte lineages. The coccoid Ostreococcus tauri is included in the Mamiellales lineage and P ycnococcus provasolii is allied with the flagellate P seudoscourfieldia marina. A previously undescribed prasinophyte lineage is comprised of the coccoid Prasinococcus cf. capsulatus (CCMP 1407) and other isolates tentatively identified as Prasinococcus sp. (CCMP 1202, CCMP 1614, and CCMP 1194), as well as three unnamed coccoids (CCMP 1193, CCMP 1413, and CCMP 1220). No flagellate organisms are known from this lineage. Organisms of this new lineage share some characteristics of both the Pycnococcaceae and the Mamiellales, although relationships among these separate lineages were not supported by bootstrap analyses. An additional unnamed coccoid isolate (CCMP 1205) is separate from all major prasinophyte lineages. The analyses did not resolve the relationships among the major prasinophyte lineages, although they support previous conclusions that the Prasinophyceae are not monophyletic.     

Phylogenetics of early branching eudicots:Comparing phylogenetic signal across plastid introns,spacers,and genes

<正>Recent phylogenetic analyses revealed a grade with Ranunculales,Sabiales,Proteales,Trochodendrales, and Buxales as first branching eudicots,with the respective positions of Proteales and Sabiales still lacking statistical confidence.As previous analyses of conserved plastid genes remain inconclusive,we aimed to use and evaluate a representative set of plastid introns(group I:trnL;group II:petD,rpll6,trnK) and intergenic spacers(trnL-F,petB-petD, atpB-rbcL,rps3-rpl16) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes. Overall patterns of micro structural mutations converged across genomic regions,underscoring the existence of a general mutational pattern throughout the plastid genome.Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK,followed by spacers,then group II and group I introns.The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content.Parsimony,maximum likelihood,and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions(14 000 aligned characters) converged to a backbone topology of eudicots with Ranunculales branching first,a Proteales-Sabiales clade second,followed by Trochodendrales and Buxales. Gunnerales generally appeared as sister to all remaining core eudicots with maximum support.Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes.The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics.     

Systematics of Amaryllidaceae based on cladistic analysis of plastid sequence data

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n = 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.     

Petenaeaceae,a new angiosperm family in Huerteales with a distant relationship to Gerrardina (Gerrardinaceae)

Petenaea cordata (from northern Central America) was first described in Elaeocarpaceae and later placed in Tiliaceae, but most authors have been uncertain about its familial affinities. It was considered a taxon incertae sedis in the Angiosperm Phylogeny Group classification (APG III). A recent collection was made in Guatemala, and analysis of both rbcL and atpB in the large Soltis et al. angiosperm matrix, the most completely sampled study published to date, indicated a moderately supported relationship to Tapiscia (Tapisciaceae, the only member of the newly recognized order Huerteales in this matrix; 81% bootstrap support). We then conducted a more restricted analysis using the Bayer et al. rbcL/atpB matrix for Malvales supplemented with the other genera of Huerteales from published studies. Our results indicate a distant, weakly supported sister‐group relationship to the African genus Gerrardina (Gerrardinaceae; Huerteales). After comparison of the characters cited in the literature and an examination of herbarium material of both genera, we could find no obvious synapomorphies for Gerrardina and Petenaea or any other relationship of the latter, and we therefore propose the new monogeneric family, Petenaeaceae. The polymorphic order Huerteales now comprises four small families: Dipentodontaceae, Gerrardinaceae, Petenaeaceae and Tapisciaceae. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 16–25.     

A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel

The class Prasinophyceae (Chlorophyta) contains several photosynthetic picoeukaryotic species described from cultured isolates. The ecology of these organisms and their contributions to the picoeukaryotic community in aquatic ecosystems have received little consideration. We have designed and tested eight new 18S ribosomal DNA oligonucleotide probes specific for different Prasinophyceae clades, genera, and species. Using fluorescent in situ hybridization associated with tyramide signal amplification, these probes, along with more general probes, have been applied to samples from a marine coastal site off Roscoff (France) collected every 2 weeks between July 2000 and September 2001. The abundance of eukaryotic picoplankton remained high (>10(3) cells ml(-1)) during the sampling period, with maxima in summer (up to 2 x 10(4) cells ml(-1)), and a single green algal species, Micromonas pusilla (Prasinophyceae), dominated the community all year round. Members of the order Prasinococcales and the species Bathycoccus prasinos (Mamiellales) displayed sporadic occurrences, while the abundances of all other Prasinophyceae groups targeted remained negligible.     

Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set

The ideal DNA barcode for plants remains to be discovered, and the candidate barcode rbcL has been met with considerable skepticism since its proposal. In fact, the variability within this gene has never been fully explored across all plant groups from algae to flowering plants, and its performance as a barcode has not been adequately tested. By analysing all of the rbcL sequences currently available in GenBank, we attempted to determine how well a region of rbcL performs as a barcode in species discrimination. We found that the rbcLb region was more variable than the frequently used rbcLa region. Both universal and plant group‐specific primers were designed to amplify rbcLb, and the performance of rbcLa and rbcLb was tested in several ways. Using blast , both regions successfully identified all families and nearly all genera; however, the successful species identification rates varied significantly among plant groups, ranging from 24.58% to 85.50% for rbcLa and from 36.67% to 90.89% for rbcLb. Successful species discrimination ranged from 5.19% to 96.33% for rbcLa and from 22.09% to 98.43% for rbcLb in species‐rich families, and from 0 to 88.73% for rbcLa and from 2.04% to 100% for rbcLb in species‐rich genera. Both regions performed better for lower plants than for higher plants, although rbcLb performed significantly better than rbcLa overall, particularly for angiosperms. Considering the applicability across plants, easy and unambiguous alignment, high primer universality, high sequence quality and high species discrimination power for lower plants, we suggest rbcLb as a universal plant barcode.     

Phylogenetic relationships within the New World subfamily Larreoideae (Zygophyllaceae) confirm polyphyly of the disjunct genus Bulnesia

The Larreoideae subfamily is the major representative of the family Zygophyllaceae in South America, where several of its members are common to dominant in arid regions of the Southern Cone. However, there are currently no phylogenetic analyses of the subfamily that may help to understand its origin and diversification. Additionally, there are taxonomic discrepancies around Bulnesia Gay (1845), one of its more important genera. Accordingly, we performed a phylogenetic analysis combining chloroplast (rbcL and trnL-F) and nuclear (ITS) DNA sequences. Bayesian and Parsimony analyses were performed to highlight the intergeneric relationships within Larreoideae. All genera with the exception of Bulnesia are monophyletic and we propose to redefine Bulnesia, dividing it in two genera. Furthermore, other taxonomic issues of the remaining genera are solved. This study represents the first approximation to clarify the phylogenetic relationships amongst all Larreoideae genera, producing a phylogenetic framework that can be used in future macro-ecological studies.     

Molecular Phylogeny of Casuarinaceae Based on rbcL and matK Gene Sequences

rbcL (1310 bp) and matK (1014 bp), using 15 species representing the family. The study included analyses of Ticodendron (Ticodendraceae) and three species of Betulaceae as close relatives, and one species each of Juglandaceae and Myricaceae as outgroups. Analyses based on matK gene sequences, which provided a much better resolution than the analyses based on rbcL gene sequences alone, resulted in a single most parsimonious tree whose topology is almost identical with the strict consensus tree generated by the combined data set of rbcL and matK gene sequences. Results showed that Casuarinaceae are monophyletic, comprising four distinct genera, Allocasuarina, Casuarina, Ceuthostoma and Gymnostoma, which were not recognized until recently. Within the family, Gymnostoma is positioned at the most basal position and sister to the remainder. Within the remainder Ceuthostoma is sister to the Allocasuarina-Casuarina clade. Morphologically the basalmost position of Gymnostoma is supported by plesiomorphies such as exposed stomata in the shallow longitudinal furrows of the branchlets, a basic chromosome number x=8 and the gynoecium composed of two fertile, biovulate carpels. The three other genera, Allocasuarina, Casuarina, and Ceuthostoma, have invisible stomata in the deep longitudinal furrows of the branchlets, a higher basic chromosome number x=9 or 10–14 (unknown in Ceuthostoma), the gynoecium composed of one fertile and one sterile carpel with a single ovule (unknown in Ceuthostoma). The diversity of infructescence morphology found in the latter three genera suggests that they may have evolved in close association with the elaboration of fruit dispersal mechanisms. Received 14 September 2001/ Accepted in revised form 12 October 2001     

18S rDNA sequence–structure phylogeny of the Euglenophyceae (Euglenozoa,Euglenida)

The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence–structure data are encoded and automatically aligned. Here, we present a sequence–structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence–structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.     

Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str.

We present phylogenetic analyses of Malpighiales, which are poorly understood with respect to relationships within the order, using sequences from rbcL, atpB, matK and 18SrDNA from 103 genera in 23 families. From several independent and variously combined analyses, a four-gene analysis using all sequence data provided the best resolution, resulting in the single most parsimonious tree. In the Malpighiales [bootstrap support (BS) 100%], more than eight major clades comprising a family or group of families successively diverged, but no clade containing more than six families received over 50% BS. Instead, ten terminal clades that supported close relationships between and among families (>50% BS) were obtained, between, for example, Balanopaceae and Chrysobalanaceae; Lacistemataceae and Salicaceae; and Phyllanthaceae and Picrodendraceae. The monophyly of Euphorbiaceae sens. str. were strongly supported (BS 100%), but its sister group was unclear. Euphorbiaceae sens. str. comprised two basally diverging clades (BS 100%): one leading to the Clutia group (Chaetocarpus, Clutia, Pera and Trigonopleura), and the other leading to the rest of the family. The latter shared a palisadal, instead of a tracheoidal exotegmen as a morphological synapomorphy. While both Acalyphoideae (excluding Dicoelia and the Clutia group) and Euphorbioideae are monophyletic, Crotonoideae were paraphyletic, requiring more comprehensive analyses.     

Timing the Eastern Asian–Eastern North American Floristic Disjunction: Molecular Clock Corroborates Paleontological Estimates

Sequence data of the chloroplast gene rbcL were used to estimate the time of the well-known eastern Asian–eastern North American floristic disjunction. Sequence divergence of rbcL was examined for 22 species of 11 genera (Campsis, Caulophyllum, Cornus, Decumaria, Liriodendron, Menispermum, Mitchella, Pachysandra, Penthorum, Podophyllum, and Phryma) representing a diverse array of flowering plants occurring disjunctly in eastern Asia and eastern North America. Divergence times of putative disjunct species pairs were estimated from synonymous substitutions, using rbcL molecular clocks calibrated for Cornus. Relative rate tests were performed to assess rate constancy of rbcL evolution among lineages. Corrections of estimates of divergence times for each species pair were made based on rate differences of rbcL between Cornus and other species pairs. Results of these analyses indicate that the time of divergence of species pairs examined ranges from 12.56 ± 4.30 million years to recent (<0.31 million years), with most within the last 10 million years (in the late Miocene and Pliocene). These results suggest that the isolation of most morphologically similar disjunct species in eastern Asia and eastern North America occurred during the global climatic cooling period that took place throughout the late Tertiary and Quaternary. This estimate is closely correlated with paleontological evidence and in agreement with the hypothesis that considers the eastern Asian–eastern North American floristic disjunction to be the result of the range restriction of a once more or less continuously distributed mixed mesophytic forest of the Northern Hemisphere that occurred during the late Tertiary and Quaternary. This implies that in most taxa the disjunction may have resulted from vicariance events. However, long-distance dispersal may explain the disjunct distribution of taxa with low divergence, such as Menispermum.     

PHYLOGENY OF THE CONJUGATING GREEN ALGAE (ZYGNEMOPHYCEAE) BASED ON rbc L SEQUENCES

Sequences of the gene encoding the large subunit of RUBISCO (rbcL) for 30 genera in the six currently recognized families of conjugating green algae (Desmidiaceae, Gonatozygaceae, Mesotaeniaceae, Peniaceae, and Zygnemataceae) were analyzed using maximum parsimony and maximum likelihood; bootstrap replications were performed as a measure of support for clades. Other Charophyceae sensu Mattox and Stewart and representative land plants were used as outgroups. All analyses supported the monophyly of the conjugating green algae. The Desmidiales, or placoderm desmids, constitute a monophyletic group, with moderate to strong support for the four component families of this assemblage (Closteriaceae, Desmidiaceae, Gonatozygaceae, and Peniaceae). The analyses showed that the two families of Zygnematales (Mesotaeniaceae, Zygnemataceae), which have plesiomorphic, unornamented and unsegmented cell walls, are not monophyletic. However, combined taxa of these two traditional families may constitute a monophyletic group. Partitioning the data by codon position revealed no significant differences across all positions or between partitions of positions one and two versus position three. The trees resulting from parsimony analyses using first plus second positions versus third position differed only in topology of branches with poor bootstrap support. The tree derived from third positions only was more resolved than the tree derived from first and second positions. The rbcL‐based phylogeny is largely congruent with published analyses of small subunit rDNA sequences for the Zygnematales. The molecular data do not support hypotheses of monophyly for groups of extant unicellular and filamentous or colonial desmid genera exhibiting a common cell shape. A trend is evident from simple omniradiate cell shapes to taxa with lobed cell and plastid shapes, which supports the hypothesis that chloroplast shape evolved generally from simple to complex. The data imply that multicellular placoderm desmids are monophyletic. Several anomalous placements of genera were found, including the saccoderm desmid Roya in the Gonatozygaceae and the zygnematacean Entransia in the Coleochaetales. The former is strongly supported, although the latter is not, and Entransia's phylogenetic position warrants further study.     

A molecular phylogeny of celtidaceae and ulmaceae (Urticales) based onrbcL Nucleotide sequences

On the basis of 1,290 bp sequences of the chloroplast generbcL, a molecular phylogeny of seven of nine genera of the Celtidaceae and four of six genera of the Ulmaceae was produced. These data were analyzed together with some other urticalean genera using three methods (i.e., maximum parsimony, maximum likelihood, and neighbor joining methods). Maximum likelihood topology among 18 trees obtained indicated that the Urticales are monophyletic with its common clade splitting basally into two: one leading to a line comprisingAmpelocera (traditionally placed in Celtidaceae) and Ulmaceae, and the other leading to a line comprising the remaining genera of Celtidaceae, Moraceae, and other Urticales. Ulmaceae, to whichAmpelocera is a sister group, are monophyletic, as supported by many lines of morphological evidence. In contrast to Ulmaceae, the monophyly of Celtidaceae (excludingAmpelocera) was not supported, and resolution of relationships of Celtidaceae with other Urticales, as well as of those within the family, is left for future study.