Systematic revision of the genus Reinboldiella (Ceramiaceae,Rhodophyta) from Taiwan based on comparative morphology and rbcL sequence analyses,including two new species of Reinboldiella

The genus Reinboldiella essentially consists of tiny, membranous blades, epiphytic on benthic red algae, with a wide distribution in the north-western Pacific Ocean (Taiwan, Korea and Japan). In this study, we re-examined the generitype R. schmitziana from Taiwan and neighbouring islands. Two new species of Reinboldiella, R. orientalis sp. nov. and R. taiwanensis sp. nov. are recognized from Taiwan based on comparative morphological studies and molecular analyses of RuBisCO large subunit (rbcL) gene sequences. Reinboldiella orientalis is characterized by its rosette-like appearance, with both erect and prostrate, membranous flat blades whereas R. taiwanensis is distinguishable by mainly consisting of erect, membranous blades with few, short prostrate blades in basal parts of the thalli. Thalli of R. schmitziana also have a rosette-like appearance, but their erect flat blades have cylindrical bases or stipes. The rbcL phylogenetic analyses also support the separation of R.‘schmitziana’ from Taiwan and R. schmitziana from Japan and Korea.     

Reinstatement of Grateloupia subpectinata (Rhodophyta, Halymeniaceae) based on morphology and rbcL sequences

Morphological observations and molecular analyses of the north‐western Pacific species of the red algal genus Grateloupia (Halymeniaceae) indicate the presence of an entity, which is somewhat similar in gross morphology to G. asiatica Kawaguchi et Wang but is distinguished from the latter species by some morphological features. These include: (i) a somewhat fleshy texture; (ii) wider and much thicker (4.5–10 mm wide and up to 1300 μm thick) axes, of which an inner cortex consists of more (6–9) cells; (iii) generally longer (up to 17 cm), marginal and surface proliferations that are clearly constricted (terete) at bases; and (iv) much elongated, oblong auxiliary cells. Phylogenetic analysis using the ribulose‐l,5‐bisphosphate carboxylase/ oxygenase (rbcL) gene of G. asiatica and the alga in question shows them to be distantly related and strongly supports the differentiation of these two entities at the species level. Judging from the literature, this entity is actually Grateloupia subpectinata Holmes, which has been placed into synonymy under G. asiatica [as G. filicina (Lamouroux) C. Agardh] or G. prolongata J. Agardh in previous reports, and therefore the Holmes name is reinstated.     

Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data

Nucleotide sequences of the chloroplast-encoded rbcL gene were used to examine phylogenetic relationships of the genus Salix together with other allied genera of the family Salicaceae. Phylogenetic analyses of rbcL sequences strongly suggest the monophyly of three commonly recognized genera (Chosenia, Salix, and Toisusu). Two monophyletic groups are recognized within the larger monophyletic group. They do not correspond with any infrageneric taxa proposed so far. With regard to character evolution, it is thought that the reduction of stamen number from more than two stamens to two might occur in at least three lineages and that fused bud scales evolved several times and/or the reverse evolution occurred from fused to free. Some types of pollen surfaces are considered to have evolved independently.     

Systematic studies of the antarctic species of the phyllophoraceae (Gigartinales,Rhodophyta) based on rbcL sequence analysis

The taxonomic placement of four antarctic species of the marine red algal family Phyllophoraceae (Gigartinales) is assessed within a preliminary molecular phylogeny of the family based on direct sequence analysis of the chloroplast gene rbcL. Parsimony analysis of rbcL sequences indicates that Gymnogongrus antarcticus and Gymnogongrus turquetii cluster in a clade consisting predominantly of southern hemisphere species currently placed in Gymnogongrus and Ahnfeltiopsis, whereas Phyllophora ahnfeltioides and Phyllophora antarctica cluster in a separate clade that is widely divergent from the northern hemisphere Phyllophora clade. Results from molecular and morphological data challenge the current taxonomic concept that type of life history is a phylogenetically valid criterion for recognition of genera in the Phyllophoraceae.     

Recent developments in the systematics of the Gigartinaceae (Gigartinales, Rhodophyta) based on rbcL sequence analysis and morphological evidence

The phylogenetic systematics of the Gigartinaceae is discussed for seven genera and three undescribed generic lineages and 65 taxa representing 62 species based on an analysis of rbcL sequences and morphological evidence. An examination of rbcL trees resulting from analyses of these taxa identifies seven lineages: (i) ‘Gigartina’ alveata; (ii) Rhodoglossum/Gigartina; (iii) Chondracanthus; (iv) Ostiophyllum; (v) Sarcothalia; (vi) ‘Gigartina’ skottsbergii; and (vii) a large clade containing Iridaea/‘Sarcothalia’, Mazzaella and Chondrus. These lineages and Chondrus are strongly supported; however, two groups, Iridaea/‘Sarcothalia’ and Mazzaella, receive no bootstrap support. The morphology of the female reproductive system is investigated with the aid of computer-generated, color-coded tracings of photographs of cystocarps seen in cross section at different developmental stages. Seven basic cystocarp types were found which corresponded to species groups seen in rbcL trees. These were: (i) a ‘Gigartina’ alveata group in which the carposporangia-bearing filaments develop apomictically from gametophytic cells; (ii) a Rhodoglossum/Gigartina group in which gonimoblast filaments penetrate the surrounding envelope fusing progessively with envelope cells; (iii) a Chondracanthus group in which gonimoblast filaments penetrate the envelope but fuse with envelope cells only at late developmental stages; (iv) a Sarcothalia group in which the gonimoblast filaments displace an envelope composed mainly of secondary gametophytic filaments and link to envelope cells by terminal tubular gonimoblast cells; (v) an Iridaea group similar to the Sarcothalia group, but with an envelope composed of a mixture of medullary cells and secondary gametophytic filaments; (vi) a Mazzaella group that lacks a true envelope and in which gonimoblast filaments connect to modified gametophytic cells by means of terminal tubular cells; (vii) a Chondrus group in which gonimoblast filaments penetrate the medulla and link to modified medullary cells by means of conjunctor cells forming secondary pit connections. The further separation of these groups into genera is based largely on tetrasporangial characters.     

Phylogeny of extant genera in the family Characeae (Charales,Charophyceae) based on rbcL,sequences and morphology

Extant genera of Characeae have been assigned to two tribes: Chareae (Chara, Lamprothamnium, Nitellopsis, and Lychnothamnus) and Nitelleae (Nitella and Tolypella), based on morphology of the thallus and reproductive structures. Character analysis of fossil and extant oogonia suggest that Tolypella is polyphyletic, the genus comprising two sections, one in each of the two tribes. Eleven morphological characters and sequence data for the Rubisco large subunit (rbcL) were used to reconstruct the phylogeny of genera, including the two sections of Tolypella. Parsimony analysis of the rbcL data, with all positions and changes weighted equally, strongly supports the monophyly of the Characeae. The two Tolypella sections form a robust monophyletic group basal to the family. Transversion weighting yielded the same tree but with a paraphyletic Tolypella. The rbcL data strongly support monophyly of tribe Chareae but tribe Nitelleae is paraphyletic. Parsimony analysis of morphological data produced one unrooted tree consistent with monophyly of the two tribes; on this tree the Tolypella sections were paraphyletic. Combining morphological with rbcL data did not change the results derived from rbcL sequences alone. The rbcL data support the monophyly of the Characeae and Coleochaete, which together form a monophyletic sister group to embryophytes.     

Phylogeny of ants (Formicidae) based on morphology and DNA sequence data

In order to reconstruct ants' phylogeny, we analysed DNA sequences for two nuclear genes, abdominal-A and Ultrabithorax, from 49 species of ants and two outgroups. As these genes control the development of the first segments of the abdomen in insects, which are very variable in ants (petiole, postpetiole, and gaster constriction), we hypothesized that the morphological variations between the subfamilies may be correlated with mutations of some abd-A or Ubx regions. Contrarily to our hypothesis, these sequences are highly conserved. The differences observed concern mainly third codon positions and present some saturation. Phylogenetic reconstructions were carried out using the genetic raw sequence data and by combining them with a set of morphological data (Total Evidence). Relations among subfamilies of ants remains poorly resolved with molecular data only, but adding these data to morphological characters confirms and reinforce the topology of : a Poneroid complex [Ponerinae, Cerapachyinae, Leptanillinae and army ants], a Formicoid complex [Dolichoderinae, Formicinae] and a Myrmecoid complex [Myrmicinae, Myrmeciinae, Pseudomyrmecinae, Nothomyrmeciinae]. Our molecular results allow resolution near the branch tips and three subfamilies (Dolichoderinae, Formicinae and Pseudomyrmecinae) always appear as monophyletic. The Formicinae and the Dolichoderinae have close relationships. The Camponotini appear as a strong clade inside the Formicinae. The Ponerinae are separated in two parts: the Ectatommini and all other tribes. The Cerapachyinae, Dorylinae, and Ecitoninae belong to the same clade, the Cerapachyinae being confirmed in their subfamily status. The Myrmicinae appears to be very heterogeneous, with the Attini forming a very stable and well-separated group.     

Phylogeny of the multivalvulidae (Myxozoa: Myxosporea) based on comparative ribosomal DNA sequence analysis

Fish parasites of the Multivalvulida (Myxozoa, Myxosporea) are widespread and can be associated with mortality or poor flesh quality in their commercially important marine hosts. Traditional classifications divide members of this order into families based on spore valve and polar capsule numbers. Analyses of the small-subunit (SSU) ribosomal DNA (rDNA) sequences from all representative families in the order (Trilosporidae, Kudoidae, Pentacapsulidae, Hexacapsulidae, and Septemcapsulidae) indicate that a revision of the taxonomy and nomenclature is warranted. In our phylogenetic analysis of (SSU and large subunit) rDNA sequences, members of Pentacapsula, Hexacapsula, and Septemcapsula root within a clade of Kudoa species with Unicapsula (Trilosporidae) as an outlier to these genera. Therefore, we propose to synonymize Pentacapsulidae, Hexacapsulidae, and Septemcapsulidae with Kudoidae alter the diagnosis of Kudoidae and Kudoa to accommodate all marine myxozoan parasites having 4 or more shell valves and polar capsules.     

The molecular systematics of some agar- and carrageenan-containing marine red algae based on rbcL sequence analysis

A hypothesis of phylogenetic relationships inferred by parsimony analysis of plastid-encoded rbcL sequences is presented for red algae containing agar- and carrageenan-like phycocolloids; rbcL encodes the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase. Previous studies have shown that Floridean families that contain sulfated galactans as cell wall components are resolved as a monophyletic clade sister to the agarophyte order Ahnfeltiales. Families that have been identified as containing kappa-type carrageenans, often in addition to lambda-type carrageenans, are resolved in three clades: (1) a complex containing the families Solieriaceae, Cystocloniaceae, Hypneaceae, Caulacanthaceae, Tichocarpaceae, Furcellariaceae, and the genera Turnerella and Opuntiella; (2) the Gigartinaceae and Phyllophoraceae, and (3) the genus Endocladia. Except for Tichocarpus and Endocladia, these are all members of the Gigartinales sensu Kylin (1956). Most of the families previously placed in the Cryptonemiales by Kylin appear to contain only lambda-type carrageenans. These fall into two groups, one that clusters with typical carrageenophyte- and the other with typical agarophyte-taxa. The first of these includes the families Polyideaceae, Kallymeniaceae, Dumontiaceae, and Rhizophyllidaceae. The second includes the type family of the Cryptonemiales, the Halymeniaceae, which is divisible into two well-supported clades, one of which possesses special lambda-like carrageenans, the aeodans, and the Schizymeniaceae, a recently created family containing two former gigartinalean genera. The agarophyte orders Gelidiales, Gracilariales and Ceramiales are well resolved as monophyletic clades, but their topological positions are poorly resolved. The Gelidiales and Ceramiales are associated, but the Gracilariales is included in a clade that contains families belonging to the Rhodymeniales, a possible agarophyte order. Finally, two groups that may contain lambda-like carrageenans, the Plocamiales and the Sarcodiaceae, are resolved as separate clades.     

Phylogenetic analysis of the Plagiotheciaceae (Musci) and its relatives based on rbcL gene sequences

Phylogenetic relationships are investigated using nucleotide sequences of the chloroplast gene, rbcL, for members of the family Plagiotheciaceae and its relatives. Nucleotide sequences of the rbcL were determined in 32 species (38 samples). In some species small differences in the nucleotide sequences of rbcL were recognized between the materials from different localities. The phylogenetic tree deduced from the sequences of the rbcL loci indicates the following: (1) pleurocarpous mosses form a monophyletic clade; (2) Plagiothecium is monophyletic; (3) Taxiphyllum is not closely related to Plagiothecium; (4) the family Hypnaceae is paraphyletic; (5) Pylaisiella is heterogeneous.     

Modeling a minimal ribosome based on comparative sequence analysis

We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto structures of the 30S and 50S subunits determined by X-ray crystallography. Several functional domains of the ribosome are conserved in their three-dimensional organization in the Archaea, Bacteria, Eucaryotic nuclear, mitochondria and chloroplast ribosomes. In contrast, other regions from both subunits have shifted their position in three-dimensional space during evolution, including the L11 binding domain and the alpha-sarcin-ricin loop (SRL). We examined conserved bridge interactions between the two ribosomal subunits, giving an indication of which contacts are more significant. The tRNA contacts that are conserved were also determined, highlighting functional interactions as the tRNA moves through the ribosome during protein synthesis. To augment these studies of a large collection of comparative structural models sampled from all major branches on the phylogenetic tree, Caenorhabditis elegans mitochondrial rRNA is considered individually because it is among the smallest rRNA sequences known. The C.elegans model supports the large collection of comparative structure models while providing insight into the evolution of mitochondrial ribosomes.     

多位点序列和比较基因组学分析对盐单胞菌科菌株JSM 104105的系统发育学研究

【目的】为了精准地判定产铁载体嗜盐新菌株JSM 104105在盐单胞菌科(Halomonadaceae)中的系统发育地位。【方法】采用基于16SrRNA基因、DNA促旋酶B亚基基因(DNAgyraseB subunit gene, gyrB)和核糖核酸聚合酶σ因子RpoD基因(RNA polymerase sigma factor RpoD gene,rpoD)序列的多位点序列分析方法(multilocus sequence analysis, MLSA),对菌株JSM 104105的系统发育地位进行初步分析;采用比较基因组学分析(comparative genomics analysis),分析该菌株与其系统发育关系密切的典型菌株之间的GC含量、平均核苷酸一致性(average nucleotide identity,ANI)和数字DNA-DNA杂交值(digital DNA-DNA hybridization, dDDH),并进行基因组系统发育学分析(phylogenomic analysis),更准确地判定菌株JSM 104105在盐单胞菌科中的系统发育地位。【结果】MLSA分析...     

Phylogeny of the Brachytheciaceae (Bryophyta) based on morphology and sequence level data

Brachytheciaceae is often considered a taxonomically difficult group of mosses. For example, morphological variation has led to difficulty in generic delimitation. We used DNA sequence data (chloroplast psbT‐H and trnL‐F and nuclear ITS2) together with morphology (63 characters) to examine the relationships within this family. The combined unaligned length of the DNA sequences used in the phylogenetic analyses varied between 1277 and 1343 bp. For phylogeny reconstruction we performed direct optimization, as implemented in POY. Analyses were performed with three different gap costs and the morphological data partition was weighted both: (1) equal to gap cost, and (2) with a weight of one. The utility of sensitivity analysis has recently been cast into doubt; hence in this study it was performed only to explore the effects of weighting on homology statements and topologies and to enable more detailed comparisons between earlier studies utilizing the direct optimization method. The wide sequence length variation of non‐coding ITS2 sequences resulted in character optimizations (i.e., “alignments”) of very different lengths when various gap costs were applied. Despite this variation, the topologies of equally parsimonious trees remained fairly stable. The inclusion of several outgroups, instead of only one, was observed to increase the congruence between data sets and to slightly increase the resolution. An inversion event in the 9 bp loop region in the chloroplast psbT‐N spacer in mosses has been postulated to include only uninformative variation, thus possibly negatively impacting the phylogeny reconstruction. Despite this inversion, its variation within Brachytheciaceae was clearly congruent with information from other sources, but inclusion of these 9 bp in the analysis had only a minor effect on the phylogenetic results. In the most parsimonious topology, which was obtained with equal weighting of all data, Meteoriaceae and Brachytheciaceae were resolved as monophyletic sister groups, which had recently been suggested based on a few shared morphological characters. Our study revealed some new generic relationships within the Brachytheciaceae, which are discussed in light of the morphological characters traditionally used for generic delimitation.     

Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences

The two families of the order Apiales (Apiaceae and Araliaceae) represent a classic example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. In Apiales, this problem is further compounded by phylogenetic confusion at almost every taxonomic level, including ordinal, interfamilial, and infrafamilial, due largely to difficulties in understanding trends in morphological evolution. Phylogenetic analyses of rbcL sequences were employed to resolve relationships at the ordinal and familial levels. The results of the ordinal analysis confirm the placement of Apiales in an expanded subclass Asteridae as the sister group to Pittosporaceae, and refute the traditional alliance of Apiales with Cornales and Rosidae. This study has also resolved relationships of a number of enigmatic genera, suggesting, for example, that Melanophylla, Aralidium, Griselinia, and Toricellia are close relatives of Apiales. Clarification of phylogenetic relationships has concomitantly provided insights into trends of morphological evolution, and suggests that the ancestral apialean taxon was probably bicarpellate, simple-leaved, woody, and paleotropical. Phylogenetic analysis at the family level suggests that apiaceous subfamily Hydrocotyloideae, often envisioned as an intermediate group between Apiaceae and Araliaceae, is polyphyletic, with some hydrocotyloids closely allied with Araliaceae rather than Apiaceae. With the exception of some hydrocotyloids, Apiaceae appear to be monophyletic. The relationship between Apiaceae and Araliaceae remains problematic. Although the shortest rbcL trees suggest that Apiaceae are derived from within a paraphyletic Araliaceae, this result is only weakly supported.     

Molecular identification and phylogenetic analysis of Aloe shadensis from Saudi Arabia based on matK,rbcL and ITS DNA barcode sequence

The Kingdom of Saudi Arabia thrives with great plant diversity, including rare plants of the family Asphodelaceae that have multiple benefits and are still being studied. Aloe shadensis is one of these plants that must be preserved and documented in its natural environment. The most appropriate molecular approach currently approved for documentation is the sequencing of some genomic markers. The current study is the first to use genomic markers to record this rare plant. In this study, the plastid genes matK (Maturase K), rbcL (Ribulose-bisphosphate carboxylase/oxygenase large subunit), and the nuclear region ITS (Internal transcribed spacer) were used to reveal their efficiency in identifying the plant under study. This study is the first to deal with this plant and document it using these genetic markers. The study showed a promising result concerning identifying the sequence of the matK gene and ITS region, while the rbcL gene did not give a good indicator through the used primers. The obtained sequences of the matK gene and the ITS region were determined through two different sets of primers in each case then deposited in GenBank. The evolutionary relatedness of Aloe shadensis was established with the different species of Aloe. The study showed that the closest species is Aloe vera with a similarity of more than 99 %. The study concludes with the possibility of using these genes to correctly identify, distinguish and document the species of Aloe shadensis.     

Comparative morphology and systematics of Chondrymenia lobata from the Mediterranean Sea and a phylogeny of the Chondrymeniaceae fam. nov. (Rhodophyta) based on rbcL sequence analyses

The Chondrymeniaceae Rodríguez-Prieto, G. Sartoni, S.-M. Lin & Hommersand, fam. nov., is proposed for Chondrymenia lobata. Analyses of rbcL sequences place the new family in a large gigartinalean assemblage that comprises the Cystocloniaceae–Solieriaceae complex. Plants are decumbent and growth takes place by division of multiple apical cells at the margin of the blade. Thalli consist of an outer cortex of subspherical to elongate cortical cells arranged in anticlinal rows, a subcortex of cells cross-linked by lateral arms, and a large central medulla composed of primary medullary filaments intermixed with numerous rhizoidal filaments. Male stages are reported in monoecious individuals. Inactive carpogonial branches consist of a two-celled filament that is directed inwards from the supporting cell. Functional carpogonial branches are oriented outwardly, with the carpogonia and trichogynes pointed towards the thallus surface. After presumed fertilization, the carpogonium fuses with the hypogynous cell and transfers the zygote nucleus. The hypogynous cell, in turn, fuses with the supporting cell which contains many haploid nuclei. The resulting fusion cell functions as an auxiliary cell that cuts off a single gonimoblast initial, which produces the gonimoblast filaments. Gametophytic cells close to the auxiliary cell unite with it to form a placental fusion network of variable size and outline, and a placental fusion cell. Proximal gonimoblast cells fuse with the placental fusion cell, while the distal cells differentiate into branched chains of subspherical carposporangia. The superficial similarity of the outwardly developed osteolate cystocarp is responsible for Kylin's (1956) placement of Chondrymenia in his family Sarcodiaceae; however, the manner in which the placenta is formed is more like that seen in the Cystocloniaceae–Solieriaceae complex.     

A phylogenetic reappraisal of the Peltophorum group (Caesalpinieae: Leguminosae) based on the chloroplast trnL-F, rbcL and rps16 sequence data

The monophyly of the Peltophorum group, one of nine informal groups recognized by Polhill in the Caesalpinieae, was tested using sequence data from the trnL-F, rbcL, and rps16 regions of the chloroplast genome. Exemplars were included from all 16 genera of the Peltophorum group, and from 15 genera representing seven of the other eight informal groups in the tribe. The data were analyzed separately and in combined analyses using parsimony and Bayesian methods. The analysis method had little effect on the topology of well-supported relationships. The molecular data recovered a generally well-supported phylogeny with many intergeneric relationships resolved. Results show that the Peltophorum group as currently delimited is polyphyletic, but that eight genera plus one undescribed genus form a core Peltophorum group, which is referred to here as the Peltophorum group sensu stricto. These genera are Bussea, Conzattia, Colvillea, Delonix, Heteroflorum (inedit.), Lemuropisum, Parkinsonia, Peltophorum, and Schizolobium. The remaining eight genera of the Peltophorum group s.l. are distributed across the Caesalpinieae. Morphological support for the redelimited Peltophorum group and the other recovered clades was assessed, and no unique synapomorphy was found for the Peltophorum group s.s. A proposal for the reclassification of the Peltophorum group s.l. is presented.