Analysis Of rbcL Gene Sequences Research Articles

Taxonomic contributions to Hapalidiales (Corallinophycidae, Rhodophyta): Boreolithothamnion gen. nov., Lithothamnion redefined and with three new species and Roseolithon with new combinations.

Phylogenetic analyses of rbcL gene sequences and of concatenated rbcL, psbA, and nuclear SSU rRNA gene sequences resolved the generitype of Lithothamnion, L. muelleri, in a clade with three other southern Australian species, L. kraftii sp. nov., L. saundersii sp. nov., and L. woelkerlingii sp. nov. Cold water boreal species currently classified in Lithothamnion and whose type specimens have been sequenced are transferred to Boreolithothamnion gen. nov., with B. glaciale comb. nov. as the generitype. The other species are B. giganteum comb. nov., B. phymatodeum comb. nov., and B. sonderi comb. nov., whose type specimens are newly sequenced, and B. lemoineae comb. nov., B. soriferum comb. nov., and B. tophiforme comb. nov., whose type specimens were already sequenced. Based on rbcL sequences from the type specimens of Lithothamnion crispatum, L. indicum, and L. superpositum, each is recognized as a distinct species and transferred to the recently described Roseolithon as R. crispatum comb. nov., R. indicum comb. nov., and R. superpositum com. nov., respectively. To correctly assign species to these three genera based only on morpho-anatomy, specimens must have multiporate conceptacles and some epithallial cells with flared walls. The discussion provides examples demonstrating that only with phylogenetic analyses of DNA sequences can the evolution of morpho-anatomical characters of non-geniculate corallines be understood and applied at the correct taxonomic rank. Finally, phylogenetic analyses of DNA sequences support recognition of the Hapalidiales as a distinct order characterized by having multiporate tetra/bisporangial conceptacles, and not as a suborder of Corallinales whose tetra/bisporangial conceptacles are uniporate.

Grateloupia oligoclora (Halymeniaceae, Rhodophyta): a new species from China based on morphological observation, life history and rbcL gene sequence analysis

ABSTRACT A new species of Grateloupia from Wenzhou Nanji Island in Zhejiang province, China, was illustrated based on morphological observation, early development, life history and rbcL gene sequence analysis, and named Grateloupia oligoclora H.W.Wang & Y.Bian sp. nov. The morphological features of this new species can be summarized as upright thalli, solitary or cespitose, dark red in colour, cartilaginous and mucilaginous in texture. The margins of the thalli were smooth, without lateral branches, proliferations, or branched, dichotomously branched or with 3–5 irregular rod-shaped branches. The thalli were consisted of cortex cells (6–9 cell layers) and medulla. The cystocarps were spherical and appeared to be speckled from the surface of the thalli. The carpogonial branch ampullae and auxiliary cell branch were typical Grateloupia-type. During the cruciate dividing of tetrasporangia, some dyads showed asynchronous phenomenon. Type of spore development and life history were typical mediate discal type and isomorphic alternation of generations. Phylogenetic analysis based on rbcL sequence indicated that the new taxon formed an independent clade from other Grateloupia species, and this clade was sister to G. subpectinata Holmes with high interspecific divergence 12 bp (1%), supporting its specific status. Accordingly, G. oligoclora H.W.Wang & Y.Bian sp. nov is proposed as a new species of Grateloupia. This study provides new resource and species diversity of marine Rhodophyta in China.

Systematic revision of the foliose Halymeniaceae (Halymeniales, Rhodophyta) from Europe, with the description of Halymenia ballesterosii sp. nov. from the Mediterranean Sea and Nesoia hommersandii from the Canary Islands

ABSTRACT In the past, large, foliose and unbranched Halymenia-like plants from Europe were often identified as ‘Halymenia latifolia’, however recent taxonomic studies have shown that ‘H. latifolia’ was a catch-all name for at least three cryptic species: Neofolia rosea, Nesoia mediterranea, and the genuine H. latifolia, which has been transferred to the recently established genus Nesoia. In this study, we further refine the taxonomy of European Halymeniaceae by examining new collections of foliose taxa from the Mediterranean Sea and Macaronesia. Analyses of rbcL gene sequences showed that unbranched foliose Halymeniaceae from Europe can be separated into five species, including three previously described species in Neofolia (N. rosea) and Nesoia (N. latifolia and N. mediterranea) and two new species belonging to Halymenia (H. ballesterosii sp. nov.) and Nesoia (N. hommersandii sp. nov.). Halymenia ballesterosii is the only known unbranched foliose species in the genus from Europe and can be separated from morphologically similar species in Neofolia and Nesoia by protruding surface cells, two-celled carpogonial branches, a basal nutritive cell cluster in the carpogonial branch ampullae, and secondary connecting filaments issued from basal cells of ampullar filaments. Nesoia hommersandii differs from N. latifolia by the lack of swollen arms in medullary stellate cells and cystocarps that slightly protrude above the thallus surface. We expect that the species diversity of foliose Halymeniaceae may increase when more foliose plants are collected and examined from different locations in Europe.

Morphological and molecular evidence for Osmundea coelenterata comb. nov. (Ceramiales, Rhodophyta) from the tropical Atlantic Ocean

Background. As part of the monographic studies on the Laurencia complex (Rhodomelaceae, Rhodophyta) from Cuba, detailed taxonomic research was carried out on Laurencia coelenterata, a diminutive species collected in Santiago de Cuba, in the eastern Cuban archipelago. The vegetative and reproductive features of the species clearly belong to the genus Osmundea, a member of the Laurencia complex: two pericentral cells per each vegetative axial segment, tetrasporangia cut off randomly from cortical cells, and filament-type spermatangial branches. Goals. In this study the morphological characteristics previously unknown to Laurencia coelenterata are shown, and in order that their taxonomic position within the Laurencia complex is discussed. Furthermore, the global geographic distribution of the Osmundea species is analysed. Methods. Morphological and molecular analysis of the rbcL gene sequences were performed allied with the preparation and interpretation of phylogenetic hypotheses. Results. The new morphological analysis of the paratype specimen (# 4451) housed in the Puertorriqueno Marine Herbarium showed that Laurencia coelenterata was incorrectly placed in the genus Laurencia. The phylogenetic position of the present species was inferred by the analysis of the chloroplast-encoded rbcL gene sequences, and the range of the genetic variation found in this analysis also supports the transfer of Laurencia coelenterata to the genus Osmundea, as O. coelenterata (D. L. Ballantine et Aponte) M.T. Fujii, Senties et Areces. Conclusions. The morphological and molecular approach in algal taxonomy is allowing consolidate the nomenclatural status of the species, and the new combination for Laurencia coelenterata as Osmundea coelenterata is not an exception.

Phylogenetic position of Zygogonium ericetorum (zygnematophyceae, charophyta) from a high alpine habitat and ultrastructural characterization of unusual aplanospores.

Zygogonium ericetorum, the type species of the genus, was studied from a natural population collected in Mt. Schönwieskopf, Tyrol, Austria. Generic concepts of Zygogonium and Zygnema were tested with atpB, psbC, and rbcL gene sequence analysis, which showed a sister relationship between Z. ericetorum and Mesotaenium, in an early branching clade sister to a grouping of Zygnema and several other filamentous and unicellular zygnematalean taxa. A variety of light, confocal, transmission electron microscopy, and cytochemical techniques provided new data on the variable chloroplast shape of Z. ericetorum, and its aplanospore structure and development, which has been previously considered taxonomically important but has been ambiguously interpreted. Zygogonium can be distinguished from other zygnematophytes (particularly Zygnema), based on the combination of two characters: (i) irregular, compressed plate-like chloroplasts and (ii) residual cytoplasmic content left in sporangia outside of the fully developed aplanospores or zygospores. The presence of a sporangial wall that separates the spores from the parent cell should be excluded from the definition of Zygogonium, because it is also observed in Zygnema. Similarly, the ecological characterization of Zygogonium as acidophilic is not unique to the genus. The names of 18 species currently belonging to Zygogonium are here changed to Zygnema, because of incompatibility with this new proposed Zygogonium concept. In the species transferred to Zygnema, chloroplasts are typically stellate in three-dimensions, and the entire content of fertile cells is transformed into the spore, so there is no cytoplasmic residue.

SYSTEMATICS OF THE GENUS ZYGNEMA (ZYGNEMATOPHYCEAE, CHAROPHYTA) FROM CALIFORNIAN WATERSHEDS(1).

Natural populations of Zygnema were collected from 80 stream sites across California, and eight species were identified and characterized morphologically. Generic and infrageneric concepts of Zygnema and Zygogonium were tested with cox3 and rbcL gene sequence analysis. Strains of Zygnema were positioned in a single monophyletic clade sister to Zygogonium tunetanum Gauth.-Lièvre. In both the rbcL and cox3 phylogenies, strains of Zygnema formed two major clades. The first clade contained species that have zygospores with a blue-colored mesospore or akinetes with a colorless mesospore. The second clade contained species that have a yellow or brown mesospore. The existing taxonomic concepts for Zygnema classification are not consistent with our molecular phylogeny and do not correspond to natural groups. We propose that mesospore color may be useful in the infrageneric classification of Zygnema. Newly described Zygnema aplanosporum sp. nov. and Zygnema californicum sp. nov. have zygospores with a blue mesospore formed in the conjugation tube and separated by a cellulosic sporangial wall. Z. aplanosporum also possessed a combination of vegetative and reproductive features characteristic of Zygogonium, such as presence of short branches, rhizoidal outgrowths, thickened vegetative cell walls, purple-colored cell content, small compressed-globular chloroplasts as well as predominant asexual reproduction. Z. aplanosporum and Z. californicum were deeply embedded in a larger clade of Zygnema both in rbcL and cox3 analyses. Based on our observations, there are no features or combination of features that separate Zygnema and Zygogonium. Therefore, we conclude that Zygogonium is probably a synonym of Zygnema.

Genetic characterisation of sexually and parthenogenetically reproductive populations of Chara canescens (Charophyceae) using AFLP, rbcL, and SNP markers

R. Schaible, I. Bergmann, M. Bögle, A. Schoor and H. Schubert. 2009. Genetic characterisation of sexually and parthenogenetically reproductive populations of Chara canescens (Charophyceae) using AFLP, rbcL, and SNP markers. Phycologia 48: 105–117. DOI: 10.2216/08-58.1Parthenogenetically reproducing Chara canescens (Charophyceae) populations have been described from several European locations. Sexually reproducing populations with female and male individuals are known only from the Neusiedler See located in Seewinkel National Park, Austria. Sexual and parthenogenetic populations probably coexist in this area, but no morphological attribute is known to differentiate between females of the two reproductive modes. To find markers associated with parthenogenesis, DNA samples from individuals of both reproductive modes were screened via amplified fragment length polymorphism (AFLP) analysis. Although no unique monomorphic loci for the reproduction systems could be identified, neighbour-joining analysis separated the individuals into two groups representing the two reproductive modes. The rbcL gene sequence analysis also revealed two nucleotide differences among these groups. Sequence characterization of the flanking region of one microsatellite locus from C. canescens individuals identified one insertion/deletion (indel) between the reproductive modes. This indel was converted via polymerase chain reaction into a marker associated with sexual reproduction. Further analysis of the AFLP data showed a high level of polymorphism and genetic diversity between and within populations of the reproductive modes. A larger sample size is needed to confirm the gene pool cluster and the degree of genetic diversity between the reproductive modes finally, but the successful development of a promising marker system for the reproduction mode provides a tool for future research to characterise geographical parthenogenesis of C. canescens in detail.

TWO TYPES OF AUXILIARY CELL AMPULLAE IN GRATELOUPIA (HALYMENIACEAE, RHODOPHYTA), INCLUDING G.TAIWANENSIS SP. NOV. AND G.ORIENTALIS SP. NOV. FROM TAIWAN BASED ON rbcL GENE SEQUENCE ANALYSIS AND CYSTOCARP DEVELOPMENT(1).

Few species in the genus Grateloupia have been investigated in detail with respect to the development of the auxiliary cell ampullae before or after diploidization. In this study, we document the vegetative and reproductive structures of two new species of Grateloupia, G.taiwanensis S.-M. Lin et H.-Y. Liang sp. nov. and G.orientalis S.-M. Lin et H.-Y. Liang sp. nov., plus a third species, G.ramosissima Okamura, from Taiwan. Two distinct patterns are reported for the development of the auxiliary cell ampullae: (1) ampullae consisting of three orders of unbranched filaments that branch after diploidization of the auxiliary cell and form a pericarp together with the surrounding secondary medullary filaments (G.taiwanensis type), and (2) ampullae composed of only two orders of unbranched filaments in which only a few cells are incorporated into a basal fusion cell after diploization of the auxiliary cell and the pericarp consists almost entirely of secondary medullary filaments (G.orientalis type). G.orientalis is positioned in a large clade based on rbcL gene sequence analysis that includes the type species of Grateloupia C. Agardh 1822, G.filicina. G. taiwanensis clusters with a clade that includes the generitype of Phyllymenia J. Agardh 1848, Ph.belangeri from South Africa; that of Prionitis J. Agardh 1851, Pr.lanceolata from Pacific North America; and that of Pachymeniopsis Y. Yamada ex Kawab. 1954, Pa.lanceolata from Japan. A reexamination of the type species of the genera Grateloupia, Phyllymenia, Prionitis, and Pachymeniopsis is required to clarify the generic and interspecific relationships among the species presently placed in Grateloupia.

MOLECULAR PHYLOGENY OF THE GREEN ALGAL ORDER PRASIOLALES (TREBOUXIOPHYCEAE, CHLOROPHYTA)1

The systematics of the Prasiolales was investigated by phylogenetic inference based on analyses of the rbcL and 18S rRNA genes for representatives of all four genera currently attributed to this order (Prasiococcus, Prasiola, Prasiolopsis, Rosenvingiella), including all type species. The rbcL gene had higher sequence divergence than the 18S rRNA gene and was more useful for phylogenetic inference at the ranks of genus and species. In the rbcL gene phylogeny, three main clades were observed, corresponding to Prasiola, Prasiolopsis, and Rosenvingiella. Prasiococcus was nested among species of Prasiola occurring in subaerial and supralittoral habitats. Trichophilus welckeri Weber Bosse, a subaerial alga occurring in the fur of sloths in Amazonia, was closely related to Prasiolopsis ramosa Vischer. The species of Prasiola were grouped into three well‐supported clades comprising (i) marine species, (ii) freshwater and terrestrial species with linear blades, and (iii) terrestrial species with rounded or fan‐shaped blades. Sequence divergence was unexpectedly low in the marine group, which included species with different morphologies. For the 18S rRNA gene, the phylogenetic analyses produced several clades observed for the rbcL gene sequence analysis, but, due to very little sequence variation, it showed considerably lower resolution for inference at the species and genus levels. Due to the low support of some internal branches, the results of the analyses did not allow an unambiguous clarification of the origin and the early evolution of the Prasiolales.

A COMBINED 18S rDNA AND rbcL PHYLOGENETIC ANALYSIS OF CHLOROMONAS AND CHLAMYDOMONAS (CHLOROPHYCEAE, VOLVOCALES) EMPHASIZING SNOW AND OTHER COLD‐TEMPERATURE HABITATS1

An extensive phylogenetic analysis of the biflagellate genera, Chlamydomonas Ehrenberg and Chloromonas Gobi emend. Wille, was undertaken using 18S rDNA and rbcL gene sequence analysis. Emphasis was placed on 21 cold‐tolerant taxa of which 10 are from snow. These taxa occurred in four distinct clades each in the 18S rDNA and rbcL phylogenies, and when taken together suggest at least five distinct origins in cold habitats. Most of these taxa occur in a single clade (A), and all snow species occurred in this clade. In the rbcL and combined rbcL–18S rDNA analyses, the snow taxa fell into three groups. Two groups occurred in subclade 1: Chlamydomonas augustae Skuja CU, Chlamydomonas augustae UTEX, and Chlamydomonas sp.‐A and Chloromonas clathrata Korshikov, Chloromonas rosae Ettl CU, and Chloromonas rosae v. psychrophila var. nov. The third snow group, subclade 2, included three species with unique cell divisions, Chloromonas brevispina (Fritsch) Hoham, Roemer et Mullet, Chloromonas pichinchae (Lagerheim) Wille, and Chloromonas sp.‐D, and the basal Chloromonas nivalis (Chodat) Hoham et Mullet with normal cell divisions. This suggests that the snow habitat has been colonized at least twice and possibly three times in the history of these biflagellates. In the 18S rDNA tree, one cold‐tolerant Chloromonas species fell outside clade A: Chloromonas subdivisa (Pascher et Jahoda) Gerloff et Ettl. In the rbcL tree, three cold‐tolerant Chloromonas species fell outside clade A: Chloromonas subdivisa, Chloromonas sp.‐ANT1, and Chloromonas sp.‐ANT3. These results support previous findings that pyrenoids have been gained and lost several times within this complex.

A molecular investigation of the systematic relationships of Sirodotia species (Batrachospermales, Rhodophyta) in North America

Six collections of the freshwater red algal genus Sirodotia from North America were sampled as follows: S. tenuissima (Collins) Skuja ex Flint from Rhode Island, S. suecica Kylin from Rhode Island and Labrador, and S. huillensis (Welwitsch ex West et G.S. West) Skuja from Texas, Mexico, and Costa Rica. To investigate relationships among these taxa, a fragment of the rbcL gene was sequenced. The ITS1–5.8S rDNA–ITS2 region, the rbcL–S spacer, and part of the rbcS gene were sequenced for all taxa and all but one collection. The rbcL gene sequence analysis showed S. suecica and S. tenuissima to be paraphyletic. The S. huillensis samples formed a monophyletic clade, with the Texas and Mexico collections being most closely related. The rbcL–S spacer and partial rbcS gene sequence data showed the same trend as the rbcL gene data, with S. suecica and S. tenuissima having identical sequence and S. huillensis samples forming a distinct, monophyletic clade. The rbcL–S spacer region may provide evidence for a closer phylogenetic relationship between Sirodotia and Batrachospermum gelatinosum (Linnaeus) DeCandolle than with the Lemaneaceae. In comparing the ITS1–5.8S rDNA–ITS2 region from S. suecica and S. tenuissima, little sequence divergence (~2%) was observed. Previous work on these two taxa revealed little morphological differentiation. Therefore, we conclude that S. suecica and S. tenuissima should be synonymized; S. suecica has priority. Based on the sequence variation among S. huillensis collections, further phylogeographic studies are recommended. The utility of ITS1–5.8S rDNA–ITS2 region data for phylogenetic and phylogeographic studies is discussed.

TOWARD A NATURAL SYSTEM OF SPECIES IN CHLOROGONIUM (VOLVOCALES, CHLOROPHYTA): A COMBINED ANALYSIS OF MORPHOLOGICAL AND rbcL GENE SEQUENCE DATA

The taxonomy of species of Chlorogonium (Volvocales, Chlorophyta) was studied based on comparative light and electron microscopy and DNA sequence data of 23 strains from five major algal culture collections. All of the 23 strains showed pyrenoids under photoautotrophic conditions, but 17 of the 23 exhibited marked reduction in size of pyrenoids, or pyrenoids were absent under photoheterotrophic conditions. The strains could clearly be delineated into six species, C. euchlorum, C. elongatum, C. fusiforme, C. capillatum, C. neglectum, and C. kasakii on the basis of differences in cell shape, number of contractile vacuoles, number and stability of pyrenoids, and ultrastructure of pyrenoids and stigmata. This distinction of species based on morphology was also supported by analyses of rbcL gene sequences. The later strongly showed that each species, C. euchlorum (seven strains), C. elongatum (three strains), and C. capillatum (10 strains), forms a robust clade. Although some morphological differences were noted within different strains of C. euchlorum and C. capillatum, these features were regarded as strain‐specific because they were not reflected in the rbcL gene phylogenies. In addition, the rbcL gene trees strongly suggested that C. neglectum and C. kasakii are closely related to each other, consistent with the similarity of the ultrastructure of pyrenoids and stigmata between the two species. However, C. kasakii can be distinguished clearly from C. neglectum by its multiple pyrenoids in the chloroplast and acute anterior and posterior ends in the vegetative cell.

A Revised Circumscription of the Genera of the Fern Family Vittariaceae

Based on phylogenetic analysis of rbcL gene sequences from species of Vittariaceae, Vittaria and Antrophyum are, respectively, polyphyletic and paraphyletic. New circumscriptions are developed with the goal of organizing the species into genera that are strictly monophyletic. Species of Vittaria are placed in three genera, Vittaria, Haplopteris, and Radiovittaria, reflecting new hypotheses of their phylogenetic relation- ships. Species with leaves 4 mm wide and paraphyses bearing narrow apical cells are retained in Vittaria. Old World species with funnelform terminal cells on paraphyses and distichous phyllotaxy are placed in Haplopteris, whereas those with funnelform terminal cells on paraphyses and spiral phyllotaxy are placed in the new genus Radiovittaria. Species of Antrophyum are divided between the monophyletic genera Antrophyumn and Scoliosorus. Antrophyum is restricted to paleotropical species with pluriseriate venation and globose- tetrahedral spores. Those species with pluriseriate venation (neotropical and African) and bilateral spores are assigned to Scoliosorus. The genera Ananthacorus, Anetium, Hecistopteris, Monogramma, and Polytaenium are retained and given clarified circumscriptions. A description of the Vittariaceae and a key to the genera of the family are presented; all genera are described and new combinations are made for a number of species.

Systematics of the Gnetales: A Review of Morphological and Molecular Evidence

Despite substantial evolutionary interest in the order Gnetales as the extant group of seed plants most similar to the angiosperms, our knowledge of systematic relationships within the genera of the group remains quite limited. The most recent worldwide monograph of Ephedra is that of Stapf (1889), while the only worldwide systematic treatment of Gnetum is that of Markgraf (1930). This article summarizes our current knowledge of the relationships among the ca. 50 species of Ephedra and the ca 39 species of Gnetum and the relationships between these two genera and the monotypic Welwitschia. Preliminary phylogenetic analyses of rbcL gene sequences, including three species each of Ephedra and Gnetum, provide further support for the monophyly of the Gnetales relative to the other extant groups of seed plants and for the sister-group relationship of Ephedra and Gnetum.

Systematic and Evolutionary Implications of rbcL Sequence Variation in Rosaceae

The angiosperm family Rosaceae poses a number of noteworthy systematic problems as well as many questions concerning morphological and chromosomal evolution. Phylogenetic analysis of rbcL gene sequences was performed to address systematic and evolutionary problems of Rosaceae. Both rbcL sequence variation and the presence of duplicated sequences near the 3' end of rbcL were useful in determining phylogenetic relationships in this family. Analyses of rbcL sequences indicate that there are groups of genera within Rosaceae comparable to the subfamilies Maloideae, Amygdaloideae, and Rosoideae, although the composition of each group differs from traditional circumscriptions. According to analysis of rbcL data, Maloideae and Amygdaloideae each include additional taxa not normally associated with them. All members of Rosoideae with x = 9 are phylogenetically well separated from the x = 8 and 7 members of the subfamily. In addition, Spiraeoideae are not monophyletic but appear to consist of several distinct evolutionary lineages. The rbcL-based phylogenies suggest that chromosome numbers are more reliable indicators of some generic alliances than the more commonly used fruit types. Sequence data are also useful in determining the alliances of several problematic genera, suggesting that the capsular and follicular-fruited genera Vauquelinia, Lindleya, and Kageneckia (usually placed in Spiraeoideae) should be included in the pome-fruited subfamily Maloideae, and that Quillaja is not a member of Rosaceae. Molecular data are consistent with several suggestions for the ancestral chromosome numbers and fruit types of Rosaceae, but do not support any one hypothesis for either. This study also suggests that the subfamily Maloideae may have descended from spiraeoid ancestors and that the pome is derived from follicular or capsular fruit types.

RbcL sequences support exclusion ofRetzia, Desfontainia, andNicodemia from theGentianales

The taxonomic positions ofRetzia, Desfontainia, andNicodemia have been much discussed, and all three genera have been included inLoganiaceae (Gentianales). We have made a cladistic analysis ofrbcL gene sequences to determine the relationships of these taxa toGentianales. Four newrbcL sequences are presented; i.e., ofRetzia, Desfontainia, Diervilla (Caprifoliaceae), andEuthystachys (Stilbaceae). Our results show thatRetzia, Desfontainia, andNicodemia are not closely related toLoganiaceae or theGentianales. Retzia is most closely related toEuthystachys and is better included inStilbaceae. The positions ofDesfontainia andNicodemia are not settled, butDesfontainia shows affinity for theDipsacales s.l. andNicodemia for theLamiales s.l.