rbcL Phylogeny Research Articles

Morphology, rbcL phylogeny and distribution of distromatic Ulva (Ulvophyceae, Chlorophyta) in Ireland and southern Britain

C.J. Loughnane, L.M. McIvor, F. Rindi, D.B. Stengel and M.D. Guiry. 2008. Morphology, rbcL phylogeny and distribution of distromatic Ulva (Ulvophyceae, Chlorophyta) in Ireland and southern Britain. Phycologia 47: 416–429. DOI: 10.2216/07-61.1Species of Ulva occur worldwide in all aquatic habitats from freshwater through brackish to fully saline environments. The scarcity of stable morphological characters and the morphological plasticity linked to environmental conditions typical of species referred to this genus make identification and circumscription problematic. In Ireland and Britain the taxonomy of Ulva species has been uncertain, and only three species have been reported: Ulva lactuca, U. rigida and U. olivascens (later reassigned to Umbraulva olivascens). We reassessed the taxonomic status of this genus by combining morphological investigations with analyses of rbcL sequence data for 24 selected specimens from the Irish and southern British shores. This combination of methods allowed the identification of seven lineages, which were considered to represent the following species: Ulva rigida, U. scandinavica, U. lactuca, U. gigantea, U. rotundata, U. californica and Umbraulva olivascens. Of these, U. scandinavica, U. gigantea, U. rotundata and U. californica are newly reported; the distribution of U. olivascens was shown to be much wider than previously thought. The use of morphological features proved to be largely inconclusive and of limited value for circumscription of species. In the rbcL phylogeny, U. olivascens formed a sister clade to all other species. The results support the conspecificity of U. rigida, U. scandinavica and U. armoricana and the conspecificity of U. pseudocurvata and U. compressa already suggested in previous studies.

A global molecular phylogeny of the fern genus Trichomanes (Hymenophyllaceae) with special reference to stem anatomy

To establish a basis for future taxonomic revisions and to infer the evolutionary traits of Trichomanes s.l., one of two large filmy fern genera, molecular phylogenetic analyses were conducted using chloroplast rbcL sequences. Sampling covered most of the global distribution range of this genus throughout the tropical and temperate zones, as well as all taxonomically significant species by the addition of 51 samples principally from Asia. The evolution of eight selected characters, which were adopted as taxonomic keys and/or putatively reflect morphological regression, was optimized on the retrieved most parsimonious rbcL trees, together with new observations on the stem anatomy of 45 species. The eight robust clades retrieved within Trichomanes in the rbcL phylogeny conflict with the existing classifications. Our results also suggest that the cup-shaped sorus, the primary diagnostic character of the genus, appears in parallel in the Hymenophyllum lineage, as demonstrated by Pleuromanes (typified by Trichomanes pallidum) included in the lineage. The suggestion that the regressive character states are homoplastic apomorphies in the evolution of the frond size, stem thickness, root system, and stem anatomy (stele and cortex) probably illustrates a strong tendency towards adaptive evolutionary transition in Trichomanes.

Vegetative morphology and rbcL phylogeny of some members of the genera Botryocladia and Irvinea (Rhodymeniaceae, Rhodophyta)

R.J. Wilkes, L. McIvor and M.D. Guiry. 2006. Vegetative morphology and rbcL phylogeny of some members of the genera Botryocladia and Irvinea (Rhodymeniaceae, Rhodophyta). Phycologia 45: 481–494. DOI: 10.2216/05-11.1Botryocladia is a genus of marine red algae (Rhodophyta) generally found in tropical, subtropical and warm temperate seas. There are currently 35 described species, but the taxonomic status of many of these remains confused. Recently, the genus was split into two genera, with the new genus, Irvinea, described based on morphological and molecular evidence. Only one species, I. ardreana, is currently assigned to the newer genus. For this study, a number of cultured Botryocladia and Irvinea strains from the Mediterranean and Caribbean were examined. Each was examined microscopically and the key features currently used for identification were evaluated. Up to 1277 bp of the rbcL gene was PCR amplified for each isolate and directly sequenced. The molecular data confirm that the species currently considered as Botryocladia do not form a monophyletic group. Botryocladia boergesenii grouped in a clade with I. ardreana with the remaining Botryocladia species in a separate grouping. We propose the transfer of B. boergesenii to the genus Irvinea on the basis of the molecular and morphological data. Morphological and molecular data for the other species examined were also evaluated although little correlation between the morphological features and the rbcL data was observed. The taxonomic utility of some of the morphological features is called into doubt, although clear differences between the genera Botryocladia and Irvinea can be seen. In addition to the morphological features currently regarded as important intergeneric characters, the presence of branched vesicles as an indicator for species of Irvinea should be added.

Origin and age of Australian Chenopodiaceae

We studied the age, origins, and possible routes of colonization of the Australian Chenopodiaceae. Using a previously published rbcL phylogeny of the Amaranthaceae–Chenopodiaceae alliance (Kadereit et al. 2003) and new ITS phylogenies of the Camphorosmeae and Salicornieae, we conclude that Australia has been reached in at least nine independent colonization events: four in the Chenopodioideae, two in the Salicornieae, and one each in the Camphorosmeae, Suaedeae, and Salsoleae. Where feasible, we used molecular clock estimates to date the ages of the respective lineages. The two oldest lineages both belong to the Chenopodioideae ( Scleroblitum and Chenopodium sect. Orthosporum/ Dysphania) and date to 42.2–26.0 and 16.1–9.9 Mya, respectively. Most lineages (Australian Camphorosmeae, the Halosarcia lineage in the Salicornieae, Sarcocornia, Chenopodium subg. Chenopodium/ Rhagodia, and Atriplex) arrived in Australia during the late Miocene to Pliocene when aridification and increasing salinity changed the landscape of many parts of the continent. The Australian Camphorosmeae and Salicornieae diversified rapidly after their arrival. The molecular-clock results clearly reject the hypothesis of an autochthonous stock of Chenopodiaceae dating back to Gondwanan times. Instead, they indicate that most lineages arrived in Australia via long-distance dispersal. Some lineages (e.g. the Halosarcia lineage) may have used the Indonesian archipelagos as stepping stones. The authors are aware that estimates of diversification times using a molecular clock can be subject to considerable levels of error. Our estimates of the age of Australian chenopod lineages based on three alternative fossils were made independently from any knowledge about shifts in climatic and geographical conditions in Australia during the times of arrival. In most cases, however, the paleoclimatic scenario indicates habitat shifts suitable for the respective chenopod colonizer, which corroborates our findings and provides a plausible scenario.

THE PRASIOLALES (CHLOROPHYTA) OF ATLANTIC EUROPE: AN ASSESSMENT BASED ON MORPHOLOGICAL, MOLECULAR, AND ECOLOGICAL DATA, INCLUDING THE CHARACTERIZATION OF ROSENVINGIELLA RADICANS (KÜTZING) COMB. NOV.1

Despite a simple morphology and intensive studies carried out for more than two centuries, the systematics of the Prasiolales still presents several unsolved problems. The taxonomic relationships of several common species of Prasiolales, mostly from northern Europe, were investigated by a combination of morphological observations, culture experiments, and molecular analyses based on rbcL sequences. The results indicate that Rosenvingiella and Prasiola are separate genera. The capacity for production of tridimensional pluriseriate gametangia and the presence of unicellular rhizoids are the morphological features that discriminate Rosenvingiella from filamentous forms of Prasiola. The molecular data indicate that uniseriate filaments can be produced in at least three different species of Prasiola. The genetic diversity of uniseriate filamentous Prasiolales is higher than their simple morphology would indicate, and the provisional retention of SchizogoniumKützing 1843 as independent genus is recommended. The rbcL phylogeny confirms that Prasiola calophylla, P. crispa, and P. stipitata are distinct species, whereas P. stipitata and P. meridionalis are probably conspecific. Rosenvingiella polyrhiza is a strictly marine alga, and most records of Rosenvingiella in Europe are referable to Rosenvingiella radicans, proposed here as a new combination based on Ulothrix radicansKützing 1849. This is a primarily terrestrial alga that can occur from upper intertidal rock to locations situated hundreds of kilometers inland. The great confusion that has arisen in Europe between these two species in the last century is mostly due to misidentifications of marine populations of R. radicans.

Unusual position of the genus Spirotaenia (Zygnematophyceae) among streptophytes revealed by SSU rDNA and rbcL sequence comparisons

Sexual reproduction by conjugation characterizes the genus Spirofaenia, and based on this character alone it has long been considered a member of the class Zygnematophyceae (Streptophyta). The similarity in chloroplast morphology between the unicellular Spirotaenia (Mesotaeniaceae) and the filamentous Spirogyra (Zygnemataceae) has led to the assumption that the two genera are evolutionarily related, a view apparently supported by rbcL sequence comparisons (McCourt et a1. 2000). We sequenced the nuclear-encoded SSU rDNA and the rbcL genes from three Spirotaenia species and analysed their molecular phylogeny together with other streptophyte green algae (including representatives of the class Zygnematophyceae) and embryophytes using maximum likelihood, distance, maximum parsimony and Bayesian inference methods. The significance of the results was tested by bootstrap analyses,deletion of long-branch taxa and user-defined tree topologies. The two genes congruently revealed an unexpected position of the genus Spirofaenia within the streptophyte algae outside the class Zygnematophyceae, but associated with Chiorokybus. In contrast to a previously published rbcL phylogeny of conjugating green algae, our results suggest that Spirotaenia is not specifically related to Spirogyra and may not belong to the class Zygnematophyceae. The absence of the well-known zygnematophycean 1506 group I intron in all SSU rONA sequences of Spirotaenia supports this conclusion.

Utility of plastid psaB gene sequences for investigating intrafamilial relationships within Orchidaceae

DNA sequences of the plastid gene psaB were completed for 182 species of Orchidaceae (representing 150 different genera) and outgroup families in Asparagales. These data were analyzed using parsimony, and resulting trees were compared to a rbcL phylogeny of Orchidaceae for the same set of taxa after an additional 30 new rbcL sequences were added to a previously published matrix. The psaB tree topology is similar to the rbcL tree, although the psaB data contain less homoplasy and provide greater bootstrap support than rbcL alone. In combination, the two-gene tree recovers the five monophyletic subfamilial clades currently recognized in Orchidaceae, but fails to resolve the positions of Cypripedioideae and Vanilloideae. These new topologies help to clarify some of the anomalous results recovered when rbcL is analyzed alone. Both genes appear to be absent from the plastid genome of several achlorophyllous orchids, but are present in the form of presumably non-functional pseudogenes in Cyrtosia. This study is the first to document the utility of psaB sequences for phylogenetic studies of plants below the family level.

Identification of north-western Atlantic Porphyra (Bangiaceae, Bangiales) based on sequence variation in nuclear SSU and plastid rbcL genes

Six species of Porphyra have commonly been recognized in the north-western Atlantic from Long Island Sound to the Canadian Maritimes: P. amplissima, P. leucosticra, P. linearis, P. miniata, P. purpurea, and P. umbilicalis. Distinguishing them with certainty has been problematic. A DNA-based system of molecular identification was developed using partial sequences of the nuclear small subunit ribosomal RNA gene (SSU) or the plastid ribulose-1,5-bisphosphate carboxylase–oxygenase large subunit gene (rbcL). Multiple samples of each taxon were surveyed for intraspecific variation. Intraspecific SSU divergences for Porphyra ‘leucosticta’, P. ‘miniata’, P. ‘umbilicalis’, and P. ‘purpurea’ ranged from 0% to 1%. There was more variation for P. ‘amplissima’ (0–2.1%) and P. ‘linearis’ (0–3.5%); however, each taxon was monophyletic. No intraspecific differences were observed for these taxa in rbcL (one to eight samples per taxon). These sequences were compared with P. yezoensis U51, introduced to Maine, and with P. ‘dioica’, a north-east Atlantic Porphyra easily confused with P. ‘purpurea’. To discriminate between P. ‘purpurea’, P. ‘umbilicalis’, and P. ‘leucosticta’, SSU variation was used to design primers for the Allele-Specific Polymerase Chain Reaction™. With molecular tools, we could classify over 80% of the monostromatic specimens surveyed, but the residue of unidentifiable specimens may indicate the existence of further monostromatic species in the north-west Atlantic. Porphyra ‘purpurea’ was found to occur further south than previously recorded. A morphologically cryptic Porphyra was discovered at Herring Cove, Nova Scotia, Canada.† Phylogenetic analyses using SSU or rbcL sequences showed ‘soft incongruence’ between gene trees, i.e. the topologies of the phylograms were similar but not identical, with only weak to moderate bootstrap support for the nodes that differed. Both trees strongly supported a clade including P. ‘purpurea’, P. ‘umbilicalis’, P. ‘linearis’, and P. ‘dioica’. Porphyra sp. Herring Cove was allied with the remaining Porphyra taxa in the SSU tree. The rbcL phylogeny was less well resolved, consisting of a polytomy of a P. ‘purpurea’–P. ‘umbilicalis’–P. ‘linearis’–P. ‘dioica’ clade, Porphyra sp. Herring Cove, a clade comprising P. ‘amplissima’ and P. ‘miniata’, and a P. ‘suborbiculata’–P. ‘leucosticta’–P. yezoensis clade.

Molecular phylogeny of conjugating green algae (Zygnemophyceae, Streptophyta) inferred from SSU rDNA sequence comparisons.

Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino-Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.

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.

GRACILARIA FROM THE GULF OF MEXICO, WITH SPECIAL EMPHASIS ON GRACILARIA TIKVAHIAE BASED ON TWO MOLECULAR DATASETS

Despite a recent body of literature, the species of Gracilaria recognized for the Gulf of Mexico are still incompletely characterized, misidentified, and species limits not well defined due to huge morphological plasticity and overlapping habits. To better characterize these taxa and evaluate their taxonomic relationships, we provide a chloroplast‐encoded rbcL phylogeny encompassing primarily Gulf, western Atlantic, and Caribbean species. Our results indicate the need to resurrect older, validly published names currently placed in synonymy under other species of Gracilaria, and to describe new species. For Gracilaria tikvahia, in particular, a combination of DNA sequences [rbcL, and internal transcribed spacer regions (ITS) of nuclear ribosomal DNA] from specimens collected across a wide biogeographic area (Nova Scotia, Canada, to Las Coloradas, Yucatan Peninsula) successfully promotes the integration and correlation of molecular phylogenies and morphology with biogeographic hypotheses.

Phylogeny of Aspleniaceae Inferred from rbcL Nucleotide Sequences

Phylogeny of Aspleniaceae Inferred from rbcL Nucleotide Sequences

Phylogenetic relationships within Araucariaceae based on rbcL gene sequences

Phylogenetic relationships were determined in the Araucariaceae, which are now found mainly in the Southern Hemisphere. This conifer family was well diversified and widely distributed in both hemispheres during the Mesozoic era. The sequence of 1322 bases of the rbcL gene of cpDNA was determined from 29 species of Araucariaceae, representing almost all the species of the family. Phylogenetic trees determined by the parsimony method indicate that Araucariaceae are well defined by rbcL sequences and also that the monophyly of Agathis or Araucaria is well supported by high bootstrap values. The topology of these trees revealed that Wollemia had derived prior to Agathis and Araucaria. The rbcL phylogeny agrees well with the present recognition of four sections within Araucaria: Araucaria, Bunya, Eutacta, and Intermedia. Morphological characteristics of the number of cotyledons, position of male cone, and cuticular micromorphologies were evaluated as being phylogenetically informative. Section Bunya was found to be derived rather than to be the oldest taxon. Infrageneric relationships of Agathis could not be well elucidated because there are few informative site changes in the rbcL gene, suggesting the more recent differentiation of the species as their fossil records indicate. The New Caledonian Araucaria and Agathis species each formed a monophyletic group with very low differentiation in rbcL sequences among them, indicating rapid adaptive radiation to new edaphic conditions, i.e., ultramafic soils, in the post-Eocene era.

Phylogenetic relationships of Biebersteinia Stephan (Geraniaceae) inferred from rbcL and atpB sequence comparisons

Phylogenetic analysis of rbcL and atpB gene sequences from Biebersteinia Stephan (represented by B. orphanidis Boiss.) and from selected taxa of the rosids I and II clades does not support traditional grouping of this genus in Geraniaceae s.s. nor in Geraniales, but indicates strong support for a position nested within Sapindales (as recently delimitated). The rbcL and atpB phylogenies obtained were congruent but differently resolved and do not link Biebersteinia to any other clade within Sapindales. Biebersteinia is on a long branch on its own which, given the particular combination of apomorphic morphological characters, justifies familial status

Molecular systematics and a revised taxonomy of the onocleoid ferns (Dryopteridaceae: Onocleeae)

Nucleotide sequences of the chloroplast-encoded rbcL gene were determined for all five species of the onocleoid ferns (Dryopteridaceae tribe Onocleeae), including both varieties of Onoclea sensibilis, and for outgroup member Blechnum glandulosum. Together with GenBank sequences of three additional onocleoid accessions and four additional taxa representing the outgroup Blechnaceae, these were analyzed cladistically under the optimality criteria of maximum parsimony and maximum likelihood. Maximum parsimony yielded a single most-parsimonious tree with the three accessions of Onoclea sensibilis var. sensibilis left as an unresolved trichotomy. Maximum likelihood yielded a single set of three optimal trees whose only topological variation was in the trivial positioning of the three accessions of Onoclea sensibilis var. sensibilis relative to each other. Thus tree topologies of the onocleoid ingroup under maximum parsimony and maximum likelihood were completely congruent. Matteuccia orientalis and M. intermedia formed the basalmost ingroup clade strongly separated from the remaining taxa and sister to them. Onoclea sensibilis is strongly separated from its sister clade of Matteuccia struthiopteris plus Onocleopsis hintonii, and the two varieties of Onoclea sensibilis are well differentiated from each other. Matteuccia struthiopteris and Onocleopsis hintonii form the least strongly supported clade. Levels of sequence divergence among onocleoid taxa are compared with values from other taxa, and morphological and chromosomal data used in previous, noncladistic studies of the onocleoids are reevaluated in light of this rbcL phylogeny. Matteuccia orientalis and M. intermedia should be recognized in their own genus Pentarhizidium, and the previously recognized varieties of Onoclea sensibilis are supported at least at varietal rank and possibly at the rank of species. Molecular and morphological data bearing on the circumscriptions of Matteuccia and Onocleopsis are equivocal but perhaps most concordant with their continued recognition as monotypic genera.

Molecular Phylogeny of the Papilionoideae (Family Leguminosae): RbcL Gene Sequences versus Chemical Taxonomy

AbstractTotal DNA was extracted from 67 species (30 genera) of the subfamily Papilionoideae (family Leguminosae). The rbcL gene was amplified by polymerase chain reaction (PCR) and sequenced directly. RbcL sequences were evaluated with character‐state (maximum parsimony; PAUP) and distance methods (neighbour‐joining; MEGA). Morphology‐based classifications of tribes and subtribes are mostly congruent with rbcL phylogeny. Differences occur for members of the genus Sophora and for intratribal relationships within the Genista/Cytisus complex: Sophora appears in two clades; one clade with S. japonica at the base of the Papilionoideae and a second more advanced group (with S. davidii, S. jaubertii, and S.flavescens) which represents a sister clade of the Thermopsideae. The Cytisus complex includes the genera Cytisus, Chamaecytisus, Calicotome and Spartocytisus but not Cytisophyllum which appears as a distinct member of the Genista complex. Chamaespartium sagittale is very close to Genista supporting the view that it does not represent an independent genus but should be treated as Genista sagittalis. Close to Genista are Teline and Spartium, whereas Argyrolobium, Retama, Cytisophyllum, Ulex, Petteria, Adenocarpus, Chamaespartium tridentatum and Laburnum can be considered as “outliers” of the Genista‐group sensu stricto. RbcL phylogeny is compared with profiles of alkaloids and other natural products. First results indicate that secondary metabolite profiles, if compared with morphology or rbcL sequences, are of limited value as a taxonomic marker.