Matt P. Ashworth

A multi-locus time-calibrated phylogeny of the siphonous green algae

The siphonous green algae are an assemblage of seaweeds that consist of a single giant cell. They comprise two sister orders, the Bryopsidales and Dasycladales. We infer the phylogenetic relationships among the siphonous green algae based on a five-locus data matrix and analyze temporal aspects of their diversification using relaxed molecular clock methods calibrated with the fossil record. The multi-locus approach resolves much of the previous phylogenetic uncertainty, but the radiation of families belonging to the core Halimedineae remains unresolved. In the Bryopsidales, three main clades were inferred, two of which correspond to previously described suborders (Bryopsidineae and Halimedineae) and a third lineage that contains only the limestone-boring genus Ostreobium. Relaxed molecular clock models indicate a Neoproterozoic origin of the siphonous green algae and a Paleozoic diversification of the orders into their families. The inferred node ages are used to resolve conflicting hypotheses about species ages in the tropical marine alga Halimeda.

A revision of the genus Cyclophora and description of Astrosyne gen. nov. (Bacillariophyta), two genera with the pyrenoids contained within pseudosepta

Ashworth M.P., Ruck E.C., Lobban C.S., Romanovicz D.K., and Theriot E.C. 2012. A revision of the genus Cyclophora and description of Astrosyne gen. nov. (Bacillariophyta), two genera with the pyrenoids contained within pseudosepta. Phycologia 51: 684–699. DOI: 10.2216/12-004.1 The araphid pennate diatom genus Cyclophora is characterized by an elliptical to circular pseudoseptum at the centre of one valve; C. tenuis is the only commonly reported species. New species have included some with pseudosepta on both valves, and we emended the generic description to accommodate these. Three species of Cyclophora were described from light and scanning electron microscopy: C. castracanei sp. nov., C. tabellariformis sp. nov. and C. minor sp. nov. Of these, C. castracanei was isovalvar with a pseudoseptum on both valves; C. tabellariformis was heterovalvar but differed in shape from the type species; and C. minor was very small and had both iso- and heterovalvar frustules. Other differences included stria density and arrangement of slits in the apical fields. Developmentally, the areolae within the boundary of the pseudoseptum filled in as the pseudoseptum grew. Also described was Astrosyne radiata gen. nov., sp. nov., which possessed a pseudoseptum in both valves but was radially symmetrical in valve outline. Transmission electron microscopy (TEM) observations of cytoplasmic ultrastructural organization and three-gene sequencing (nuclear-encoded small subunit rRNA, rbcL and psbC) of cultured cells was carried out on all except C. minor. TEM showed that pyrenoids were localized within the pseudoseptum in both Cyclophora and Astrosyne. Phylogenetic analysis of the DNA sequences also supported the close relationship between these genera. While A. radiata was not the first radially symmetrical diatom suggested to be derived from an araphid pennate lineage, the localization of pyrenoids within a central pseudoseptum in the valve may be the most distinctive synaopomorphy amongst diatoms with such different valve outlines.

Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae)

The ocellate and pseudocellate diatoms in the Eupodiscaceae and Biddulphiaceae (respectively) are common inhabitants of the marine littoral (and plankton zone) with a rich fossil history making them important components of marine stratigraphic studies and good candidates for molecular dating work. These diatoms are important for un‐derstanding the phylogeny of the diatoms as a whole, as molecular phylogenies have blurred the traditional distinction between the pennate and multipolar non‐pennate diatoms. However, the convoluted taxonomic history of these groups has the potential to disrupt both stratigraphic and molecular dating studies. Although efforts have been made to examine frustule morphology of several ocellate and pseudocellate diatoms and develop a morphological scheme to define genera, very little work has been done to determine how these groups are interrelated. In this study, we use nuclear and chloroplast molecular markers to construct a phylogeny of a diverse sampling of Eupodiscaceae and Biddulphiaceae taxa. The ocellus‐bearing taxa (Eupodiscaceae) are monophyletic, and thus the ocellus may be a useful character in delimiting the Eupodiscaceae, the Biddulphiaceae are polyphyletic and scattered across a number of lineages of multipolar non‐pennate diatoms. Hypothesis testing aimed at assessing the likeliness of several morphology based hypotheses against the molecular data highlights uncertainty in both types of data. We present evidence that there are monophyletic genera within both the Biddulphiaceae and Eupodiscaceae, and recommend the taxa within the Odontella mobilensis/sinensis/regia clade be transferred to a new genus: Trieres Ashworth & Theriot.

Status of the pursuit of the diatom phylogeny : Are traditional views and new molecular paradigms really that different?

Diatoms are often referred to one of six structural groups. The two major groups are centrics and pennates, and each is further subdivided. Centrics are either radial centrics or (bi-)multipolar (or simply polar) centrics. The former typically are circular and lack any prominent structures which may be paired or multiply arranged so as to give some sort of visually prominent polarity to the cell. Polar centrics have such structures and often have elongate outlines. Pennates are either araphid pennates or raphid pennates, depending on whether or not they possess a raphe. These structural groups have been arranged differently through time, whether the source of data was morphology and the method of analysis noncanonical or whether the data were molecular and analyzed by more formal methods. Both congruence and conflict between these various approaches have been claimed. Diatomists have rejected traditional views because they conflict with molecular results in some instances, and yet reject molecular results because they conflict with morphologically based results in others. Such conflicts are rarely formally tested. Here, we formally test several traditional hypotheses and a recent molecular-based reclassification of diatoms against a three-gene combined molecular dataset. Centrics are strongly rejected as monophyletic. However, some relationships could not be rejected. Monophyly of araphids is not statistically worse than the best tree (in which araphids are recovered as a grade). Monophyly of radial centrics and of polar centrics cannot be rejected, nor can a competing hypothesis (in which radial centrics are a grade and the Thalassiosirales are part of that grade). This last result is congruent with complex morphological characters and is an example of the value of formally testing conflict and congruence between datasets, and of the potential value of formal phylogenetic analysis of diatom morphology.

AN UNRECOGNIZED ANCIENT LINEAGE OF GREEN PLANTS PERSISTS IN DEEP MARINE WATERS 1

We provide molecular phylogenetic evidence that the obscure genera Palmophyllum Kütz. and Verdigellas D. L. Ballant. et J. N. Norris form a distinct and early diverging lineage of green algae. These palmelloid seaweeds generally persist in deep waters, where grazing pressure and competition for space are reduced. Their distinctness warrants recognition as a new order, the Palmophyllales. Although phylogenetic analyses of both the 18S rRNA gene and two chloroplast genes (atpB and rbcL) are in agreement with a deep‐branching Palmophyllales, the genes are in conflict about its exact phylogenetic placement. Analysis of the nuclear ribosomal DNA allies the Palmophyllales with the prasinophyte genera Prasinococcus and Prasinoderma (Prasinococcales), while the plastid gene phylogeny placed Palmophyllum and Verdigellas as sister clade to all other Chlorophyta.

New Insights into Plagiogrammaceae (Bacillariophyta) Based on Multigene Phylogenies and Morphological Characteristics with the Description of a New Genus and Three New Species

Plagiogrammaceae, a poorly described family of diatoms, are common inhabitants of the shallow marine littoral zone, occurring either in the sediments or as epiphytes. Previous molecular phylogenies of the Plagiogrammaceae were inferred but included only up to six genera: Plagiogramma, Dimeregramma, Neofragilaria, Talaroneis, Psammogramma and Psammoneis. In this paper, we describe a new plagiogrammoid genus, Orizaformis, obtained from Bohai Sea (China) and present molecular phylogenies of the family based on three and four genes (nuclear-encoded large and small subunit ribosomal RNAs and chloroplast-encoded rbcL and psbC). Also included in the new phylogenies is Glyphodesmis. The phylogenies suggest that the Plagiogrammaceae is composed of two major clades: one consisting of Talaroneis, Orizaformis and Psammoneis, and the second of Glyphodesmis, Psammogramma, Neofragilaria, Dimeregramma and Plagiogramma. In addition, we describe three new species within established genera: Psammoneis obaidii, which was collected from the Red Sea, Saudi Arabia; and Neofragilaria stilus and Talaroneis biacutifrons from the Mozambique Channel, Indian Ocean, and illustrate two new combination taxa: Neofragilaria anomala and Neofragilaria lineata. Our observations suggest that the biodiversity of the family is strongly needed to be researched, and the phylogenetic analyses provide a useful framework for future studies of Plagiogrammaceae.

Metabolomic Profiling of 13 Diatom Cultures and Their Adaptation to Nitrate-Limited Growth Conditions

Diatoms are very efficient in their use of available nutrients. Changes in nutrient availability influence the metabolism and the composition of the cell constituents. Since diatoms are valuable candidates to search for oil producing algae, measurements of diatom-produced compounds can be very useful for biotechnology. In order to explore the diversity of lipophilic compounds produced by diatoms, we describe the results from an analysis of 13 diatom strains. With the help of a lipidomics platform, which combines an UPLC separation with a high resolution/high mass accuracy mass spectrometer, we were able to measure and annotate 142 lipid species. Out of these, 32 were present in all 13 cultures. The annotated lipid features belong to six classes of glycerolipids. The data obtained from the measurements were used to create lipidomic profiles. The metabolomic overview of analysed cultures is amended by the measurement of 96 polar compounds. To further increase the lipid diversity and gain insight into metabolomic adaptation to nitrogen limitation, diatoms were cultured in media with high and low concentrations of nitrate. The growth in nitrogen-deplete or nitrogen-replete conditions affects metabolite accumulation but has no major influence on the species-specific metabolomic profile. Thus, the genetic component is stronger in determining metabolic patterns than nitrogen levels. Therefore, lipid profiling is powerful enough to be used as a molecular fingerprint for diatom cultures. Furthermore, an increase of triacylglycerol (TAG) accumulation was observed in low nitrogen samples, although this trend was not consistent across all 13 diatom strains. Overall, our results expand the current understanding of metabolomics diversity in diatoms and confirm their potential value for producing lipids for either bioenergy or as feed stock.

Marine necklace-chain Fragilariaceae (Bacillariophyceae) from Guam, including descriptions of Koernerella and Perideraion, genera nova

Light microscopy (LM) and scanning electron microscopy (SEM) studies of necklace‐chain forming colonial diatoms from benthic habitats in Guam revealed five species. Bleakeleya notata (Grunow in Van Heurck) Round is widespread and well‐known. Asterionella notata var. recticostata Körner has been reported only twice before; we describe the plastids for the first time. On phylogenetic grounds we assign A. notata var. recticostata to a new genus, Koernerella, and emend the description of Bleakeleya. Three new species belonging in a new genus, Perideraion, are described as P. montgomeryi, P. decipiens and P. elongatum. Cultures from single‐cell isolates yielded four gene sequences for three of these taxa. The genera are easy to identify in the LM and SEM. Perideraion differs from Bleakeleya and Koernerella in having two large H‐shaped plastids, as reported for Asterionellopsis and Asteroplanus, and is further distinguished from all these genera by the following character set: a distinct rim around the basal field of circular pores, an apical rimoportula laterally on the valve mantle, pores in the valves that are unlike those in the basal pore field, and absence of apical slits. Although the basal pole attachment and colony morphology seem synapomorphic, molecular evidence suggests that the Bleakeleya‐Koernerella‐Perideraion clade is separate from the Asterionellopsis‐Asteroplanus clade and these five genera do not form one monophyletic group. It remains to be seen whether they are part of a somewhat larger group at the base of the araphid grade or if the genera we studied are truly separate.

Conserved Gene Order and Expanded Inverted Repeats Characterize Plastid Genomes of Thalassiosirales

Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: Thalassiosira weissflogii, Roundia cardiophora, Cyclotella sp. WC03_2, Cyclotella sp. L04_2, and three additional non-Thalassiosirales species Chaetoceros simplex, Cerataulina daemon, and Rhizosolenia imbricata. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in Thalassiosira oceanica. Cyclotella nana, Thalassiosira weissflogii and Roundia cardiophora share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two Cyclotella species by a single inversion. The genes ilvB and ilvH are missing in all six diatom plastid genomes except for Cerataulina daemon, suggesting an independent gain of these genes in this species. The acpP1 gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, psaE, psaI, psaM, are missing in Rhizosolenia imbricata, which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes.

Climaconeis species (Bacillariophyceae: Berkeleyaceae) from western Pacific islands, including C. petersonii sp. nov. and C. guamensis sp. nov., with emphasis on the plastids

Plastids of Climaconeis (Okedenia) were originally characterized by Mereschkowsky as H-shaped in girdle view with pyrenoids but recent descriptions implicitly or explicitly indicate that the H-shape is seen in valve view. We observed five known taxa–one a variety that we raise to species rank–and two new species: C. silvae, C. riddleae, C. guamensis sp. nov. and C. inflexa (curved species); C. lorenzii (straight species with craticular bars); a straight species without bars that matches Navicula scopulorum var. triundulata = Climaconeis undulata comb. nov.; and a new straight species without bars, C. petersonii sp. nov. In the species with multiple plastids, plastids are plate-like, usually with a pyrenoid in the centre, arranged in pairs along the girdle faces of the cells. In some species with few plastids, including C. riddleae, and possibly C. inflexa, the pyrenoid is also visible in valve view between opposing plastids, such that these species do appear to have plastids that are H-shaped in valve view. We describe the two new species and confirm published SEM observations on other species, including features of the pores that help distinguish C. guamensis from the very similar C. riddleae.