Edward C. Theriot

PHYLOGENY OF THE ULVOPHYCEAE (CHLOROPHYTA): CLADISTIC ANALYSIS OF NUCLEAR-ENCODED rRNA SEQUENCE DATA1

Cladistic analysis of nuclear‐encoded rRNA sequence data provided us with the basis for some new hypotheses of relationships within the green algal class Ulvophyceae. The orders Ulotrichales and Ulvales are separated from the clade formed by the remaining orders of siphonous and siphonocladous Ulvophyceae (Caulerpales, Siphonocladales /Cladophorales [S/C] complex, and the Dasycladales), by the Chlorophyceae and Pleurastrophyceae. Our results suggest that the Ulvophyceae is not a monophyletic group. Examination of inter‐ and intra‐ordinal relationships within the siphonous and siphonocladous ulvophycean algae revealed that Cladophora, Chaetomorpha, Anadyomene, Microdictyon, Cladophoropsis and Dictyosphaeria form a clade. Thus the hypothesis, based on ultrastructural features, that the Siphonocladales and Cladophorales are closely related is supported. Also, the Caulerpales is a monophyletic group with two lineages; Caulerpa, Halimeda, and Udotea comprise one, and Bryopsis and Codium comprise the other. The Dasycladales (Cymopolia and Batophora) also forms a clade, but this clade is not inferred to be the sister group to the S/C complex as has been proposed. Instead, it is either the sister taxon to the Caulerpales or basal to the Caulerpales and S/C clade The Trentepohliales is also included at the base of the siphonous and siphonocladous ulvophycean clade. The Pleurastrophyceae, which, like the Ulvophyceae, posses a counter‐clockwise arrangement of flagellar basal bodies, are more closely related to the Chlorophyceae than to the Ulvophyceae based on rRNA sequences. Thus, the arrangement of basal bodies does not diagnose a monophyletic group. Previously reported hypotheses of phylogenetic relationships of ulvophycean algae were tested. In each case, additional evolutionary steps were required to obtain the proposed relationships. Relationships of ulvophycean algae to other classes of green algae are discussed.

USE OF RIBOSOMAL DNA INTERNAL TRANSCRIBED SPACERS FOR PHYLOGENETIC STUDIES IN DIATOMS1

Sequence variation of ribosomal DNA internal transcribed spacers (ITS) among populations, species, and genera of the diatom genus Stephanodiscus was investigated. ITS 1 and ITS 2, including the 5.8S gene, were sequenced from geographically distant and nearby populations of S. niagarae Ehrenberg. In addition, repeats from S. hantzschii Grunow and Cyclotella meneghiniana Kützing were sequenced to determine the taxonomic range over which the ITS region could be used for diatom systematics. The morphologically distinct S. yellowstonensis Theriot & Stoermer, thought to have evolved from S. niagarae in Yellowstone Lake between 12,000 and 8000 years ago, also was sequenced to assess its relationship to nearby S. niagarae populations. The organization and relative sizes of ITS 1 and ITS 2 in Stephanodiscus species were similar to those reported for other eukaryotes. In general, ITS 2 was slightly larger and more variable than ITS 1. Cladistic analysis of ITS sequences did not resolve relationships of nearby S. niagarae and S. yellowstonensis populations. However, central North American S. niagarae populations were in a clade supported by two nucleotide changes. For Cyclotella, much of the ITS region was not alignable with that for Stephanodiscus species; therefore, generic‐level comparison within the Thalassiosiraceae may not be possible. The variation (95–96% similarity) between S. hantzschii and other Stephanodiscus species suggests that interspecific relationships could be assessed with ITS sequences. Although S. yellowstonensis is morphologically distinct from S. niagarae, no autapomorphic nucleotide sites were identified. Two S. niagarae populations (Heart and Lewis Lakes), however, did possess autapomorphic ITS sites.

THE PLEURASTROPHYCEAE AND MICROMONADOPHYCEAE: A CLADISTIC ANALYSIS OF NUCLEAR rRNA SEQUENCE DATA1

Partial sequences from the nuclear‐encoded 18S and 26S ribosomal RNA molecules from representatives of the five classes of Chlorophyta sensu Mattox and Stewart (1984) were analyzed cladistically in a study of the phylogenetic relationships among the Micromonadophyceae, Pleurastrophyceae, and other green algae. The sequence data indicate that the Micromonadophyceae (= Prasinophyceae) is not monophyletic but comprises at least three lineages occupying a basal position among the green algae. Though the Pleurastrophyceae and the Ulvophyceae both possess counter‐clockwise basal body orientations, the sequence data indicate that the Pleurastrophyceae is the sister group to the Chlorophyceae. The molecular data alone do not resolve the monophyly of the Pleurastrophyceae or the Ulvophyceae; however, a combined data set of molecular and non‐molecular characters support a monophyletic Pleurastrophyceae. Analyses with user‐defined tree topologies and the bootstrap method of character resampling indicate that the relationships shown in the most parasimonious cladograms are well supported by the character data.

PHYLOGENETIC SYSTEMATICS AS A GUIDE TO UNDERSTANDING FEATURES AND POTENTIAL MORPHOLOGICAL CHARACTERS OF THE CENTRIC DIATOM FAMILY THALASSIOSIRACEAE

We list features of the siliceous cell wall which may be of use in the systematics of the Thalassiosiraceae. Many, but not all, of these features have been used in taxonomy of the members of the family. We have subdivided or redefined some previously used features such as “complex alveoli” into component parts. Discussion for potential characters are based on first principles of phylogenetic systematics rather than on agreement with current or desired taxonomic results. Features are considered as potential homologous characters if they share some degree of similarity and can be argued to be discretely heritable. The resultant list is large (over 80 features), but by no means complete because many details of Thalassiosiraceae frustule morphology remain unreported and unobserved. In fact, one of our objectives is to encourage microscopists to give more attention to the girdle bands and to better resolve so-called “minutiae” such as fultoportule cowlings (a new term defined and illustrated here).

Cell wall morphology and systematic importance of Thalassiosira ritscheri (Hustedt) hasle, with a description of Shionodiscus gen. nov

The centric diatom order Thalassiosirales includes all diatoms with a fultoportula (strutted process), a feature now recognized as a synapomorphy for the lineage. Within Thalassiosirales, Thalassiosira is perhaps the most taxonomically and morphologically diverse genus, and at least two distinct morphological groups have been recognized within it. Group “A” Thalassiosira species, which include the type species, T. nordenskioeldii, have short inward and long outward extensions of the strutted processes and a labiate process on the valve mantle. Group “B” species have exceptionally long inward and reduced outward extensions of the strutted processes, and a labiate process on the valve face. We collected and cultured Thalassiosira ritscheri, which has a combination of group A and B characters. It has a labiate process on the valve face and reduced outward extensions of the strutted processes. We show for the first time that T. ritscheri has short inward, A-type extensions of the strutted processes. A phylogenetic interpretation of these conditions suggests a close relationship between T. ritscheri and the traditionally held group “B” species. Species diagnosed by the autapomorphic condition of a labiate process away from the valve mantle, including many group “B” Thalassiosira species, are transferred into Shionodiscus gen. nov.

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.

INFERRING DIATOM PHYLOGENY: A CLADISTIC PERSPECTIVE

The true phylogeny of a lineage can never be known, only estimated. Phylogenetic Systematics or Cladistics represents one approach to inferring genealogical relationships of diatoms. The assumptions of the cladistic approach and its associated methodology are outlined, and examples are presented for the diatoms. The relevance of recognising monophyletic groups to phylogenetic reconstruction is discussed.

Comparative analysis of the interaction between habitat and growth form in diatoms

We characterized the evolutionary history of growth form (solitary–colonial) and its interaction with species’ habitat (planktonic–benthic) across a multi-gene phylogeny encompassing a broad sample of the order-level diversity of diatoms. We treated these characters broadly, modeling the evolution of aggregation of cells into a colony irrespective of the way aggregation is achieved, and relating the growth form to a broad concept of niche location: in the plankton or benthos. The results showed that habitat shifts are rare implying conservatism in niche location at the level of large clades. On the other hand, the evolutionary history of growth form is more dynamic with evolutionary rates that vary across the tree. Analyses of a possible interaction revealed that shifts in growth form are independent of habitat and that traversing between habitats does not hinge upon species’ growth form. Our findings help to fill a gap in the understanding of diatom niche and growth form macroevolution and contribute toward a platform for the comparative study of the mechanisms underlying diatom species and functional diversity.

Phylogenetic analysis and a review of the history of the accidental phytoplankter, Phaeodactylum tricornutum Bohlin (Bacillariophyta)

The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.