The Ulvophyceae, one of the four classes of the Chlorophyta, is of particular evolutionary interest because it features an unrivaled morphological and cytological diversity. Morphological types range from unicells and simple multicellular filaments to sheet-like and complex corticated thalli. Cytological layouts range from typical small cells containing a single nucleus and chloroplast to giant cells containing millions of nuclei and chloroplasts. In order to understand the evolution of these morphological and cytological types, the present paper aims to assess whether the Ulvophyceae are monophyletic and elucidate the ancient relationships among its orders. Our approach consists of phylogenetic analyses (maximum likelihood and Bayesian inference) of seven nuclear genes, small subunit nuclear ribosomal DNA and two plastid markers with carefully chosen partitioning strategies, and models of sequence evolution. We introduce a procedure for fast site removal (site stripping) targeted at improving phylogenetic signal in a particular epoch of interest and evaluate the specificity of fast site removal to retain signal about ancient relationships. From our phylogenetic analyses, we conclude that the ancestral ulvophyte likely was a unicellular uninucleate organism and that macroscopic growth was achieved independently in various lineages involving radically different mechanisms: either by evolving multicellularity with coupled mitosis and cytokinesis (Ulvales-Ulotrichales and Trentepohliales), by obtaining a multinucleate siphonocladous organization where every nucleus provides for its own cytoplasmic domain (Cladophorales and Blastophysa), or by developing a siphonous organization characterized by either one macronucleus or millions of small nuclei and cytoplasmic streaming (Bryopsidales and Dasycladales). We compare different evolutionary scenarios giving rise to siphonous and siphonocladous cytologies and argue that these did not necessarily evolve from a multicellular or even multinucleate state but instead could have evolved independently from a unicellular ancestor.

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Species-level taxonomy of Bryopsidalean genera is often based on quantifiable morphological characters. Yet there are relatively few examples of statistically founded morphometric studies within this group of siphonous algae and macroalgae in general. Molecular phylogenetic studies have revealed cases of cryptic diversity in several Bryopsidalean genera and call for new approaches toward taxonomy. We present a combined molecular and morphometric approach toward Halimeda taxonomy using a selection of specimens representing the five natural lineages within the genus. A phylogeny was inferred from partial nuclear rDNA sequences (3 0 end of small subunit, internal transcribed spacer region 1, 5.8S, internal transcribed spacer region 2, and 5 0 end of large subunit) from our and previously studied specimens. Segment size and shape descriptors were acquired using different techniques, including landmark analysis and elliptic Fourier analysis. A broad range of anatomical structures was measured. Taxonomic utility of the different methods and characters was assessed using predictive discriminant analysis. Molecular data were used to delimit species groups. Segment morphological characters proved fairly good predictors for species membership, but anatomical variables yielded the best results. The good performance of morphometric taxon predictors offers perspectives, not only for future taxonomic case studies within problematic species complexes, but also for thorough examinations of the rich fossil record of Halimeda. Statistically founded morphometric studies can probably help elucidate taxonomic issues within other Bryopsidalean genera as well.Key index words: anatomy; Bryopsidales; Halimeda; morphology; morphometrics; phylogeny; siphonous algae; taxonomy Abbreviations: DA, discriminant analysis; EFA, elliptic Fourier analysis; ITS, internal transcribed spacer; TBR, tree bisection-reconnection Morphometric analysis, the mathematical investigation of shape, allows objective and statistically sound evaluation of morphological variation to answer a broad spectrum of biological questions. Macroalgae are at first sight less suited for morphometric investigation because their structures and branching patterns are marked by considerable stochastic variation and plasticity. Contrary to botanists and zoologists, phycologists do not have the habit of embracing morphometrics to answer their taxonomic and ecological questions. Nonetheless, during the last 5 years, a raise in interest for morphometrics could be observed (Sherwood and Sheath 1999, Kraan et al. 2001, Krellwitz et al. 2001, Collado-Vides 2002, Hubbard and Garbary 2002, Vieira and Necchi 2002, de Senerpont Domis et al. 2003, Kamiya et al. 2003, Haywood et al. 2004, Murray et al. 2004. Achievements of these studies include reports of morphological differences between taxa and the description of taxon boundaries.In the present study, we explore the taxonomic utility of morphometric methods in the genus Halimeda. This genus belongs to the Bryopsidales, a group of algae ch...

BackgroundA non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and non-canonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code.ResultsThis study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique.ConclusionsWe compare different evolutionary scenarios for the complex phylogenetic distribution of this non-canonical genetic code. A single transition to the non-canonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are also unlikely because the same deviant code has evolved in all lineages. Instead we favor a stepwise acquisition model, congruent with the ambiguous intermediate model, whereby the non-canonical code observed in these green algal orders has a single origin. We suggest that the final steps from an ambiguous intermediate situation to a non-canonical code have been completed in the Trentepohliales, Dasycladales, Cladophorales and Blastophysa but not in the Bryopsidales. We hypothesize that in the latter lineage an initial stage characterized by translational ambiguity was not followed by final reassignment of both stop codons to glutamine. Instead the standard code was retained by the disappearance of the ambiguously decoding tRNAs from the genome. We correlate the emergence of a non-canonical genetic code in the Ulvophyceae to their multinucleate nature.

The microfilamentous green alga Uronema curvatum is widely distributed along the western and eastern coasts of the north Atlantic Ocean where it typically grows on crustose red algae and on haptera of kelps in subtidal habitats. The placement of this marine species in a genus of freshwater Chlorophyceae had been questioned. Molecular phylogenetic analysis of nuclearencoded small and large subunit rDNA sequences reveal that U. curvatum is closely related to the ulvophycean order Cladophorales, with which it shares a number of morphological features, including a siphonocladous level of organization and zoidangial development. The divergent phylogenetic position of U. curvatum, sister to the rest of the Cladophorales, along with a combination of distinctive morphological features, such as the absence of pyrenoids, the diminutive size of the unbranched filaments and the discoid holdfast, warrants the recognition of a separate genus, Okellya, within a new family of Cladophorales, Okellyaceae. The epiphytic Urospora microscopica from Norway, which has been allied with U. curvatum, is revealed as a member of the cladophoralean genus Chaetomorpha and is herein transferred to that genus as C. norvegica nom. nov.