Frederick W. Zechman

Phylogenetic Relationships of the "Green Algae" and "Bryophytes"

Considerable progress has been made recently, based on classical morphological characters and newly described ultrastructural features, in understanding the phylogenetic relationships of the tracheophytes to the green algae and bryophytes. Recent technological advances in molecular biology, particularly the advent of the polymerase chain reaction (PCR), have allowed nucleotide sequence data relevant to such large-scale phylogenetic questions to accumulate, especially ribosomal RNA gene sequences (both the large and small subunits) from the nucleus and the chloroplast. We present synthetic cladistic analyses of the green plants that combine and compare available morphological and molecular data sets

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.

Into the deep: new discoveries at the base of the green plant phylogeny

Recent data have provided evidence for an unrecognised ancient lineage of green plants that persists in marine deep‐water environments. The green plants are a major group of photosynthetic eukaryotes that have played a prominent role in the global ecosystem for millions of years. A schism early in their evolution gave rise to two major lineages, one of which diversified in the worlds oceans and gave rise to a large diversity of marine and freshwater green algae (Chlorophyta) while the other gave rise to a diverse array of freshwater green algae and the land plants (Streptophyta). It is generally believed that the earliest‐diverging Chlorophyta were motile planktonic unicellular organisms, but the discovery of an ancient group of deep‐water seaweeds has challenged our understanding of the basal branches of the green plant phylogeny. In this review, we discuss current insights into the origin and diversification of the green plant lineage.

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.

PHYLOGENETIC ANALYSES OF THE BRYOPSIDALES (ULVOPHYCEAE, CHLOROPHYTA) BASED ON RUBISCO LARGE SUBUNIT GENE SEQUENCES1

Current taxonomy of the Bryopsidales recognizes eight families; most of which are further categorized into two suborders, the Bryopsidineae and Halimedineae. This concept was supported by early molecular phylogenetic analyses based on rRNA sequence data, but subsequent cladistic analyses of morphological characters inferred monophyly in only the Halimedineae. These conflicting results prompted the current analysis of 32 taxa from this diverse group of green algae based on plastid‐encoded RUBISCO large subunit (rbcL) gene sequences. Results of these analyses suggested that the Halimedineae and Bryopsidineae are distinct monophyletic lineages. The families Bryopsidaceae, Caulerpaceae, Codiaceae, Derbesiaceae, and Halimediaceae were inferred as monophyletic, however the Udoteaceae was inferred as non‐monophyletic. The phylogenetic position of two taxa with uncertain subordinal affinity, Dichotomosiphon tuberosus Lawson and Pseudocodium floridanum Dawes & Mathieson, were also inferred. Pseudocodium was consistently placed within the halimedinean clade suggesting its inclusion into this suborder, however familial affinity was not resolved. D. tuberosus was the inferred sister taxon of the Halimedineae based on analyses of rbcL sequence data and thus a possible member of this suborder.

PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA, ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES1

The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast‐encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family‐level classification. The genus Cymopolia Lamouroux was inferred to be the basal‐most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier‐Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition‐to‐transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g1 values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies.

Gain and loss of elongation factor genes in green algae

BackgroundTwo key genes of the translational apparatus, elongation factor-1 alpha (EF-1α) and elongation factor-like (EFL) have an almost mutually exclusive distribution in eukaryotes. In the green plant lineage, the Chlorophyta encode EFL except Acetabularia where EF-1α is found, and the Streptophyta possess EF-1α except Mesostigma, which has EFL. These results raise questions about evolutionary patterns of gain and loss of EF-1α and EFL. A previous study launched the hypothesis that EF-1α was the primitive state and that EFL was gained once in the ancestor of the green plants, followed by differential loss of EF-1α or EFL in the principal clades of the Viridiplantae. In order to gain more insight in the distribution of EF-1α and EFL in green plants and test this hypothesis we screened the presence of the genes in a large sample of green algae and analyzed their gain-loss dynamics in a maximum likelihood framework using continuous-time Markov models.ResultsWithin the Chlorophyta, EF-1α is shown to be present in three ulvophycean orders (i.e., Dasycladales, Bryopsidales, Siphonocladales) and the genus Ignatius. Models describing gene gain-loss dynamics revealed that the presence of EF-1α, EFL or both genes along the backbone of the green plant phylogeny is highly uncertain due to sensitivity to branch lengths and lack of prior knowledge about ancestral states or rates of gene gain and loss. Model refinements based on insights gained from the EF-1α phylogeny reduce uncertainty but still imply several equally likely possibilities: a primitive EF-1α state with multiple independent EFL gains or coexistence of both genes in the ancestor of the Viridiplantae or Chlorophyta followed by differential loss of one or the other gene in the various lineages.ConclusionEF-1α is much more common among green algae than previously thought. The mutually exclusive distribution of EF-1α and EFL is confirmed in a large sample of green plants. Hypotheses about the gain-loss dynamics of elongation factor genes are hard to test analytically due to a relatively flat likelihood surface, even if prior knowledge is incorporated. Phylogenetic analysis of EFL genes indicates misinterpretations in the recent literature due to uncertainty regarding the root position.

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.