Frederik Leliaert

Phylogeny and molecular evolution of the green algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.

Limits to gene flow in a cosmopolitan marine planktonic diatom

The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.

DNA-based species delimitation in algae

Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming the standard for delimiting species and testing their traditional boundaries. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation. We review these recent developments in DNA-based species delimitation methods, and discuss how they have changed and continue to change our understanding of algal species boundaries. Although single-locus approaches have proven effective for a first rapid and large-scale assessment of species diversity, species delimitation based on single gene trees falls short due to gene tree–species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization and introgression. Data from unlinked loci and multi-species coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors. Several of these methods also provide statistical support regarding species boundaries, which is important because speciation is a process and therefore uncertainty about precise species boundaries is inevitable in recently diverged lineages.

Identity of the Qingdao algal bloom.

In early July 2008, news agencies worldwide reported on a vast algal bloom that was threatening the upcoming Olympic sailing events in Qingdao, China. The identity of the culpable alga, however, remained undiscussed. We have identified the alga that caused the bloom by means of morphological and molecular data, including sequence data of the plastid encoded large subunit ribulose 1,5‐bisphosphate carboxylase gene (rbcL) and the nuclear encoded rDNA internal transcribed spacer (ITS) region. The bloom‐forming alga falls within the morphological limits of the green seaweed Ulva prolifera O.F. Müller (‘Enteromorpha prolifera (O.F. Müller) J. Agardh’) but our phylogenetic analyses show that it forms a clade with representatives of the Ulva linza‐procera‐prolifera (LPP) complex. The Chinese rbcL sequences are identical to those of specimens collected from Japan, New Zealand, Finland and Portugal, suggesting that the taxon is widely distributed. rDNA ITS sequences showed a close affinity with Japanese isolates of the species complex. The Qingdao bloom is a typical illustration of a green tide, which occurs increasingly along several coasts worldwide.

Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia

Recent data revealed that metazoans such as mites and springtails have persisted in Antarctica throughout several glacial–interglacial cycles, which contradicts the existing paradigm that terrestrial life was wiped out by successive glacial events and that the current inhabitants are recent colonizers. We used molecular phylogenetic techniques to study Antarctic microchlorophyte strains isolated from lacustrine habitats from maritime and continental Antarctica. The 14 distinct chlorophycean and trebouxiophycean lineages observed point to a wide phylogenetic diversity of apparently endemic Antarctic lineages at different taxonomic levels. This supports the hypothesis that long-term survival took place in glacial refugia, resulting in a specific Antarctic flora. The majority of the lineages have estimated ages between 17 and 84 Ma and probably diverged from their closest relatives around the time of the opening of Drake Passage (30–45 Ma), while some lineages with longer branch lengths have estimated ages that precede the break-up of Gondwana. The variation in branch length and estimated age points to several independent but rare colonization events.

DNA taxonomy in morphologically plastic taxa: Algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales)

DNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially in organisms in which morphological discrimination is difficult or impossible, such as many algal taxa. A group with a long history of confusing species circumscriptions is the morphologically plastic Boodlea complex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and Struveopsis. In this study, we elucidate species boundaries in the Boodlea complex by analysing nrDNA internal transcribed spacer sequences from 175 specimens collected from a wide geographical range. Algorithmic methods of sequence-based species delineation were applied, including statistical parsimony network analysis, and a maximum likelihood approach that uses a mixed Yule-coalescent model and detects species boundaries based on differences in branching rates at the level of species and populations. Sequence analyses resulted in the recognition of 13 phylogenetic species, although we failed to detect sharp species boundaries, possibly as a result of incomplete reproductive isolation. We found considerable conflict between traditional and phylogenetic species definitions. Identical morphological forms were distributed in different clades (cryptic diversity), and at the same time most of the phylogenetic species contained a mixture of different morphologies (indicating intraspecific morphological variation). Sampling outside the morphological range of the Boodlea complex revealed that the enigmatic, sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis, also falls within the Boodlea complex. Given the observed evolutionary complexity and nomenclatural problems associated with establishing a Linnaean taxonomy for this group, we propose to discard provisionally the misleading morphospecies and genus names, and refer to clade numbers within a single genus, Boodlea.

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.

What we can learn from sushi: a review on seaweed-bacterial associations.

Many eukaryotes are closely associated with bacteria which enable them to expand their physiological capacities. Associations between algae (photosynthetic eukaryotes) and bacteria have been described for over a hundred years. A wide range of beneficial and detrimental interactions exists between macroalgae (seaweeds) and epi- and endosymbiotic bacteria that reside either on the surface or within the algal cells. While it has been shown that these chemically mediated interactions are based on the exchange of nutrients, minerals, and secondary metabolites, the diversity and specificity of macroalgal-bacterial relationships have not been thoroughly investigated. Some of these alliances have been found to be algal or bacterial species-specific, whereas others are widespread among different symbiotic partners. Reviewing 161 macroalgal-bacterial studies from the last 55 years, a definite bacterial core community, consisting of Gammaproteobacteria, CFB group, Alphaproteobacteria, Firmicutes, and Actinobacteria species, seems to exist which is specifically (functionally) adapted to an algal host-associated lifestyle. Because seaweed-bacterial associations are appealing from evolutionary and applied perspectives, future studies should integrate the aspects of diverse biological fields.

Evolution and Cytological Diversification of the Green Seaweeds (Ulvophyceae)

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.

Lack of Phylogeographic Structure in the Freshwater Cyanobacterium Microcystis aeruginosa Suggests Global Dispersal

Background Free-living microorganisms have long been assumed to have ubiquitous distributions with little biogeographic signature because they typically exhibit high dispersal potential and large population sizes. However, molecular data provide contrasting results and it is far from clear to what extent dispersal limitation determines geographic structuring of microbial populations. We aimed to determine biogeographical patterns of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. Being widely distributed on a global scale but patchily on a regional scale, this prokaryote is an ideal model organism to study microbial dispersal and biogeography. Methodology/Principal Findings The phylogeography of M. aeruginosa was studied based on a dataset of 311 rDNA internal transcribed spacer (ITS) sequences sampled from six continents. Richness of ITS sequences was high (239 ITS types were detected). Genetic divergence among ITS types averaged 4% (maximum pairwise divergence was 13%). Preliminary analyses revealed nearly completely unresolved phylogenetic relationships and a lack of genetic structure among all sequences due to extensive homoplasy at multiple hypervariable sites. After correcting for this, still no clear phylogeographic structure was detected, and no pattern of isolation by distance was found on a global scale. Concomitantly, genetic differentiation among continents was marginal, whereas variation within continents was high and was mostly shared with all other continents. Similarly, no genetic structure across climate zones was detected. Conclusions/Significance The high overall diversity and wide global distribution of common ITS types in combination with the lack of phylogeographic structure suggest that intercontinental dispersal of M. aeruginosa ITS types is not rare, and that this species might have a truly cosmopolitan distribution.