The Southern Line Islands in the central Pacific Ocean are some of the most remote islands on earth. Their coral reefs are almost pristine, but knowledge on their marine biodiversity is fragmented, and we know very little about their seaweeds.
During two recent expeditions, researchers from Scripps Institution of Oceanography spotted a striking green alga that was widespread in the area, but looked very unusual. Our morphological and molecular research shows that the alga represents a new species, and indeed, a new genus. We named it Brilliantia kiribatiensis referring to its bright colour and the island nation of Kiribati where it grows.
The new seaweed has a very simple architecture of unbranched filaments that attach to rocky surfaces. It also has a unique mode of cell division that is only found in one group of green algae, the Cladophorales.
The species appears to only grow in the Southern Line Islands region. The discovery of a new endemic genus confirms the uniqueness of these ecosystems, and the importance of protecting them. Although isolated and pristine, the islands are subject to global climate change. More research and conservation work in these remote coral reefs is urgently needed.
Leliaert F, Kelly EL, Janouškovec J, Fox MD, Johnson MD, Redfern FM, Eria T, Haas AF, Sala E, Sandin SA. 2022. Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean.Journal of Phycology 58: 183-197 full text
The strange world of the Ediacarian (630-542 million years ago), a period in which green seaweeds were able to diversify after the severe ice ages of the Cryogenian (Wikimedia Commons contributors, “File:Life in the Ediacaran sea.jpg” (accessed January 3, 2020) (CC BY-SA 2.0).
In a new study we explore the origin and diversification of green seaweeds, which are major primary producers in marine environments. Green seaweeds likely shaped early animal evolution by altering benthic ecosystems and furnishing novel ecological niches. However, the evolutionary origin and morphological diversification of green seaweeds remain unclear. We used a phylogenomic approach to resolve evolutionary relationships among the Chlorophyta, the core group of extant green algae that includes green seaweeds. Analysis of hundreds of protein-coding nuclear genes from 55 species deduced from 15 genomes and 40 transcriptomes yielded a phylogenetic tree that was subsequently time-calibrated using molecular clock and fossil data.
Hypothesis for the evolution of multicellularity and macroscopic growth in the green seaweeds.
The tree suggests that core Chlorophyta likely emerged in the Neoproterozoic Era, around 1,000-700 million years ago, and that green seaweeds likely originated and diversified just before or during the late Tonian and Cryogenian Periods, which were marked by global glaciation events. During the ice ages, isolated refuges likely served as safe-harbors for the survival of unicellular and simple multicellular ancestors of green seaweeds, with some lineages adopting a benthic lifestyle. As the ice retreated benthic environments became abundantly available, and green seaweeds were able to disperse and diversify extensively, which likely enabled their repeated efflorescence into riotously diverse macroscopic forms-a process aided by increased nutrient supply and grazing pressure. Our findings provide a window into the evolution of green seaweeds, which continue to play important ecological roles in modern oceans.
Del Cortona A., Jackson C. J., Bucchini F., Van Bel M., D’hondt S., Škaloud P., Delwiche C. F., Knoll A. H., Raven J. A., Verbruggen H., Vandepoele K., De Clerck O. & Leliaert F. (2019) Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. PNAS: www.pnas.org/cgi/doi/10.1073/pnas.1910060117
In a paper just published in Journal of Phycology, we describe a recent evolutionary radiation of macroalgae in the oldest lake in the world. Lake Baikal is home to spectacular biodiversity and extraordinary levels of endemism, and many of the animal species flocks in this lake are well known examples of evolutionary radiations.
Lake Baikal is also known to harbor a wide diversity of endemic algae, but their evolutionary affinities are poorly understood. The endemic taxa of the green algal order Cladophorales show a range of divergent morphologies that led to their classification in four genera in two families.
Morphological variation of the endemic Cladophorales species of Lake Baikal
We show that these endemic taxa form a clade within the genus Rhizoclonium, and exhibit very low genetic differentiation. The Baikal clade appears to represent a recent radiation, and we argue that the large morphological variation results from diversification in sympatry from a common ancestor in Lake Baikal.
Phylogeny of the Cladophorales, showing the Baikal clade within the genus Rhizoclonium
Boedeker C, Leliaert F, Timoshkin OA, Vishnyakov V, Diaz Martinez S & Zuccarello GC (2018) The endemic Cladophorales (Ulvophyceae) of ancient Lake Baikal represent a monophyletic group of very closely related but morphologically diverse species. Journal of Phycologyfull text
In a study recently published in Journal of Biogeography, we gain a better understanding on the evolutionary processes underlying Indo-Pacific biodiversity. Although seaweeds are a dominant group of marine organisms, biogeographical patterns and processes have been explored far less extensively than in marine invertebrates and fishes.
One of the many cryptic species of Portieria, collected from de Mariana Islands. Photo: Tom Schils.
We used the common Indo-Pacific red seaweed Portieria as a model. DNA-based methods show that species diversity is far greater than the five species currently named. We delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo-Malay Archipelago, also known as the Coral Triangle, a region known as a marine biodiversity hotspot for several animal groups.
Geographical pattern of Portieria species richness. Geographical distributions were based on location data of 802 sequenced specimens.
Phylogenetic analyses indicate that the genus Portieria is ancient, and likely originated during the late Cretaceous in the area that is now the Central Indo-Pacific. We suggest that the long geological history of the Indo-Malay Archipelago played an important role in shaping Portieria diversity. High species richness in the region resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Diversity in peripheral regions resulted from repeated dispersal events from the Coral Triangle, followed by diversification within those regions, and limited dispersal back to the Coral Triangle.
Historical biogeographical reconstruction of the genus Portieria.
Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both ‘centres of origin’ and ‘centres of accumulation’, and corroborate previous findings for invertebrates and fishes that there is no single unifying model explaining the biological diversity within the central Indo-Pacific.
Summary of biogeographical events for the Indo-Pacific genus Portieria.
Leliaert F, Payo DA, Gurgel CFD, Schils T, Draisma SGA, Saunders GW, Kamiya M, Sherwood AR, Lin S-M, Huisman JM, Le Gall L, Anderson RJ, Bolton JJ, Mattio L, Zubia M, Spokes T, Vieira C, Payri CE, Coppejans E, D’Hondt S, Verbruggen H & De Clerck O (2018) Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeographyfull text
This volume of the “Süßwasserflora von Mitteleuropa” covers the freshwater, aerophytic, and terrestrial species of Ulvophyceae, one of the main classes of green algae. Although most of the species diversity of Ulvophyceae is found in the marine environment, a substantial number of species also occurs in brackish, freshwater, and aero-terrestrial habitats. These species are found in nine orders: Ulvales and Ulotrichales, which contain most freshwater species, the Trentepohliales which is exclusively aero-terrestrial, the smaller orders Chlorocystidales, Oltmannsiellopsidales, Scotinosphaerales, and Ignatiales, and the large but mainly marine orders Cladophorales and Bryopsidales. One other order, Dasycladales, only includes marine species and is thus not included in the present volume.
Current view of phylogenetic relationships of the core Chlorophyta
Freshwater ulvophycean algae display a wide variety of thallus morphologies, ranging from microscopic unicellular organisms to larger, filamentous or parenchymatic algae.
Species are also found in a wide diversity of habitats, generally attached, or sometimes free-floating. Several marine species occur over a broad salinity range, and are found in brackish to freshwater and semi-terrestrial habitats. Other species are restricted to freshwater or aero-terrestrial habitats. Several species are found in highly specialized habitats such as epizoic on freshwater snails or on carapaces of freshwater turtles, epiphytic on aquatic lichens or as lichen phycobionts, or endophytic in filamentous algae or mesophyll of vascular plants. This volume serves as a reference work for identifying these ulvophyte green algae by providing keys, detailed descriptions, and illustrations of the more than 100 European species. As in other volumes of this series, this treatment is not restricted to European taxa, and includes descriptions and illustrations of more than other 100 taxa found on other continents. The present study incorporates the latest findings in molecular phylogeny, ultrastructure and morphology for the classification, delimitation and identification of the species. In addition, it significantly revises the taxonomy of ulvophytes, in particular the orders Ulvales and Ulotrichales, based on new molecular phylogenetic data, combined with morphological data.
Phylogeny of the Ulvales
Phylogeny of the Ulotrichales
We propose to resurrect one order and family (Chlorocystidales and Chlorocystidaceae), and describe five new families (Binucleariaceae, Planophilaceae, Hazeniaceae, Sarcinofilaceae, and Tupiellaceae). In addition, we formally describe the order Ignatiales and family Ignatiaceae based on published molecular and ultrastructural data. This book is one of the first comprehensive treatments of species diversity of nonmarine Ulvophyceae, and we hope that it will be a useful tool in green algal research worldwide.
Škaloud, P., Rindi, F., Boedeker, C. & Leliaert, F. (2018) Freshwater Flora of Central Europe, Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa, Bd. 13: Chlorophyta: Ulvophyceae). Springer Spektrum, Berlin, Heidelberg. http://www.springer.com/gp/book/9783662554944
After more than 10 years of research, and sequencing millions of reads, we were finally able to uncover secrets of the chloroplast genome of Cladophorales green algae. In stark contrast to other algae, little was known about the gene content and structure of the chloroplast genome in this ecologically important group of marine and freshwater green algae. Most previous attempts to amplify common chloroplast genes have failed, and an atypical plastid genome has been suggested by the presence of abundant plasmid-like DNA in the chloroplasts of several species. Pioneering work of John La Claire and colleagues in the 1990-ies revealed that these structures are single-stranded DNA molecules of 1.5-3.0 kb that fold in a hairpin configuration, and contain putatively transcribed sequences with similarity to chloroplast genes.
In a recent study, we describe intriguing features of the plastid genome of Cladophorales. Through the integration of different DNA sequencing methods, combined with RNA sequencing, we found that chloroplast protein-coding genes are highly expressed and encoded on 1-7 kb linear single-stranded DNA molecules. Due to the wide-spread presence of inverted repeats, these molecules fold into a hairpin configuration. The chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in plastid genome architecture.
Schematic representation of Boodlea chloroplast genome
Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. 2017. The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes. Current Biology 24:3771–3782 doi:10.1016/j.cub.2017.11.004.
Smith DR. 2017. Evolution: In Chloroplast Genomes, Anything Goes. Current Biology 27:R1305-R1307 doi:10.1016/j.cub.2017.10.049.
The existence of massive cryptic diversity in algae makes linking DNA-based lineages to existing taxa exceedingly difficult. A better integration of historical collections into modern taxonomic research is therefore highly desirable. Using the brown algal genus Lobophora as a test case, we explore the feasibility of linking taxonomic names to clades in modern phylogenies.
Phylogeny of Lobophora with holotypes indicated in red and epitypes and a neotype in green
Despite Lobophora being a pantropical genus with probably more than 100 species, traditionally only a handful of species have been recognized. In this study we reevaluated the identity of 17 historical taxa thought to belong to Lobophora by attempting DNA amplification of herbarium material as well as specimens recently collected from the type localities (epitypes). In an attempt to assign them to Molecular Operational Taxonomic Units, the obtained sequences were integrated in a global Lobophora phylogeny based upon data derived from more than 650 specimens. Our results indicate that although five sequences were obtained from type specimens, exclusive reliance on information preserved in type specimens is problematic. Epitype material proved a more successful way forward, but this route often comes with a considerable degree of uncertainty, especially in tropical regions where the extent of sympatry among Lobophora lineages is often considerable. More problematic from a broader perspective is the fact that for 35% of historical taxa, either the type could not be traced or permission was not granted to extract DNA from the types. Such a low accessibility rate may reduce our reliance on type material and jeopardize future efforts to integrate historical taxa into a framework of a modern DNA-based taxonomy.
Vieira C, Camacho O, Wynne MJ, Mattio L, Anderson RJ, Bolton JJ, Sansón M, D’Hondt S, Leliaert F, Fredericq S, Payri C, De Clerck O. 2016. Shedding new light on old algae: Matching names and sequences in the brown algal genus Lobophora (Dictyotales, Phaeophyceae). Taxon 65:689-707.
In a recent study, published in Scientific Reports, we provide solid phylogenetic evidence that the enigmatic green seaweed order Palmophyllales together with the unicellular planktonic Prasinococcales (= prasinophyte clade VI) form the deepest-branching clade of the Chlorophyta. Our analyses are based on chloroplast genomic, and nuclear rDNA data.
Phylogeny of the green plants inferred from 71 concatenated plastid genes showing the position of the new class Palmophyllophyceae.
Species of Palmophyllales typically grow in deep marine waters and other shady habitats. The group is characterized by a unique form of multicellularity, forming macroscopic plants that are composed of isolated and undifferentiated spherical cells embedded in an amorphous gelatinous matrix. In 2010, we showed that the Palmophyllales formed an early-diverging lineage of green plants, but the exact phylogenetic position could not be determined with certainty.
Our phylogenetic results improve our understanding of morphological evolution in the green algae. Until present, the early-diverging lineages of the Chlorophyta (the prasinophytes) were only known to comprise unicellular planktonic algae. Our results point to an independent origin of macroscopic growth and multicellularity outside of the core Chlorophyta.
Our study also contributes to a better understanding of plastid genome evolution in green plants. 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.
Leliaert F, Tronholm A, Lemieux C, Turmel M, et al. 2016. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Scientific Reports 6:25367. article
Leliaert F, Verbruggen H, Zechman FW. 2011. Into the deep: New discoveries at the base of the green plant phylogeny. BioEssays 33:683-692. article
Zechman FW, Verbruggen H, Leliaert F, Ashworth M, et al. 2010. An unrecognized ancient lineage of green plants persists in deep marine waters. Journal of Phycology 46:1288-1295. article
The first chloroplast and mitochondrial genomes from the ecologically and economically important marine green alga Ulva have just been published. If you want to know more: here is the paper.
Gene map of Ulva sp. UNA00071828 chloroplast and mitochondrial genomes
Hot off the press: Part 2/1 of Engler’s Syllabus of Plant Families – Photoautotrophic eukaryotic Algae provides a thorough treatise of the world-wide morphological and molecular diversity of the Glaucocystophyta, Cryptophyta, Dinophyta/Dinozoa, Haptophyta, Heterokontophyta/Ochrophyta, Chlorarachniophyta/Cercozoa, Euglenophyta/Euglenozoa, Chlorophyta, and Streptophyta (p.p.) (The red algae will be treated in Part 2/2).
Part 2/1 of Engler’s Syllabus of Plant Families – Photoautotrophic eukaryotic Algae
Engler’s Syllabus of Plant Families has since its first publication in 1887 aimed to provide a concise survey of the plant kingdom as a whole, presenting all higher systematic units right down to families and genera of plants and fungi. In 1954, more than 60 years ago, the 12th edition of the well-known “Syllabus der Pflanzenfamilien” (“Syllabus of Plant Families”) was published.
Now, the completely restructured and revised 13th edition of Engler’s Syllabus published in 5 parts and in English language for the first time also considers molecular data, which have only recently become available in order to provide an up-to-date evolutionary and systematic overview of the plant groups treated.
Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. In a paper we recently published in BMC Genomics, we report on the complete cpDNAs of Bryopsis plumosa and Tydemania expeditionis, as well as a re-annotated cpDNA of B. hypnoides (which was shown to contain a higher number of genes than originally published).
Gene maps of the chloroplast genomes of Bryopsis plumosa and Tydemania expeditionis. The red arcs indicate gene regions of bacterial origin.
The cpDNAs of B. plumosa and T. expeditionis are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta, and both lack a large inverted repeat.
Both chloroplast genomes contain DNA regions with genes of bacterial origin, including rhs-family genes, and several genes involved in mobile functions, such as transposases, integrases, DNA polymerases, and phage/plasmid DNA primases. Another unexpected finding was the presence of two genes in T. expeditionis showing close similarity to bacterial DNA methyltransferases, a family of genes that have up till now not been found in any plastid genome.
The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae. Our data adds to the scarce knowledge of horizontal transfer of bacterial DNA to plastid genomes.
In addition, chloroplast genomic data were used to evaluate phylogenetic hypotheses in the Chlorophyta. These analyses, however, were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.
Phylogenetic trees of Chlorophyta inferred from a 50-gene dataset (A: protein dataset, B: nucleotide dataset).
The genus Pseudoderbesia is characterized by minute, dichotomously branched green siphons, and was originally described from the Caribbean coast of Colombia and the Canary Islands. However, the genus has remained unnoticed until today, possibly because the original publication was in Spanish, in a journal (Caldasia) not widely read by phycologists.Therefore, we want to bring the genus back to the attention. In a paper submitted to Cryptogamie Algologie, we report on a recent collection of Pseudoderbesia from Rhodes, Greece, representing the first report of the genus after its original description, and the first record from the Mediterranean Sea. Molecular phylogenetic analysis shows a sister relationship with the common and species-rich genus Bryopsis.
Cultured plants of Pseudoderbesia, characterized by upright, regularly dichotomously branched siphons, developing from stolonoid siphons.
Accurate species delimitation is a central assumption in studies of biodiversity, systematics, biogeography and ecology. In algae, morphology-based species delimitation is often problematic, and hence DNA sequence data are becoming the standard for delimiting species. 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.
In a paper that we recently submitted to the European Journal of Phycology we review these recent developments in DNA-based species delimitation methods, and discuss how they have and will continue to change our understanding of algal species boundaries.
Single-locus (DNA barcoding) approaches have proven effective for rapid and large-scale assessment of algal species diversity. However, 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, hybridisation and introgression. Data from unlinked loci and multispecies coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors.
Neutral coalescence process running within a species tree, and consequences for species delimitation – read more.
Although we realize that many algal taxonomists may feel uncomfortable with the idea of delimiting species based solely on DNA sequence data, we argue that DNA sequence data serve as a reliable source of data for testing species boundaries even in the absence of additional phenotypic evidence. The hundreds of new species discovered using DNA sequences have profoundly reshaped our ideas on algal diversity and present a telling case of our inability to accurately assess species diversity based on phenotypic characters alone.
Because speciation is a process and not a single event in time, uncertainty about species boundaries is inevitable in recently diverged lineages. One of the strengths of DNA-based species delimitation methods is that this uncertainty can be taken into account and quantified by incorporating probabilistic tests for species boundaries that provide statistical support plus a level of uncertainty regarding species boundaries.
In species delimitation approaches, it is important to keep in mind the moving target that we are trying to circumscribe, a species. The question of species definition and delimitation is tied to the process of speciation, which has idiosyncratic components involving multiple populations, individuals with different life cycles and reproductive successes, different selective histories, and which contains a large component of stochasticity. Elucidating the relative importance of these components in the speciation process defines the beauty of systematic biology. The use of molecular markers in species delimitation has pointed phycologists toward more realistic species boundaries. We anticipate that multispecies coalescent methods based on multi-locus data will further refine our view on algal species, especially in recently diverged lineages, in which factors such as incomplete lineage sorting, hybridisation and introgression may confound species boundaries. These methods will increase the statistical rigour and objectivity of species delimitation, and are likely to result in the recognition of less inclusive entities, which in turn will have implications for estimates of algal species diversity. Resetting species boundaries towards a point where they truly reflect the biological reality will make the study of speciation processes more expedient. But quite likely, the question of “what is a species?” will remain with us as long as we want to study the process of evolution that produces these apparent discontinuities that we call “species”.
I started a new post-doc in the lab of Juan Lopez-Bautista at the University of Alabama where I will be working on the green and red algae tree of life projects.
Roll tide!
The Phycolab at the South Eastern Phycological Colloquium (September 2013, Dauphin Island)
Frederik Leliaert 
