Line Le Gall

The revised classification of eukaryotes.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.

DNA BARCODING IS A POWERFUL TOOL TO UNCOVER ALGAL DIVERSITY: A CASE STUDY OF THE PHYLLOPHORACEAE (GIGARTINALES, RHODOPHYTA) IN THE CANADIAN FLORA

Previous studies have established that the 5′ end of the mitochondrial gene COI (cytochrome oxidase subunit I) is useful for rapid and reliable identification of red algal species and have demonstrated that our understanding of red algal biodiversity and biogeography is fragmentary. In this context, we are completing a thorough sampling along the Canadian coast and using the DNA barcode for the assignment of collections to genetic species to explore algal diversity in the Canadian flora. In the present study, we provide results regarding diversity of members of the red algal family Phyllophoraceae. We have analyzed 354 individuals from the Arctic, Atlantic, and Pacific coasts of Canada, as well as 26 specimens from the USA, Europe, and Australia, resolving 29 species based on the analyses of the DNA barcode. Twenty‐three of these genetic species were present in Canada where only 18 species are currently recognized, including Ceratocolax hartzii Rosenv., which was in the same genetic species group as its host Coccotylus truncatus (Pall.) M. J. Wynne et N. J. Heine and is thus transferred to Coccotylus, C. hartzii (Rosenv.) comb. nov., but retained as a distinct species owing to its unique habit and phenology. Our results revealed the presence of cryptic diversity within the genera Coccotylus, Mastocarpus, Ozophora, and Stenogramme, for which we resurrect Coccotylus brodiei (Turner) Kütz. and describe Mastocarpus pachenicus sp. nov., Ozophora lanceolata sp. nov., and Stenogramme bamfieldiensis sp. nov., leaving a multitude of unnamed Mastocarpus spp. in need of further taxonomic study. In addition, we report range extensions into British Columbia of Besa papillaeformis Setch., previously known only from its type and nearby localities in California; Gymnogongrus crenulatus (Turner) J. Agardh, recorded only from the Atlantic; and Stenogramme cf. rhodymenioides Joly et Alveal, previously only known from South America. Finally, the phylogenetic affinities of the Canadian species of Phyllophoraceae characterized in this study were investigated using LSU rDNA, RUBISCO LSU (rbcL), and combined analyses.

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

BackgroundThe assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.ResultsPhylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches.ConclusionsOur study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.

REVIEW: Predictive ecology in a changing world

1. In a rapidly changing world, ecology has the potential to move from empirical and conceptual stages to application and management issues. It is now possible to make large-scale predictions up to continental or global scales, ranging from the future distribution of biological diversity to changes in ecosystem functioning and services. With these recent developments, ecology has a historical opportunity to become a major actor in the development of a sustainable human society. With this opportunity, however, also comes an important responsibility in developing appropriate predictive models, correctly interpreting their outcomes and communicating their limitations. There is also a danger that predictions grow faster than our understanding of ecological systems, resulting in a gap between the scientists generating the predictions and stakeholders using them (conservation biologists, environmental managers, journalists, policymakers). 2. Here, we use the context provided by the current surge of ecological predictions on the future of biodiversity to clarify what prediction means, and to pinpoint the challenges that should be addressed in order to improve predictive ecological models and the way they are understood and used. 3. Synthesis and applications. Ecologists face several challenges to ensure the healthy development of an operational predictive ecological science: (i) clarity on the distinction between explanatory and anticipatory predictions; (ii) developing new theories at the interface between explanatory and anticipatory predictions; (iii) open data to test and validate predictions; (iv) making predictions operational; and (v) developing a genuine ethics of prediction.

Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes

Systematics of the red algal order Corallinales has a long and convoluted history. In the present study, molecular approaches were used to assess the phylogenetic relationships based on the analyses of two datasets: a large dataset of SSU sequences including mainly sequences from GenBank; and a combined dataset including four molecular markers (two nuclear: SSU, LSU; one plastidial: psbA; and one mitochondrial: COI). Phylogenetic analyses of both datasets re-affirmed the monophyly of the Corallinales as well as the two families (Corallinaceae and Hapalidiaceae) currently recognized within the order. Three of the four subfamilies of the Corallinaceae (Corallinoideae, Lithophylloideae, Metagoniolithoideae) were also resolved as a monophyletic lineage whereas members of the Mastophoroideae were resolved as four distinct lineages. We therefore propose to restrict the Mastophoroideae to the genera Mastophora, Metamastophora, and possibly Lithoporella in the aim of rendering this subfamily monophyletic. In addition, our phylogenies resolved the genus Hydrolithon in two unrelated lineages, one containing the generitype Hydrolithon reinboldii and the second containing Hydrolithon onkodes, which used to be the generitype of the now defunct genus Porolithon. We therefore propose to resurrect the genus Porolithon for the second lineage encompassing those species with primarily monomerous thalli, and trichocyte arrangements in large pustulate horizontal rows. Moreover, our phylogenetic analyses revealed the presence of cryptic diversity in several taxa, shedding light on the need for further studies to better circumscribe species frontiers within the diverse order Corallinales, especially in the genera Mesophyllum and Neogoniolithon.

Multigene phylogenetic analyses support recognition of the Sporolithales ord. nov.

a Centre for Environmental and Molecular Algal Research, Department of Biology, P.O. Box 4400, University of New Brunswick, Fredericton, NB, Canada E3B 5A3 b UMR 7138/UR R148. ‘‘Systématique, Adaptation, Evolution”, Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa cedex, Nouvelle-Calédonie, France c UMR 7138 ‘‘Systématique, Adaptation, Evolution”, Département ‘‘Systématique et évolution”, Muséum National d’Histoire Naturelle, CP 39, 75231 Paris cedex 05, France

Phylogenetic analyses of the Laurencia complex (Rhodomelaceae, Ceramiales) support recognition of five genera: Chondrophycus, Laurencia, Osmundea, Palisada and Yuzurua stat. nov.

Molecular phylogenies inferred from rbcL sequences including 39 representative members of the Laurencia complex confirm the four genera currently recognised within the complex: Laurencia sensu stricto, Osmundea, Chondrophycus and the recently described genus Palisada. Furthermore, Palisada poiteaui was resolved as a fifth independent lineage suggesting that the complex is actually composed of five rather than four genera. Palisada poiteaui is the type species of the subgenus Yuzurua, and elevation of this subgenus to generic rank is proposed. This new genus allied strongly with Laurencia s.s. However, the other intergeneric relationships were not well supported, suggesting that rbcL sequences may not have sufficient signal to clarify infrageneric relationships fully within the Laurencia complex.

A Multilocus Species Delimitation Reveals a Striking Number of Species of Coralline Algae Forming Maerl in the OSPAR Maritime Area

Maerl beds are sensitive biogenic habitats built by an accumulation of loose-lying, non-geniculate coralline algae. While these habitats are considered hot-spots of marine biodiversity, the number and distribution of maerl-forming species is uncertain because homoplasy and plasticity of morphological characters are common. As a result, species discrimination based on morphological features is notoriously challenging, making these coralline algae the ideal candidates for a DNA barcoding study. Here, mitochondrial (COI-5P DNA barcode fragment) and plastidial (psbA gene) sequence data were used in a two-step approach to delimit species in 224 collections of maerl sampled from Svalbard (78°96’N) to the Canary Islands (28°64’N) that represented 10 morphospecies from four genera and two families. First, the COI-5P dataset was analyzed with two methods based on distinct criteria (ABGD and GMYC) to delineate 16 primary species hypotheses (PSHs) arranged into four major lineages. Second, chloroplast (psbA) sequence data served to consolidate these PSHs into 13 secondary species hypotheses (SSHs) that showed biologically plausible ranges. Using several lines of evidence (e.g. morphological characters, known species distributions, sequences from type and topotype material), six SSHs were assigned to available species names that included the geographically widespread Phymatolithon calcareum, Lithothamnion corallioides, and L. glaciale; possible identities of other SSHs are discussed. Concordance between SSHs and morphospecies was minimal, highlighting the convenience of DNA barcoding for an accurate identification of maerl specimens. Our survey indicated that a majority of maerl forming species have small distribution ranges and revealed a gradual replacement of species with latitude.

PHYLOGENETIC ANALYSES OF THE RED ALGAL ORDER RHODYMENIALES SUPPORTS RECOGNITION OF THE HYMENOCLADIACEAE FAM. NOV., FRYEELLACEAE FAM. NOV., AND NEOGASTROCLONIUM GEN. NOV.(1).

Systematics of the red algal order Rhodymeniales was investigated using combined large‐subunit nuclear ribosomal DNA (LSU) and elongation factor 2 (EF2) analyses. These data were subjected to distance, parsimony, and Bayesian analyses, and the resulting phylogenies were largely congruent with previously published SSU results in that the four currently recognized rhodymenialean families (Champiaceae, Faucheaceae, Lomentariaceae, and Rhodymeniaceae) were resolved as monophyletic lineages (with the exception of Coelothrix, which is here transferred to the Champiaceae from the Rhodymeniaceae). In addition, taxa presently considered as incertae sedis consisted of two lineages (Fryeella lineage and Hymenocladia lineage). Based on these results, two new families are proposed: (i) the Fryeellaceae fam. nov. to accommodate the genera Fryeella, Hymenocladiopsis, and a new taxon from Tasmania, Australia; and (ii) the Hymenocladiaceae fam. nov., to accommodate Asteromenia, Hymenocladia, and Erythrymenia. In addition to resolving familial relationships, these analyses resolved some novel interspecific affinities, and we propose a new genus, Neogastroclonium gen. nov., for Gastroclonium subarticulatum, a species that differs significantly in both morphology and molecular data from genuine species of Gastroclonium. Relationships among additional faucheacean and lomentariacean taxa were investigated using LSU data only, and these results are discussed. The familial classification of the Rhodymeniales proposed herein is discussed in light of vegetative and reproductive anatomy, most notably the ontogeny of the tetrasporangia.

Contrasting genetic diversity patterns in two sister kelp species co-distributed along the coast of Brittany, France

We investigated patterns of genetic structure in two sister kelp species to explore how distribution width along the shore, zonation, latitudinal distribution and historical factors contribute to contrasting patterns of genetic diversity. We implemented a hierarchical sampling scheme to compare patterns of genetic diversity and structure in these two kelp species co‐distributed along the coasts of Brittany (France) using a total of 12 microsatellites, nine for Laminaria hyperborea and 11 for Laminaria digitata, of which eight amplified in both species. The genetic diversity and connectivity of L. hyperborea populations were greater than those of L. digitata populations in accordance with the larger cross‐shore distribution width along the coast and the greater depth occupied by L. hyperborea populations in contrast to L. digitata populations. In addition, marginal populations showed reduced genetic diversity and connectivity, which erased isolation‐by‐distance patterns in both species. As L. digitata encounters its southern range limit in southern Brittany (SBr) while L. hyperborea extends down to mid‐Portugal, it was possible to distinguish the effect of habitat continuity from range edge effects. We found that L. digitata did not harbour high regional diversity at its southern edge, as expected in a typical rear edge, suggesting that refuges from the last glacial maximum for L. digitata were probably not located in SBr, but most likely further north. For both species, the highest levels of genetic diversity were found in the Iroise Sea and Morlaix Bay, the two regions in which they are being currently harvested. Preserving genetic diversity of these two foundation species in these areas should, thus, be a priority for the management of this resource in Brittany.