This revision of the classification of eukaryotes, which updates that of Adl et al. (2005), 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.

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [ J. Euk. Microbiol . 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

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. Supporting InformationAdditional Supporting Information may be found in the online version of this article.Appendix S1. Characteristics of mechanistic and phenomenological models in ecology.Appendix S2. Non-exhaustive list, of international initiatives of the scientific community aiming for sharing ecological data.

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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.

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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.

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.