Genetic Diversity and Phylogeography of a Turf-Forming Cosmopolitan Marine Alga, Gelidium crinale (Gelidiales, Rhodo-Phyta).

Cosmopolitan species are rare in red algae, which have a low-dispersal capacity unless they are dispersed by human-mediated introductions. Gelidium crinale, a turf-forming red alga, has a widespread distribution in tropical and temperate waters. To decipher the genetic diversity and phylogeography of G. crinale, we analyzed mitochondrial COI-5P and plastid rbcL sequences from collections in the Atlantic, Indian, and Pacific Oceans. Phylogenies of both markers statistically supported the monophyly of G. crinale, with a close relationship to G. americanum and G. calidum from the Western Atlantic. Based on the molecular analysis from these materials, Pterocladia heteroplatos from India is here merged with G. crinale. Phylogeny and TCS networks of COI-5P haplotypes revealed a geographic structure of five groups: (i) Atlantic-Mediterranean, (ii) Ionian, (iii) Asian, (iv) Adriatic-Ionian, and (v) Australasia-India-Tanzania-Easter Island. The most common ancestor of G. crinale likely diverged during the Pleistocene. The Bayesian Skyline Plots suggested the pre-LGM population expansion. Based on geographical structure, lineage-specific private haplotypes, the absence of shared haplotypes between lineages, and AMOVA, we propose that the cosmopolitan distribution of G. crinale has been shaped by Pleistocene relicts. The survival of the turf species under environmental stresses is briefly discussed.

Major loss of coralline algal diversity in response to ocean acidification.

Calcified coralline algae are ecologically important in rocky habitats in the marine photic zone worldwide and there is growing concern that ocean acidification will severely impact them. Laboratory studies of these algae in simulated ocean acidification conditions have revealed wide variability in growth, photosynthesis and calcification responses, making it difficult to assess their future biodiversity, abundance and contribution to ecosystem function. Here, we apply molecular systematic tools to assess the impact of natural gradients in seawater carbonate chemistry on the biodiversity of coralline algae in the Mediterranean and the NW Pacific, link this to their evolutionary history and evaluate their potential future biodiversity and abundance. We found a decrease in the taxonomic diversity of coralline algae with increasing acidification with more than half of the species lost in high pCO2 conditions. Sporolithales is the oldest order (Lower Cretaceous) and diversified when ocean chemistry favoured low Mg calcite deposition; it is less diverse today and was the most sensitive to ocean acidification. Corallinales were also reduced in cover and diversity but several species survived at high pCO2 ; it is the most recent order of coralline algae and originated when ocean chemistry favoured aragonite and high Mg calcite deposition. The sharp decline in cover and thickness of coralline algal carbonate deposits at high pCO2 highlighted their lower fitness in response to ocean acidification. Reductions in CO2 emissions are needed to limit the risk of losing coralline algal diversity.

DNA sequencing of type material and newly collected specimens reveals two heterotypic synonyms for Harveylithon munitum (Metagoniolithoideae, Corallinales, Rhodophyta) and three new species.

Nongeniculate coralline algae are difficult to identify based solely on morpho-anatomy. To address the systematics of several taxonomically challenging taxa, we analyzed DNA sequences of a short portion (118-296 base pairs) of the 3' end of the rbcL gene from three type specimens. The analyses revealed that Harveylithon munitum (basionym: Lithophyllum munitum), described in 1906 from Cave Cays, Exuma Chain, Bahamas, is conspecific with both Goniolithon accretum and Goniolithon affine, described in 1906 from Sand Key, Florida and in 1907 from Culebra Island, Puerto Rico, respectively. Lithophyllum munitum and G. accretum were described in the same 1906 publication and have equal priority. We have selected the currently accepted and most commonly used name H. munitum to apply to this entity. Comparative analyses of rbcL, psbA, UPA, COI, and LSU sequences from contemporary field-collected specimens revealed that H. munitum currently inhabits mesophotic rhodolith beds in the northwestern Gulf of Mexico, as well as the intertidal zone in the Florida Keys, Honduras, Atlantic Mexico, Caribbean Panama, and Guadeloupe, French West Indies. Species delimitation analyses reveal that the Western Atlantic and Australian H. munitum populations may be separate species. Two new species of Harveylithon from the northwestern Gulf of Mexico and one new species from the southwestern Gulf of Mexico, the Caribbean, and the Red Sea were also identified in the analyses and are described.

Corallinapetrales and Corallinapetraceae: A new order and family of coralline red algae including Corallinapetra gabrielii comb. nov.

The coralline algal genus Corallinapetra is currently monospecific and was established on the species Corallinapetra novaezelandiae, known from a single collection from north-eastern New Zealand. On the basis of multi-gene phylogenetic analyses, Corallinapetra has been resolved apart from all currently recognized families and orders within the Corallinophycidae. We analyzed DNA sequence data from the holotype of Lithothamnion gabrielii, which has been considered a heterotypic synonym of L. muelleri, and an unidentified sample collected from Stewart Island in New Zealand, using psbA, rbcL, and COI-5P genes. We also observed detailed morpho-anatomical characters with light and scanning electron microscopy. Our phylogenetic analyses showed that L. gabrielii and the sample from New Zealand belonged to the same clade as Corallinapetra, distinct from other families and orders in the Corallinophycidae. Members of this clade are distinguishable from other families and orders in the Corallinophycidae by possessing sporangia that are surrounded by remnant sterile filaments that are weakly calcified in mature multiporate sporangial conceptacles that produce zonately divided tetrasporangia. Therefore, we propose that Corallinapetra be placed in its own family, Corallinapetraceae and order, Corallinapetrales, and that L. gabrielii should be assigned to Corallinapetra, as C. gabrielii, to reflect their phylogenetic relationships. We also obtained a partial rbcL sequence data from the lectotype of L. muelleri, the generitype of Lithothamnion. Comparison of the L. muelleri type sequence with L. gabrielii unambiguously demonstrated that these two species are not conspecific, and confirm the placement of L. muelleri within the Hapalidiales.

Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny.

The subclass Corallinophycidae is the only group of red algae characterized by the presence of calcite crystals in their cell walls. Except for the Rhodogorgonales, the remaining orders - collectively called corallines - are diverse and widely distributed, having calcified cell walls and highly variable morphology. Corallines constitute the group with the richest fossil record among marine algae. In the present study, we investigate the evolutionary history of the subclass Corallinophycidae and provide a time-calibrated phylogeny to date the radiation of the crown group and its main lineages. We use a multi-locus dataset with an extensive taxon sampling and comprehensive collection of fossil records, carefully assigned to corallines, to reconstruct a time-calibrated phylogeny of this subclass. Our molecular clock analyses suggest that the onset of crown group diversification of Corallinophycidae started in the Lower Jurassic and sped up in the Lower Cretaceous. The divergence time of the oldest order Sporolithales is estimated in the Lower Cretaceous followed by the remaining orders. We discuss the long period of more than 300 million years between the early Paleozoic records attributed to the stem group of Corallinophycidae and the radiation of the crown group. Our inferred phylogeny yields three highly-supported suprageneric lineages for the order Corallinales; we confirm the family Mastophoraceae and amend circumscription of the families Corallinaceae and Lithophyllaceae. These three families are distinguished by a combination of vegetative and reproductive features. In light of the phylogeny, we discuss the evolutionary trends of eleven morphological characters. In addition, we also highlight homoplasious characters and selected autapomorphies emerging in particular taxa.

From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats.

Ecosystem engineering species alter the physical structure of their environment and can create or modify habitats, having a massive impact on local biodiversity. Coralligenous reefs are highly diverse habitats endemic to the Mediterranean Sea built by calcareous benthic organisms among which Crustose Coralline Algae are the main engineering species. We analyzed the diversity of Lithophyllum stictiforme or L. cabiochiae in coralligenous habitats combining a multiple barcode and a population genomics approach with seascape features. Population genomics allowed disentangling pure spatial effects from environmental effects. We found that these taxa form a complex of eight highly divergent cryptic species that are easily identifiable using classic barcode markers (psbA, LSU, COI). Three factors have a significant effect on the relative abundances of these cryptic species: the location along the French Mediterranean coast, depth and Photosynthetic Active Radiation (PAR). The analysis of around 5000 SNPs for the most abundant species revealed genetic differentiation among localities in the Bay of Marseille but no differentiation between depths within locality. Thus, the effect of depth and PAR on cryptic species communities is not a consequence of restricted connectivity but rather due to differential settlement or survival among cryptic species. This differential is more likely driven by irradiance levels rather than by pressure or temperature. Both the genetic and species diversity patterns are congruent with the main patterns of currents in the Bay. Ecological differentiation among these engineering cryptic species, sensitive to ocean warming and acidification, could have important consequences on the diversity and structure of the coralligenous communities.

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.

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.

Adeylithon bosencei gen. et sp. nov. (Corallinales, Rhodophyta): a new reef-building genus with anatomical affinities with the fossil Aethesolithon.

Adeylithon gen. nov. with one species, A. bosencei sp. nov., belonging to the subfamily Hydrolithoideae is described from Pacific coral reefs based on psbA sequences and morpho-anatomy. In contrast with Hydrolithon, A. bosencei showed layers of large polygonal "cells," which resulted from extensive lateral fusions of perithallial cells, interspersed among layers of vegetative cells. This anatomical feature is shared with the fossil Aethesolithon, but lacking DNA sequences from the fossils and the fragmentary nature of Aethesolithon type material, we cannot ascertain if Adeylithon and Aethesolithon are congeneric. Morpho-anatomical features of A. bosencei were generally congruent with diagnostic features of the subfamily Hydrolithoideae: (i) outline of cell filaments entirely lost in large portions due to pervasive and extensive cell fusions, (ii) trichocytes not arranged in tightly packed horizontal fields, (iii) basal layer without palisade cells, and (iv) cells lining the canal pore oriented more or less perpendicular to roof surface and not protruding into the canal. However, it showed a predominant monomerous thallus organization and trichocytes were disposed in large pustulate, horizontal fields, although they were not tightly packed and did not become distinctly buried in the thallus. Only mature tetrasporangial conceptacles were observed, therefore the type of conceptacle roof formation remained undetermined. Adeylithon bosencei occurs on shallow coral reefs, in Australia, Papua New Guinea, and South Pacific islands (Fiji, Vanuatu). Fossil Aethesolithon is considered an important component of shallow coral reefs since the Miocene; fossil records showed a broad Indo-Pacific distribution, but a long-term process of range contraction in the last 2.6 million years, resulting in an overlap with the distribution of the extant Adeylithon. While the congeneric nature of extant and fossil taxa remained uncertain, similarities in morpho-anatomy, habitat, and distribution may indicate that both taxa likely shared a common ancestor.

Mediterranean Lithophyllum stictiforme (Corallinales, Rhodophyta) is a genetically diverse species complex: implications for species circumscription, biogeography and conservation of coralligenous habitats.

Lithophyllum species in the Mediterranean Sea function as algal bioconstructors, contributing to the formation of biogenic habitats such as coralligenous concretions. In such habitats, thalli of Lithophyllum, consisting of crusts or lamellae with entire or lobed margins, have been variously referred to as either one species, L. stictiforme, or two species, L. stictiforme and L. cabiochiae, in the recent literature. We investigated species diversity and phylogenetic relationships in these algae by sequencing three markers (psbA and rbcL genes, cox2,3 spacer), in conjunction with methods for algorithmic delimitation of species (ABGD and GMYC). Mediterranean subtidal Lithophyllum belong to a well-supported lineage, hereby called the L. stictiforme complex, which also includes two species described from the Atlantic, L. lobatum and L. searlesii. Our results indicate that the L. stictiforme complex consists of at least 13 species. Among the Mediterranean species, some are widely distributed and span most of the western and central Mediterranean, whereas others appear to be restricted to specific localities. These patterns are interpreted as possibly resulting from allopatric speciation events that took place during the Messinian Salinity Crisis and subsequent glacial periods. A partial rbcL sequence from the lectotype of L. stictiforme unambiguously indicates that this name applies to the most common subtidal Lithophyllum in the central Mediterranean. We agree with recent treatments that considered L. cabiochiae and L. stictiforme conspecific. The diversity of Lithophyllum in Mediterranean coralligenous habitats has been substantially underestimated, and future work on these and other Mediterranean corallines should use identifications based on DNA sequences.

Discrimination and Characterization of Two Mediterranean Species from the Laurencia Complex (Rhodomelacea) Using an NMR-Based Metabolomic Approach.

Generic and specific determination among the Laurencia complex is a challenging task. DNA barcoding combined with phenotypic investigations are mandatory for species differentiation. In this study, two morphologically different members of the Laurencia complex were investigated using untargeted 1 H-NMR-based metabolomics. Twenty-one population samples were collected in order to evaluate both temporal and geographical homogeneity. Data obtained from 1 H-NMR analysis followed by statistical analysis allowed a clear separation of all the samples into two groups. DNA mitochondrial tests confirmed this pattern and identified the two species as Laurenciella sp. and Laurencia obtusa. In addition, metabolites responsible of this discrimination were investigated directly in crude extracts by 13 C-NMR using an in-house computer-assisted method. The combination of both untargeted (1 H) and targeted (13 C) NMR-based metabolomic approaches proves to be a powerful and complementary approach to discriminate species from the Laurencia complex.

A novel phylogeny of the Gelidiales (Rhodophyta) based on five genes including the nuclear CesA, with descriptions of Orthogonacladia gen. nov. and Orthogonacladiaceae fam. nov.

Although the Gelidiales are economically important marine red algae producing agar and agarose, the phylogeny of this order remains poorly resolved. The present study provides a molecular phylogeny based on a novel marker, nuclear-encoded CesA, plus plastid-encoded psaA, psbA, rbcL, and mitochondria-encoded cox1 from subsets of 107 species from all ten genera within the Gelidiales. Analyses of individual and combined datasets support the monophyly of three currently recognized families, and reveal a new clade. On the basis of these results, the new family Orthogonacladiaceae is described to accommodate Aphanta and a new genus Orthogonacladia that includes species previously classified as Gelidium madagascariense and Pterocladia rectangularis. Acanthopeltis is merged with Gelidium, which has nomenclatural priority. Nuclear-encoded CesA was found to be useful for improving the resolution of phylogenetic relationships within the Gelidiales and is likely to be valuable for the inference of phylogenetic relationship among other red algal taxa.

Multigene analyses resolve early diverging lineages in the Rhodymeniophycidae (Florideophyceae, Rhodophyta).

Multigene phylogenetic analyses were directed at resolving the earliest divergences in the red algal subclass Rhodymeniophycidae. The inclusion of key taxa (new to science and/or previously lacking molecular data), additional sequence data (SSU, LSU, EF2, rbcL, COI-5P), and phylogenetic analyses removing the most variable sites (site stripping) have provided resolution for the first time at these deep nodes. The earliest diverging lineage within the subclass was the enigmatic Catenellopsis oligarthra from New Zealand (Catenellopsidaceae), which is here placed in the Catenellopsidales ord. nov. In our analyses, Atractophora hypnoides was not allied with the other included Bonnemaisoniales, but resolved as sister to the Peyssonneliales, and is here assigned to Atractophoraceae fam. nov. in the Atractophorales ord. nov. Inclusion of Acrothesaurum gemellifilum gen. et sp. nov. from Tasmania has greatly improved our understanding of the Acrosymphytales, to which we assign three families, the Acrosymphytaceae, Acrothesauraceae fam. nov. and Schimmelmanniaceae fam. nov.

Species diversity of the genus Osmundea (Ceramiales, Rhodophyta) in the Macaronesian region.

Species diversity within the genus Osmundea in the Macaronesian region was explored by conducting a comprehensive sampling in the Azores, the Canary, and the Madeira archipelagos. Toward identification, all specimens were first observed alive to verify the absence of corps en cerise, a diagnostic character for the genus and morphometric data were measured (thallus length and width, first-order branches length and width, branchlets length and width, cortical cell length and width in surface view, cortical cell length and width in transverse section). Specimens were sequenced for COI-5P (39 specimens) and three species delimitation methods (Generalized Mixed Yule Coalescent, Automatic Barcode Gap Discovery method, and Poisson Tree Processes) were used to assess the threshold between infra- and interspecific relationships. Subsequently, one or several sequences of plastid-encoded large subunit of RuBisCO (21 specimens) per delimited species were generated to assess the phylogenetic relationships among Macaronesian Osmundea. Moreover, for each delineated species, vegetative and reproductive anatomy was thoroughly documented and, when possible, specimens were either assigned to existing taxa or described as novel species. This integrative approach has provided data for (i) the presence of O. oederi, O. pinnatifida, and O. truncata in Macaronesia; (ii) the proposal of two novel species, O. prudhommevanreinei sp. nov. and O. silvae sp. nov.; and (iii) evidence of an additional species referred as "Osmundea sp.1," which is a sister taxon of O. hybrida.

How does molecular-assisted identification affect our estimation of α, ß and γ biodiversity? An example from understory red seaweeds (Rhodophyta) of Laminaria kelp forests in Brittany, France.

Using two distinct identification methods, one based on morphological characters only and the other combining morphological and molecular characters (integrative identification method), we investigated the differences in the biodiversity patterns of red seaweed communities associated with kelp forests at various spatial scales: the regional diversity of Brittany, France (γ-diversity), the local diversity at different Breton sites (α-diversity) and the differentiation in species diversity and abundances among those sites (ß-diversity). To characterise α and ß diversities, we conducted an initial survey in winter 2011 at 20 sites belonging to four different sub-regions, with specimens collected from six quadrats of 0.10 m(2) at each site, three in the tidal zone dominated by Laminaria digitata and three in the zone dominated by Laminaria hyperborea. To further characterise the regional diversity, we carried out another survey combining several sampling methods (quadrats and visual census) in different seasons (winter, spring and summer) and different years (2011 and 2012). In all, we collected 1990 specimens that were assigned to 76 taxa with the identification method based on morphological characters and 139 taxa using the integrative method. For γ and α diversity, the use of molecular characters revealed several cases of cryptic diversity and both increased the number of identified taxa and improved their taxonomic resolution. However, the addition of molecular characters for specimen identification only slightly affected estimates of ß-diversity.

Molecular evidence for the coexistence of two sibling species in Pylaiella littoralis (Ectocarpales, Phaeophyceae) along the Brittany coast.

The great phenotypic variability and the lack of diagnostic characters in the genus Pylaiella render the systematic study of this genus problematic. In this study, we investigated the diversity of Pylaiella littoralis along the Brittany (France) coast using a DNA barcoding multilocus approach with mitochondrial (cox1, nad1, and atp9) and chloroplastic (rbcL and atpB) markers associated with a population genetics approach using 10 microsatellite markers. In addition, spatio-temporal sampling was conducted along the Brittany coast. We sampled 140 individuals from four sites located between Saint-Malo and Concarneau (380 km) from April to October. Mitochondrial sequence data revealed the occurrence of two sibling species, with a minimum of 2.4% divergence between them. Microsatellite genotypic data congruently revealed two well-supported clusters matching the two mitochondrial clades of Pylaiella. Although gene flow is limited between species, occurrence of genetic admixtures in some populations suggested that reproductive isolation is not complete. Our study highlighted the complementarity of barcoding and population genetics approaches to shed light on the evolutionary processes that lead to speciation.

Sequencing type material resolves the identity and distribution of the generitype Lithophyllum incrustans, and related European species L. hibernicum and L. bathyporum (Corallinales, Rhodophyta).

DNA sequences from type material in the nongeniculate coralline genus Lithophyllum were used to unambiguously link some European species names to field-collected specimens, thus providing a great advance over morpho-anatomical identifi-cation. In particular, sequence comparisons of rbcL, COI and psbA genes from field-collected specimens allowed the following conclusion: the generitype species, L. incrustans, occurs mostly as subtidal rhodoliths and crusts on both Atlantic and Mediterranean coasts, and not as the common, NE Atlantic, epilithic, intertidal crust reported in the literature. The heterotypic type material of L. hibernicum was narrowed to one rhodolith belonging in Lithophyllum. As well as occurring as a subtidal rhodolith, L. hibernicum is a common, epilithic and epizoic crust in the intertidal zone from Ireland south to Mediterranean France. A set of four features distinguished L. incrustans from L. hibernicum, including epithallial cell diameter, pore canal shape of sporangial conceptacles and sporangium height and diameter. An rbcL sequence of the lectotype of Lithophyllum bathyporum, which was recently proposed to accommodate Atlantic intertidal collections of L. incrustans, corresponded to a distinct taxon hitherto known only from Brittany as the subtidal, bisporangial, lectotype, but also occurs intertidally in Atlantic Spain. Specimens from Ireland and France morpho-anatomically identified as L. fasciculatum and a specimen from Cornwall likewise identified as L. duckerae were resolved as L. incrustans and L. hibernicum, respectively.

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.

Levelling-up rhodolith-bed science to address global-scale conservation challenges.

Global marine conservation remains fractured by an imbalance in research efforts and policy actions, limiting progression towards sustainability. Rhodolith beds represent a prime example, as they have ecological importance on a global scale, provide a wealth of ecosystem functions and services, including biodiversity provision and potential climate change mitigation, but remain disproportionately understudied, compared to other coastal ecosystems (tropical coral reefs, kelp forests, mangroves, seagrasses). Although rhodolith beds have gained some recognition, as important and sensitive habitats at national/regional levels during the last decade, there is still a notable lack of information and, consequently, specific conservation efforts. We argue that the lack of information about these habitats, and the significant ecosystem services they provide, is hindering the development of effective conservation measures and limiting wider marine conservation success. This is becoming a pressing issue, considering the multiple severe pressures and threats these habitats are exposed to (e.g., pollution, fishing activities, climate change), which may lead to an erosion of their ecological function and ecosystem services. By synthesizing the current knowledge, we provide arguments to highlight the importance and urgency of levelling-up research efforts focused on rhodolith beds, combating rhodolith bed degradation and avoiding the loss of associated biodiversity, thus ensuring the sustainability of future conservation programs.

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.

Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella.

We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier-a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.