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Caribbean coral reefs are experiencing a shift to algal dominance at the expense of stony corals. Determining the factors leading to algal phase shifts is crucial for assuring the survival of Caribbean coral reefs. In this study, factors controlling the growth of the abundant brown macroalgae Dictyota spp. were investigated by varying herbivory pressure (caging) and nutrients (fertilizer addition) on coral reefs near St. Thomas (US Virgin Islands). Experiment 1 measured Dictyota heights and percent cover at 3 sites (11-20 m depth) and showed no growth response to nutrient addition and a weak negative response to herbivory. To confirm results of Experiment 1, a caging and nutrient manipulation (Experiment 2) was conducted at one site (14 m depth) using the dependent variable Dictyota biomass. A strong negative response of growth to nutrient addition was shown, presumably because of nutrient inhibition, and an equally negative response to herbivory (loss of ~50% biomass over 21 d). The inhibitory effect of fertilization on growth was confirmed in a third experiment that showed increasing biomass loss over 4 treatment levels of increasing fertilizer addition (0 [ambient], 5, 10, 20 g). Overall, Dictyota was not nutrient limited at any sites, and was weakly controlled by herbivore populations. Factors responsible for Dictyota abundance on Caribbean reefs may reflect decreased herbivory caused by overfishing and reductions in coral cover and do not appear to be affected by recent changes in nitrogen or phosphorus load. This study reinforces the need for conservation and management of herbivores in coral reef ecosystems, to mitigate the effects from anthropogenic stressors.

Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically, we test whether the evolutionary processes that shaped the latitudinal diversity patterns in these clades are in line with the tropical conservatism, out-of-the-tropics or diversification rate hypotheses. Location: Global coastal benthic marine environments. Taxon: Dictyotales (Phaeophyceae). Methods: Species diversity was inferred using DNA-based species delineation, addressing cryptic diversity and circumventing taxonomic problems. A six-gene time-calibrated phylogeny, distribution data of 3,755 specimens and probabilistic modelling of geographical range evolution were used to infer historical biogeographical patterns. The phylogeny was tested against different trait-dependent models to compare diversification rates for different geographical units as well as different thermal affinities. Results: Our results indicate that Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo-Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Our results suggest that three major clades underwent a major diversification burst in the early Cenozoic, with Dictyota and Padina expanding their distribution into temperate regions while Lobophora retained a predominantly tropical niche. Main conclusions: Our results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (Lobophora), and the out-of-the-tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (Dictyota, Padina).

Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically, we test whether the evolutionary processes that shaped the latitudinal diversity patterns in these clades are in line with the tropical conservatism, out-of-the-tropics or diversification rate hypotheses. Location: Global coastal benthic marine environments. Taxon: Dictyotales (Phaeophyceae). Methods: Species diversity was inferred using DNA-based species delineation, addressing cryptic diversity and circumventing taxonomic problems. A six-gene time-calibrated phylogeny, distribution data of 3,755 specimens and probabilistic modelling of geographical range evolution were used to infer historical biogeographical patterns. The phylogeny was tested against different trait-dependent models to compare diversification rates for different geographical units as well as different thermal affinities. Results: Our results indicate that Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo-Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Our results suggest that three major clades underwent a major diversification burst in the early Cenozoic, with Dictyota and Padina expanding their distribution into temperate regions while Lobophora retained a predominantly tropical niche. Main conclusions: Our results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (Lobophora), and the out-of-the-tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (Dictyota, Padina).

Many tropical marine cyanobacteria are prolific producers of bioactive secondary metabolites with ecological relevance and promising pharmaceutical applications. One species of chemically rich, tropical marine cyanobacteria that was previously identified as Symploca hydnoides or Symploca sp. corresponds to the traditional taxonomic definition of Phormidium penicillatum. In this study, we clarified the taxonomy of this biomedically and ecologically important cyanobacterium by comparing recently collected specimens with the original type material and the taxonomic description of P. penicillatum. Molecular phylogenetic analyses of the 16S rRNA gene and the 16S-23S internal transcribed spacer regions showed that P. penicillatum formed an independent clade sister to the genus Symploca, and distantly related to Phormidium and Lyngbya. We propose the new genus Caldora for this clade, with Caldora penicillata comb. nov. as the type species and designate as the epitype the recently collected strain FK13-1. Furthermore, the production of bioactive secondary metabolites among various geographically dispersed collections of C. penicillata showed that this species consistently produced the metabolite dolastatin 10 and/or the related compound symplostatin 1, which appear to be robust autapomorphic characters and chemotaxonomic markers for this taxon.

Cyanobacteria comprise an extraordinarily diverse group of microorganisms and, as revealed by increasing molecular information, this biodiversity is even more extensive than previously estimated. In this sense, the cyanobacterial genus Lyngbya is a highly polyphyletic group composed of many unrelated taxa with morphological similarities. In this study, the new genus Dapis was erected from the genus Lyngbya, based on a combined molecular, chemical, and morphological approach. Herein, two new species of cyanobacteria are described: D. pleousa and D. pnigousa. Our analyses found these species to be widely distributed and abundant in tropical and subtropical marine habitats. Seasonally, both species have the ability to form extensive algal blooms in marine habitats: D. pleousa in shallow-water, soft bottom habitats and D. pnigousa on coral reefs below depths of 10 m. Electron microscopy showed that D. pleousa contains gas vesicles, a character not previously reported in Lyngbya. These gas vesicles, in conjunction with a mesh-like network of filaments that trap oxygen released from photosynthesis, provide this species with an unusual mechanism to disperse in coastal marine waters, allowing D. pleousa to be present in both benthic and planktonic forms. In addition, both D. pleousa and D. pnigousa contained nitrogen-fixing genes as well as bioactive secondary metabolites. Several specimens of D. pnigousa biosynthesized the secondary metabolite lyngbic acid, a molecule that has also been isolated from many other marine cyanobacteria. Dapis pleousa consistently produced the secondary metabolite malyngolide, which may provide a promising chemotaxonomic marker for this species.

We reassessed the taxonomy of dentate Dictyota species formerly attributed to D. ciliolata and D. crenulata. Both taxa have long been assumed to be broadly distributed in tropical to warm-temperate seas. Recent molecular data, however, provided evidence that D. crenulata constituted a complex of at least four species with restricted geographical distributions. Based on those results and careful morphological examination, we split D. crenulata sensu lato into D. crenulata sensu stricto restricted to Pacific Central America, D. jamaicensis with a tropical amphi-Atlantic distribution and D. canariensis and D. pleiacantha sp. nov. from Macaronesia. Morphological analysis showed that these species were distinguished by subtle morphological differences. In contrast to D. crenulata sensu lato, the wide tropical distribution of D. ciliolata was confirmed by DNA data. In addition, psbA sequence analysis did not provide evidence to segregate D. menstrualis and D. plectens from D. ciliolata.

The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. 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.

Coexistence in a homogeneous environment requires species to specialize in distinct niches. Sympatry of cryptic species is of special interest to both ecologists and evolutionary biologists because the mechanisms that facilitate their persistent coexistence are obscure. In this study, we report on two sympatric Dictyota species, D. dichotoma (Huds.) J. V. Lamour. and the newly described species D. cymatophila sp. nov., from the Canary Islands. Gene sequence data (rbcL, psbA, nad1, cox1, cox3, and LSU rDNA) demonstrate that D. dichotoma and D. cymatophila do not represent sister species. Rather, D. cymatophila and D. dichotoma have converged on a nearly identical morphology, only to be distinguished with detailed morphometric observations. Both species co-occur in eulittoral pools and the shallow subtidal in Tenerife. Even though D. cymatophila was more dominant in wave-exposed places and D. dichotoma in less exposed areas, the spatial distribution of both species overlapped in intermediate habitats. The species display radically different phenologies. D. dichotoma reached its highest density in winter and early spring and disappeared nearly completely in autumn, while D. cymatophila dominated the study site from July until November. The timing of gamete release also differs between both species, D. dichotoma releasing gametes twice every lunar cycle, while the release of gametes in D. cymatophila occurred roughly every other day.

Although it has been suggested that the distribution of Dictyota dichotoma is probably restricted to the European Atlantic Ocean and the Mediterranean Sea, its occurrence in the Canary Islands (new southernmost distribution limit) is confirmed by nuclear ribosomal sequence data (LSU rDNA). Even though D. dichotoma has been described and illustrated prominently in early studies of brown algae, the species remains difficult to characterize due to considerable morphological plasticity. An exhaustive analysis of several quantitative characters confirms significant morphological variation both seasonally and between life-cycle phases. The species may be characterized in the Canary Islands only by the following qualitative features: erect thallus attached by a single holdfast, subdichotomous branches always of similar width, straight terminal segments and smooth margins and an entirely unilayered medulla. In the Canary Islands, D. dichotoma is an aseasonal annual with at least three overlapping generations in which sporophytes and gametophytes grow simultaneously. Thallus life span seems to be less than 3 months. The species occurs throughout the year, but as cryptic microthalli in autumn. Two abundance peaks were detected with the maximum value in February (6.2 thalli m-2). The optimum reproductive stage (88.3% fertile specimens) occurred in winter and the maximum vegetative stage (maximum thallus length: 18.6 cm) in summer. Sporophytes outnumbered gametophytes throughout the year, with ratios decreasing from 13.2±1.1 in winter to 1.9±0.2 in summer. Gametophytes made up to 25% of the population and fertile thalli were always dominant. The populations from the Canaries exhibited a temporal displacement compared to northern populations with the favorable period in the coldest season (winter) and the resting period in the warmest season (autumn).

Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).

Seagrasses are among the most productive habitats in the marine realm, performing several crucial physical and biological ecosystem services. One group of seagrasses is the family Zosteraceae, which includes three to four genera and >20 species inhabiting temperate waters of both the northern and southern hemisphere. Species delineation depends on the type of data used, ranging from morphological to molecular. The main goal of this study was to better understand the evolution and divergence within the family, using a broad taxon sampling (>90 individuals) representing all species across the entire biogeographical range in both hemispheres and a four-locus approach (ITS1, matK, rbcL, psbA-trnH). The concatenated four-locus analysis supported earlier studies showing four genera in the family: Phyllospadix, Zostera, Nanozostera and Heterozostera. Four species were resolved within the genus Zostera, four within Nanozostera and two within Heterozostera. No distinction was revealed between H. nigracaulis (Australia) and H. chiliensis (Chile), suggesting a very recent introduction to Chile. A time-calibrated phylogeny using the rbcL gene revealed an early divergence of Zostera-Nanozostera/Heterozostera at 14.4 Ma, followed by a late Miocene radiation of Nanozostera-Heterozostera at 6.4 Ma, and the H. polychalymas-H. nigracaulis/tasmanica/chiliensis split at 2.3 Ma. Zostera asiatica diverged from other species of Zostera at 4.6 Ma. Phylogenetic analyses indicated that matK was the most informative single locus, whereas psbA-trnH (a widely used barcoding locus) was unable to resolve any entities within the Zosteraceae. A commonly used barcoding combination for plants, rbcL/matK, distinguished all genera, but was unable to resolve several species.

The control of RNA splicing is often modulated by exonic motifs near splice sites. Chief among these are exonic splice enhancers (ESEs). Well-described ESEs in mammals are purine rich and cause predictable skews in codon and amino acid usage toward exonic ends. Looking across species, those with relatively abundant intronic sequence are those with themore profound end of exon skews, indicative of exonization of splice site recognition. To date, the only intron-rich species that have been analyzed are mammals, precluding any conclusions about the likely ancestral condition.Here,we examine the patterns of codon and amino acid usage in the vicinity of exon-intron junctions in the brown alga Ectocarpus siliculosus, a species with abundant large introns, known SR proteins, and classical splice sites.We find that amino acids and codons preferred/avoided at both 3' and 5' ends in Ectocarpus, ofwhichthere aremany, tend, on average, to also be preferred/avoided at the same exon ends in humans. Moreover, the preferences observed at the 5' ends of exons are largely the same as those at the 3' ends, a symmetry trend only previously observed in animals. We predict putative hexameric ESEs inEctocarpus and show that these are purine rich and that there are many more of these identified as functional ESEs in humans than expected by chance. These results are consistent with deep phylogenetic conservation of SR protein binding motifs. Assuming codons preferred near boundaries are "splice optimal" codons, in Ectocarpus, unlike Drosophila, splice optimal and translationally optimal codons are not mutually exclusive. The exclusivity of translationally optimal and splice optimal codon sets is thus not universal.

We reassessed the taxonomy of dentate Dictyota species formerly attributed to D. ciliolata and D. crenulata. Both taxa have long been assumed to be broadly distributed in tropical to warm-temperate seas. Recent molecular data, however, provided evidence that D. crenulata constituted a complex of at least four species with restricted geographical distributions. Based on those results and careful morphological examination, we split D. crenulata sensu lato into D. crenulata sensu stricto restricted to Pacific Central America, D. jamaicensis with a tropical amphi-Atlantic distribution and D. canariensis and D. pleiacantha sp. nov. from Macaronesia. Morphological analysis showed that these species were distinguished by subtle morphological differences. In contrast to D. crenulata sensu lato, the wide tropical distribution of D. ciliolata was confirmed by DNA data. In addition, psbA sequence analysis did not provide evidence to segregate D. menstrualis and D. plectens from D. ciliolata.

Coexistence in a homogeneous environment requires species to specialize in distinct niches. Sympatry of cryptic species is of special interest to both ecologists and evolutionary biologists because the mechanisms that facilitate their persistent coexistence are obscure. In this study, we report on two sympatric Dictyota species, D. dichotoma (Huds.) J. V. Lamour. and the newly described species D. cymatophila sp. nov., from the Canary Islands. Gene sequence data (rbcL, psbA, nad1, cox1, cox3, and LSU rDNA) demonstrate that D. dichotoma and D. cymatophila do not represent sister species. Rather, D. cymatophila and D. dichotoma have converged on a nearly identical morphology, only to be distinguished with detailed morphometric observations. Both species co-occur in eulittoral pools and the shallow subtidal in Tenerife. Even though D. cymatophila was more dominant in wave-exposed places and D. dichotoma in less exposed areas, the spatial distribution of both species overlapped in intermediate habitats. The species display radically different phenologies. D. dichotoma reached its highest density in winter and early spring and disappeared nearly completely in autumn, while D. cymatophila dominated the study site from July until November. The timing of gamete release also differs between both species, D. dichotoma releasing gametes twice every lunar cycle, while the release of gametes in D. cymatophila occurred roughly every other day.

Coexistence in a homogeneous environment requires species to specialize in distinct niches. Sympatry of cryptic species is of special interest to both ecologists and evolutionary biologists because the mechanisms that facilitate their persistent coexistence are obscure. In this study, we report on two sympatric Dictyota species, D. dichotoma (Huds.) J. V. Lamour. and the newly described species D. cymatophila sp. nov., from the Canary Islands. Gene sequence data (rbcL, psbA, nad1, cox1, cox3, and LSU rDNA) demonstrate that D. dichotoma and D. cymatophila do not represent sister species. Rather, D. cymatophila and D. dichotoma have converged on a nearly identical morphology, only to be distinguished with detailed morphometric observations. Both species co-occur in eulittoral pools and the shallow subtidal in Tenerife. Even though D. cymatophila was more dominant in wave-exposed places and D. dichotoma in less exposed areas, the spatial distribution of both species overlapped in intermediate habitats. The species display radically different phenologies. D. dichotoma reached its highest density in winter and early spring and disappeared nearly completely in autumn, while D. cymatophila dominated the study site from July until November. The timing of gamete release also differs between both species, D. dichotoma releasing gametes twice every lunar cycle, while the release of gametes in D. cymatophila occurred roughly every other day

Taxonomy of the brown algal genus Dictyota has a long and troubled history. Our inability to distinguish morphological plasticity from fixed diagnostic traits that separate the various species has severely confounded species delineation. From continental Europe, more than 60 species and intraspecific taxa have been described over the last two centuries. Using a molecular approach, we addressed the diversity of the genus in European waters and made necessary taxonomic changes. A densely sampled DNA data set demonstrated the presence of six evolutionarily significant units (ESUs): Dictyota dichotoma (Huds.) J. V. Lamour., D. fasciola (Roth) J. V. Lamour., D. implexa J. V. Lamour., D. mediterranea (Schiffn.) G. Furnari, D. spiralis Mont., and the newly described D. cyanoloma sp. nov., which was previously reported as D. ciliolata from the Mediterranean Sea. Species distributions, based on DNA-confirmed occurrence records, indicate that all species are geographically confined to the NE Atlantic Ocean with the exception of D. dichotoma and D. implexa, which also occur in South Africa and Bermuda, respectively. To investigate potential hybridization between D. dichotoma and D. implexa, which were previously shown to be sexually compatible in culture, we compiled and analyzed sets of mitochondrial, plastid, and nuclear markers to detect putative hybrids or introgression in natural populations. Failure to detect natural hybrids indicates that effective pre- and postzygotic isolation mechanisms are at play in natural populations and supports the by-product hypothesis of reproductive isolation.

Veinticinco especies de algas marinas bentónicas (cinco Cyanophyta, catorce Rhodophyta y seis Chlorophyta) son citadas por primera vez para la isla de El Hierro. Las especies fueron recolectadas en el eulitoral y el sublitoral en la zona de uso tradicional de la ‘Reserva Marina del Mar de Las Calmas’. Se presentan datos sobre el hábitat y la distribución regional de las especies. Twenty-five species of benthic marine algae (five Cyanophyta, fourteen Rhodophyta, and six Chlorophyta) are reported for the first time for the island of El Hierro. Species were collected in the eulittoral and sublittoral in the zone for traditional activities of the ‘Reserva Marina del Mar de Las Calmas’. Data concerning the habitat and the regional distribution of the species are presented.

Background : Many tropical marine macroalgae are reported from all three ocean basins, though these very wide distributions may simply be an artifact resulting from inadequate taxonomy that fails to take into account cryptic diversity. Alternatively, pantropical distributions challenge the belief of limited intrinsic dispersal capacity of marine seaweeds and the effectiveness of the north-south oriented continents as dispersal barriers. We aimed to re-assess the distribution of two allegedly circumtropical brown algae, Dictyota ciliolata and D. crenulata, and interpret the realized geographical range of the respective species in relation to their thermal tolerance and major tectonic and climatic events during the Cenozoic. Methodology/Principal Findings : Species delimitation was based on 184 chloroplast encoded psbA sequences, using a Generalized Mixed Yule Coalescent method. Phylogenetic relationships were inferred by analyzing a six-gene dataset. Divergence times were estimated using relaxed molecular clock methods and published calibration data. Distribution ranges of the species were inferred from DNA-confirmed records, complemented with credible literature data and herbarium vouchers. Temperature tolerances of the species were determined by correlating distribution records with local SST values. We found considerable conflict between traditional and DNA-based species definitions. Dictyota crenulata consists of several pseudocryptic species, which have restricted distributions in the Atlantic Ocean and Pacific Central America. In contrast, the pantropical distribution of D. ciliolata is confirmed and linked to its significantly wider temperature tolerance. Conclusions/Significance : Tectonically driven rearrangements of physical barriers left an unequivocal imprint on the current diversity patterns of marine macroalgae, as witnessed by the D. crenulata–complex. The nearly circumglobal tropical distribution of D. ciliolata, however, demonstrates that the north-south oriented continents do not present absolute dispersal barriers for species characterized by wide temperature tolerances.