Molecular phylogeny of two unusual brown algae,Phaeostrophion irregulare and Platysiphon glacialis,proposal of the Stschapoviales ord. nov. and Platysiphonaceae fam. nov., and a re‐examination of divergence times for brown algal orders

The molecular phylogeny of brown algae was examined using concatenated DNA sequences of seven chloroplast and mitochondrial genes (atpB, psaA, psaB, psbA, psbC, rbcL, and cox1). The study was carried out mostly from unialgal cultures; we included Phaeostrophion irregulare and Platysiphon glacialis because their ordinal taxonomic positions were unclear. Overall, the molecular phylogeny agreed with previously published studies, however, Platysiphon clustered with Halosiphon and Stschapovia and was paraphyletic with the Tilopteridales. Platysiphon resembled Stschapovia in showing remarkable morphological changes between young and mature thalli. Platysiphon, Halosiphon and Stschapovia also shared parenchymatous, terete, erect thalli with assimilatory filaments in whorls or on the distal end. Based on these results, we proposed a new order Stschapoviales and a new family Platysiphonaceae. We proposed to include Phaeostrophion in the Sphacelariales, and we emended the order to include this foliose member. Finally, using basal taxa not included in earlier studies, the origin and divergence times for brown algae were re‐investigated. Results showed that the Phaeophyceae branched from Schizocladiophyceae ~260 Ma during the Permian Period. The early diverging brown algae had isomorphic life histories, whereas the derived taxa with heteromorphic life histories evolved 155–110 Ma when they branched from the basal taxa. Based on these results, we propose that the development of heteromorphic life histories and their success in the temperate and cold‐water regions was induced by the development of the remarkable seasonality caused by the breakup of Pangaea. Most brown algal orders had diverged by roughly 60 Ma, around the last mass extinction event during the Cretaceous Period, and therefore a drastic climate change might have triggered the divergence of brown algae.     

THE RECLASSIFICATION OF LESSONIA LAMINARIOIDES (LAMINARIALES,PHAEOPHYCEAE): PSEUDOLESSONIA GEN. NOV.1

A new genus, Pseudolessonia, is proposed for the kelp Lessonia laminarioides Postels et Ruprecht (Laminariales, Phaeophyceae), which occurs on the northwest side of the Sea of Okhotsk, in the northwest Pacific Ocean. Pseudolessonia is monotypic and differs from Lessonia in its short primary stipes and its corrugated, unilaterally arranged blades with entire margins. This species is transferred on the basis of morphology and plastid gene sequence comparisons. We determined psaA and rbcL gene sequences from 17 taxa of Pseudolessonia, Lessonia, and putative relatives. Analyses of individual and combined data sets resulted in congruent trees showing a clear separation of Pseudolessonia laminarioides from Lessonia, but suggesting its sister relationships with the clade of Nereocystis, Macrocystis, Pelagophycus, and Postelsia in the North Pacific Ocean. On the other hand, Lessonia species from the South Pacific Ocean formed a strongly supported clade. The results indicate that the basal splitting of the blade, which has been considered a diagnostic character for the family Lessoniaceae, is a result of convergent evolution.     

Comparative Genome Analysis Reveals Cyanidiococcus gen. nov., A New Extremophilic Red Algal Genus Sister to Cyanidioschyzon (Cyanidioschyzonaceae,Rhodophyta)

The taxonomic placement of strains belonging to the extremophilic red alga Galdieria maxima has been controversial due to the inconsistent phylogenetic position inferred from molecular phylogenetic analyses. Galdieria maxima nom. inval. was classified in this genus based on morphology and molecular data in the early work, but some subsequent molecular phylogenetic analyses have inferred strains of G. maxima to be closely related to the genus Cyanidioschyzon. To address this controversy, an isolated strain identified as G. maxima using the rbcL gene sequence as the genetic barcode was examined using a comprehensive analysis across morphological, physiological, and genomic traits. Herein are reported the chloroplast-, mitochondrion-, and chromosome-level nuclear genome assemblies. Comparative analysis of orthologous gene clusters and genome arrangements suggested that the genome structure of this strain was more similar to that of the generitype of Cyanidioschyzon, C. merolae than to the generitype of Galdieria, G. sulphuraria. While the ability to uptake various forms of organic carbon for growth is an important physiological trait of Galdieria, this strain was identified as an ecologically obligate photoautotroph (i.e., the inability to utilize the natural concentrations of organic carbons) and lacked various gene models predicted as sugar transporters. Based on the genomic, morphological, and physiological traits, we propose this strain to be a new genus and species, Cyanidiococcus yangmingshanensis. Re-evaluation of the 18S rRNA and rbcL gene sequences of the authentic strain of G. maxima, IPPAS-P507, with those of C. yangmingshanensis suggests that the rbcL sequences of “G. maxima” deposited in GenBank correspond to misidentified isolates.     

Multi‐gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov.

Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi‐gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.     

A NEW LOOK AT AN ANCIENT ORDER: GENERIC REVISION OF THE BANGIALES (RHODOPHYTA)1

The red algal order Bangiales has been revised as a result of detailed regional studies and the development of expert local knowledge of Bangiales floras, followed by collaborative global analyses based on wide taxon sampling and molecular analyses. Combined analyses of the nuclear SSU rRNA gene and the plastid RUBISCO LSU (rbcL) gene for 157 Bangiales taxa have been conducted. Fifteen genera of Bangiales, seven filamentous and eight foliose, are recognized. This classification includes five newly described and two resurrected genera. This revision constitutes a major change in understanding relationships and evolution in this order. The genus Porphyra is now restricted to five described species and a number of undescribed species. Other foliose taxa previously placed in Porphyra are now recognized to belong to the genera Boreophyllum gen. nov., Clymene gen. nov., Fuscifolium gen. nov., Lysithea gen. nov., Miuraea gen. nov., Pyropia, and Wildemania. Four of the seven filamentous genera recognized in our analyses already have generic names (Bangia, Dione, Minerva, and Pseudobangia), and are all currently monotypic. The unnamed filamentous genera are clearly composed of multiple species, and few of these species have names. Further research is required: the genus to which the marine taxon Bangia fuscopurpurea belongs is not known, and there are also a large number of species previously described as Porphyra for which nuclear SSU ribosomal RNA (nrSSU) or rbcL sequence data should be obtained so that they can be assigned to the appropriate genus.     

NEW GENERA AND SPECIES OF CERAMIACEAE (RHODOPHYTA) FROM THE SOUTHEASTERN UNITED STATES1

Five Ceramiaceae (Rhodophyta) are reported from the offshore waters of the southeastern, warm temperate coast of the United States. These include two new monotypic genera, Calliclavula trifurcate Schneider in the Griffithsieae and Nwynea grandispora Searles in the Sphondylothamnieae, and three new species, Callithamniella silvae Searles, Ptilothamnion occidentale Searles, and Lejolisia exposita Schneider et Searles.     

MOLECULAR PHYLOGENY,ULTRASTRUCTURE, AND TAXONOMIC REVISION OF CHLOROGONIUM (CHLOROPHYTA): EMENDATION OF CHLOROGONIUM AND DESCRIPTION OF GUNGNIR GEN. NOV. AND RUSALKA GEN. NOV.1

We examined the molecular phylogeny and ultrastructure of Chlorogonium and related species to establish the natural taxonomy at the generic level. Phylogenetic analyses of 18S rRNA and RUBISCO LSU (rbcL) gene sequences revealed two separate clades of Chlorogonium from which Chlorogonium (Cg.) fusiforme Matv. was robustly separated. One clade comprised Cg. neglectum Pascher and Cg. kasakii Nozaki, whereas the other clade included the type species Cg. euchlorum (Ehrenb.) Ehrenb., Cg. elongatum (P. A. Dang.) Francé, and Cg. capillatum Nozaki, M. Watanabe et Aizawa. On the basis of unique ultrastructural characteristics, we described Gungnir Nakada gen. nov. comprising three species: G. neglectum (Pascher) Nakada comb. nov., G. mantoniae (H. Ettl) Nakada comb. nov., and G. kasakii (Nozaki) Nakada comb. nov. We also emended Chlorogonium as a monophyletic genus composed of Cg. euchlorum, Cg. elongatum, and Cg. capillatum. Because Cg. fusiforme was distinguished from the redefined Chlorogonium and Gungnir by the structure of its starch plate, which is associated with pyrenoids, we reclassified this species as Rusalka fusiformis (Matv.) Nakada gen. et comb. nov.     

Proposal of Microsquama subgen. nov. for Nephroselmis pyriformis (Carter) Ettl (Nephroselmidophyceae,Chlorophyta)

A new subgenus, Microsquama, is proposed for Nephroselmis pyriformis based on its phylogenetic position and some ultrastructural characters, such as the absence of large stellate scales. Other species of the genus are classified in the subgenus Nephroselmis.     

A phylogenetic re‐appraisal of the family Liagoraceae sensu lato (Nemaliales,Rhodophyta) based on sequence analyses of two plastid genes and postfertilization development

The marine red algal family Liagoraceae sensu lato is shown to be polyphyletic based on analyses of a combined rbcL and psaA data set and the pattern of carposporophyte development. Fifteen of eighteen genera analyzed formed a monophyletic lineage that included the genus Liagora. Nemalion did not cluster with Liagoraceae sensu stricto, and Nemaliaceae is reinstated, characterized morphologically by the formation of the primary gonimolobes by longitudinal divisions of the gonimoblast initial. Yamadaella and Liagoropsis, previously placed in the Dermonemataceae, are shown to be independent lineages and are recognized as two new families Yamadaellaceae and Liagoropsidaceae. Yamadaellaceae is characterized by two gonimoblast initials cut off bilaterally from the fertilized carpogonium and diffusely spreading gonimoblast filaments. Liagoropsidaceae is characterized by at least three gonimoblast initials cut off by longitudinal septa from the fertilized carpogonium. In contrast, Liagoraceae sensu stricto is characterized by a single gonimoblast initial cut off transversely or diagonally from the fertilized carpogonium. Reproductive features, such as diffuse gonimoblasts and unfused carpogonial branches following postfertilization, appear to have evolved on more than one occasion in the Nemaliales and are therefore not taxonomically diagnostic at the family level, although they may be useful in recognizing genera.     

Molecular phylogeny of Zeacarpa (Ralfsiales,Phaeophyceae) proposing a new family Zeacarpaceae and its transfer to Nemodermatales

Zeacarpa leiomorpha is a crustose brown alga endemic to South Africa. The species has been tentatively placed in Ralfsiaceae, but its ordinal assignment has been uncertain. The molecular phylogeny of brown algae based on concatenated DNA sequences of seven chloroplast and mitochondrial gene sequences (atpB, psaA, psaB, psbA, psbC, rbcL, and cox1) of taxa covering most of the orders revealed the most related phylogenetic relationship of Z. leiomorpha to Nemoderma tingitanum (Nemodermatales) rather than Ralfsiaceae (Ralfsiales). Morphologically, Zeacarpa and Nemoderma share crustose thallus structure and multiple discoidal chloroplasts without pyrenoids in each cell, however, the formation of lateral unilocular zoidangia in tufts in loose upright filaments in Zeacarpa is distinctive in brown algae. Considering the relatively distant genetic divergence between the two taxa, comparable to that among families or orders in representative brown algae, in addition to the above‐mentioned unique morphological features, we propose the classification of Zeacarpa in a new family Zeacarpaceae in the order Nemodermatales.     

Utility of rbcS gene as a novel target DNA region for brown algal molecular systematics

The usefulness of molecular phylogenetic studies has increased remarkably as the quantity and quality of available DNA sequences has increased. When compared with the progress that has occurred in angiosperms and animals, there have been relatively few target DNA regions identified for use in taxonomic studies of brown algae. Therefore, in this study, we developed a new set of primers to amplify Rubisco small subunit (rbcS) gene sequences and determined the rbcS gene sequences of various species of brown algae including those belonging to Dictyotales, Ectocarpales, Fucales and Sphacelariales. The level of sequence variations in the rbcS gene varied according to the brown algal lineages. When focusing on the relationship of species within the genus Sargassum, the rbcS gene sequences provided useful information regarding the phylogenetic relationship among sections of the subgenus Bactrophycus. Based on the broad applicability and phylogenetic utility of the rbcS gene, we suggest that the sequence be used as a new target region for the molecular systematics of brown algae.     

Systematic revision of the freshwater snail Margarya Nevill, 1877 (Mollusca: Viviparidae) endemic to the ancient lakes of Yunnan,China, with description of new taxa

The systematics of the viviparid freshwater snail genus Margarya endemic to the ancient lakes of Yunnan, China, is revised based on comparative analyses of morphological features, including shell, operculum, radula, and genital anatomy, and molecular phylogenetic analyses of partial sequences of the mitochondrial 16S rDNA (16S) and cytochrome c oxidase subunit I (COI) genes, as well as the nuclear Internal Transcribed Spacer 2 (ITS2). The taxonomic utility of key anatomical and morphological features in this group is evaluated. The genus Margarya as delimited previously is split into three genera in order to retain monophyletic taxa: (1) Margarya s.s., consisting of four species, i.e. the type species Margarya melanioides plus Margarya francheti, Margarya oxytropoides, and Margarya monodi; (2) the previously introduced subgenus Tchangmargarya is elevated to an independent genus containing two species, Tchangmargarya yangtsunghaiensis and the new species T changmargarya multilabiata sp. nov. ; and (3) a new genus, A nularya gen. nov. , is described, also containing two species, i.e. Anularya mansuyi and Anularya bicostata. Molecular phylogenies based on analyses of three gene fragments have identical topologies, supporting the monophyly of these genera. The sister group of Margarya s.s. is Cipangopaludina, whereas the sister group of Anularya is Sinotaia; Tchangmargarya is sister to a clade containing all the aforementioned groups. Features of the operculum and the right male tentacle (penis) are particularly informative on the generic level, whereas shell and radular characters are especially useful to differentiate species. The phylogenetic relationships recovered here are consistent with orogenic patterns of the Yunnan Mountains. Changes in the river system and water area of ancient lakes caused by tectonic activities probably play an important role in speciation and shaping the current pattern of species distribution in Yunnan. © 2015 The Linnean Society of London     

TAXONOMIC STUDY OF TWO NEW GENERA OF FUSIFORM GREEN FLAGELLATES,TABRIS GEN. NOV. AND HAMAKKO GEN. NOV. (VOLVOCALES,CHLOROPHYCEAE)1

On the basis of LM, we isolated strains of two species of fusiform green flagellates that could be assigned to former Chlorogonium (Cg.) Ehrenb. One species, “Cg.”heimii Bourr., lacked a pyrenoid in its vegetative cells and required organic compounds for growth. The other was similar to Cg. elongatum (P. A. Dang.) Francé and “Cg.”acus Nayal, but with slightly smaller vegetative cells. Their molecular phylogeny was also studied based on combined 18S rRNA, RUBISCO LSU (rbcL), and P700 chl a‐apoprotein A2 (psaB) gene sequences. Both species were separated from Chlorogonium emend., Gungnir Nakada and Rusalka Nakada, which were formerly assigned to Chlorogonium. They were accordingly assigned to new genera, Tabris Nakada gen. nov. and Hamakko (Hk.) Nakada gen. nov. as T. heimii (Bourr.) Nakada comb. nov. and Hk. caudatus Nakada sp. nov., respectively. Tabris is differentiated from other genera of fusiform green flagellates by its vegetative cells, which only have two apical contractile vacuoles and lack a pyrenoid in the chloroplast. Hamakko, on the other hand, is distinguishable by the fact that its pyrenoids in vegetative cells are penetrated by flattened thylakoid lamellae.     

Taxonomic revision of the Agaraceae with a description of Neoagarum gen. nov. and reinstatement of Thalassiophyllum

We confirmed the monophyly of the Agaraceae based on phylogenetic analyses of six mitochondrial and six chloroplast gene sequences from Agarum, Costaria, Dictyoneurum, and Thalassiophyllum species, as well as representative species from other laminarialean families. However, the genus Agarum was paraphyletic, comprising two independent clades, A. clathratum/A. turneri and A. fimbriatum/A. oharaense. The latter clade was genetically most closely related to Dictyoneurum spp., and morphologically, the species shared a flattened stipe bearing fimbriae (potential secondary haptera) in the mid‐ to upper portion. The phylogenetic position of Thalassiophyllum differed between the two datasets: in the chloroplast gene phylogeny, Thalassiophyllum was included in the A. clathratum/A. turneri clade, but in the mitochondrial gene phylogeny, it formed an independent clade at the base of the Agaraceae, the same position it took in the phylogeny when the data from both genomes were combined despite a larger number of bp being contributed by the chloroplast gene sequences. Considering the remarkable morphological differences between Thalassiophyllum and other Agaraceae, and the molecular support, we conclude that Thalassiophyllum should be reinstated as an independent genus. Dictyoneurum reticulatum was morphologically distinguishable from D. californicum due to its midrib, but because of their close genetic relationship, further investigations are needed to clarify species‐level taxonomy. In summary, we propose the establishment of a new genus Neoagarum to accommodate A. fimbriatum and A. oharanese and the reinstatement of the genus Thalassiophyllum.