Molecular phylogeny and evolution of phenotype in silica‐scaled chrysophyte genus Mallomonas

The evolution of phenotypes is highly understudied in protists, due to the dearth of morphological characters, missing fossil record, and/or unresolved phylogeny in the majority of taxa. The chrysophyte genus Mallomonas (Stramenopiles) forms species‐specific silica scales with extraordinary diversity of their ornamentation. In this paper, we molecularly characterized three additional species to provide an updated phylogeny of 43 species, and combined this with evaluations of 24 morphological traits. Using phylogenetic comparative methods, we evaluated phylogenetic signal in traits, reconstructed the trait evolution, and compared the overall phylogenetic and morphological diversity. The majority of traits showed strong phylogenetic signal and mostly dynamic evolution. Phylogenetic relatedness was often reflected by the phenotypic similarity. Both V‐rib and dome are very conservative structures that are presumably involved in precise scale overlap and bristle attachment, respectively. Based on modern species, it seems the dome firstly appeared on apical and/or caudal scales, and only later emerged on body scales. Bristle was presumably present in the common ancestor and gradually elongated ever since. However, most other morphological traits readily changed during the evolution of Mallomonas.     

Taxonomic significance of asymmetrical helmet and lance bristles in the genus Mallomonas (Synurophyceae) and their discovery in Eocene lake sediments

Complex bristle types formed by species in the genus Mallomonas include those with helmet or lance-shaped apices. The ornamentation on each side of the helmet has been thought to be equivalent or symmetrical, whereas on a lance-shaped bristle an expanded portion folds over one side of the shaft to form an asymmetrical structure. We describe, for the first time, helmet bristles with a distinctly asymmetrical design, also formed by the folding of a siliceous membrane over one side of the helmet. We postulate that the asymmetrical helmet represents a structure that combines the formation of a symmetrical helmet and a lance-shaped design on the same bristle. Further, we report structurally similar asymmetrical helmet bristles, lance-shaped bristles and scales that are unambiguously assigned to Mallomonas asmundiae in Middle Eocene sediments from a maar lake in northern Canada, supporting the hypothesis that scale and bristle morphology in the Synurophyceae has undergone extensive prolonged evolutionary stasis. Given differences in scale morphology and the presence of asymmetrical helmet bristles, we transfer the North American endemic Mallomonas acaroides var. muskokana to the rank of species. Further, we formally describe Mallomonas dispar and M. lancea, fossil species with asymmetrical helmet bristles and lance-shaped bristles, respectively. The taxonomic and biogeographic significance of asymmetrical and lance-bearing bristles is discussed.     

Phylogenetic study of benthic, spine-bearing prorocentroids, including Prorocentrum fukuyoi sp. nov.

Species of prorocentroid dinoflagellates are common in marine benthic sediment and epibenthic habitats, as well as in planktonic habitats. Marine planktonic prorocentroids typically possess a small spine in the apical region. In this study, we describe a new, potentially widely distributed benthic species of Prorocentrum, P. fukuyoi sp. nov., from tidal sand habitats in several sites in Australia and from central Japan. This species was found to possess an apical spine or flange and was sister species to P. emarginatum. We analyzed the phylogeny of the group including this new species, based on large subunit (LSU) rDNA sequences. The genus contained a high level of divergence in LSU rDNA, in some cases among sister taxa. P. fukuyoi and P. emarginatum were found to be most closely related to a clade of generally planktonic taxa. Several morphological features may constitute more informative synapomorphies than habitat in distinguishing clades of prorocentroid species.     

Mallomonas jejuensis sp. nov. (Synurophyceae) from Jeju Island,South Korea

A new species of Mallomonas (Synurophyceae), Mallomonas jejuensis sp. nov., has been found in Jeju Island, South Korea. This species is placed in the series Mangoferae (section Torquatae) because it has a collar of elongated domed scales, domeless body scales, rear scales with spines and all scales ornamented with papillae. The morphological characteristics of the scales and bristle of the new species are described by EM and compared with those reported for the other species of the series Mangoferae.     

SEPERATION OF MALLOMONAS DUERRSCHMIDTIAE SP. NOV. FROM M. CRASSISQUAMA AND M. PSEUDOCORONATA: IMPLICATIONS FOR PALEOLIMNOLOGICAL RESEARCH1

A new species, Mallomonas duerrschmidtiae, with characteristics common to both Mallomonas crassisquama (Asmund) Fott and Mallomonas pseudocoronata Prescott, is described from acidic lakes low in specific conductance and total phosphorus concentration. Characteristics of scales, bristles and spines serve to separate the three taxa. The length and area of scales of M. duerrschmidtiae are significantly larger than those of M. crassisquama but smaller than those of M. pseudocoronata. Although the anterior submarginal ribs of scales of M. duerrschmidtiae may become extended to form short wings, the scales lack the large forward projecting anterior wings characteristic of scales of M. pseudocoronata. Features of the dome and junction between the arms of the V-rib and anterior submarginal ribs also serve to distinguish between the three species. Cells of M. duerrschmidtiae also possess long, smooth and thick spines on their posterior scales and lack helmet bristles. M. duerrschmidtiae has different maxima along pH, temperature, specific conductance, total phosphorus and seasonal gradients than either M. crassisquama or M. pseudocoronata. Discriminant analysis, based on nine morphological characters, was used to successfully classify body scales of the three species. The importance of M. duerrschmidtiae as a bioindicator in future lake monitoring and paleolimnological inference studies is discussed.     

Combining geometric morphometrics,molecular phylogeny,and micropaleontology to assess evolutionary patterns in Mallomonas (Synurophyceae: Heterokontophyta)

Synurophytes, also known as scaled chrysophytes, are ecologically important algae that produce an array of siliceous structures upon which their taxonomy is based. Despite occupying a key position within the photosynthetic heterokonts, the evolutionary history of synurophytes remains poorly constrained. Here, modern and Middle Eocene siliceous scales of the morphotaxon Mallomonas insignis are used as a model to investigate synurophyte evolutionary patterns. Structural details of scale morphology were examined comparatively with scanning electron microscopy and scored for geometric morphometric analyses to assess the stability of shape characters. Although consistent size differences exist (modern scales are larger than Eocene counterparts), the populations cannot be differentiated on the basis of shape or microstructural detail, implying considerable evolutionary stasis in scale morphology. A time‐calibrated relaxed molecular clock analysis using a three‐gene concatenated data set (27 strains) suggests that the M. insignis lineage predates the available fossil record, having diverged from closest congeneric taxa in the Cretaceous (≥94 Ma). However, the molecular analysis also implies that considerable genetic variability is present within several morphotaxa of Mallomonas, implying that substantial genetic variability has arisen despite the retention of uniform scale morphologies, and resulting in the widespread occurrence of cryptic taxa. Results from the synurophyte lineage are consistent with the notion of protracted ghost ranges (>10 Ma) implied by the molecular phylogenies of other algal groups, together pointing to the paucity of the fossil record of these organisms on these timescales.     

Scale Biogenesis in Synurophycean Protists: Phylogenetic Implications

The Synurophyceae is a class of golden-brown, freshwater, photosynthetic flagellates with a world-wide distribution. A well-developed taxonomy exists where genera and species are distinguished by colony or cell morphology or by the siliceous scales that cover the cells. However, phylogenetic relationships within the class are poorly understood, and incongruous taxonomic concepts occur. This study reviews scale morphology from field-collected samples and controlled culturing experiments as well as from studies of scale biogenesis. The information is used to identify homologous silicification surfaces among taxa and to document the diversity of the resulting scale structures. Thirty-two character states are coded into 11 characters in a cladistic analysis of 13 pivotal taxa. Colonial species are emphasized. One most-parsimonious phylogenetic tree is found (HI = 0, CI = 1). Synura lapponica is shown to be most closely related to Tessellaria volvocina. S. sphagnicola emerges at the base of the tree. Mallomonas caudata and the S. petersenii clade emerge from within Sectio Synura. Chrysodidymus synuroideus appears as an ancestral taxon in the Synura spinosa-like clade (i.e., Series Spinosae). The poorly understood developmental bases for some characters, especially secondary scale structures, are identified and may help focus future research.     

Phylogenetic placement of <Emphasis Type="Italic">Marasmiellus juniperinus</Emphasis>

Recent collections and the type specimen of Marasmiellus juniperinus, the type species of the genus, were examined. Phylogenetic placement, based on ribosomal large subunit (LSU) and internally transcribed spacer (ITS) sequences, is within the lentinuloid clade, nested among Gymnopus taxa. This placement dictates genus name usage and phylogenetic position of other putative species of Marasmiellus. The mating system is tetrapolar.     

Two new species of Mallomonas (Synurophyceae) from the Ocala National Forest, Florida, U.S.A.

Two new species of Mallomonas, M. ocalensis and M. caerula , are described from a clearwater, acidic and oligotrophic waterbody in the Ocala National Forest, Florida, U.S.A. Mallomonas ocalensis , in the Series Doignonianae of the Section Torquatae, consists of relatively small cells with scales that have a series of parallel shield ribs with alternating thicknesses, collar scales with very short bristles and posterior scales with small protruding spines. Mallomonas ocalensis is most similar to Mallomonas dickii , but is distinguished from the latter species based on the highly variable thicknesses of the shield ribs and significantly larger scales. Mallomonas caerula , in the Series Mallomonas of the Section Mallomonas, consists of relatively large cells that bear large domed and dorneless scales, and long, robust and ribbed bristles. Bristles with and without helmets can be found. The shield, especially the distal portion, and the posterior flange of scales consists of series of more or less parallel ribs. Mallomonas caerula appears to be most closely related to Mallomonas acaroides var. acaroides and Mallomonas acaroides var. muskokana , but can be distinguished from the latter taxa on the basis of scale type, scale structure and bristle morphology. Both new species were found in the plankton and surface sediments of Blue Sink Pond.     

Records of chrysophytes with siliceous scales (Mallomonadaceae and Paraphysomonadaceae) from Finnish inland waters

Seventy-three taxa of silica-scaled chrysophytes were found with LM and TEM in 264 samples from 141 Finnish water bodies, including the genera Mallomonas (40 taxa), Synura (9), Chrysosphaerella (3), Spiniferomonas (8) and Paraphysomonas (13). More than half of the taxa are recorded for the first time from Finland and five (Mallomonas actinoloma v. actinoloma, M. favosa, M. mangofera f. gracilis, M. scrobiculata and Spiniferomonas serrata) are new to Europe. Most taxa are illustrated with TEM micrographs and the taxonomy of some interesting species is discussed in detail. The seasonal occurrence of the commonest species is described.     

Mallomonas alphaphora (Chrysophyceae), a new species from Western Australia

A new species ofMallomonas, M. alphaphora (Chrysophyceae), was found in freshwater ponds in the Perth region, Western Australia. It is distinguished from other species ofMallomonas by its very distinctive scale and bristle morphology and is placed in a new section,Alphaphorae, of the genusMallomonas. Dedicated to Prof. DrL. Geitler on the occasion of the 90th anniversary of his birthday.     

Multigene phylogeny of Synura (Synurophyceae) and descriptions of four new species based on morphological and DNA evidence

We used phylogenetic analyses based on multiple gene sequences (partial nr SSU and LSU rDNA, partial pt LSU rDNA, psaA and rbcL) from 148 strains (including three outgroups) and scale ultrastructure to examine phylogenetic relationships among species of the colonial genera Synura and Tessellaria. The phylogenetic tree based on the combined dataset was congruent with ultrastructural characteristics of the scales. Synura was divided into three major clades, two including species in section Synura, and one representing section Peterseniae. One clade, consisting of seven strains of S. uvella (section Synura), diverged at the base of the genus. The second clade consisted of the remaining species belonging to the section Synura. The third clade, containing organisms in the section Peterseniae and characterized by scales possessing a keel, was monophyletic with strong support values. Based on our findings, S. uvella needs to be in a separate section from other spine-bearing species, and we therefore propose new sectional ranks; Synura, Peterseniae, Curtispinae (presence of body scales with slender spines, tubular scales and caudal scales). We further propose four new species based on phylogenetic analyses and unique scale characters: S. longitubularis sp. nov., S. sungminbooi sp. nov., S. soroconopea sp. nov. and S. lanceolata sp. nov. Lastly, we propose a new genus name, Neotessella, to replace the invalid use of the name Tessellaria.     

A further phylogenetic study of the heterotrophic dinoflagellate genus, Protoperidinium (Dinophyceae) based on small and large subunit ribosomal RNA gene sequences

The heterotrophic marine dinoflagellate genus Protoperidinium is the largest genus in the Dinophyceae. Previously, we reported on the intrageneric and intergeneric phylogenetic relationships of 10 species of Protoperidinium, from four sections, based on small subunit (SSU) rDNA sequences. The present paper reports on the impact of data from an additional 5 species and, therefore, an additional two sections, using the SSU rDNA data, but now also incorporating sequence data from the large subunit (LSU) rDNA. These sequences, in isolation and in combination, were used to reconstruct the evolutionary history of the genus. The LSU rDNA trees support a monophyletic genus, but the phylogenetic position within the Dinophyceae remains ambiguous. The SSU, LSU and SSU + LSU rDNA phylogenies support monophyly in the sections Avellana, Divergentia, Oceanica and Protoperidinium, but the section Conica is paraphyletic. Therefore, the concept of discrete taxonomic sections based on the shape of 1′ plate and 2a plate is upheld by molecular phylogeny. Furthermore, the section Oceanica is indicated as having an early divergence from other groups within the genus. The sections Avellana and Excentrica and a clade combining the sections Divergentia/Protoperidinium derived from Conica‐type dinoflagellates independently. Analysis of the LSU rDNA data resulted in the same phylogeny as that obtained using SSU rDNA data and, with increased taxon sampling, including members of new sections, a clearer idea of the evolution of morphological features within the genus Protoperidinium was obtained. Intraspecific variation was found in Protoperidinium conicum (Gran) Balech, Protoperidinium excentricum (Paulsen) Balech and Protoperidinium pellucidum Bergh based on SSU rDNA data and also in Protoperidinium claudicans (Paulsen) Balech, P. conicum and Protoperidinium denticulatum (Gran et Braarud) Balech based on LSU rDNA sequences. The common occurrence of base pair substitutions in P. conicum is indicative of the presence of cryptic species.     

A new peronosporomycete, <Emphasis Type="Italic">Halioticida noduliformans</Emphasis> gen. et sp. nov., isolated from white nodules in the abalone <Emphasis Type="Italic">Haliotis</Emphasis> spp. from Japan

Four strains belonging to the Peronosporomycetes (formerly Oomycetes) were isolated from white nodules found on the mantle of three species of abalone. In artificial seawater, the four isolates formed fragments such as in the genus Haliphthoros, but the protoplasm constriction was weaker, and fragments were longer, with smaller spaces between them, than those of Haliphthoros. The four strains form one or more discharge tubes from each zoosporangium. The four strains were similar, but not identical, to the genus Haliphthoros based on morphological characteristics. As a result, the four isolates were classified in a new genus and species, Halioticida noduliformans gen. et sp. nov. Phylogenetic analysis of the D1/D2 region of the large subunit ribosomal RNA gene (LSU rDNA) was performed, and the four isolates showed 100%–99.8% concordance. In the phylogenetic tree, the four isolates were not classified in the subclass Peronosporomycetidae, Saprolegniomycetidae, or Rhipidiomycetidae. However, the four isolates formed a new clade with genera Haliphthoros and Halocrusticida in Peronosporomycetes. Within this new clade, the four isolates, Haliphthoros spp. and Halocrusticida spp., were grouped in their respective independent subclades. These results showed that these were the new genus and species from the morphological characteristics.     

Molecular Phylogeny and Taxonomy of the Genus Minidiscus (Bacillariophyceae), with Description of Mediolabrus gen. nov

The genus Minidiscus comprises a group of ecologically-important and globally-distributed planktonic diatoms that are characterized by their small cell size, high mantle and processes more or less concentrated in the valve center. Monoclonal strains were established from collections along the Chinese coast. In the phylogenetic analyses inferred from a LSU and SSU dataset, six Minidiscus species clustered into two well-supported clades. The first clade was located within a larger clade formed mainly by Thalassiosira taxa, and the second clade appeared as sister to a clade comprising the genus Skeletonema. Hence, presently known Minidiscus do not form a monophyletic clade, but rather make up a phenotypic grouping. Based on the morphology of the type species, M. trioculatus, as well as morphological characters of all taxa in the clade with M. trioculatus, Minidiscus is characterized by having fultoportula(e) in the valve center or sub-centered close to a single rimoportula, and the cells are usually cylindrical. Mediolabrus gen. nov. is proposed to accommodate species in the second clade. The main difference between Minidiscus and Mediolabrus is the type of process found in the valve (sub-)center, with fultoportula(e) close to a rimoportula in the former, and only a single rimoportula in the latter. According to the above criteria, previously described Minidiscus taxa were re-examined, and either retained in Minidiscus or transferred to Mediolabrus.     

Freshwater scaled chrysophytes,heliozoa and thaumatomonad flagellates from Edo State,Nigeria

A total of nine silica-scaled chrysophytes (Chrysophyceae: two species each in Spiniferomonas and Paraphysomonas; Synurophyceae: five Mallomonas species), 16 heliozoa, and two scaled flagellates were recorded from 19 samples collected from Edo State, Nigeria, over a period covering both dry and rainy seasons in 2006–2007. Identifications were based on transmission electron microscopy. Eleven are new records for Africa, including a new species of Mallomonas, M. cribridomus. Also observed were two siliceous scaled colourless free-living thaumatomonad flagellates, Thaumatomastix nigeriensis and Gyromitus limax, the latter also a new record for Africa.     

Mallomonas wujekii (Synurophyceae), a new species from Florida, U.S.A.

A new species of Mallomonas, M. wujekii sp. nov., belonging to the Series Tonsuratae is described from a dilute, acidic locality in Florida, U.S.A. Bristle bearing domed scales are restricted to the anterior end, and scales are orientated with their longitudinal axes at a 60° to 90° angle with the longitudinal axis of the cell. Cells have three types of scales, domed anterior scales, domeless body scales and spined posterior scales. All scales possess papillae that are restricted to the shield and have one rib positioned on each end of the posterior flange. The new species is believed to be most closely related to Mallomonas tonsurata and M. galeiformis . The combination of characters of the bristles is unique among taxa of Mallomonas .     

PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA1

Previous studies using the nuclear SSU rDNA and partial LSU rDNA have demonstrated that the euglenoid loricate taxa form a monophyletic clade within the photosynthetic euglenoid lineage. It was unclear, however, whether the loricate genera Trachelomonas and Strombomonas were monophyletic. In order to determine the relationships among the loricate taxa, SSU and LSU nuclear rDNA sequences were obtained for eight Strombomonas and 25 Trachelomonas strains and combined in a multigene phylogenetic analysis. Conserved regions of the aligned data set were used to generate maximum‐likelihood (ML) and Bayesian phylogenies. Both methods recovered a strongly supported monophyletic loricate clade with Strombomonas and Trachelomonas species separated into two sister clades. Taxa in the genus Strombomonas sorted into three subclades. Within the genus Trachelomonas, five strongly supported subclades were recovered in all analyses. Key morphological features could be attributed to each of the subclades, with the major separation being that all of the spine‐bearing taxa were located in two sister subclades, while the more rounded, spineless taxa formed the remaining three subclades. The separation of genera and subclades was supported by 42 distinct molecular signatures (33 in Trachelomonas and nine in Strombomonas). The morphological and molecular data supported the retention of Trachelomonas and Strombomonas as separate loricate genera.     

Exploring Cryptic Diversity and Distribution Patterns in the Mallomonas kalinae/rasilis Species Complex with a Description of a New Taxon—Mallomonas furtiva sp. nov.

A complex of closely related Mallomonas taxa belonging to the section Papillosae, M. kalinae ?ezá?ová and M. rasilis Dürrschmidt, has been studied in detail by molecular and morphometric methods. Our investigations uncovered the existence of a new species found in water bodies in Vietnam, which we describe here as Mallomonas furtiva sp. nov. This taxon is morphologically very similar to M. kalinae , from which it differs by minute, but statistically significant morphological differences on the structure of silica scales. Indeed, the principal component analysis of morphological traits measured on silica scales significantly separates all three species in the complex. Mallomonas kalinae and M . furtiva differ by number of papillae on the shield and the dome, as well as by the scale sizes. Likewise, Mallomonas rasilis and M. furtiva are primarily differentiated by the absence of submarginal anterior ribs on silica scales of the former species. Phylogenetic analyses showed that Mallomonas furtiva is closely related to M . kalinae , with which it formed a highly supported lineage. Distribution patterns of all three studied taxa are further discussed.