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The large population sizes and high dispersal potential of microbes suggests that a given microbial species should be found in all suitable habitats worldwide. Consequently, microbes should not exhibit the kinds of biogeographic patterns seen in macroorganisms. This paradigm is challenged by a growing list of exotic microbes with biogeographic disjunctions that instead promotes microbial dispersal as inherently limited. We sampled water bodies in the United States and compiled records from the literature and public databases to characterize the distribution of the freshwater planktonic diatom, Discostella asterocostata (Xie, Lin, and Cai) Houk and Klee. Discostella asterocostata was thought to be restricted to the Far East, but we report its presence in ecologically similar water bodies across the eastern United States. Populations from the U.S. and China are indistinguishable morphometrically, suggesting they may be recently separated—a hypothesis supported by paleolimnological data, which support an introduction of D. asterocostata into the U.S. as recently as the mid-1980s. The overlapping distributions of D. asterocostata and invasive carp species, in both their native and nonnative ranges, highlighted Asian carp as a possible vector for introduction of the diatom in the U.S. The existence of exotic diatoms underscores natural constraints on microbial dispersal, resulting in biogeographic distributions that can be upended through human activity.

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of S. marinoi grown in a common garden. Our experiment included eight genotypes from source populations spanning the Baltic Sea salinity cline. Changes in gene expression revealed a shared response to salinity across genotypes, where low salinities induced profound changes in cellular metabolism, including upregulation of carbon fixation and storage compound biosynthesis, and increased nutrient demand and oxidative stress. Nevertheless, the genotype effect overshadowed the salinity effect, as genotypes differed significantly in their response, both in the magnitude and direction of gene expression. Intraspecific differences included regulation of transcription and translation, nitrogen metabolism, cell signaling, and aerobic respiration. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond and adapt to environmental change.

Public health laboratories obtain whole-genome sequences of pathogens to confirm outbreaks and identify transmission routes. Here, we present tinselR, an open-source and user-friendly application for visualization and annotation of relatedness among pathogens with phylogenetic trees. By combining annotation and phylogenetics, we simplify one critical step in the pathogen analysis workflow.

We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.

Summary Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework.We constructed a time‐calibrated, 11‐gene, 1151‐taxon phylogeny of diatoms – the most inclusive diatom species tree to date. We used this phylogeny, together with a comprehensive inventory of first–last occurrences of Cenozoic fossil diatoms, to estimate ranges of expected species richness, diversification and its variation through time and across lineages.Diversification rates varied with life history traits. Although anisogamous lineages diversified faster than oogamous ones, this increase was restricted to a nested clade with active motility in the vegetative cells.We propose that the evolution of motility in vegetative cells, following an earlier transition from oogamy to anisogamy, facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence across a variety of novel habitats. Together, these contributed to a species radiation that gave rise to the majority of present‐day diatom diversity.

How diatoms respond to fluctuations in osmotic pressure is important from both ecological and applied perspectives. It is well known that osmotic stress affects photosynthesis and can result in the accumulation of compounds desirable in pharmaceutical and alternative fuel industries. Gene expression responses to osmotic stress have been studied in short-term trials, but it is unclear whether the same mechanisms are recruited during long-term acclimation. We used RNA-seq to study the genome-wide transcription patterns in the euryhaline diatom, Cyclotella cryptica, following long-term acclimation to salinity that spanned the natural range of fresh to oceanic water. Long-term acclimated C. cryptica exhibited induced synthesis or repressed degradation of the osmolytes glycine betaine, taurine and dimethylsulfoniopropionate (DMSP). Although changes in proline concentration is one of the main responses in short-term osmotic stress, we did not detect a transcriptional change in proline biosynthetic pathways in our long-term experiment. Expression of membrane transporters showed a general tendency for increased import of potassium and export of sodium, consistent with the electrochemical gradients and dependence on co-transported molecules. Our results show substantial between-genotype differences in growth and gene expression reaction norms and suggest that the regulation of proline synthesis important in short-term osmotic stress might not be maintained in long-term acclimation. Further examination using time-course gene expression experiments, metabolomics and genetic validation of gene functions would reinforce patterns inferred from RNA-seq data.

Climate warming impacts ecosystems through multiple interacting pathways, including via direct thermal responses of individual taxa and the combined responses of closely interacting species. In this study we examined how warming and infection by an oomycete parasite affect the dominant zooplankter of Russia’s Lake Baikal, the endemic cold-adapted stenotherm Epischura baikalensis (Copepoda). We used a combination of laboratory experiments, long-term monitoring data and population modeling. Experiments showed large thermal mismatch between host and parasite, with strong negative effects of warm temperatures on E. baikalensis survival and reproduction and a negative synergistic effect of Saprolegnia infection. However, Saprolegnia infection had an unexpected positive effect on E. baikalensis reproductive output, which may be consistent with fecundity compensation by infected females. Long-term monitoring data showed that Saprolegnia infections were most common during the warmest periods of the year and that infected individuals tended to accumulate in deep water. Population models, parameterized with experimental and literature data, correctly predicted the timing of Saprolegnia epizootics, but overestimated the negative effect of warming on E.baikalensis populations. Models suggest that diel vertical migration may allow E. baikalensis to escape the negative effects of increasing temperatures and parasitism and enable E. baikalensis to persist as Lake Baikal warms. Our results contribute to understanding of how multiple interacting stressors affect warming pelagic ecosystems of cold lakes and oceans and show that the population-level consequences of thermal mismatch between hosts and parasites can vary seasonally, interannual and spatially.

PREMISE OF THE STUDY Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of "apochloritic" diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic Nitzschia suggests a single loss of photosynthesis in their common ancestor, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. METHODS We analyzed genes from the nuclear, plastid, and mitochondrial genomes for a broad set of taxa to test whether photosynthesis was lost one or multiple times in Bacillariales. We also sequenced and characterized the plastid genome of a nonphotosynthetic Nitzschia species. KEY RESULTS Phylogenetic analyses showed that genes from all three genetic compartments either supported or failed to reject monophyly of apochloritic Nitzschia species, consistent with a single loss of photosynthesis in this group. The plastid genomes of two apochloritic Nitzschia are highly similar in all respects, indicating streamlining of the plastid genome before the split of these two species. CONCLUSIONS A better understanding of the phylogeny and ecology of apochloritic Nitzschia, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group of diatoms. Finally, some habitats host diverse communities of co-occurring nonphotosynthetic diatoms, reflecting resource abundance or resource partitioning in ecologically favorable habitats.

Many clades that span the marine-freshwater boundary are disproportionately more diverse in the younger, shorter-lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate-associated (benthic) lineages are several-fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden-state speciation and extinction models we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton-benthos contrast was also consistent with state-dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric, and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.

Loss of photosynthesis is a common and often repeated trajectory in nearly all major groups of photosynthetic eukaryotes. One small subset of ‘apochloritic’ diatoms in the genus Nitzschia have lost their ability to photosynthesize and require extracellular carbon for growth. Similar to other secondarily nonphotosynthetic taxa, apochloritic diatoms maintain colorless plastids with highly reduced plastid genomes. Although the narrow taxonomic breadth of apochloritic diatoms suggests a single loss of photosynthesis in the common ancestor of these species, previous phylogenetic analyses suggested that photosynthesis was lost multiple times. We sequenced additional phylogenetic markers from the nuclear and mitochondrial genomes for a larger set of taxa and found that the best trees for datasets representing all three genetic compartments provided low to moderate support for monophyly of apochloritic Nitzschia, consistent with a single loss of photosynthesis in diatoms. We sequenced the plastid genome of one apochloritic species and found that it was highly similar in all respects to the plastid genome of another apochloritic Nitzschia species, indicating that streamlining of the plastid genome had completed prior to the split of these two species. Finally, it is increasingly clear that some locales host relatively large numbers apochloritic Nitzschia species that span the phylogenetic diversity of the group, indicating that these species co-exist because of resource abundance or resource partitioning in ecologically favorable habitats. A better understanding of the phylogeny and ecology of this group, together with emerging genomic resources, will help identify the factors that have driven and maintained the loss of photosynthesis in this group, a rare event in diatoms.

Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively lower Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a metabarcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some have had more time to diversify than others. However, species richness was largely independent of genus age, suggesting that disparities in species richness among genera were better explained by variation in rates of speciation and extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.

Using a broadly sampled, time-calibrated phylogeny of Cyanobacteria and photosynthetic eukaryotes, Sanchez-Baracaldo et al. (1) report that the most-recent common ancestor (MRCA) of Archaeplastida likely inhabited a low-salinity (freshwater) habitat, providing an advance on a longstanding debate about the ecological context for the origin of plastids (2). The freshwater ancestry for Cyanobacteria and Archaeplastida was based on reconstructions that assumed equal transition rates among marine, brackish, and freshwater habitats (1), which likely oversimplified the 2.5-billion-year history of these groups. We relaxed the assumption of a single transition rate by fitting a model with additional parameters for independent transition rates among marine, brackish, and freshwater habitats. This model provided a … [↵][1]1To whom correspondence should be addressed. Email: tnakov{at}uark.edu. [1]: #xref-corresp-1-1

Premise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively higher Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a meta-barcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some had more time to diversify than others. Still, species richness was only weakly correlated with genus age, highlighting variation in rates of speciation and/or extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.

The diatom genus Entomoneis is known from the benthos and plankton of marine, brackish, and freshwaters. Entomoneis includes diatoms with a bilobate keel elevated above the valve surface, a sigmoid canal raphe, and numerous girdle bands. Owing mostly to the scarcity of molecular data for a diverse set of species, the phylogeny of Entomoneis has not been investigated in depth. The few previous studies that included Entomoneis were focused on broader questions and the available data were from a small number of either unidentified Entomoneis or well-known species (e.g., E. paludosa). Since the first description of new species combining both molecular and morphological characters (E. tenera), we have continued to cultivate and investigate Entomoneis in the plankton of the Adriatic Sea. Combined multigene phylogeny (SSU rDNA sequences, rbcL, and psbC genes) and morphological observations (LM, SEM and TEM) revealed six new Entomoneis species supported by phylogenetic and morphological data: E. pusilla, E. gracilis, E. vilicicii, E. infula, E. adriatica, and E. umbratica. The most important morphological features for species delineation were cell shape, the degree and mode of torsion, valve apices, the appearance and structure of the transition between keel and valve body, the ultrastructure and the shape of the girdle bands, and the arrangement and density of perforations along the valve and valvocopulae. Our results highlight the underappreciated diversity of Entomoneis and call for a more in-depth morphological and molecular investigation of this genus especially in planktonic habitats.

We characterized the evolutionary history of growth form (solitary-colonial) and its interaction with species' habitat (planktonic-benthic) across a multi-gene phylogeny encompassing a broad sample of the order-level diversity of diatoms. We treated these characters broadly, modeling the evolution of aggregation of cells into a colony irrespective of the way aggregation is achieved, and relating the growth form to a broad concept of niche location: in the plankton or benthos. The results showed that habitat shifts are rare implying conservatism in niche location at the level of large clades. On the other hand, the evolutionary history of growth form is more dynamic with evolutionary rates that vary across the tree. Analyses of a possible interaction revealed that shifts in growth form are independent of habitat and that traversing between habitats does not hinge upon species' growth form. Our findings help to fill a gap in the understanding of diatom niche and growth form macroevolution and contribute toward a platform for the comparative study of the mechanisms underlying diatom species and functional diversity.

We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was...

Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages.

Strategies for optimizing fitness in a dilute, competitive, and changing environment are thought to underlie cell size evolution in phytoplankton. Support for cell size as an adaptive trait comes from observed shifts in cell size distributions in response to environmental cues at geologic time scales and across environmental gradients. Physicochemical differences between marine and freshwater environments are thought to drive diatom cell size evolution in opposite directions, with larger sizes conferring benefits in marine habitats and small sizes in freshwater habitats. We tested this hypothesis in one lineage of diatoms, the Thalassiosirales, which spans marine and freshwater habitats, has a well-supported phylogeny, and whose members are relatively homogenous with respect to cell shape, growth habit, and habitat preference. A comparison of adaptive models for cell size evolution supports the hypothesis for different cell size optima between marine and freshwater habitats. The data are best explained by a model with separate selective regimes for marine and freshwater lineages. However, a scenario of stabilizing selection towards a single global cell size optimum irrespective of habitat cannot be completely discounted. Understanding of the processes that shape cell size evolution in phytoplankton would benefit from models that incorporate phylogeny, intrinsic properties of species (e.g., cell shape, colony formation, and motility), and more specific habitat characterization, as well as genetic and genomic properties of different phytoplankton groups.

The ocellate and pseudocellate diatoms in the Eupodiscaceae and Biddulphiaceae (respectively) are common inhabitants of the marine littoral (and plankton zone) with a rich fossil history making them important components of marine stratigraphic studies and good candidates for molecular dating work. These diatoms are important for un-derstanding the phylogeny of the diatoms as a whole, as molecular phylogenies have blurred the traditional distinction between the pennate and multipolar non-pennate diatoms. However, the convoluted taxonomic history of these groups has the potential to disrupt both stratigraphic and molecular dating studies. Although efforts have been made to examine frustule morphology of several ocellate and pseudocellate diatoms and develop a morphological scheme to define genera, very little work has been done to determine how these groups are interrelated. In this study, we use nuclear and chloroplast molecular markers to construct a phylogeny of a diverse sampling of Eupodiscaceae and Biddulphiaceae taxa. The ocellus-bearing taxa (Eupodiscaceae) are monophyletic, and thus the ocellus may be a useful character in delimiting the Eupodiscaceae, the Biddulphiaceae are polyphyletic and scattered across a number of lineages of multipolar non-pennate diatoms. Hypothesis testing aimed at assessing the likeliness of several morphology based hypotheses against the molecular data highlights uncertainty in both types of data. We present evidence that there are monophyletic genera within both the Biddulphiaceae and Eupodiscaceae, and recommend the taxa within the Odontella mobilensis/sinensis/regia clade be transferred to a new genus: Trieres Ashworth & Theriot.

Lake Ohrid is an important biodiversity hotspot, including diatom diversity and endemism. Numerous, putatively endemic diatom species have been described from the lake, alongside reports of relict taxa otherwise known only as fossils from European Neogene deposits. Diploneis Ehrenberg ex Cleve is considered to be one of the species-rich genera in Lake Ohrid. This study presents a detailed account of Diploneis in Lake Ohrid, providing additional information on some of the infrequently recorded taxa. In addition, sediment core samples from Lake Ohrid were used to provide an historical account of some of the more abundant taxa and to determine the morphological similarity between fossil (core samples) and extant populations. To this end, detailed light and scanning electron microscope observations were carried out to ascertain the identity and describe the morphological variation of Diploneis taxa. As a result, 15 Diploneis taxa from Lake Ohrid are reported with four potentially endemic species described as ...

Although the plastid genomes of diatoms maintain a conserved architecture and core gene set, considerable variation about this core theme exists and can be traced to several different processes. Gene duplication, pseudogenization, and loss, as well as intracellular transfer of genes to the nuclear genome, have all contributed to variation in gene content among diatom species. In addition, some noncoding sequences have highly restricted phylogenetic distributions that suggest a recent foreign origin. We sequenced the plastid genome of the marine diatom, Toxarium undulatum, and found that the genome contains three genes (chlB, chlL, and chlN) involved in light-independent chlorophyll a biosynthesis that were not previously known from diatoms. Phylogenetic and syntenic data suggest that these genes were differentially retained in this one lineage as they were repeatedly lost from most other diatoms. Unique among diatoms and other heterokont algae sequenced so far, the genome also contains a large group II intron within an otherwise intact psaA gene. Although the intron is most similar to one in the plastid-encoded psaA gene of some green algae, high sequence divergence between the diatom and green algal introns rules out recent shared ancestry. We conclude that the psaA intron was likely introduced into the plastid genome of T. undulatum, or some earlier ancestor, by horizontal transfer from an unknown donor. This genome further highlights the myriad processes driving variation in gene and intron content in the plastid genomes of diatoms, one of the world's foremost primary producers.

The Surirellales and Rhopalodiales are large, widespread, and morphologically diverse groups of raphid pennate diatoms (Bacillariphyta) whose raphe, a structure that facilitates active motility, opens internally into a siliceous canal. We collected 202 representatives of the lineage and sequenced genes from the nuclear, plastid, and mitochondrial genomes to infer phylogenetic relationships as a basis for comparative study of ecology and morphological evolution as well as reclassification. The lineage was ancestrally marine, and we report the first evidence for a ‘stepping stone’ model of marine–freshwater transitions in which freshwater invasions were preceded by adaptation to intermediate brackish habitats. Phylogenetic comparative analyses also showed that the shift from an apical (e.g., Entomoneis) to transapical major axis of development (e.g., Surirella) did not have to proceed through subcircular intermediate forms (i.e., Campylodiscus). Rather, subcircular forms evolved both within lineages with longer apical axis or longer transapical axis. We also used the inferred phylogeny as a basis for genus-level reclassification of the lineage. Campylodiscus now includes the fastuosoid members of Surirella and Campylodiscus, but excludes other marine Campylodiscus which are now classified as Coronia. Surirella includes the Surirella striatula clade, Surirella Pinnatae group, and species formerly classified as Cymatopleura. We resurrected the genus Iconella to accommodate Stenopterobia and the robustoid members of Surirella and Campylodiscus. We broadened Epithemia to include members of the paraphyletic genus Rhopalodia. Finally, we discuss the challenges of constructing a classification that best leverages available phylogenetic data, while minimizing disruption to the research community and recognizing practical considerations stemming from the slow rate of progress on systematic studies of understudied organisms.

A new Rhoicosphenia species, R. tenuis Levkov & Nakov is described from Lake Ohrid. It is characterized by its narrow linear valves (valve width up to 4.5 μm), which differentiate it from the otherwise similar R. curvata. This species has an ultrastructure typical of the rest of the freshwater representatives of the genus Rhoicosphenia. The concave valve possesses the typical raphe system, while the convex valve has a reduced raphe system. A well developed pseudoseptum is present at the poles, and both valves possess an apical pore field at their foot pole. According to valve morphology and ultrastructure, R. tenuis is closer to R. curvatathan to Rhoicosphenia macedonica, another species described from Lake Ohrid

SUMMARY The name Navicula hasta is regularly applied to large, heavily silicified Navicula specimens with lanceolate outlines, protracted ends, and relatively coarse, radiate, and lineolate striae that are more irregularly spaced around the central area. As such, Navicula hasta has been reported from numerous localities such as brackish water fossil sediments, oligotrophic ancient lakes and postglacial lakes. When the data for distribution of Navicula hasta are summarized, this species appears to be geographically and temporally widespread with a broad range of ecologic tolerances. Published reports for size range show that diatomists during the last century have differing concepts of the species starting with the disagreement between the protologue and one of the figures given by Pantocsek. Furthermore, an informal ‘type’ of Navicula hasta reported in 1980 does not match the protologue and is not unambiguously based on material Pantocsek had in his hands when describing his new species. We studied published reports of Navicula hasta and investigated material reported to contain Navicula hasta and its allies from the type locality (Kopecz), one of the fossil deposits reported to contain N. hasta (Bodos) and from ancient and other younger lakes worldwide. From our analyses, we document the variation and underappreciated diversity within the Navicula hasta group and set the stage for formal recognition of new species in subsequent papers. Herein, we formally propose a lectotype from among the original illustrations and designate an epitype for Navicula hasta based on Pantocsek's Kopecz material. Additionally, two new species, Navicula krenneri spec. nov. and Navicula pseudohasta spec. nov. are described and a lectotype of Navicula superhasta Lange-Bertalot and Metzeltin is proposed.

Lake Prespa belongs to the group of ancient lakes. By subterranean channels it is connected with Lake Ohrid. In the past two decades, Lake Prespa has been characterized by a decrease of its water level and an increased cultural and natural eutrophication. In this period, very few ecological studies were performed, based mainly on composition and biomass of the phytoplankton community. From June 2002 to May 2003 analyses of 18 physical and chemical parameters and composition of benthic diatoms were performed on 12 sampling sites of Lake Macro Prespa. About 300 diatom taxa were identified in the lake. Relative abundances were calculated by counting 200 diatom valves, and 143 diatom taxa had abundances of more than 1 % in at least one sampling site. Deep benthic communities were dominated by Cyclotella ocellata and Diploneis mauleri, while in the littoral region these communities were dominated by small Navicula sensu lato species. For statistical analyses, the 17 most abundant diatom taxa (> 1 % in total abundance) were used. Contrarily to the expectations, TP had a negligible influence on diatom community structure. The main environmental factors controlling species distribution and abundances were ammonium and metallic cations (Cu, Mn, K) and, secondarily, dissolved oxygen and Secchi depth, as inferred from both correlation and multivariate (CCA) analysis.

Ohrid and Prespa lakes belong to a group of ancient lakes having an age of ca. 3 million years. Both lakes are characterized by a highly diverse diatom flora and endemism. Recent studies on the diatom flora led to the description of several new taxa. Observations on taxa closely related to the Sellaphora bacillum (Ehrenberg) Mereschkowsky complex showed the presence of two previously undescribed species. In this study, two new species, Sellaphora krsticii sp. nov. and Sellaphora perbacilloides sp. nov., are described. Furthermore a new combination, Sellaphora bacilloides (Hustedt) Levkov, Krstic & Nakov comb. nov. is proposed.

The subgenus DECUSSATA R.M. Patrick was recently elevated to generic status as Decussata (R.M. Patrick) H. Lange-Bertalot & Metzeltin in Lange-Bertalot (2000. Iconographica Diatomologica, 9, 670–673) to accommodate Navicula placenta Ehrenberg and its allies. The description of Decussata is based on characteristics of the valve: solitary cells, flat, broadly elliptic valves with various ends, and areolae with circular foramina arranged in regular quincunx patterns crossing at 60°-80°. A collection from Cedar Hills Sand Prairie in Black Hawk Co., Iowa (U.S.A.), had abundant live Decussata placenta (Ehrenberg) Lange Bertalot & Metzeltin in Lange-Bertalot, the generitype, and a collection from near Prava Reka, Macedonia, had numerous specimens of Decussata hexagona (Torka) Lange-Bertalot. These collections permitted a first observation of living Decussata and a detailed study of their valve and cingulum ultrastructure. Based on this material we place Decussata in the Order Mastogloiales and Family Mastogloiac...

The diatom microflora collected from glacial lakes, peat-bogs, springs, streams, rivers and wetlands on 352 localities on Shara Mountain and 124 localities on Nidze Mountain, Macedonia, was investigated between 1995 and 2003. A total of 418 taxa from 76 genera, were identified. The taxa are predominantly oligotrophic or dystrophic. Total floristic similarity between the neighbouring mountain sytems (100 km apart) was only 22.74%. One of the sites has been influenced by glaciation, while the other contained habitats that served as glacial refugia. Taxa from the refugia are highly similar to the those of the ancient Ohrid and Prespa lakes in Macedonia. The morphological features and taxomic position of 11 taxa are discussed.

Previous analyses of single diatom chloroplast protein-encoded genes recovered results highly incongruent with both traditional phylogenies and phylogenies derived from the nuclear encoded small subunit (SSU) gene. Our analysis here of six individual chloroplast genes (atpB, psaA, psaB, psbA, psbC and rbcL) obtained similar anomalous results. However, phylogenetic noise in these genes did not appear to be correlated, and their concatenation appeared to effectively sum their collective signal. We empirically demonstrated the value of combining phylogenetic information profiling, partitioned Bremer support and entropy analysis in examining the utility of various partitions in phylogenetic analysis. Noise was low in the 1st and 2nd codon positions, but so was signal. Conversely, high noise levels in the 3rd codon position was accompanied by high signal. Perhaps counterintuitively, simple exclusion experiments demonstrated this was especially true at deeper nodes where the 3rd codon position contributed most to a result congruent with morphology and SSU (and the total evidence tree here). Correlated with our empirical findings, probability of correct signal (derived from information profiling) increased and the statistical significance of substitutional saturation decreased as data were aggregated. In this regard, the aggregated 3rd codon position performed as well or better than more slowly evolving sites. Simply put, direct methods of noise removal (elimination of fast-evolving sites) disproportionately removed signal. Information profiling and partitioned Bremer support suggest that addition of chloroplast data will rapidly improve our understanding of the diatom phylogeny, but conversely also illustrate that some parts of the diatom tree are likely to remain recalcitrant to addition of molecular data. The methods based on information profiling have been criticized for their numerous assumptions and parameter estimates and the fact that they are based on quartets of taxa. Our empirical results support theoretical arguments that the simplifying assumptions made in these methods are robust to “real-life” situations.

A lectotype and isolectotype for Navicula budayana Pantocsek = Diploneis budayana (Pantocsek) Hustedt, Navicula ostracodarum Pantocsek = Diploneis ostracodarum (Pantocsek) Jovanovska, Nakov & Levkov and Navicula praeclara Pantocsek = Diploneis praeclara (Pantocsek) Cleve-Euler from Kopecz, Neogene fossil deposits in Romania have been made. Typification for each species was based on Pantocsek’s original images and material deposited at the Hungarian Natural History Museum (BP). Unfortunately, the type slides for Diploneis budayana , D. ostracodarum and D. praeclara were lost or destroyed during the course of World War II. Therefore, authentic material from the type locality Kopecz at BP was used to designate the lectotypes for these three species. Detailed LM and SEM observations have been assigned for each taxon, in order to ascertain the variation in valve morphology. Taxonomic descriptions and comments are made for each species. Typification of taxa described by Pantocsek would potentially affect further stratigraphic, comparative or molecular phylogenetic work not just for Tertiary floras but for Recent floras as well. In particular, studies concerning comparisons of these species between localities, such as Lake Ohrid, will greatly benefit from this work. The outcome of such studies will shed light on the evolutionary and biogeographic history of diatoms in the context of geologic events on the Balkan Peninsula.

Diatoms are often referred to one of six structural groups. The two major groups are centrics and pennates, and each is further subdivided. Centrics are either radial centrics or (bi-)multipolar (or simply polar) centrics. The former typically are circular and lack any prominent structures which may be paired or multiply arranged so as to give some sort of visually prominent polarity to the cell. Polar centrics have such structures and often have elongate outlines. Pennates are either araphid pennates or raphid pennates, depending on whether or not they possess a raphe. These structural groups have been arranged differently through time, whether the source of data was morphology and the method of analysis noncanonical or whether the data were molecular and analyzed by more formal methods. Both congruence and conflict between these various approaches have been claimed. Diatomists have rejected traditional views because they conflict with molecular results in some instances, and yet reject molecular results because they conflict with morphologically based results in others. Such conflicts are rarely formally tested. Here, we formally test several traditional hypotheses and a recent molecular-based reclassification of diatoms against a three-gene combined molecular dataset. Centrics are strongly rejected as monophyletic. However, some relationships could not be rejected. Monophyly of araphids is not statistically worse than the best tree (in which araphids are recovered as a grade). Monophyly of radial centrics and of polar centrics cannot be rejected, nor can a competing hypothesis (in which radial centrics are a grade and the Thalassiosirales are part of that grade). This last result is congruent with complex morphological characters and is an example of the value of formally testing conflict and congruence between datasets, and of the potential value of formal phylogenetic analysis of diatom morphology.

Cyclotella is a commonly encountered name in the diatom literature. The name is attached, however, to a historically vaguely defined and polyphyletic genus whose taxonomy and systematics remain muddled despite numerous taxonomic treatments. One recent chapter in this history concerns species informally known as the “Cyclotella comta” group, which have one or more rimoportulae on the valve face. These species were grouped into a new genus, Puncticulata, a name that has been applied inconsistently since its introduction. The name Puncticulata eventually was shown to be illegitimate, as some species had once been classified within Handmannia, which had nomenclatural priority. An inventory of names within Cyclotella sensu lato revealed that both Puncticulata and Handmannia are later synonyms of Lindavia. We identify a rimoportula positioned on the valve face as a synapomorphy for a group of taxa with the Cyclotella comta and C. ocellata bauplans (including Pliocaenicus), and accordingly, we transfer taxa with this synapomorphy into the genus Lindavia.