Teofil Nakov

Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae)

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.

Status of the pursuit of the diatom phylogeny : Are traditional views and new molecular paradigms really that different?

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.

Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms.

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.

Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites

Abstract: 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 found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modelling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling, and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values, therefore, seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect.

Diatom assemblages on Shara and Nidze Mountains, Macedonia

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.

Observations of the genus Diploneis from Lake Ohrid, Macedonia

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 new: D. parabudayana, D. rotunda, D. pulchra and D. vetusa. Among the remaining taxa, two endemic species (D. heisingeriae Jurilj and D. tavcharii Jurilj) previously described from Lake Ohrid were observed, along with nine widespread species commonly reported throughout Europe and elsewhere.

RHOICOSPHENIA TENUIS, A NEW DIATOM SPECIES FROM LAKE OHRID

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,

Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)

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.

Comparative analysis of the interaction between habitat and growth form in diatoms

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.

AN EMENDED DESCRIPTION OF DECUSSATA (PATRICK) LANGE-BERTALOT & METZELTIN THAT INCLUDES PROTOPLAST ORGANIZATION AND DETAILED VALVE AND CINGULUM ULTRASTRUCTURE

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 Mastogloiaceae, and provide an emended description of the genus to include details of valve ultrastructure including structure of the cingulum, areolae occluded by internal convex hymenes, and the protoplast characters of a central nucleus, two chloroplaste per cell, one toward each pole, H-shaped in girdle view, variably invaginated in valve view, with a pyrenoid in the plastid bridge.