Diatom Lineages Research Articles

Pre-Neogene non-marine diatom biochronology with new data from the late Eocene Florissant Formation of Colorado, USA

Studies of the non-marine diatom assemblages from Eocene deposits in North America extend the fossil record of a number of extant freshwater diatom lineages. These and other accounts show that the earliest documented appearances of non-marine diatoms consisted of 7 genera from late Cretaceous deposits, followed by 36 more from the Eocene, and 4 additional genera from Oligocene to early Miocene localities. A total of 47 diatom genera, 45 of which are extant, therefore, are known from pre-Neogene (>23.8 Ma) non-marine deposits. The chronological extension of these first-occurrences of genera has implications for terrestrial diatom biostratigraphy, paleoclimate, and diatom phylogenetic studies. An overview of the pre-Neogene non-marine diatom biochronology from published records and original work provides the geologic and geographic context for the more current findings. Two geologic range charts synthesize the data from the pre-Neogene non-marine (fresh and brackish water) diatom floras from the 9 published localities, supplemented by additional findings from a recent floristics study of the Florissant site in Colorado. These charts allow easy comparison of the timing, floral composition, and taxon-richness at the genus level and higher for the 9 sites. Among the pre-Neogene sites discussed here are early and middle Eocene deposits in Canada and middle Eocene deposits in Idaho andWyoming that provide evidence of an early pulse in the post-Cretaceous radiation of freshwater diatoms. The survey of the fossil diatoms from lake sediments of the Florissant Formation in Colorado showed that this deposit contains the most diverse (genus-rich) early freshwater diatom flora on record. This late Eocene flora suggests a later pulse in freshwater diatom radiation during pre-Neogene time that contributed to the rich taxonomic diversity of today. The Florissant fossil diatom investigations yield a total of 33 freshwater diatom genera. This number exceeds by 20 genera any other single known non-marine diatom-bearing Eocene and older deposit. The Florissant diatom flora consists of taxa with decidedly modern affinities, has superior diversity (taxon-richness), and yields the first-reported occurrence in the geologic record of 14 freshwater genera. From the 9 featured pre-Neogene sites, genera of centric, araphid, biraphid, and monoraphid morphologic groups are represented. While the findings of these studies are not inconsistent with the previously predicted timing of the first appearance of the major morphological diatom groups, the actual known fossil record post-dates the presumed timing of such morphological differentiation. Although the first occurrences in these deposits must be treated as apparent first occurrences due to the innate incompleteness of the fossil record, such findings confirm that species of many of the modern non-marine diatom genera had evolved prior to the end of the Eocene. It is anticipated that this synthesis of the pre-Neogene non-marine diatom floras will provide necessary paleontological evidence for interpreting the true geologic ranges of several diatom lineages. This work could facilitate future application of diatoms in biostratigraphic studies of fossil lake beds in hydrologic and climate change studies and in hydrocarbon exploration. Perhaps such data will generate insights to diatom phylogenetics that may lead to a greater understanding of their evolutionary histories. Further research could potentially relate changes in diatom forms to global events that might include climate shifts.

Complete Chloroplast Genome Sequence of Freshwater Araphid Pennate Diatom Alga Synedra acus from Lake Baikal

Complete chloroplast genome of diatom alga Synedra acus possesses canonical quadripartite structure with two inverted repeats containing ribosomal RNA gene loci that separate small and large single-copy regions. Chloroplast genome maps as a circular molecule of 116 251 bp. It encodes 27 tRNAs, three rRNAs, two small RNA genes, and 128 protein-coding genes. Comparison of the genic features across diatom chloroplast genomes reveals the absence of an overlap between atpD and atpF gene coding sequences that is present in other plastid genomes of diatom origin. This feature is a clear synapomorphy of S. acus plastid genome that is likely a result of either relaxed constraints or extensive selection forces acting upon atpF gene. We also characterized nuclear-encoded acyl-carrier protein gene with chloroplastic targeting in S. acus . The transfer of acpp gene into the nuclear host genome is hypothesized to have occurred independently in several lineages of diatoms.

Evolution of the Lake Titicaca basin and its diatom flora over the last ~ 370,000 years

In recent years, deep drilling undertaken as part of the International Continental Drilling Program has generated multiple long lacustrine sedimentary records to reconstruct continental paleoclimate. In many cases, the tectonic and geomorphic history of these basins is under-constrained and poorly known, which affects the interpretation of climate history from geophysical, geochemical, and paleobiotic proxies in the sedimentary record. In addition, non-analog biotic assemblages that reflect evolutionary processes may constrain the reconstruction of past environments. In the drill-core record of Lake Titicaca, spanning the last ~370ka, the diatom stratigraphy reflects both the influence of climate and the long-term evolution of the lake basin and its biota. In the upper part of the drill-core sequence, glacial intervals were deep and dominated by freshwater planktic taxa, and peak interglacial intervals were shallow and dominated by benthic species, some with saline affinities. In the basal sections of the drill-core record, benthic diatoms are dominant in both glacial and interglacial units, with freshwater taxa dominating the glacial strata. This suggests that the ancient lake basin was shallower during intervals of both wet and dry climate, and that the modern deep lake may result from a progressive subsidence and deepening of the basin over time. In addition, morphological evolution in one of the major lineages of planktic diatoms, Cyclostephanos, indicates substantial change in the limnological environment that affected species morphology and may have driven speciation.

Origin and Evolution of the Canal Raphe System in Diatoms

One lineage of pennate diatoms has a slit through the siliceous cell wall, called a "raphe," that functions in motility. Raphid pennate diatoms number in the perhaps tens of thousands of species, with the diversity of raphe forms potentially matching this number. Three lineages-the Bacillariales, Rhopalodiales, and Surirellales-possess a complex and presumably highly derived raphe that is physically separated from the cell interior, most often by a set of siliceous braces. Because the relationship among these three lineages is unclear, the number of origins of the canal raphe system and the homology of it and its constitutive parts among these lineages, is equally unclear. We reconstructed the phylogeny of raphid pennate diatoms and included, for the first time, members of all three canal raphid diatom lineages, and used the phylogeny to test specific hypotheses about the origin of the canal raphe. The canal raphe appears to have evolved twice, once in the common ancestor of Bacillariales and once in the common ancestor of Rhopalodiales and Surirellales, which form a monophyletic group in our analyses. These results recommend careful follow-up morphogenesis studies of the canal raphe in these two lineages to determine the underlying developmental basis for this remarkable case of parallel evolution.

Density dependent expression of a diatom retrotransposon

Retrotransposons are mobile genetic elements that encode for their own replication. Many studies have linked their expression to stress caused by environmental factors. Genome sequencing and EST libraries of the coastal diatom Phaeodactylum tricornutum indicate that this organism has an active copia-like retrotransposon ( Blackbeard), which is variably expressed under different culture conditions. In this study, we induce physiologic stress in P. tricornutum and measure Blackbeard expression over time. However, we find the dominant pattern of Blackbeard expression is related to cell culture density, not short-term physiologic stress. Density dependent expression of a retrotransposon in a diatom provides significant insight into the biogeography of diatom genome mutation. We suggest the shallow coastal ocean, where diatom densities are high, may be the geographic locus for generating genomic diversity in diatom lineages.

Cretaceous Records of Diatom Evolution, Radiation, and Expansion

New information and discussions regarding Mesozoic diatoms presented over the last decade advanced our knowledge of their origin and early history. The oldest confirmed centric diatom fossils are presented here from the earliest Cretaceous, and araphid and raphid pennate diatoms now date from the Late Cretaceous; all from terrestrial sediments. Molecular sequencing helped clarify relationships between diatom lineages, and verify the position of diatoms within the heterokontophytes. Molecular clock approaches estimate a diatom origin near ~135 Ma, but not before 240 Ma. Biomarkers in marine sediments are able to trace a diatom presence back to the mid-Cretaceous, even when siliceous fossils are absent. Seasonal growth and encystment cycles in Late Cretaceous planktonic marine diatoms are now well documented. A biostratigraphic framework for the Late Cretaceous Arctic will aid regional and global biostratigraphic correlations. The systematic position of many new taxonomic groups is now included within a more natural classification scheme that better reflects phylogenetic relationships evident in molecular data and affirmed by biostratigraphic micropaleontology. Discussions regarding the impact of diatoms on several global systems are maturing, as more information becomes available. Four stages in diatom evolution are proposed to explain the history of radiation, extinction, and expansion into new environments and habitats during the Mesozoic.

Strong purifying selection in the silicon transporters of marine and freshwater diatoms

Marine and freshwater diatoms show several important differences in silicon physiology. In addition to containing an order of magnitude more silica in their cell walls, freshwater diatoms also appear to have a less efficient silicic acid uptake mechanism. A novel set of silicon transporters (SITs), encoded by a small gene family, import silicic acid from the environment into the diatom cell. Some evidence suggests that the disparity in uptake efficiency between marine and freshwater diatoms might be attributable to different demands on SITs in the two environments. To test this hypothesis, partial SIT genes were cloned and sequenced from 45 species of Thalassiosirales, a diatom lineage with high diversity in marine and freshwaters. Phylogenetically based codon substitution models were used to test whether SITs from marine and freshwater taxa were under similar selective constraints and whether codons in different structural locations of the protein were under similar functional constraints. Purifying selection is the predominant evolutionary force acting on SITs, irrespective of location in the protein, and differences in efficiency of silicic acid uptake between marine and freshwater diatoms are not due to sequence differences in SITs.

A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution

A molecular phylogenetic dating study, using the PATHd8 program, was conducted to infer the time frame within which the diatoms originated and diversified. A Proterozoic to Early Paleozoic origin was rejected while an Early Triassic (i.e. 250 Ma) to Early Jurassic (i.e. 183 Ma) evolution of the group was supported. However, when considering the inconsistencies in the divergence dates, caused by the somewhat contradictory fixages, the diatoms may have evolved between the late Permian (i.e. 267 Ma) and the Middle Jurassic (i.e. 162 Ma). According to the chronogram of the original PATHd8 analysis, modern “centric diatoms” already existed in the Early Jurassic, “araphid pennates” should be discovered in Lower Cretaceous sediments and the “raphid pennates” are expected to be present in Upper Cretaceous deposits. Uncertainties in the divergence times, due to the disagreements between the fixed calibration dates, suggested that the modern “centrics” may, in fact, have evolved in the Middle Jurassic. However, the evolutionary time spans of the “araphids” and “raphids”, inferred by the original PATHd8 study, were not challenged by the discrepancies among the fixages. The molecular time estimates obtained for the evolution of many diatom lineages were generally between 10 and 65 Ma older than their first paleontlogical appearance dates. Exceptions were Thalassiosirales and Paralia which show “ghost ranges” of approximately 92 million and 84 Ma, respectively. The first appearance of Aulacoseira species in the paleontological record about 48.6 Ma ago is consistent with the time indicated by the molecular dating analysis. However, the chronogram shows that the lineage to which Aulacoseira belongs is approximately 98.7 Ma old, possibly suggesting a “gap” in our knowledge of the fossil record and the taxonomy of the group. Stratigraphic ranges devoid of diatom species, but expected to be present based on molecular dating analyses, may be due to erroneously classified/diagnosed taxa, poor preservation but also because of unreliable molecular timescales/phylogenies. It is suggested that the rRNA timescale, proposed here, can function as a guideline to identify geological time periods and taxa that potentially need additional analyses in order to provide a more complete picture of diatom evolution.

Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms

Salinity imposes a significant barrier to the distribution of many organisms, including diatoms. Diatoms are ancestrally marine, and the number of times they have independently colonized fresh waters and the physiological adaptations that facilitated these transitions remain outstanding questions in diatom evolution. The colonization of fresh waters by diatoms has been compared to “crossing the Rubicon,” implying that successful colonization events are rare, irreversible, and lead to substantial species diversification. To test these hypotheses, we reconstructed the phylogeny of Thalassiosirales, a diatom lineage with high diversity in both marine and fresh waters. We collected ∼5.3 kb of DNA sequence data from the nuclear ( SSU and partial LSU rDNA) and chloroplast genomes ( psbC and rbcL) and reconstructed the phylogeny using parsimony and Bayesian methods. Alternative topology tests strongly reject all previous colonization hypotheses, including monophyly of the predominantly freshwater Stephanodiscaceae. Results showed at least three independent colonizations of fresh waters, and whereas previous accounts of freshwater-to-marine transitions have been discounted, these results provide compelling evidence for as many as three independent re-colonizations of the marine habitat, two of which led to speciation events. This study adds valuable phylogenetic context to previous debate about the nature of the salinity barrier in diatoms and provides compelling evidence that, at least for Thalassiosirales, the salinity barrier might be less formidable than previously thought.

THEORETICAL MORPHOSPACE AND ITS RELATION TO FRESHWATER GOMPHONEMOID–CYMBELLOID DIATOM (BACILLARIOPHYTA) LINEAGES

A number of basic forms in the gomphonemoid–cymbelloid diatom lineages were generated using three-dimensional (3D) parametric equations. The same boundary intervals and differentials for the parameters were used for all forms. From this, the absolute value of the Riemann sum of differences was determined for each variable between pairs of forms. The results were coordinate triplets, and they were plotted in 3D morphospace. Naviculoid forms occupied lower-valued morphospace in contrast to gomphonemoid and cymbelloid morphospaces. However, gomphonemoid and cymbelloid forms occupied different morphospaces. Forms representing Brebissonia occupied morphospace at the base of gomphonemoid forms, but occupied high-valued morphospace with respect to cymbelloid forms. Forms representing Encyonema had lower-valued coordinates compared to other cymbelloid forms. These results support hypotheses of Kociolek and Stoermer that state that naviculoid forms (and in particular, Placoneis) are ancestral to gomphonemoid and cymbelloid forms, Brebissonia is basal to gomphonemoid (but not cymbelloid) forms, and Encyonema is more primitive than other cymbelloid forms. This approach was useful in inferring the relation between theoretical morphospace and hypothesized phylogenies in the gomphonemoid–cymbelloid diatom lineages.

BOLIDOMONAS: A NEW GENUS WITH TWO SPECIES BELONGING TO A NEW ALGAL CLASS, THE BOLIDOPHYCEAE (HETEROKONTA)

A new algal class, the Bolidophyceae (Heterokonta), is described from one genus, Bolidomonas, gen. nov., and two species, Bolidomonas pacifica, sp. nov and Bolidomonas mediterranea, sp. nov., isolated from the equatorial Pacific Ocean and the Mediterranean Sea, respectively. Both species are approximately 1.2 μm in diameter and have two unequal flagella; the longer flagellum bears tubular hairs, whereas the shorter is smooth. The flagellar basal apparatus is restricted to two basal bodies, and there is no transitional helix. Cells are naked, devoid of walls or siliceous structures. The internal cellular organization is simple with a single plastid containing a ring genophore and a girdle lamella, one mitochondrion with tubular cristae, and one Golgi apparatus close to the basal bodies. The Mediterranean and the Pacific species differ in the insertion angle between their flagella and their pattern of swimming, these differences possibly being linked to each other. Analyses of the SSU rDNA gene place the two strains as a sister group to the diatoms. Moreover, pigment analyses confirm this position, as fucoxanthin is found as the major carotenoid in both lineages. These data strongly suggest that the ancestral heterokont that gave rise to the diatom lineage was probably a biflagellated unicell.

Iterative evolution in the diatom genus Rhizosolenia Ehrenberg

Sorhannus, U., Fenster, E. J., Hoffman, A. & Burckle, L. 1991 01 15: Iterative evolution in the diatom genus Rhizosolenia Ehrenberg. Lethaia, Vol. 24, pp. 39–44. Oslo. ISSN 0024–1164. Two late Pliocene planktic diatom lineages, Rhizosolenia sigmoida Sörhannus and Rhizosolenia praebergonii Mukhina, originated consecutively from Rhizosolenia bergonii Peragallo in the eastern equatorial Pacific Ocean. This morphological iteration is closely associated with two successive shifts in the oxygen isotope record (18O/16O) at approximately 3.3 Ma and 2.9 Ma. suggesting that palcoenvironmental factors may have been directly or indirectly involved in initiating these events. Iterative evolution, pseudoextinction. diatom, oxygen isotope record.

Speciation and morphological divergence between two Neogene diatom lineages

Speciation and morphological divergence between two Neogene diatom lineages

Punctuated morphological change in a Neogene diatom lineage: “Local” evolution or migration?

A biometric analysis of the morphology of a late Pliocene planktic diatom lineage, Rhizosolenia praebergonii Mukhina indicates that it appeared abruptly in the fossil record in the Indian Ocean at 2.9 Ma after which it remained virtually unchanged. The observed pattern can be explained by “local”; evolution from the ancestral form Rhizosolenia bergonii, Peragallo or by migration from thecentral Pacific Ocean, where it originated gradually, in conjunction with an accelerated rate of evolution. At present time, it is not possible to conclude which one of the two hypotheses is more likely.