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Edward C Theriot - One of the best experts on this subject based on the ideXlab platform.
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PHYLOGENETIC ANALYSIS OF THE MARINE AND FRESHWATER THALAS‐SIOSIROID DIATOMS
Journal of Phycology, 2020Co-Authors: Matthew L Julius, Edward C TheriotAbstract:The thalassiosiroid centric diatoms are distinguished by at least one synapomorphy, the strutted process or fultoportula. Variously classified as a family (Thalassiosiraceae) or an order (Thalassiosirales) among centric diatoms, it is generally conceded that the group of several hundred fossil and living species is monophyletic as a whole. There are two ecological groups of thalassiosiroids, marine and freshwater. It has been hypothesized, based on an ecletic, non-rigorous, evolutionary taxonomy perspective that both the marine and freshwater ecological groups are also monophyletic, but this hypothesis has never been tested in a rigorous framework. Likewise, the freshwater thalassiosiroid species have been grouped into several genera and subgenera using an evolutionary taxonomic approach, but these hypotheses have not fully been tested using cladistic analysis. Focusing mainly on freshwater species, but including at least one representative of each marine genus and one representative from each of several proposed subgeneric groupings of the genus Thalassiosira, we scored morphological characters for fossil and living marine and freshwater Thalassiosiraceae to test these hypotheses. Our cladistic results provide strong support for monophyly for the freshwater group, but it seems unlikely that the marine group is monophyletic. The cladistic results are corroborated to greater or lesser degrees by the fossil record. The implications for evolution in the group and for taxon sampling in molecular studies we are conducting will be discussed.
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conserved gene order and expanded inverted repeats characterize plastid genomes of Thalassiosirales
PLOS ONE, 2014Co-Authors: Jamal S M Sabir, Mengjie Yu, Matt P Ashworth, Nabih A Baeshen, Mohammad N Baeshen, Ahmed Bahieldin, Edward C Theriot, Robert K JansenAbstract:Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: Thalassiosira weissflogii, Roundia cardiophora, Cyclotella sp. WC03_2, Cyclotella sp. L04_2, and three additional non-Thalassiosirales species Chaetoceros simplex, Cerataulina daemon, and Rhizosolenia imbricata. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in Thalassiosira oceanica. Cyclotella nana, Thalassiosira weissflogii and Roundia cardiophora share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two Cyclotella species by a single inversion. The genes ilvB and ilvH are missing in all six diatom plastid genomes except for Cerataulina daemon, suggesting an independent gain of these genes in this species. The acpP1 gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, psaE, psaI, psaM, are missing in Rhizosolenia imbricata, which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes.
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Using phylogeny to model cell size evolution in marine and freshwater diatoms
Limnology and Oceanography, 2014Co-Authors: Teofil Nakov, Edward C Theriot, Andrew J AlversonAbstract: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.
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Status of the pursuit of the diatom phylogeny : Are traditional views and new molecular paradigms really that different?
The Diatom World, 2011Co-Authors: Edward C Theriot, Matt P Ashworth, Teofil Nakov, Elizabeth C. Ruck, Robert K JansenAbstract: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.
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application of phylogenetic principles to testing evolutionary scenarios a comment on kaczmarska et al molecular phylogeny of selected members of the order Thalassiosirales bacillariophyta and evolution of the fultoportula
Journal of Phycology, 2008Co-Authors: Edward C TheriotAbstract:: While rigorous techniques have usually been used to generate phylogenetic trees from molecular data, morphological analysis has sometimes been more informal. A recent example was a study of the evolution of the fultoportula in the diatom order Thalassiosirales (Kaczmarska et al. 2006). Phylogeny was inferred using modern phylogenetic principles applied to nuclear SSU rDNA sequences, but inferences about morphological character evolution were made using noncanonical reasoning and evolutionary scenario building. The preferred hypothesis posited that marginal fultoportulae evolved from the marginal ridge of Lithodesmiales. A related hypothesis suggested that fultoportulae in the valve center were not homologous with those near the valve margin. Shared symplesiomorphies, shared homoplasies, gaps in the fossil record, and subtle morphological differences between central- and marginal-area fultoportulae were offered as the primary evidence for these scenarios. The literature has demonstrated such arguments to be either irrelevant or logically weaker than inferences made under the tests of similarity, conjunction, and congruence. Five prior hypotheses about the origin and evolution of the fultoportula were examined in this study using these tests. The hypothesis that the areola evolved into the multistrutted process, which evolved into the fultoportula, was best supported.
Andrew J Alverson - One of the best experts on this subject based on the ideXlab platform.
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Timing marine–freshwater transitions in the diatom order Thalassiosirales
Paleobiology, 2020Co-Authors: Andrew J AlversonAbstract:With species found throughout both marine and fresh waters, the diatom order Thalassiosirales is one of the most phylogenetically and ecologically diverse lineages of planktonic diatoms. A clear understanding of the timescale of Thalassiosirales evolution would provide novel insights into the rates and patterns of species diversification associated with major habitat shifts, as well as provide valuable context for understanding the age and evolutionary history of the model species, Cyclotella nana (¼Thalassiosira pseudonana). The freshwater fossil record for Thalassiosirales is extensive, well characterized, and generally supportive of a Miocene origin for the major freshwater lineages. The marine record is, by comparison, more sparse and in many cases, unverified. The discovery of freshwater thalassiosiroids in Eocene sediments pushed the freshwater fossil record considerably further back in time, highlighting an apparent gap of some 30 million years. An alternative interpretation is that the Miocene and Eocene reports represent competing hypotheses. In the absence of additional independent and decisive fossil data, I explored the relative plausibility of these two scenarios with Bayesian relaxed molecular clock methods under a range of fossil calibration schemes. Although I found no support for the Eocene fossil dates, the two major freshwater colonization events probably occurred much earlier than previously thought—as early as the Paleocene for Cyclotella, followed by an Eocene origin for the cyclostephanoid lineage. Much of the extant freshwater diversity in both lineages traces back to the Miocene, however, giving the impression of a single Miocene origin. Efforts to infer the timescale of Thalassiosirales evolution more accurately would benefit from a systematic reevaluation of the marine fossil record and formal integration of fossil species into existing phylogenetic hypotheses.
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a phylogenetic re definition of the diatom genus bacterosira Thalassiosirales bacillariophyta with the transfer of thalassiosira constricta based on morphological and molecular characters
Phytotaxa, 2016Co-Authors: Joon Sang Park, Andrew J AlversonAbstract:Thalassiosira constricta was first described from Tromso in the Norwegian Sea. The species was placed in the large and morphologically diverse genus Thalassiosira based on the presence of classical features of that genus, including the formation of chains held together by β-chitin threads extruded from central fultoportulae. We recently discovered T . constricta in Korean coastal waters near Sinsi Island. Detailed morphological analyses revealed the following cell wall features: i) cells arranged in chains, with adjacent cells directly abutting one another or distinctly separated and linked by β-chitin threads extruded from a central cluster of 0–14 fultoportulae, ii) delicate, biseriate poroid areolae along radial ribs on the valve face and coarse loculate areolae on the valve mantle, iii) a cingulum structure consisting of finely perforated valvocoupla and copula and scratched pleurae, iv) distinct antiligula on the valve, v) a single ring of marginal fultoportulae, vi) one rimoportula located within the ring of marginal fultoportulae, vii) fultoportulae with internal extensions that lack opercula, and viii) fultoportulate with four fully exposed satellite pores, each in a depression and surrounded by a defined cowling. Phylogenetic analysis of nuclear and plastid markers revealed a sister relationship with Bacterosira bathyomphala . Based on these findings, we transfer T . constricta to Bacterosira as Bacterosira constricta comb . nov . and offer an emended the description of the genus Bacterosira , which appears to be one of only a few monophyletic marine genera in Thalassiosirales.
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Using phylogeny to model cell size evolution in marine and freshwater diatoms
Limnology and Oceanography, 2014Co-Authors: Teofil Nakov, Edward C Theriot, Andrew J AlversonAbstract: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.
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timing marine freshwater transitions in the diatom order Thalassiosirales
Paleobiology, 2014Co-Authors: Andrew J AlversonAbstract:With species found throughout both marine and fresh waters, the diatom order Thalassiosirales is one of the most phylogenetically and ecologically diverse lineages of planktonic diatoms. A clear understanding of the timescale of Thalassiosirales evolution would provide novel insights into the rates and patterns of species diversification associated with major habitat shifts, as well as provide valuable context for understanding the age and evolutionary history of the model species, Cyclotella nana (= Thalassiosira pseudonana ). The freshwater fossil record for Thalassiosirales is extensive, well characterized, and generally supportive of a Miocene origin for the major freshwater lineages. The marine record is, by comparison, more sparse and in many cases, unverified. The discovery of freshwater thalassiosiroids in Eocene sediments pushed the freshwater fossil record considerably further back in time, highlighting an apparent gap of some 30 million years. An alternative interpretation is that the Miocene and Eocene reports represent competing hypotheses. In the absence of additional independent and decisive fossil data, I explored the relative plausibility of these two scenarios with Bayesian relaxed molecular clock methods under a range of fossil calibration schemes. Although I found no support for the Eocene fossil dates, the two major freshwater colonization events probably occurred much earlier than previously thought—as early as the Paleocene for Cyclotella , followed by an Eocene origin for the cyclostephanoid lineage. Much of the extant freshwater diversity in both lineages traces back to the Miocene, however, giving the impression of a single Miocene origin. Efforts to infer the timescale of Thalassiosirales evolution more accurately would benefit from a systematic reevaluation of the marine fossil record and formal integration of fossil species into existing phylogenetic hypotheses.
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Strong purifying selection in the silicon transporters of marine and freshwater diatoms
Limnology and Oceanography, 2007Co-Authors: Andrew J AlversonAbstract: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.
Irena Kaczmarska - One of the best experts on this subject based on the ideXlab platform.
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species rich meta communities of the diatom order Thalassiosirales in the arctic and northern atlantic ocean
Journal of Plankton Research, 2016Co-Authors: Ian A Luddington, Connie Lovejoy, Irena KaczmarskaAbstract:The marine planktonic diatom order Thalassiosirales are used as climate proxies with reported characteristic temperate and Polar species. However, a systematic analysis of the genetic variability and species limits is lacking. Here, we combined molecular and morphological approaches to identify Thalassiosirales from 7 Beaufort Sea sea-ice samples and 27 water-column samples collected from across the Canadian Arctic at different times of the year and the Scotia Shelf, North Atlantic in spring. While many species were found in both oceanic regions, there were two distinct Thalassiosirales communities: the first from sea ice and ice-influenced water columns and the second Arctic late summer and North Atlantic spring communities. Thalassiosirales formed genetically coherent Boreal-Arctic meta-communities, inclusive of intra-specific variants. Genetic similarity between the Arctic and North Atlantic meta-communities would be reinforced by counter-clockwise dominant surface current systems. Local patterns of spatial and temporal distributions of planktonic thalassiosiroids were best explained by latitudinal gradients and phosphate and silicate concentrations, suggesting that climate-mediated changes in Arctic and North Atlantic hydrography could have a marked effect on species distribution. Our analysis also revealed a need for taxonomic revision of several species complexes reported from the region before they can be reliably used as bio-indicators.
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Distance and Character-Based Evaluation of the V4 Region of the 18S rRNA Gene for the Identification of Diatoms (Bacillariophyceae)
PLOS ONE, 2012Co-Authors: Ian A Luddington, Irena Kaczmarska, Connie LovejoyAbstract:DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p-distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis.
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molecular phylogeny of selected members of the order Thalassiosirales bacillariophyta and evolution of the fultoportula1
Journal of Phycology, 2006Co-Authors: Irena Kaczmarska, Margaret J Beaton, Anita C Benoit, Linda K MedlinAbstract:Recent phylogenetic studies of the diatoms indicate that members of the order Thalassiosirales occupy an interesting position in the diatom evolutionary tree. Despite their radial morphology and scaly auxospores, they are consistently recovered in molecular analyses as a member of subdivision Bacillariophytina and a sister clade to non-fultoportulate and non-radial lithodesmioids. This study included 46 species from nine traditionally accepted extant genera, and analyzed 43 nuclear small subunit (SSU) rRNA sequences in parallel with a survey of the variation in fultoportula structure. Three possible scenarios leading to the evolution of the fultoportula are discussed in the context of molecular and morphological similarities between the examined Thalassiosirales and their SSU rRNA sister clade Lithodesmiales. We speculate that the fultoportula might be derived by a modification of either a cribrum in an areola (fultoportula within an areola), or structures similar to marginal ridges now seen in lithodesmioids around a cluster of poroids (fultoportula in a tube), or finally, that the central fultoportula may have an origin different from the marginal fultoportulae. Our data confirm that fultoportula-bearing diatoms constitute a natural phylogenetic group. The families Thalassiosiraceae, Skeletonemaceae, and Stephanodiscaceae and the genus Thalassiosira Cleve were unexpectedly found to be paraphyletic. Further, Cyclotella Kutz. and Stephanodiscus Ehr. may not be closely related and some species of these genera are more closely allied to other species of Thalassiosira. The generitype, T. nordenskioeldii, is embedded within a large poorly structured cluster of species that includes several members of Thalassiosira, Planktoniella sol, Minidiscus trioculatus, and two members of Stephanodiscus. An emendment of the order Lithodesmiales and the family Lauderiaceae are proposed.
Linda K Medlin - One of the best experts on this subject based on the ideXlab platform.
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Mini Review: The evoltution of the diatoms and a report on the current status of their classification
2020Co-Authors: Linda K MedlinAbstract:This mini review describes the newest classification of diatoms based on their evolution, which was obtained from molecular data. Because centric forms were found earlier in the geological record it is assumed that the pennate diatoms evolved from the centric forms and 3 classes were described: the centric diatoms, the araphid pennate and the raphid pennate diatoms. However, molecular data showed that the centric diatoms are most likely paraphyletic and the diatoms are now divided into two groups: Clade 1 contains the radial centric diatoms and Clade 2 contains two subClades: the first sub-Clade contains the bipolar centrics and the Thalassiosirales and the second sub-Clade contains the pennate diatoms to which many of the microphytobenthos species belong. These Clades and additional morphological support for this new taxonomy is discussed in this mini review.
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molecular phylogeny of selected members of the order Thalassiosirales bacillariophyta and evolution of the fultoportula1
Journal of Phycology, 2006Co-Authors: Irena Kaczmarska, Margaret J Beaton, Anita C Benoit, Linda K MedlinAbstract:Recent phylogenetic studies of the diatoms indicate that members of the order Thalassiosirales occupy an interesting position in the diatom evolutionary tree. Despite their radial morphology and scaly auxospores, they are consistently recovered in molecular analyses as a member of subdivision Bacillariophytina and a sister clade to non-fultoportulate and non-radial lithodesmioids. This study included 46 species from nine traditionally accepted extant genera, and analyzed 43 nuclear small subunit (SSU) rRNA sequences in parallel with a survey of the variation in fultoportula structure. Three possible scenarios leading to the evolution of the fultoportula are discussed in the context of molecular and morphological similarities between the examined Thalassiosirales and their SSU rRNA sister clade Lithodesmiales. We speculate that the fultoportula might be derived by a modification of either a cribrum in an areola (fultoportula within an areola), or structures similar to marginal ridges now seen in lithodesmioids around a cluster of poroids (fultoportula in a tube), or finally, that the central fultoportula may have an origin different from the marginal fultoportulae. Our data confirm that fultoportula-bearing diatoms constitute a natural phylogenetic group. The families Thalassiosiraceae, Skeletonemaceae, and Stephanodiscaceae and the genus Thalassiosira Cleve were unexpectedly found to be paraphyletic. Further, Cyclotella Kutz. and Stephanodiscus Ehr. may not be closely related and some species of these genera are more closely allied to other species of Thalassiosira. The generitype, T. nordenskioeldii, is embedded within a large poorly structured cluster of species that includes several members of Thalassiosira, Planktoniella sol, Minidiscus trioculatus, and two members of Stephanodiscus. An emendment of the order Lithodesmiales and the family Lauderiaceae are proposed.
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Evolution of the Diatoms (Bacillariophyta): IV. A Reconstruction of Their Age from Small Subunit rRNA Coding Regions and the Fossil Record
Molecular Phylogenetics and Evolution, 1996Co-Authors: Wiebe H. C. F. Kooistra, Linda K MedlinAbstract:Abstract Small subunit ribosomal RNA (ssu rRNA) coding regions from 30 diatoms, 3 oomycetes, and 6 pelagophytes were used to construct linearized trees, maximum-likelihood trees, and neighbor-joining trees inferred from both unweighted and weighted distances. Stochastic accumulation of sequence substitutions among the diatoms was assessed with relative rate tests. Pennate diatoms evolved relatively slowly but within the limits set by a stochastic model; centric diatoms exceeded those limits. A rate distribution test was devised to identify those taxa showing an aberrant distribution of base substitutions within the ssu rRNA coding region. First appearance dates of diatom taxa from the fossil record were regressed against their corresponding branch lengths to infer the average and earliest possible age for the origin of the diatoms, the pennate diatoms, and the centric diatom order Thalassiosirales. Our most lenient age estimate (based on the median-evolving diatom taxon in the maximum-likelihood tree or on the average branch length in a linearized tree) suggests that their average age is approximately 164–166 Ma, which is close to their earliest fossil record. Both calculations suggest that it is unlikely that diatoms existed prior to 238–266 Ma. Rate variation among the diatoms' ssu rRNA coding regions and uncertainties associated with the origin of extant taxa in the fossil record contribute significantly to the variation in age estimates obtained. Different evolutionary models and the exclusion of fast or slow evolving taxa did not significantly affect age estimates; however, the inclusion of aberrantly fast evolving taxa did. Our molecular clock calibrations indicate that the rRNA coding regions in the diatoms are evolving at approximately 1% per 18 to 26 Ma, which is the fastest substitution rate reported in any pro- or eukaryotic group of organisms to date.
Robert K Jansen - One of the best experts on this subject based on the ideXlab platform.
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conserved gene order and expanded inverted repeats characterize plastid genomes of Thalassiosirales
PLOS ONE, 2014Co-Authors: Jamal S M Sabir, Mengjie Yu, Matt P Ashworth, Nabih A Baeshen, Mohammad N Baeshen, Ahmed Bahieldin, Edward C Theriot, Robert K JansenAbstract:Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: Thalassiosira weissflogii, Roundia cardiophora, Cyclotella sp. WC03_2, Cyclotella sp. L04_2, and three additional non-Thalassiosirales species Chaetoceros simplex, Cerataulina daemon, and Rhizosolenia imbricata. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in Thalassiosira oceanica. Cyclotella nana, Thalassiosira weissflogii and Roundia cardiophora share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two Cyclotella species by a single inversion. The genes ilvB and ilvH are missing in all six diatom plastid genomes except for Cerataulina daemon, suggesting an independent gain of these genes in this species. The acpP1 gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, psaE, psaI, psaM, are missing in Rhizosolenia imbricata, which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes.
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Status of the pursuit of the diatom phylogeny : Are traditional views and new molecular paradigms really that different?
The Diatom World, 2011Co-Authors: Edward C Theriot, Matt P Ashworth, Teofil Nakov, Elizabeth C. Ruck, Robert K JansenAbstract: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.
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Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms
Molecular Phylogenetics and Evolution, 2007Co-Authors: Andrew J Alverson, Robert K Jansen, Edward C TheriotAbstract:Abstract 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.