The Experts below are selected from a list of 234 Experts worldwide ranked by ideXlab platform
Thomas Cavalier-smith - One of the best experts on this subject based on the ideXlab platform.
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Megaphylogeny, Cell Body Plans, Adaptive Zones : Causes and Timing of Eukaryote Basal Radiations
Journal of Eukaryotic Microbiology, 2020Co-Authors: Thomas Cavalier-smithAbstract:ABSTRACT. I discuss eukaryote megaphylogeny and the timing of major innovations in the light of multigene trees and the rarity of marine/freshwater evolutionary transitions. The first eukaryotes were aerobic Phagotrophs, probably substratum-associated heterotrophic amoeboflagellates. The primary eukaryote bifurcation generated unikonts (ancestrally probably unicentriolar, with a conical microtubular [MT] cytoskeleton) and bikonts (ciliary transformation from anterior cilium to ancestrally gliding posterior cilium; cytoskeleton of ventral MT bands). Unikonts diverged into Amoebozoa with anterior cilia, lost when lobosan broad pseudopods evolved for locomotion, and Choanozoa with posterior cilium and filose pseudopods that became unbranched tentacles/microvilli in holozoa and eventually the choanoflagellate/choanocyte collar. Of choanozoan ancestry, animals evolved epithelia, fibroblasts, eggs, and sperm. Fungi and Ichthyosporea evolved walls. Bikonts, ancestrally with ventral grooves, include three adaptively divergent megagroups: Rhizaria (Retaria and Cercozoa, ancestrally reticulofilose soft-surfaced gliding amoeboflagellates), and the originally planktonic Excavata, and the corticates (Plantae and chromalveolates) that suppressed pseudopodia. Excavata evolved cilia-generated feeding currents for grooval ingestion; corticates evolved cortical alveoli and ciliary hairs. Symbiogenetic origin and transfers of chloroplasts stimulated an explosive radiation of corticates—hard to resolve on multigene trees—and opisthokonts, and ensuing Cambrian explosions of animals and protists. Plantae lost Phagotrophy and multiply evolved walls and macroalgae. Apusozoa, with dorsal pellicle and ventral pseudopods, are probably the most divergent bikonts or related to opisthokonts. Eukaryotes probably originated 800–850 My ago. Amoebozoa, Apusozoa, Loukozoa, and Metamonada may be the only extant eukaryote phyla pre-dating Neoproterozoic snowball earth. New subphyla are established for Choanozoa and Loukozoa; Amoebozoa are divided into three revised subphyla, with Variosea transferred into Conosa.
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Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences
Protoplasma, 2018Co-Authors: Thomas Cavalier-smithAbstract:In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing Phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained Phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated ‘endocytosis’ from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans -Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa ), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.
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Scale evolution in Paraphysomonadida (Chrysophyceae): Sequence phylogeny and revised taxonomy of Paraphysomonas, new genus Clathromonas, and 25 new species
European Journal of Protistology, 2014Co-Authors: Josephine Margaret Scoble, Thomas Cavalier-smithAbstract:Heterotrophic chrysomonads of the genus Paraphysomonas are ubiquitous Phagotrophs with diverse silica scale morphology. Over 50 named species have been described by electron microscopy from uncultured environmental samples. Sequence data exist for very few, but the literature reveals misidentification or lumping of most previously sequenced. For critically integrating scale and sequence data, 59 clonal cultures were studied light microscopically, by sequencing 18S ribosomal DNA, and recording scale morphology by transmission electron microscopy. We found strong congruence between variations in scale morphology and rDNA sequences, and unexpectedly deep genetic diversity. We now restrict Paraphysomonas to species with nail-like spine scales, establishing 23 new species and eight subspecies (Paraphysomonadidae). Species having base-plates with dense margins form three distinct subclades; those with a simple margin only two. We move 29 former Paraphysomonas species with basket scales into a new genus, Clathromonas, and describe two new species. Clathromonas belongs to a very distinct rDNA clade (Clathromonadidae fam. n.), possibly distantly sister to Paraphysomonas. Molecular and morphological data are mutually reinforcing; both are needed for evaluating paraphysomonad diversity and confirm excessive past lumping. Former Paraphysomonas species with neither nail-like nor basket scales are here excluded from Paraphysomonas and will be assigned to new genera elsewhere.
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Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution
Biology Direct, 2010Co-Authors: Thomas Cavalier-smithAbstract:Background The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. Results I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of Phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. Conclusion Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others. Reviewers This article was reviewed by Anthony Poole, Gáspár Jékely and Eugene Koonin.
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Molecular phylogeny, scale evolution and taxonomy of centrohelid heliozoa
Molecular Phylogenetics and Evolution, 2007Co-Authors: Thomas Cavalier-smith, Sophie Von Der HeydenAbstract:Heliozoa are ubiquitous, unicellular Phagotrophs with slender radiating axopodia for trapping prey. We sequenced 18S rRNA genes from 35 cultured centrohelid heliozoa (18 studied by electron microscopy) and 28 environmental libraries (18 freshwater, 10 marine), yielding 97 new sequences, this exceeding described species. Phylogenetic analyses show two major groups and that ancestral centrohelids probably had inner plate-like tangential and distinct outer radial silica scales, the latter diverging early into contrasting scale types seen in extant Pterocystis/Choanocystis and Acanthocystis/Raphidiophryidae. Scales were lost at least thrice. Pterocystis is paraphyletic, as was the classical family Acanthocystidae; Heterophrys was polyphyletic. Using scale morphology and rRNA sequences, we establish new families Pterocystidae (Pterocystis, Raineriophrys, Chlamydaster), Marophryidae (type Marophrys (Heterophrys) marina gen. et comb. nov.) and Choanocystidae, new suborders Pterocystina (Pterocystidae, Choanocystidae, Heterophryidae) and Acanthocystina (Acanthocystidae, Raphidiophryidae, Marophryidae), and ten new Pterocystis, Acanthocystis and Choanocystis species. Most clades are exclusively freshwater or exclusively marine; evolutionary transitions between these habitats have been rare.
Robert A. Andersen - One of the best experts on this subject based on the ideXlab platform.
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Single cell genome analysis supports a link between Phagotrophy and primary plastid endosymbiosis
Scientific Reports, 2012Co-Authors: Debashish Bhattacharya, Dana C. Price, Hwan Su Yoon, Eun Chan Yang, Nicole J. Poulton, Robert A. AndersenAbstract:Two cases of primary plastid endosymbiosis are known. The first occurred ca. 1.6 billion years ago and putatively gave rise to the canonical plastid in algae and plants. The second is restricted to a genus of rhizarian amoebae that includes Paulinella chromatophora . Photosynthetic Paulinella species gained their plastid from an α-cyanobacterial source and are sister to plastid-lacking Phagotrophs such as Paulinella ovalis that ingest cyanobacteria. To study the role of feeding behavior in plastid origin, we analyzed single-cell genome assemblies from six P. ovalis -like cells isolated from Chesapeake Bay, USA. Dozens of contigs in these cell assemblies were derived from prey DNA of α-cyanobacterial origin and associated cyanophages. We found two examples of horizontal gene transfer (HGT) in P. ovalis -like nuclear DNA from cyanobacterial sources. This work suggests the first evidence of a link between feeding behavior in wild-caught cells, HGT and plastid primary endosymbiosis in the monophyletic Paulinella lineage.
Joseph E. Boxhorn - One of the best experts on this subject based on the ideXlab platform.
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Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity
Evolutionary Ecology, 1998Co-Authors: Martin E. Boraas, Dianne B. Seale, Joseph E. BoxhornAbstract:Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a Phagotrophic flagellated protist (‘flagellate’). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10–20 generations in the presence of the Phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.
Antoine Guisan - One of the best experts on this subject based on the ideXlab platform.
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Soil protist diversity in the Swiss western Alps is better predicted by topo‐climatic than by edaphic variables
Journal of Biogeography, 2020Co-Authors: Christophe Victor W. Seppey, David Singer, Edward A. D. Mitchell, Olivier Broennimann, Aline Buri, Erika Yashiro, Eric Pinto-figueroa, Quentin Blandenier, Hélène Niculita-hirzel, Antoine GuisanAbstract:Aim: Trends in spatial patterns of macroscopic organisms diversity can be well predicted from correlative models, using topo-climatic variables for plants and animals allowing inference over large scales. By contrast, soil microorganisms diversity is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo-climatic vs. edaphic variables for predicting the diversity of various soil protist groups at the regional scale. Location: Swiss western Alps. Taxa: Full protist community and nine clades belonging respectively to three functional groups: parasites (Apicomplexa, Peronosporomycetes, Phytomyxea), Phagotrophs (Sarcomonadea, Tubulinea, Spirotrichea) phototrophs (Chlorophyta, Trebouxiophyceae, Diatomeae). Methods: We extracted soil DNA from 178 sites along a wide range of elevations with a random-stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the rRNA small sub-unit gene. We assessed and modelled the diversity (Shannon index) patterns of all above-mentioned taxonomic groups based on topo-climatic (topography, slope southness, slope steepness and average summer temperature) and edaphic (soil temperature, relative humidity, pH, electroconductivity, phosphorus percentage, carbon/nitrogen, loss on ignition and shale percentage) variables in Generalized Additive Models (GAM). Results: The respective significance of topo-climatic and edaphic variables varied among taxonomic and – to a certain extent – functional groups: while many variables explained significantly the diversity of the three phototrophs this was less the case for the three parasites. Topo-climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic groups. Main conclusions: Topo-climatic variables (particularly slope steepness and summer temperature if we consider their significance in the GAMs) were, on average, better predictors of protist diversity at the landscape scale than edaphic variables. However, the predictive power of these variables on diversity differed considerably among taxonomic groups; such relationships may be due to direct and/or indirect (e.g. biotic) influences (like with parasitic taxa, where low predictive power is most likely explained by the absence of information on the hosts distribution). Future prospects include using such spatial models to predict hotspots of diversity and disease outbreaks.
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Soil protist diversity in the Swiss western Alps is better predicted by topo-climatic than by edaphic variables
bioRxiv, 2019Co-Authors: Christophe Victor W. Seppey, David Singer, Edward A. D. Mitchell, Olivier Broennimann, Aline Buri, Erika Yashiro, Eric Pinto-figueroa, Quentin Blandenier, Helene Niculita Hirzel, Antoine GuisanAbstract:Aim: General trends in spatial patterns of macroscopic organisms diversity can be reasonably well predicted from correlative models, using for instance topo-climatic variables for plants and animals allowing inference over large scales. By contrast, soil microorganisms diversity is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo-climatic vs. edaphic variables for predicting the diversity of various soil protist groups at the regional scale. Location: Swiss western Alps. Taxa: Full protist community and nine clades belonging to three functional groups: parasites (Apicomplexa, Oomycota, Phytomyxea), Phagotrophs (Sarcomonadea, Tubulinea, Spirotrichea) and phototrophs (Chlorophyta, Trebouxiophyceae, Bacillariophyta). Methods: We extracted soil environmental DNA from 178 sites along a wide range of elevations with a random-stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the ribosomal RNA small sub-unit gene. We assessed and modelled the diversity (Shannon index) patterns of all selected groups as a function of topo-climatic and edaphic variables using Generalized Additive Models. Results: The respective significance of topo-climatic and edaphic variables varied among taxonomic and - to a certain extent - functional groups: while many variables explained significantly the diversity of phototrophs this was less the case for parasites. Generally, topo-climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic and functional groups. Main conclusions: Topo-climatic variables are, on average, better predictors of protist diversity at the landscape scale than edaphic variables, which opens the way to wide-scale sampling designs avoiding costly and time-consuming laboratory protocols. However, predictors of diversity differ considerably among taxonomic and functional groups; such relationships may be due to direct and/or indirect, e.g. biotic influences. Future prospects include using such spatial models to predict hotspots of diversity or pathogens outbreaks. Keywords: edaphic variables, predictive modelling, protist diversity, soils, spatial modelling, Swiss western Alps, topo-climatic variables.
Kevin J Flynn - One of the best experts on this subject based on the ideXlab platform.
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Niche separation between different functional types of mixoplankton: results from NPZ-style N-based model simulations
Marine Biology, 2019Co-Authors: Anna-a Anschütz, Kevin J FlynnAbstract:Protist plankton comprise phytoplankton (incapable of Phagotrophy), protozooplankton (incapable of phototrophy) and mixoplankton (capable of phototrophy and Phagotrophy). Of these, only phytoplankton and zooplankton are typically described in models. Over the last decade, however, the importance of mixoplankton across all marine biomes has risen to prominence. We thus need descriptions of mixoplankton within marine models. Here we present a simple yet flexible N-based model describing any one of the five basic patterns of protist plankton: phytoplankton, protozooplankton, and the three functional groups of mixoplankton: general non-constitutive mixoplankton (GNCM), specialist non-constitutive mixoplankton (SNCM), and constitutive mixoplankton (CM). By manipulation of a few input switch values, the same model can be used to describe any of these patterns, while adjustment of salient features, such as the percent of C-fixation required for mixotrophic growth, and the rate of phototrophic prey ingestion required to enable growth of GNCM and SNCM types, readily provides fine tuning. Example outputs are presented showing how the performance of these different protist configurations accords with expectations (set against empirical evidence). Simulations demonstrate clear niche separations between these protist functional groups according to nutrient, prey and light resource availabilities. This addition to classic NPZ plankton models provides for the exploration of the implications of mixoplankton activity in a simple yet robust fashion.
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Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition: Incorporation of Diverse Mixotrophic Strategies
Protist, 2016Co-Authors: Aditee Mitra, John A. Raven, Kevin J Flynn, Diane K. Stoecker, Urban Tillmann, David A. Caron, Per Juel Hansen, Gustaaf M. Hallegraeff, Robert W SandersAbstract:Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic "phytoplankton" and Phagotrophic "microzooplankton". However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and Phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an eco-physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking Phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as Phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks.
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morphological controls on cannibalism in a planktonic marine Phagotroph
Protist, 2008Co-Authors: Claire M. Martel, Kevin J FlynnAbstract:The ingestion preferences of planktonic protozoa influence the structure and succession of microbial communities and thus biogeochemical cycling within aquatic environments. Some predatory ciliates and flagellates are reported to switch to cannibalism when no suitable non-self prey items are available for consumption. However, the importance of cannibalism as a survival strategy, and its ubiquity within the planktonic protozoa is not known. We report the first attempt to quantify cannibalism in a Phagotrophic marine dinoflagellate (Oxyrrhis marina). Cannibalistic Oxyrrhis cells seldom comprised >2% of any experimental population, including those in which all non-self prey items had been grazed to extinction. Such ‘prey-deplete’ cultures became dominated by homogeneous populations of highly motile Oxyrrhis that were morphologically unable (too similar in size) to cannibalise. That cannibalism can only occur when ‘victim’ and ‘cannibal’ cell size-classes of sufficient difference collide, suggests that cannibalism may be of limited use as a long-term survival strategy in Phagotrophic protozoa.