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Eukaryote kingdoms: Seven or nine?

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Abstract

The primary taxa of eukaryote classification should be monophyletic and based on fundamental cell structure rather than nutritional adaptive zones. The classical two kingdom classification into “plants” and “animals” and the newer four kingdom classifications into “protist”, “fungi”, “animals” and “plants” are therefore both unsatisfactory. Eukaryotes can be classified into nine kingdoms each defined in terms of a unique constellation of cell structures. Five kingdoms have plate-like mitochondrial cristae: (1) Eufungi (the non-ciliated fungi, which unlike the other eight kingdoms have unstacked Golgi cisternae), (2) Ciliofungi (the posteriorly ciliated fungi), (3) Animalia (Animals, sponges, mesozoa, and choanociliates; phagotrophs with basically posterior ciliation), (4) Biliphyta (Non-phagotrophic, phycobilisome-containing, algae; i.e. the Glaucophyceae and Rhodophyceae), (5) Viridiplantae (Non-phagotrophic green plants, with starch-containing plastids). Kingdom (6), the Euglenozoa, has disc-shaped cristae and an intraciliary dense rod and may be phagotrophic and/or phototrophic with plastids with three-membraned envelopes. Kingdom (7), the Cryptophyta, has flattened tubular cristae, tubular mastigonemes on both cilia, and starch in the compartment between the plastid endoplasmic reticulum and the plastid envelope; their plastids, if present, have phycobilins inside the paired thylakoids and chlorophyll c2. Kingdom (8), the Chromophyta, has tubular cristae, together with tubular mastigonemes on one anterior cilium and/or a plastid endoplasmic reticulum and chlorophyll c2 + c2. Members of the ninth kingdom, the Protozoa, are mainly phagotrophic, and have tubular or vesicular cristae (or lack mitochondria altogether), and lack tubular mastigonemes on their (primitively anterior) cilia; plastids if present have three-envelope membranes, chlorophyll c2, and no internal starch, and a plastid endoplasmic reticulum is absent. Kingdoms 4–9 are primitively anteriorly biciliate.Detailed definitions of the new kingdoms and lists of the phyla comprising them are given. Advantages of the new system and its main phylogenetic implications are discussed. A simpler system of five kingdoms suitable for very elementary teaching is possible by grouping the photosynthetic and fungal kingdoms in pairs. Various compromises are possible between the nine and five kingdom systems; it is suggested that the best one for general scientific use is a system of seven kingdoms in which the Eufungi and Ciliofungi become subkingdoms of the Kingdom Fungi, and the Cryptophyta and Chromophyta subkingdoms of the Kingdom Chromista; the Fungi, Viridiplantae, Biliphyta, and Chromista can be subject to the Botanical Code of Nomenclature, while the Zoological Code can govern the Kingdoms Animalia, Protozoa and Euglenozoa. If one accepts the idea that the Ciliofungi evolved directly from a eufungus (or vice versa) and that the Chromophyta evolved from a cryptophyte, then these seven kingdoms would probably be monophyletic and preferable to the nine-kingdom system, which is my own view. The nine-kingdom system is independent of these particular phylogenetic assumptions and may therefore be preferred by those who reject them.

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... It stemmed from realising that discoverers of Rhodelphis (Gawryluk et al. 2019), a remarkable heterotrophic flagellate with an unseen relict plastid unexpectedly related to red algae, had overlooked key aspects of its TZ structure that give compelling evidence for an evolutionary relationship with both glaucophyte algae and another heterotroph of uncertain affinity, Picomonas (Seenivasan et al. 2013). This led me to reconsider classification of plant subkingdom Biliphyta and the origin of the remarkable stellate structure of green plant TZs (a major reason for establishing subkingdom Viridiplantae: Cavalier -Smith 1981), during which I found overlooked tomographic evidence for a star-like substructure of the Chlamydomonas TP periphery (O'Toole et al. 2003) and was able to generalise star pattern elements to other corticate eukaryotes and find differences in their TZ structure from other discaria. This allowed me to explain the origin of green plant stellate structures by evolutionary hypertrophy of selected parts of the standard corticate TP and/or its more widespread accessory structures. ...
... Four decades ago classical kingdom Plantae of Haeckel (1866) was refined by restricting it to those eukaryotes possessing plastids located in the cytosol and bounded by only two membranes and considered to have evolved by one common ancestral enslavement of a cyanobacterium (Cavalier-Smith 1981). Eukaryote algae with plastids located instead within the rough endoplasmic reticulum (ER) and with an intervening periplastid membrane (PPM) were placed instead in a new kingdom Chromista thought to have evolved by one secondary enslavement of a plant cell whose plasma membrane became the periplastid membrane; algae with plastids in the cytosol but with three bounding membranes were then placed in kingdom Protozoa, where euglenoid algae remain, though dinoflagellate algae are now in Chromista as their ancestor secondarily lost the PPM (Cavalier-Smith 2018). ...
... Plantae as thus defined fall into two subgroups with very different chloroplasts: (1) subkingdom Biliphyta comprising phyla Glaucophyta and Rhodophyta (red algae), which both retained blue or red phycobilisomes and so also unstacked thylakoids as in ancestral cyanobacteria; (2) Viridiplantae (green plants) which ancestrally lost phycobilisomes and use chlorophyll b instead of phycobilins as secondary antenna pigment and whose thylakoids are stacked for greater photosynthetic efficiency (Cavalier-Smith 1981, 1998. Viridiplantae are also united by sharing a ciliary transition zone (TZ) basal cylinder surrounded by a characteristic stellate structure, this TZ structure being unique in eukaryotes, and a particularly important cell evolutionary character as Manton (1965) first emphasised. ...
Article
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I thoroughly discuss ciliary transition zone (TZ) evolution, highlighting many overlooked evolutionarily significant ultrastructural details. I establish fundamental principles of TZ ultrastructure and evolution throughout eukaryotes, inferring unrecognised ancestral TZ patterns for Fungi, opisthokonts, and Corticata (i.e., kingdoms Plantae and Chromista). Typical TZs have a dense transitional plate (TP), with a previously overlooked complex lattice as skeleton. I show most eukaryotes have centriole/TZ junction acorn-V filaments (whose ancestral function was arguably supporting central pair microtubule-nucleating sites; I discuss their role in centriole growth). Uniquely simple malawimonad TZs (without TP, simpler acorn) pinpoint the eukaryote tree's root between them and TP-bearers, highlighting novel superclades. I integrate TZ/ciliary evolution with the best multiprotein trees, naming newly recognised major eukaryote clades and revise megaclassification of basal kingdom Protozoa. Recent discovery of non-photosynthetic phagotrophic flagellates with genome-free plastids (Rhodelphis), the sister group to phylum Rhodophyta (red algae), illuminates plant and chromist early evolution. I show previously overlooked marked similarities in cell ultrastructure between Rhodelphis and Picomonas, formerly considered an early diverging chromist. In both a nonagonal tube lies between their TP and an annular septum surrounding their 9+2 ciliary axoneme. Mitochondrial dense condensations and mitochondrion-linked smooth endomembrane cytoplasmic partitioning cisternae further support grouping Picomonadea and Rhodelphea as new plant phylum Pararhoda. As Pararhoda/Rhodophyta form a robust clade on site-heterogeneous multiprotein trees, I group Pararhoda and Rhodophyta as new infrakingdom Rhodaria of Plantae within subkingdom Biliphyta, which also includes Glaucophyta with fundamentally similar TZ, uniquely in eukaryotes. I explain how biliphyte TZs generated viridiplant stellate-structures.
... During the same period, the increasing availability of molecular sequences has been an increasingly valuable source of independent phylogenetic information. The establishment of the predominantly photosynthetic kingdom Chromista (brown algae and diatoms and their various relatives) in 1981 (17) and the primitively amitochondrial kingdom Archezoa in 1987 (26), and an ultrastructurally based redefinition of the kingdom Plantae (17,29), excluded a large residue of mainly phagotrophic and aerobic protists whose classification is the subject of the present review. Although there might be some merit in subdividing these protists into several kingdoms along phylogenetic lines, I here adopt the more conservative approach of including them all in a single kingdom, Protozoa, and subdividing this into subkingdoms, infrakingdoms, parvkingdoms, and superphyla. ...
... During the same period, the increasing availability of molecular sequences has been an increasingly valuable source of independent phylogenetic information. The establishment of the predominantly photosynthetic kingdom Chromista (brown algae and diatoms and their various relatives) in 1981 (17) and the primitively amitochondrial kingdom Archezoa in 1987 (26), and an ultrastructurally based redefinition of the kingdom Plantae (17,29), excluded a large residue of mainly phagotrophic and aerobic protists whose classification is the subject of the present review. Although there might be some merit in subdividing these protists into several kingdoms along phylogenetic lines, I here adopt the more conservative approach of including them all in a single kingdom, Protozoa, and subdividing this into subkingdoms, infrakingdoms, parvkingdoms, and superphyla. ...
... But for many years neither this proposal nor Haeckel's proposal of a similar, but narrower, kingdom Protista (52,67) became accepted, primarily because of the difficulty of demarcating Protozoa from the kingdoms Animalia and Plantae. Eventually, electron microscopy provided many new criteria for this demarcation and helped to reinforce a growing preference for multikingdom systems of classification over the old animal-or-vegetable dichotomy (16,17,19,21,31,52,76,77,90,95,96,99,101,124,147). Though it is widely agreed that Protozoa are too diverse to constitute a single phylum and must be distributed among a fairly large number of phyla (17,31,52,77,83,89,90,98,124), there has been no general consensus as to how this should be done or, indeed, whether or not Protozoa should even remain a formal taxon. ...
Article
The demarcation of protist kingdoms is reviewed, a complete revised classification down to the level of subclass is provided for the kingdoms Protozoa, Archezoa, and Chromista, and the phylogenetic basis of the revised classification is outlined. Removal of Archezoa because of their ancestral absence of mitochondria, peroxisomes, and Golgi dictyosomes makes the kingdom Protozoa much more homogeneous: they all either have mitochondria and peroxisomes or have secondarily lost them. Predominantly phagotrophic, Protozoa are distinguished from the mainly photosynthetic kingdom Chromista (Chlorarachniophyta, Cryptista, Heterokonta, and Haptophyta) by the absence of epiciliary retronemes (rigid thrust-reversing tubular ciliary hairs) and by the lack of two additional membranes outside their chloroplast envelopes. The kingdom Protozoa has two subkingdoms: Adictyozoa, without Golgi dictyosomes, containing only the phylum Percolozoa (flagellates and amoeboflagellates); and Dictyozoa, made up of 17 phyla with Golgi dictyosomes. Dictyozoa are divided into two branches: (i) Parabasalia, a single phylum with hydrogenosomes and 70S ribosomes but no mitochondria, Golgi dictyosomes associated with striated roots, and a kinetid of four or five cilia; and (ii) Bikonta (16 unicellular or plasmodial phyla with mitochondria and bikinetids and in which Golgi dictyosomes are not associated with striated ciliary roots), which are divided into two infrakingdoms: Euglenozoa (flagellates with discoid mitochondrial cristae and trans-splicing of miniexons for all nuclear genes) and Neozoa (15 phyla of more advanced protozoa with tubular or flat [usually nondiscoid] mitochondrial cristae and cis-spliced spliceosomal introns). Neozoa are divided into seven parvkingdoms: (i) Ciliomyxa (three predominantly ciliated phyla with tubular mitochondrial cristae but no cortical alveoli, i.e., Opalozoa [flagellates with tubular cristae], Mycetozoa [slime molds], and Choanozoa [choanoflagellates, with flattened cristae]); (ii) Alveolata (three phyla with cortical alveoli and tubular mitochondrial cristae, i.e., Dinozoa [Dinoflagellata and Protalveolata], Apicomplexa, and Ciliophora); (iii) Neosarcodina (phyla Rhizopoda [lobose and filose amoebae] and Reticulosa [foraminifera; reticulopodial amoebae], usually with tubular cristae); (iv) Actinopoda (two phyla with axopodia: Heliozoa and Radiozoa [Radiolaria, Acantharia]); (v) Entamoebia (a single phylum of amoebae with no mitochondria, peroxisomes, hydrogenosomes, or cilia and with transient intranuclear centrosomes); (vi) Myxozoa (three endoparasitic phyla with multicellular spores, mitochondria, and no cilia: Myxosporidia, Haplosporidia, and Paramyxia); and (vii) Mesozoa (multicells with tubular mitochondrial cristae, included in Protozoa because, unlike animals, they lack collagenous connective tissue).
... and the Algaebase (https:// www.algaebase.org/). Both databases adopted the Cavalier-Smith's taxonomic classification system (Cavalier-Smith 1981). In this classification system, Chromista were established to include all chromophyte algae (those with chlorophyll c, not b) considered to have evolved by symbiogenetic enslavement of another eukaryote (a red alga), as well as heterotrophic protists that descended from them by loss of photosynthesis or entire plastids (Cavalier-Smith 1981, Ruggiero et al. 2015, which in our lists include the phyla: Bigyira, Cercozoa, Ciliophora, Cryptophyta, Foraminifera, Haptophyta, Myzozoa and Ochrophyta. ...
... Both databases adopted the Cavalier-Smith's taxonomic classification system (Cavalier-Smith 1981). In this classification system, Chromista were established to include all chromophyte algae (those with chlorophyll c, not b) considered to have evolved by symbiogenetic enslavement of another eukaryote (a red alga), as well as heterotrophic protists that descended from them by loss of photosynthesis or entire plastids (Cavalier-Smith 1981, Ruggiero et al. 2015, which in our lists include the phyla: Bigyira, Cercozoa, Ciliophora, Cryptophyta, Foraminifera, Haptophyta, Myzozoa and Ochrophyta. All records without species level identifications were removed from the lists. ...
Article
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DNA metabarcoding has the capacity to bolster current biodiversity assessment techniques, including the early detection and monitoring of non-indigenous species (NIS). However, the success of this approach is greatly dependent on the availability, taxonomic coverage and reliability of reference sequences in genetic databases, whose deficiencies can potentially compromise species identifications at the taxonomic assignment step. In this study we assessed lacunae in availability of DNA sequence data from four barcodes (COI, 18S, rbcL and matK) for NIS occurring in European marine and coastal environments. NIS checklists were based on EASIN and AquaNIS databases. The highest coverage was found for COI for Animalia and rbcL for Plantae (up to 63%, for both) and 18S for Chromista (up to 51%), that greatly increased when only high impact species were taken into account (up to 82 to 89%). Results show that different markers have unbalanced representations in genetic databases, implying that the parallel use of more than one marker can act complimentarily and may greatly increase NIS identification rates through DNA-based tools. Furthermore, based on the COI marker, data for approximately 30% of the species had maximum intra-specific distances higher than 3%, suggesting that many NIS may have undescribed or cryptic diversity. Although completing the gaps in reference libraries is essential to make the most of the potential of the DNA-based tools, a careful compilation, verification and annotation of available sequences is fundamental to assemble large curated and reliable reference libraries that provide support for rigorous species identifications.
... В частности, исследования структуры жгутиков, крист митохондрий, хлоропластов, клеточных покровов и т.п., а также типов митоза и цитокинеза, позволили по-новому взглянуть на многие таксоны эукариот, и еще до "эры молекулярной биологии" высказать предположения относительно моно-/полифилии некоторых групп. Одним из первых, кто использовал для характеристики макротаксонов (царств) эукариот ультраструктурные признаки (строение крист митохондрий, жгутиков, аппарата Гольджи, хлоропластов и т.д.) был британский биолог Т. Кавалье-Смит, который утверждал, что при построении естественной системы необходимо основываться на фундаментальных структурах клетки (Cavalier-Smith, 1978, 1981. Например, именно анализ ультраструктурных признаков позволил предположить, что криптомонады (отдел Cryptophyta) правомочно выделять в отдельное царство (Cavalier-Smith, 1981), что, в настоящее время, подтверждается молекулярно-генетическими исследованиями (см. ...
... Одним из первых, кто использовал для характеристики макротаксонов (царств) эукариот ультраструктурные признаки (строение крист митохондрий, жгутиков, аппарата Гольджи, хлоропластов и т.д.) был британский биолог Т. Кавалье-Смит, который утверждал, что при построении естественной системы необходимо основываться на фундаментальных структурах клетки (Cavalier-Smith, 1978, 1981. Например, именно анализ ультраструктурных признаков позволил предположить, что криптомонады (отдел Cryptophyta) правомочно выделять в отдельное царство (Cavalier-Smith, 1981), что, в настоящее время, подтверждается молекулярно-генетическими исследованиями (см. ниже). ...
Article
Different problems concerned the evolution of algal chloroplasts are reviewed. Progress in the studies on the classification of eukaryotes and understanding of the position of algae on the Tree of Life are discussed. Currently, among the numerous monophyletic supergroups of eukaryotes, five supergroups contain representatives of algae: Archaeplastida (Glaucocystophyta, Rhodophyta, Prasinodermophyta, Chlorophyta, Charophyta), TSAR (Ochrophyta, Dinophyta, Chlorachniophyta, and photosynthetic Chromera, Vetrella and Paulinella), Haptista (Prymnesiophyta, Rappemonads), Cryptista (Cryptophyta) and Discoba (Euglenophyta). Short diagnoses of the phyla and supergroups containing different phyla of algae are given.
... Sporná tvrzení byla dále ověřována v algologické literatuře, případně v dalších odborných textech. Nedostatky v systematickém zařazení v publikacích (Cavalier-Smith, 1981, 1986, Rosypal et al., 1992. Další odborné nedostatky v publikacích (Cyrus & Hindák, 1978;Hindák, 1978;Ettl, 1983, Ambrozová, 1999Knox, 2000;Granéli & Turner, 2002;Víden, 2005;Nedbalová & Lukavský, 2007;Šmarda, 2009;Lukavský, 2014;Vrtiška, 2014;Guiry & Guiry, 2017a;Kaštovský & Hauer, 2017a). ...
... Vysokoškolská učebnice Kaliny a Váni (2005), na kterou naše studie odkazuje, vychází z uspořádání organismů do pěti říší -Protozoa, Chromista, Plantae, Fungi a Animalia, které publikoval v druhé polovině minulého století Cavalier-Smith (1981, 1986. Aktuálně uznávaný systém organismů uvádějí Keeling et al. (2009) ...
Article
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Studie je zaměřena na zpracování tématu Řasy v osmi učebnicích přírodopisu. Cílem výzkumu bylo zjistit odborné nedostatky v učivu o řasách. Metodou výzkumu byla obsahová analýza (Gavora, 2010, 2015). Zjištěné nedostatky byly rozděleny na dvě kategorie – nedostatky týkající se zařazení řas do systému a další odborné nedostatky. Celkem byly v učebnicích zjištěny 4 typy nedostatků v systematickém zařazení řas a 61 dalších odborných nedostatků. V diskusi jsou porovnány výsledky studie se zjištěními jiných autorů a vyvozovány dopady na vzdělávání žáků. Článek je doplněn přílohou s uvedením odborné správnosti determinovaných chyb.
... Plants are mainly photosynthetic eukaryotic multicellular organisms which belong to kingdom plantae. They are comprised of conifers, flowering plants and gymnosperms [1]. The term "medicinal plants" refers to a large group of plants which are used in the field of herbalism [2]. ...
... Klasifikacija živih bića na Zemlji u rangu carstva može se pratiti i u publikacijama od 1735 do danas (Linnaeus, 1735;Haeckel, 1866;Chatton, 1925;Copeland, 1938;Whittaker, 1969;Woese et al, 1977;Woese et al, 1990;Cavalier-Smith, 1981;1993;2010) tabela 1. ...
... Trypanosoma brucei is the causative agent of African sleeping sickness [1] intramitochondrial Pi pool either in exchange with OHor in symport with protons [21,22]. 49 ...
Article
Conserved amongst all eukaryotes is a family of mitochondrial carrier proteins (SLC25A) responsible for the import of various solutes across the inner mitochondrial membrane. We previously reported that the human parasite Trypanosoma brucei possesses 26 SLC25A proteins (TbMCPs) amongst which two, TbMCP11 and TbMCP8, were predicted to function as phosphate importers. The transport of inorganic phosphate into the mitochondrion is a prerequisite to drive ATP synthesis by substrate level and oxidative phosphorylation and thus crucial for cell viability. In this paper we describe the functional characterization of TbMCP11. In procyclic form T. brucei, the RNAi of TbMCP11 blocked ATP synthesis on mitochondrial substrates, caused a drop of the mitochondrial oxygen consumption and drastically reduced cell viability. The functional complementation in yeast and mitochondrial swelling experiments suggested a role for TbMCP11 as inorganic phosphate carrier. Interestingly, procyclic form T. brucei cells in which TbMCP11 was depleted displayed an inability to either replicate or divide the kinetoplast DNA, which resulted in a severe cytokinesis defect.
... Estos microorganismos pertenecen al reino Cromista, división Haptophyta (Cavalier-Smith 1981. La clasificación de los cocolitóforos está dada principalmente por la morfología de los cocolitos, siendo la familia el nivel taxonómico más aceptado (Young y Bown 1997). ...
Thesis
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Coccolithophores are unicellular marine phytoplankton (primary producers) that are a significant part of the biogeochemical carbon cycle. They secrete tiny plates of CaCO3 called coccoliths and their sinking represents one of the main mechanisms for the export of particulate inorganic carbon to the sea floor. Quantifying their flux in the ocean is a prerequisite to understanding the global carbon cycle. As a part of a multidisciplinary program, the material collected from a time-series sediment trap has been used to determine the settling of coccoliths in La Paz Bay (Alfonso Basin). In this thesis the various coccoliths are analyzed, the species are identified, the diversity of the coccoliths (in the thanatocenosis) is documented and the mass flux of calcite associated with coccoliths is calculated. Additionally, the atmospheric and oceanographic conditions in the bay are characterized to infer their influence on the fluxes. Finally, the species preserved in the underlying marine sediments are identified and compared with the assemblages that settle in the basin. The sediment trap was moored at 360 m depth in the bay (50 m above the bottom) from January 2002 to October 2003. The device collected detritus produced in the surface waters over 7 to 14 day sampling intervals, providing a total of 64 samples. The collected material was first subdivided into 10 aliquots using a rotary splitter and a 1/10 split was further subdivided to provide splits of 1/300-1/450. Theses splits were filtered onto a Nucleopore® filter membrane. A portion of each membrane was prepared for examination under a fully automated scanning electron microscope. 10 to 15 fields of view each providing 1000 to 1500 images of 57.68 x 46.14 µm2) that were stored digitally. A total of 85,200 images (an area of 4 mm2) were analyzed. The number and taxonomic composition of the coccoliths was counted on each imagine using AnalySIS® software on a personal computer. Subsequently, the numeric fluxes and diversity were determined from a software database and the CaCO 3 mass was calculated using published algorithms and measures of the coccolith length. The assemblages of coccoliths in the surface sediments were studied using a petrographic microscope. To characterize the bay, a series of wind, sea surface temperature and chlorophyll a databases were downloaded from the internet from SeaWinds, AVHRR and SeaWiFS-level-3 remote sensors. In addition, Conductivity-Temperature-Depth profiles were collected from 6 oceanographic cruises and a database was also obtained from the La Paz meteorological observatory. In total, 121,181 coccoliths were counted and 42 different taxa were identified. The coccolith numeric fluxes varied weekly and seasonally, with high fluxes occurring in autumn-winter (64.7 x108 coccoliths m-2 d-1) and low fluxes in spring-summer (0.02 x108 coccoliths m-2 d-1). September 2003 recorded the highest fluxes (128.9 x108 coccoliths m-2 d- 1). The overall average was 22 x108 coccoliths m-2 d-1. The coccolith assemblage was dominated by Gephyrocapsa oceanica (43.6 %), Emiliania huxleyi (15.7 %) and Florisphaera profunda (15.7 %). The coccolith diversity as Shannon Index and BergerParker Index varied between 1.7-2.2 and 0.3-0.8, respectively. The coccolith calcite flux varied from 0 to 0.09 g m-2 d-1and the average was 0.027 g m-2 d-1. The main contributors to the calcite flux were G. oceanica (57.3 %), Calcidiscus leptoporus (10.7 %) and Helicosphaera carteri (9.1 %). The same five species dominating the fluxes in the trap samples were also dominant in the surface sediment. Within the bay the direction and magnitude of the winds record a behavior inversely to the sea surface temperature. The high coccolith fluxes in autumn-winter are related tostrong winds from north (that generate an upper ocean mixed layer up to 30 m in depth) and low chlorophyll a concentrations. The coccolith assemblage of G. oceanica, E. huxleyi and F. profunda are associated in the literature with turbidity in the water, increase of nutrients and upwelling. The low fluxes in spring-summer are related to the weak winds from south that permits stratification in the water and high concentrations of chlorophyll a, where diatoms probably dominate the phytoplankton in the bay. In September 2003 F. profunda recorded the highest individual coccoliths fluxes associated with two tropical cyclones (low intensity of the light and high nutrient supply due to mixing and land drainage). Coccolithophores are responsible for the export of 757 tons/year of calcite in the basin (75 km2) based upon the average coccolith carbonate flux. Coccoliths contribute an average of 23 % of the total carbonate export (determined in a parallel study) which is twice the mean value reported from 13 traps moored in different ocean environments. The coccoliths fluxes documented in this work are one of the highest reported from the ocean and provides some clues for future paleoceanographic studies with nanoplankton in Alfonso Basin and other marginal basin in the Gulf of California.
... Presently, the notion of Plantae follows a funnel spectrum, with the broadest definition of Linnaeus, successively narrowed into the Archaeplastida comprising the red algae "Rhodophyta" and the glaucophyte algae "Glaucophyta" in addition to the green plants (Cavalier-Smith 1981), the Virdiplantae holding only green algae and the emerging land plants characterized by the presence of cellulosic cell wall, chlorophylls a and b, and plastids as sites for photosynthesis (Copeland 1956), and finally the narrowest is the Embryophyta which includes land plants as liverworts, hornworts, mosses, and vascular plants (Whittaker 1969). ...
Thesis
In the context of climate change, plants are facing recurrent environmental constraints that negatively affect their productivity and survival. The elevations and abrupt fluctuations of temperature expose plants to thermal stresses that are critical to their development. Additionally, the flooding events associated with the rise of sea level increase the salinity of soils which endangers wild and cultivated plants. Therefore, a major concern of plant biology is defining strategies to cope with these stresses to maintain the biodiversity and the agricultural productivity. In this scope, the plant acclimation and adaptation to abiotic stresses have been massively studied at different levels and in multiple aspects. Being sessile organisms, plants have restricted dispersal that limits their migration to regions of more convenient climatic frames. However, they are capable of achieving rapid acclimation to novel environmental conditions via their phenotypic plasticity. Additionally, they can adapt to their local microenvironments on the long term via natural selection, which enhances their fitness to their living niche. This mechanism is the basis of natural diversity. Indeed, natural diversity is a powerful tool to investigate the plant's response to environmental changes. Arabidopsis thaliana has been adopted as a model species for within-species (also called intraspecific) natural diversity. In this study, A. thaliana natural populations from the French Pyrenees were characterized for their phenotypic and transcriptomic plasticity in response to thermal and saline stresses. The particular interest in these populations is that they originate from a geographically restricted area, but with highly contrasted climates due to its mountainous nature. Additionally, the study focused on the plasticity displayed at the level of roots. Roots represent half of the plant's body, and they serve fundamental roles throughout its lifecycle. Accordingly, the molecular regulations of reactive oxygen species (ROS) during root development were reviewed. Also, the root development of thirty A. thaliana Pyrenean populations in addition to Columbia (Col-0, Poland, 200 m) and Shahdara (Sha, Tajikistan, 3400 m) was phenotyped under combination of thermal and saline stresses. Lastly, transcriptomic analyses were performed at the whole-genome level via RNA sequencing to highlight changes in the gene regulation in selected A. thaliana Pyrenean populations that displayed stress-tolerant phenotypes. The obtained results revealed the enormous phenotypic plasticity between the studied populations in response to cold-, heat-, and/or saline stresses. The integrative analyses of the phenotypic data distinguished populations as stress-tolerant/sensitive, with their roots being slightly/highly impacted by the abiotic constraint. Moreover, the transcriptomic analyses of the tolerant populations shed light on the variations of their gene expression under the applied stresses. A particular focus was made on cell wall- and ROS homeostasis- related genes since they are highly correlated with the observed phenotypes. The results showed that in the stress-tolerant populations, more genes coding for cell wall, lignin, and anthocyanin biosynthesis were upregulated. Additionally, the ROS gene network was highly implicated in the plant response to the environmental constraints. In fact, tolerant populations activated novel genes such as class III peroxidases in their acclimation response.
... Cavalier-Smith) [9,10] Family Neuropteridae Dilcher, et al. [11] Genus Cyclopteris sensu Brongniart [1] Type species: Cyclopteris orbicularis OUMNH E.3439. ...
Article
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A new species of Cyclopteris sensu was discovered in the upper sandstone beds of the Placid Shale. New species is distinguished by chevronate veins present between major radiating veins characteristic of Cyclopteris. Discovery of this species expands this genus into the Carboniferous delta deposits of Central Texas, and demonstrates the need to revisit these classic sites.
... (Modified and redrawn from Chadefaud 1960; Gorenflot and Guern 1989;Boudouresque and Gómez 1995) phylogeny, the great similarity between "brown algae" and "Oomycetes" had been established. Mereschkowsky (1910) had fully understood the consequences, in an earlier polyphyletic vision of algae and fungi that Cavalier- Smith (1981) recognized and reassessed in his kingdom of Chromista, which brought together Stramenopiles, Haptobionta, and Cryptobionta in this book. As in the case of the kingdom of Archaeplastida (cf. ...
... Consistent with the current opinion, plants (Plantae; sensu Cavalier- Smith, 1981) are photosynthetic organisms whose plastids are of primary endosymbiotic origin. 5 This branch on the Coral of Life emerged around 1,450 million years ago (mya), when a nonphotosynthetic unicellular eukaryote engulfed a cyanobacterium, which was then integrated into the host cell as a new organelle -the plastid. ...
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The present article has two primary objectives. First, the article provides a historical overview of graphical tools used in the past centuries for summarizing the classification and phylogeny of plants. It is emphasized that each published diagram focuses on only a single or a few aspects of the present and past of plant life on Earth. Therefore, these diagrams are less useful for communicating general knowledge in botanical research and education. Second, the article offers a solution by describing the principles and methods of constructing a lesser- known image type, the coral, whose potential usefulness in phylogenetics was first raised by Charles Darwin. Cladogram topology, phylogenetic classification and nomenclature, diversity of taxonomic groups, geological timescale, paleontological records, and other relevant information on the evolution of Archaeplastida are simultaneously condensed for the first time into the same figure – the Coral of Plants. This image is shown in two differently scaled parts to efficiently visualize as many details as possible, because the evolutionary timescale is much longer, and the extant diversity is much lower for red and green algae than for embryophytes. A fundamental property of coral diagrams, that is their self-similarity, allows for the redrawing of any part of the diagram at smaller scales.
... The phylum Blastocadiomycota comprises a relatively small group of zoosporic fungi with diverse morphological and ecological traits. Before its promotion to a phylum level based on molecular phylogenetic studies (James et al., 2006b), the group was already recognized as monophyletic based on ultrastructural similarities (Cavalier-Smith, 1981), uniting them with terrestrial fungi. Unlike other zoosporic fungi, Blastocladiomycota present alternation of gametophytic and sporophytic generations. ...
Article
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The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum‐level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.
... Unicellular organisms possessing a primary plastid all derive from the same first endosymbiosis event. They are called Archaeplastida (Adl et al., 2005) and radiated into three major lineages, the Glaucophyta, the Rhodophyceae or red algae, and the Chloroplastida (Adl et al., 2005), also known as Viridiplantae (Cavalier-Smith, 1981). Recently, Li et al. (2020) described the new phylum/division Prasinodermophyta and demonstrated that Prasinodermophyta belongs to Viridiplantae . ...
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The Heterokonta or Stramenopile phylum comprises clades of unicellular photosynthetic species, which are promising for a broad range of biotechnological applications, based on their capacity to capture atmospheric CO2 via photosynthesis and produce biomolecules of interest. These molecules include triacylglycerol (TAG) loaded inside specific cytosolic bodies, called the lipid droplets (LDs). Understanding TAG production and LD biogenesis and function in photosynthetic stramenopiles is therefore essential, and is mostly based on the study of a few emerging models, such as the pennate diatom Phaeodactylum tricornutum and eustigmatophytes, such as Nannochloropsis and Microchloropsis species. The biogenesis of cytosolic LD usually occurs at the level of the endoplasmic reticulum. However, stramenopile cells contain a complex plastid deriving from a secondary endosymbiosis, limited by four membranes, the outermost one being connected to the endomembrane system. Recent cell imaging and proteomic studies suggest that at least some cytosolic LDs might be associated to the surface of the complex plastid, via still uncharacterized contact sites. The carbon length and number of double bonds of the acyl groups contained in the TAG molecules depend on their origin. De novo synthesis produces long-chain saturated or monounsaturated fatty acids (SFA, MUFA), whereas subsequent maturation processes lead to very long-chain polyunsaturated FA (VLC-PUFA). TAG composition in SFA, MUFA, and VLC-PUFA reflects therefore the metabolic context that gave rise to the formation of the LD, either via an early partitioning of carbon following FA de novo synthesis and/or a recycling of FA from membrane lipids, e.g., plastid galactolipids or endomembrane phosphor- or betaine lipids. In this review, we address the relationship between cytosolic LDs and the complex membrane compartmentalization within stramenopile cells, the metabolic routes leading to TAG accumulation, and the physiological conditions that trigger LD production, in response to various environmental factors.
... Les Straménopiles (ou hétérocontes) présentent une histoire évolutive commune avec les Alvéolés basée sur la présence de plastes dans de nombreux organismes qui auraient dérivés d'une algue rouge par endosymbiose secondaire (hypothèse Chromoalvéolée, (Cavalier-Smith, 1981, Delwiche, 1999 (Bourelly, 1968). En moyenne, en milieu lacustre, la classe des Chrysophyceae représente près de 18% de la diversité décrite dans l'épilimnion par les techniques de biologie moléculaire. ...
... • Carstvo Plantae, Haeckel (1866) • Podcarstvo Viridaeplantae, Cavalier-Smith (1981) • Razred Tracheophyta, Sinnott (1935) ex Cavalier-Smith (1998) • Podrazred Euphyllophytina • Klasa Magnoliopsida, Brongniart (1843) • Podklasa Hamamelididae, Takhtajan (1967) • Nadred Faganae, (Engler 1892) Takhtajan (1997) • Red Fagales, Engler (1892) • Porodica Fagaceae, Dumortier (1829) • Potporodica Fagaceideae • Rod Fagus, Linnaeus (1753) • Fagus sylvatica, Linnaeus (1753) -obična bukva Osnovne karakteristike nekih taksonomskih jedinica 1. Divizija: Magnoliophyta -skrivenosjemenice Skrivenosjemenice (Magnoliophyta, Angiospermae) su najveća skupina zelenih kopnenih biljaka kod kojih se sjeme nalazi unutar ploda. Skrivenosjemenice u većini slučajeva čine najveću biomasu u ekosistemu i svojim izgledom i brojnošću određuju izgled i strukturu ekosistema. ...
... Yet, it is worth mentioning that free-living bodonids (e.g., Bodo saltans) are better comparators for parasitism [10,11]. The relationship between euglenids and kinetoplastids has been first proposed by T. Cavalier-Smith based on ultrastructural similarities (e.g., "mitochondrial cristae shaped like a flattened disc with a narrow neck") [12], then supported by other lines of evidence, such as alignments of nuclear rRNA [13], the addition of a leader sequence to nuclear pre-mRNAs [14] and the presence of trypanothione reductase in E. gracilis, previously found only in kinetoplastids [15]. ...
Article
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Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.
... ). These three lineages are collectively called Plantae or Archaeplastida(Cavalier-Smith, 1981; Adl et. al., 2005). ...
Chapter
Conservation and assessment of Floral diversity of Kaiga Reserve Forest of Western Chats (Karnataka) India
... An important aspect of kinetoplastid phylogeny is the massive evolutionary change of their 18S rRNA gene, due to which they are found at the base of the eukaryotic phylogenetic trees (Simpson et al., 2006;Janouškovec et al., 2017;Strassert et al., 2019). Kinetoplastids, along with diplonemids and euglenids belong to the phylum Euglenozoa (Cavalier-Smith, 1981), where the free-living and occasionally parasitic group diplonemids are their closest relatives (Lara et al., 2009). The euglenozoans diverged from other eukaryotes (Moreira et al., 2004;Vlcek et al., 2010) and are known as basal eukaryotes (Cavalier-Smith, 2009). ...
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Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers. Kinetoplastids were abundant in the deep waters of all the lakes, contributing up to 53.6% of total nanoeukaryotes. Despite this significant contribution, kinetoplastids remain undetected by amplicon sequencing using universal primers that are widely used in eukaryotic diversity studies. However, they were detected with specific primers, and the communities were characterized by both ubiquitous and lake-specific unique OTUs. Oligotyping of a ubiquitous and dominant OTU revealed the presence of lake-specific sequence types (oligotypes). Remarkably, we also detected diplonemids (a sister group of kinetoplastids and considered to be specific in the marine habitat) using kinetoplastid-specific primers, showing their presence in freshwaters. Underestimation of kinetoplastids and diplonemids using universal primers indicates that euglenozoan flagellates are overlooked in diversity studies worldwide. The present study highlighted the importance of kinetoplastids in the hypolimnion of deep lakes, thereby indicating their role in material cycling in deep waters.
... In retrospect, the true position and affinities of dinoflagellates among eukaryotes could not be clearly established by these early analyses, but more detailed secondary structure-driven analysis of 25 eukaryote lineages showed dinoflagellates diverged near or within the eukaryotic "crown radiation" (Sogin, 1989), dispelling the ancient mesokaryote hypothesis. Wolters' (1991) analysis of >40 eukaryote taxa subsequently confirmed the hypothesized affinity of dinoflagellates with ciliates and apicomplexans (Dinozoa, sensu Cavalier- Smith, 1981), and their close relationship to the Chromista (golden brown algae). While new lineages and sub-groupings have emerged, along with various controversies, the majority of work affirms dinoflagellates evolutionary position among the Alveolata. ...
Chapter
Dinoflagellates are a functionally diverse group of organisms, rich in morphological complexity and features, that has formed the basis of a well-developed classical taxonomy. Their extensive fossil record of resistant resting stages (dinocysts) is unique among protists and has supported a comparatively early development of detailed evolutionary theories to explain their apparent morphological diversity. This chapter presents a historical perspective of the application and impact of molecular approaches on the taxonomy, systematics, and phylogenetic theory of dinoflagellates. Application of molecular approaches are described as overlapping phases, beginning in the 1980s with early investigations of DNA structure and phylogenetic affinities among other protists; followed by four phases of molecular-driven discovery: (I) Challenging existing evolutionary theories; (II) Discovering widespread cryptic diversity; (III) Increased taxon and gene sampling; and (IV) Technology-accelerated diversity discovery. Current hurdles to all-of community molecular identification are discussed, and the potential of integrated molecular, fluidics, and imaging to enable high-throughput single-cell ‘omics and identity-linked molecular data for dinoflagellate taxonomy.
... 35 weaker molecular phylogenetic evidence and shared derived cell-biological features. Archaeplastida and Chromalveolata were each identified by the presence of similar plastids [17,18], with sequences from plastid genomes supporting an ancestral endosymbiotic origin of plastids in each group [19,20]. Excavata, meanwhile, was distinguished by the inference that taxa shared a derived, complex flagellar apparatus cytoskeleton [21]. ...
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For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels.
... Estas diferencias indican que el Filo Euglenozoa es un linaje muy diferente al resto, como ya ha sido evidenciado por otros autores que, incluso, proponen que se puede tratar de otro reino (T. Cavalier -Smith, 1981;Thomas Cavalier-Smith, 2016;Thomas Cavalier-Smith et al., 2018). Además, es necesario entender que organismos como L. braziliensis, sufren transformaciones exhaustivas capaces de apartarla del resto del grupo que corresponde (Figuras 1-4). ...
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La clasificación de los organismos vivos ha sido modificada numerosas veces, debido a que algunos grupos han sido difíciles de catalogar. Actualmente se reconocen siete reinos: Animalia, Plantea, Protozoa, Fungí, Archaea, Bacteria y Chromista. Este último es un grupo polifilético, muy variable morfológicamente, importante en ecosistemas marinos. La filogénia molecular permite clasificar de acuerdo con relaciones de parentesco. En este estudio se analizó la región ITS para verificar las relaciones entre diferentes filos del reino Chromista. Se seleccionaron 46 secuencias de ADN de especies diferentes de las bases de datos, se procesaron y analizaron, empleando métodos bioinformáticos de distancia y filogenia. Todos los dendrogramas mostraron una distribución de especies de acuerdo con la clasificación vigente, evidenciando que los chromistas forman un linaje diferente de los protozoos. Finalmente, es necesario realizar más estudios para descifrar mejor la evolución, fisiología y ecología; y así desarrollar estrategias de conservación, manejo y biotecnologías.
... Темп, с которым Кавалье-Смит менял свои эволюционные сценарии, был таков, что иногда за несколько летних конференций участники могли наблюдать эволюцию его идей [47]. Работы Кавалье-Смита в области мегасистематики эукариот покрывают период с 1978 по 2020 гг., и их анализ показывает, что первые системы его являлись «артистическими манифестациями» (так, в 1978 г. он выводил всех эукариот из красных водорослей [48], а в 1981 г.из безжгутиковых грибов [49]), а последние в целом вписывались в контуры консенсусной системы живого [50]. ...
Article
Eukaryotes represent a group of rich biotechnological potential, and its classification having high heuristic power and great predictive capabilities is needed by the biotechnological community. The requirements for biological classification by applied sciences can be reduced to 1) the stability of the classification system and 2) its adequacy to the nature relationships. The present paper provides a retrospective review of eukaryotic megataxonomy, assesses the stability of current system, and outlines approaches to building an interface that ensures a crosstalk of taxonomic and biotechnological communities.
... The Euglenozoa are a diverse group of protists well-known for their distinctive cellular features. They are flagellates with a (mostly) complete corset of microtubules supporting the cell membrane, a characteristic, elongated feeding apparatus (at least ancestrally), and usually two flagella, each with a different type of paraxonemal rod [1,2]. Euglenozoa are divided into three major groups: euglenids, kinetoplastids, and diplonemids [2,3]; a fourth group, symbiontids, is either sister to euglenids or a subgroup within them-see [4]. ...
Article
Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive trans -splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive trans -splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and trans -splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.
... Reino CHROMISTA Cavalier-Smith, 1981 Divisão (Filo) HAPTOPHYTA Hibberd ex Cavalier-Smith, 1986 Classe PRYMNESIOPHYCEAE Hibberd, 1976 Subclasse PRYMNESIOPHYCIDAE Cavalier-Smith, 1986 Ordem DISCOASTERALES Hay, 1977 Família DISCOASTERACEAE Tan, 1927 Gênero Discoaster Tan, 1927 Grupo DISCOASTER BROUWERI de Young (1998) Discoaster asymmetricus Gartner, 1969Figuras 4a-b 1969 Discoaster asymmetricus Gartner,p. 595,est. 1, Descrição: Asterolitos delgados com cinco raios. ...
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Os discoasteres são nanofósseis calcários de ampla distribuição e especiação no Cenozoico, apresentando formas de estrelas ou rosetas. No Neógeno, este gênero orienta a detecção de diversas biozonas, através de seus surgimentos e extinções. Porém, por possuírem raios compostos por calcitas de hábito tabular, são mais suscetíveis aos efeitos de supercrescimento e recristalização que os cocólitos, sendo muitos indivíduos, morfologicamente diferentes, englobados numa mesma espécie, e apresentados como variações preservacionais. Ao investigarmos os estratos mio-pliocênicos da Elevação do Rio Grande e Canal de Vema, nos deparamos com quantidades representativas destas variantes preservacionais, que são discutidas neste trabalho. Vinte e três táxons foram descritos e oito variantes foram destacadas, de forma a apresentarmos novas observações e discussões, visando possíveis aplicações bioestratigráficas em investigações futuras
... coccolithoporids), Pelagophyceae, Phaeophyceae (brown algae), Prasinophyceae, Raphidophyceae, and Xanthophyceae (yellow-green algae). Note that other parallel classifications exist (Cavalier-Smith, 1981) and that only the most important algal groups are listed here. ...
Article
During the early Toarcian (Early Jurassic, ~183 Ma) global climate and environmental change profoundly impacted biogeochemical cycles and marine ecosystems culminating in the early Toarcian Oceanic Anoxic Event (T-OAE). The T-OAE exhibited a global temperature rise and carbon cycle perturbation that manifested in a stepwise negative Toarcian carbon isotope excursion. While the response of marine invertebrates towards early Toarcian environmental change is well documented, that of marine primary producers is only poorly constrained and is mainly inferred from changes in algae groups producing hard parts, such as calcareous nannoplankton and organic-walled dinoflagellates. Both biotic groups, however, represent only a small part of the marine phytoplankton, the majority of which lack parts with preservation potential in the geosphere. In order to obtain a holistic view on the response of marine primary producers towards the early Toarcian environmental perturbation, we here conducted a high-resolution study based on the combined application of molecular fossils (biomarker) and calcareous nannofossils. Upon the climax of the T-OAE our data indicate that the marine phytoplankton community structure was dominated by eukaryotic algae, which experienced at least five distinct paleoecological events. Each of these was characterized by a demise of red algae groups and shallow- and deep-dwelling calcareous nannoplankton, and a contemporaneous proliferation of opportunistic green algae groups. An increase of poorly developed coccoliths (resembling protococcoliths) during each phytoplankton event attests to periodically harsh environmental conditions in surface waters. Each phytoplankton event was followed by a recovery of pre-event algal communities, indicative of a cyclicity in unstable and fluctuating environmental conditions. During the onset of the T-OAE, phytoplankton events align with negative δ13C shifts, suggesting that changes in the global carbon cycle and the climate system impacted on marine primary producers. Phytoplankton events, particularly during the onset of the T-OAE, were accompanied by recurrent freshening of surface waters during warming periods, suggesting these were the most important ecological drivers. Cyclicity in phytoplankton events followed the short eccentricity (100 kyr) orbital frequency, emphasizing the role of orbital forcing in early Toarcian environmental change and ecosystem disturbances. Ecosystem change and extinction were not driven by a single event, but resulted from multiple disturbances that occurred superimposed onto long-term environmental change and culminated in the early Toarcian ecosystem crisis.
... A large body of molecular, morphological, and fossil data demonstrates that primary plastids are derived from an ancient (≥1 Ga, up to 1.6 Ga; Butterfield 2000; Yoon et al. 2004;Parfrey et al. 2011;Blank 2013;Bengtson et al. 2017;Sánchez-Baracaldo et al. 2017) primary cyanobacterial endosymbiosis. This event occurred in the single common ancestor of three extant photosynthetic lineages collectively known as the Plantae, and more recently, the Archaeplastida (Cavalier-Smith 1981;Margulis 1981;Reyes-Prieto et al. 2007;Adl et al. 2005;Price et al. 2012;Cavalier-Smith 2017). These lineages include the Glaucophyta (glaucophyte algae), the Rhodophyta (red algae), and the Viridiplantae (green algae and land plants) that share a two-membrane bound photosynthetic plastid organelle. ...
Chapter
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It is now widely recognized that photosynthetic eukaryotes (algae and plants) have polyphyletic origins in the eukaryotic tree of life (ETOL). The primary endosymbiosis that gave rise to the first photosynthetic organelle (plastid) occurred ca. 1.6 billion years ago via the capture and retention of a free-living cyanobacterium by a single-celled protist. This proto-alga is the ancestor of the Archaeplastida that includes the photosynthetic glaucophytes, red algae, and the green lineage. The Archaeplastida plastid spread into other protist lineages through serial endosymbiosis, giving rise to dominant marine phytoplankton such as diatoms and dinoflagellates. A significant effort has been expended on elucidating plastid origin, function, and its impacts on global primary productivity and geochemical cycles. Here we focus on the placement of algae in the ETOL, with particular emphasis on the major groups: Archaeplastida, SAR (stramenopiles, alveolates, rhizarians), haptophytes, and cryptophytes. Our approach is to rely on the analysis of ortholog groups identified in recently generated genomic and transcriptomic data to infer the ETOL, rather than using a subset of manually chosen and curated genes. We show that bioinformatic pipelines effectively, and with minimal curation recover a robust ETOL, when compared to the classical approach of utilizing “designer datasets” in multiple analyses.
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This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.
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Se propuso un modelo sedimentológico de las sucesiones sedimentarias del Mioceno de la cuenca Térraba. Este se llevó a cabo a partir de levantamientos sedimentológicos en tres transectos ubicados en los alrededores de: 1) Pejibaye, siguiendo los cauces de los ríos Platanares, Pejibaye, Águila y quebrada Veracruz; 2) Pilas, en los cauces de los ríos Fresco, Pilas y Concepción y 3) Curré, al lado de la carretera Interamericana Sur entre Lagarto y La Escuadra. Con la información obtenida y los análisis petrográficos se identificaron facies de lodolita (F1), wacke (F2) y wacke-conglomerado (F3), que fueron agrupadas en asociaciones de facies deltaica y de delta gravoso. La Asociación de facies deltaica se caracterizó por la predominancia de F2 métricas masivas intercaladas por algunas F1 métricas y pocas F3. La Asociación de facies de delta gravoso presentó, igualmente, F2 métricas masivas intercaladas por F1, pero, con mayor proporción de F3, y también, con un aumento en la presencia de granos gruesos en F2. Se interpretó que ambas asociaciones de facies tuvieron influencia volcaniclástica, en ambientes deltaicos (más proximales en la Asociación de facies de delta gravoso) con escasez de oxígeno y hostilidad a trazas fósiles. Ante la falta de información que permitiera emplear la estratigrafía de secuencias, sin que se interpretaran secuencias deposicionales ni discontinuidades que las delimitaran, se definieron las sucesiones deltaicas fina y gruesa: 1) La Sucesión deltaica fina fue representada por la Asociación de facies deltaica. La recurrencia de paquetes masivos de F2 intercalados por F1 sugirió una construcción del relleno por agradación. El ambiente deltaico indicó la somerización de la cuenca, con una alta subsidencia, según los grandes espesores, y una alta tasa de sedimentación. Fue datada como Mioceno inferior-medio. Se consideró como una unidad inferior de la Formación Curré. 2) La Sucesión deltaica gruesa fue representada por la Asociación de facies de delta gravoso. El orden estratigráfico de las facies, similar al de la Asociación de facies anterior, sugirió una construcción del relleno por agradación, y la mayor proporción en los materiales de grano grueso, y los grandes espesores, indicaron progradación, con un incremento en el aporte sedimentario. Fue datada como Mioceno medio-superior. Se consideró como una unidad superior de la Formación Curré. El modelo sedimentológico mostró la somerización de la cuenca Térraba en el Mioceno, según las dos asociaciones de facies deltaicas. La cuenca evolucionó desde un período de alta profundidad y tasa de sedimentación en el Mioceno inferior, representado por la Sucesión deltaica fina, a uno de compresión tectónica, con alta tasa de erosión y un incremento del aporte de materiales gruesos, en el Mioceno medio-superior, mostrado en la Sucesión deltaica gruesa. El área fuente se ubicó en el arco volcánico de Talamanca, y se mostraron evidencias de la influencia del vulcanismo. La distribución sedimentaria se habría dado desde el sureste del área de estudio. En ese sitio se presentó más deformación, y menor al noroeste. Se propuso que se extienda el rango temporal de la Formación Curré a todo el Mioceno.
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The endosymbiosis theory most widely accepted variant surmises the engulfment of bacterial cell by archaeal cell. For decades, this scenario was reputed to be an unconfirmed hypothesis, and only recently it has obtained an indirect proof in Asgard archaea environmental DNA encoding eukaryotic signatures − actin cytoskeleton, small GTPases, and ESCRT complex. In view of growing interest to this aspect of the endosymbiosis theory, it seemed timely to revisit basic terms eukaryotic cell/eukaryotes/nucleated organisms. The article highlights inadequate applications of these terms, and seeks for their consistency with regard to phylogeny and taxonomy. Additionally, new name Caryosignifera is proposed for the archaeal phylum represented by: (1) several underexplored representatives of Asgard archaea manifested by above-mentioned DNA; (2) extant descendants of extinct engulfing archaea; (3) eukaryotic host cell lineages in modern nucleated organisms (protists, algae, plants, fungi, and animals).
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Статья посвящена разработке классической периодизации филогенеза психики А.Н.Леонтьева в контексте современных научных фактов о психической и морфофизиологической организации различных групп живых организмов. Обосновывается тезис о том, что на современном этапе развития науки сплошное деление эволюции психики на ряд стадий и уровней не отражает всей специфики данного процесса. На основе теории А.Н.Северцова выделяются главные направления эволюции психики: ароморфоз, идиоадаптация, дегенерация. В первой части статьи на основе онтологического и дифференционно-интеграционного подходов разрабатывается инструментарий анализа эволюции психического образа; далее с его помощью анализируются основные ароморфозы психического развития. Показывается, как от общего ствола эволюции постепенно отделяются боковые идиоадаптационные и дегенеративные линии эволюции психики.
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Salt-marsh foraminiferal assemblages serve as a key proxy for reconstructing sea level on multi-decadal to multi-millennial timescales, enabling reconstruction of sea level to potentially within 5 to 15-cm precision. The genus Trochamminita, common in salt-marsh environments, has proven unclear in recent decades with regard to the number of species represented within it. Because different species may possess different preferred elevations relative to sea level, it is important that the number of taxa be elucidated, to ensure future sea-level reconstructions using foraminifera are as precise as possible. Here, using new specimens identified from Pauatahanui Inlet, southern North Island of New Zealand, and Aramoana salt marsh, southern South Island, the agglutinated species Trochamminita irregularis is recognised as likely distinct from Trochamminita salsa, and a new species, Pseudotrochamminita malcolmi (n. gen., n. sp.), is named, having been identified in earlier studies either as specimens of T. irregularis, or of the unrelated species Polysaccammina ipohalina. Trochamminita irregularis and Ps. malcolmi differ from one another in chamber morphology, apertural morphology and number, chamber texture, geographical distribution, and optimal heights relative to sea level.
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Neutron tomographic reconstructions, macrophotography, transmitted light microscopy and fluorescence microscopy are employed to assess the quality of organic preservation, determine organ associations, identify insect damage, and document fungal interactions with selected Santonian–lower Campanian plant fossils from the northern Kristianstad Basin, southern Sweden. Fricia nathorstii (Conwentz) comb. nov., is proposed for a composite fossil comprising an anatomically preserved (permineralized) cupressacean conifer cone and its subtending, concealed, leafy axis (preserved as a mould) in the Ryedal Sandstone. Several other impressions of conifer and angiosperm leaf-bearing axes and isolated leaves are described under open nomenclature. Three cuticle types are described from the non-marine plant-bearing beds in the basal part of the succession exposed at Åsen, but these are only assigned to informal morphotypes pending a comprehensive review of the extensive fossil cuticle flora. Two species of ascomycote epiphyllous fungi from Åsen are established: Stomiopeltites ivoeensis sp. nov. (Micropeltidales) and Meliolinites scanicus sp. nov. (Meliolales). The latter provides an important calibration point for dating the divergence of Meliolales, being the first pre-Cenozoic representative of the order. Various additional fungal remains, including thyriothecia, scolecospores, chlamydospores, putative germlings, and hyphae, are described from the cuticular surfaces of conifer and angiosperm leaves from Åsen. Insect herbivory is expressed in the form of both margin-feeding and piercing-and-sucking damage on angiosperm leaves. The Santonian–early Campanian vegetation is inferred to have grown in strongly humid, mid-latitude, coastal plain settings based on the depositional context of the assemblages, leaf morphology, and the pervasive distribution of epiphyllous fungi.
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Plant population dynamics research has a long history, and data collection rates have increased through time. The inclusion of this information in databases enables researchers to investigate the drivers of demographic patterns globally and study life history evolution. Studies aiming to generalise demographic patterns rely on data being derived from a representative sample of populations. However, the data are likely to be biased, both in terms of the species and ecoregions investigated and in how the original studies were conducted. Matrix population models (MPMs) are a widely-used tool in plant demography, so an assessment of publications that have used MPMs is a convenient way to assess the distribution of plant demographic knowledge. We assessed bias in this knowledge using data from the COMPADRE Plant Matrix Database, which contains MPMs for almost 800 plant species. We show that tree species and tropical ecoregions are under-represented, while herbaceous perennials and temperate ecoregions are over-represented. In addition, there is a positive association between the number of studies per country and the wealth of the country. Furthermore, we found a strong tendency towards low spatiotemporal replication: More than 50% of the studies were conducted over fewer than 4 years, and only 17% of the studies have replication across >3 sites. This limited spatiotemporal coverage means that the data may not be representative of the environmental conditions experienced by the species. Synthesis: The biases and knowledge gaps we identify are a challenge for the progress of theory and limit the usefulness of current data for determining patterns that would be useful for conservation decisions, such as determining general responses to climate change. We urge researchers to close these knowledge gaps with novel data collection.
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Estos Apuntes pueden servir de base para estudiar Fitopatología a diferentes niveles. Por su lenguaje simple y abundantes ilustraciones, son fácilmente comprensibles por estudiantes, productores y aficionados. La obra incluye aspectos básicos de las enfermedades e información práctica para su manejo. Marta Rivera y Eduardo Wright son Profesores de Fitopatología en la Facultad de Agronomía de la Universidad de Buenos Aires. La Dra. Rivera es investigadora en INTA.
Thesis
The discovery and characterisation in this laboratory of a 35 kilobase plastid genome from the malaria parasite, Plasmodium, has led to intense speculation concerning its origins and function. This thesis describes how sequence data were garnered from malaria's distant apicomplexan cousins, the coccidians and piroplasms, and used to make an evolutionary analysis of their corresponding plastid DNAs. From the sequence data produced it appears highly likely that the plastid DNA was gained by an ancient progenitor of the Apicomplexa, and singularly reorganised upon the adoption of a parasitic lifestyle. Previously, the identification in this laboratory of a Plasmodium plastid encoded open reading frame with homologues in rhodoplast genomes led to the suggestion that the apicomplexan organelle has a red algal origin. However, phylogenetic analysis of the tuf gene, which encodes the ubiquitous plastid and prokaryotic elongation factor Tu, provides support for the hypothesis that the organelle was derived through endosymbiosis of a green alga. The highly conserved nature of the extrachromosomal DNA found across the range of parasites studied here suggests that the organelle within which the genome is housed performs a vital cellular role. However, the results presented provide no indication of its particular function. The sequence data generated also led to the speculation that certain plastid encoded products may provide targets for novel anti-apicomplexan chemotherapeutics. Finally, it is inferred from the sequence of the plastid DNA of the coccidians, Toxoplasma gondii and Eimeria tenella, that opal stop codons are occasionally used as tryptophan codons. Such a system would be the first identified in a plastid organelle.
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Mesofossils from the Upper Cretaceous of Lower Silesia are escribed from the Nowogrodziec Member of the Czerna Formation. The vestigated strata are part of the North Sudetic Synclinorium and are of either late Coniacian or early Santonian age. The flora comprises egaspores of lycophytes, conifer and angiosperm mesofossils, and insect-related fossils (coprolite, eggs). Megaspores are assigned to the genus Ricinospora. Fragments of the sterile conifer twigs unninghamites sp. and Geinitzia formosa are associated with isolated seeds of the conifer genera Seletya and Alapaja. The greatest diversity is found among reproductive structures of angiosperms within the Normapolles complex. They are assigned to Caryanthus communis, Caryanthus trebecensis, Caryanthus triasseris, Caryanthus sp., Zlivifructus vachae, and Zlivifructus microtriasseris. Additionally, there are several unidentified reproductive structures showing affinities with plants of the Normapolles complex. Finally, there is a single insect coprolite and a few possible insect eggs assigned to Costatheca striata.
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A Elevação Ceará é uma feição assísmica localizada no Oceano Atlântico Equatorial, entre o Cone Amazônico e a Planície Abissal do Ceará, que representa uma área chave para a compreensão de fácies oceânicas profundas. Na área de Petróleo e Gás, a identificação de biozonas com base em nanofósseis calcários é importante para o posicionamento temporal e entendimento da evolução deposicional de estratos sedimentares. O estudo da sucessão oligocênica com base em nanofósseis calcários na Elevação Ceará colaborou na detecção de inferências paleoecológicas para o Oceano Atlântico Equatorial durante o Oligoceno. Com o auxílio de um microscópio óptico de luz polarizada, foram observados, descritos e contabilizados quarenta e quatro táxons em quinze amostras (1-2 amostras por Core), o que permitiu o biozoneamento do Site 929A, que engloba as biozonas NP23, NP24, NP25 do zoneamento padrão para nanofósseis, assim como a biozona NP26 - Clausicoccus fenestratus, recentemente proposta. Dentre as espécies encontradas, destacam-se os Sphenolithus ciperoensis, Sphenolithus distentus e Sphenolithus predistentus, importantes marcadores bioestratigráficos do Oligoceno. Através da quantificação dos fósseis, foi possível dividir a seção estudada em oito intervalos distintos de acordo com as variações nos valores dos paleoproxies e dos índices de diversidade: Intervalo A (CP17: Rupeliano): apresentando uma associação típica de águas superficiais mais aquecidas e oligotróficas; Intervalo B (CP18: Rupeliano): apresentando uma associação típica de águas superficiais mais temperadas e mesotróficas/eutróficas; Intervalo C (CP18 e CP19a: Rupeliano/Chattiano): apresentando uma associação típica de águas superficiais mais aquecidas e oligotróficas; Intervalo D (CP19a e CP19b: Chattiano): apresentando uma associação típica de águas superficiais mais temperadas e mesotróficas/eutróficas; Intervalo E (CP19b: Chattiano): apresentando uma associação típica de águas superficiais mais aquecidas e oligotróficas; Intervalo F (CP19b: Chattiano): apresentando uma associação típica de águas superficiais mais temperadas e oligotróficas; Intervalo G (CP19b: Chattiano): apresentando uma associação típica de águas superficiais mais temperadas e oligotróficas; Intervalo H (CN1a: Chattiano): apresentando uma associação típica de águas superficiais mais temperadas e eutróficas.
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Green euglenophyte are a group of eukaryote with ancient origin. In order to understand the evolution of the group, it is interesting to know which characteristics are more primitive. Here, a phylogenetic tree of green euglenophytes based on the 18S rRNA gene was constructed, and ancestral states were reconstructed based on eight morphological characters. This research clarifies the phylogenetic relationships of green euglenophytes and provides a basis for the study of the origin of these plants. The phylogenetic tree, which was constructed by Bayesian inference, revealed that: Eutreptia and Eutreptiella were sister groups and that Lepocinclis, Phacus and Discoplastis were close relatives; Euglena, Cryptoglena, Monomorphina, and Colacium were closely related in addition to Trachelomonas and Strombomonas; and Euglena was not monophyletic. An ancestral reconstruction based on morphological characters revealed seven primitive character states: ductile surface, spirally striated, slightly narrowing or sharp elongated cauda, absence of a lorica, chloroplast lamellar, shield or large discoid, pyrenoid with sheath, and with many small paramylon grains. However, the ancestral state of the length of the flagellum could not be inferred. Euglena and Euglenaria, which both possessed all of the ancestral character states, might represent the most ancient lineages of green euglenophytes.
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The charophyte flora from Socotra Island, Indian Ocean, studied for the first time from streams waterbodies that distributed at the northern part of the Island. The recognized charophyte taxa were taxonomically investigated, and four dominant species belonging to family Characeae are identified as Chara braunii, C. globularis, C. hispida and Lamprothamnium papulosum. These taxa are reported as a new record for algal flora of Socotra Island. A brief account of the environment where the charophytes were found is provided, as a first evaluation of the ecological requirements of Indian charophytes. A taxonomically diverse of charophyte assemblage and ecological variables explain abiotic features of biotope as shallow (max 1.3 m), alkaline fresh (pH 7.5–8.4), slightly saline, and moderate eutrophic.
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Biological classification is the scientific procedure of arranging the organisms in a hierarchical series of groups and sub-groups on the basis of their similarities and dissimilarities. Many biologists have contributed to this method of classification, which took years for researchers to decide the most fundamental characteristics for the classification. The history of kingdom system in classification is started with Linnaeus (1735), who laid the foundation of modern biological classification by classifying the organisms into two kingdoms namely Plantae and Animalia. The two kingdom system was followed by three, four, five and six kingdom systems respectively. In present discussion, authors tried to discuss the current status of different animal phyla with respect to different kingdom systems.
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Five kingdom system of biological classification was proposed. These kingdoms were: Monera, Protista, Fungi, Plantae and Animalia. The history of kingdom system started, laid the foundation of modern biological classification by classifying the organisms into two kingdoms namely Plantae and Animalia. The two kingdom system were followed by three, four and five kingdom systems respectively. In present discussion, author tried to discuss the evolution, merits, demerits and relevancy of “five kingdom system” in modern context.
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Resumo GATTO, André. Nanofósseis calcários neógenos da Elevação do Rio Grande e Canal de Vema (Atlântico Sul): Bioestratigrafia e dinâmica paleoceanográfica. Rio de Janeiro, 2020. xviii, 259 f. Tese de Doutorado - Programa de Pós-graduação em Geologia, Instituto de Geociências, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 2020. A Elevação do Rio Grande é uma feição assísmica, no Oceano Atlântico Sudoeste, que por ser seccionada de Sul para Norte pelo Canal de Vema, em ambiente abissal, permite a entrada da Água de Fundo da Antártica na Bacia Oceânica do Brasil. Para investigar o histórico deposicional das vasas biogênicas da região durante o Neógeno, foi realizado um estudo bioestratigráfico e paleoecológico, com base em associações de nanofósseis calcários, nos Sites 516, 516A e 518 do DSDP. Noventa e dois táxons foram identificados e contados. Dez biozonas e quatro associações foram detectadas no Site 516, englobando um intervalo do Burdigaliano ao Piacenziano, oito biozonas e uma associação para o Site 516A, do Tortoniano ao Piacenziano e quatro biozonas e uma associação no Site 518, do Langhiano ao Piacenziano. Mudanças na preservação, principalmente dos discoasteres de cinco pontas, Amaurolithus spp. e Ceratolithus spp., revelaram possível interferência na identificação de biozonas em estudos anteriores na região. A abundância relativa dos proxies selecionados, índices ecológicos e os resultados dos agrupamentos CONISS, revelaram dezessete intervalos paleoecológicos nas seções estudadas: quatro intervalos oligotróficos (O1-O4), sete intervalos mesotróficos (M1-M7), cinco intervalos eutróficos (E1-E5) e um intervalo de Ressurgência (R1), que foram discutidos perante as principais mudanças paleoceanográficas globais do Neógeno, como o Ótimo Climático do Mioceno médio, a Crise de salinidade do Messiniano, a Inundação Zancleana, a formação do Ístimo do Panamá e a expansão do Manto de Gelo da Antártica Oriental, com destaque para o intervalo de ressurgência (R1), datado do Tortoniano. Abstract GATTO, André. Nanofósseis Calcários Neógenos Da Elevação Do Rio Grande E Canal De Vema (Atlântico Sul): Bioestratigrafia e dinâmica paleoceanográfica. [Neogene calcareous nannofossils from the Rio Grande Rise and Vema Seachannel: Biostratigraphy and paleoceanographic dynamics.] Rio de Janeiro, 2020. xviii, 259 f. Tese de Doutorado (Geologia) - Programa de Pós-graduação em Geologia, Instituto de Geociências, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 2020. The Rio Grande Rise is an asismic feature in Southwestern Atlantic Ocean, which is intercepted by the Vema Seachannel at ultradeep depths, enabling the input of the Antartic Bottom Water into the Brazil Oceanic Basin. In order to investigate the carbonate depositional history of the area during the Neogene, a bioestratigraphic and paleoecological study was conducte, based on calcareous nannofossil assemblages fom DSDP Sites 516, 516A and 518. Ninety-two taxa were identified and counted. Ten biozones and four associations were detected at Site 516, encompassing a range from Burdigalian to Piacenzian ages, eight biozones and an association at Site 516A, comprising a section from Tortonian to Piacenzian ages and four biozones and an association at Site 518, encompassing a section of Langhian to Piacenzian ages. Preservation changes, mainly on five-rayed discoasters, Amaurolithus spp. and Ceratolithus spp., revealed possible preservational interference in the identification of biozones in previous studies at this region. The relative abundance of the selected proxies, ecological indexes and the results of the CONISS clustering, revealed seventeen paleoecological intervals in the studied sections: four oligotrophic intervals (O1-O4), seven mesotrophic intervals (M1-M7), five eutrophic intervals (E1-E5) and an upwelling interval (R1), which were discussed in the light of the main global paleoceanographic changes of the Neogene, such as the Middle Miocene Climatic Optimum, the Messinian Salinity Crisis, the Zanclean Flood, the formation of the Isthmus of Panama and the expansion of the East Antarctic Ice Sheet, with emphasis on the upwelling interval (R1), dated of the Tortonian.
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Representatives of phycobiliprotein-containing algae such as Anabaena cylindrica, Anacystis nidulans, Gloeotrichia echinulata (Cyanophyceae), Chroomonas spec., Hemiselmis rufescens, Rhodomonas spec. (Cryptophyceae), Porphyridium cruentum, Rhodella violacea (Rhodophyceae) along with the unicellular Cyanidium caldarium (unspecified systematic status) have been investigated for their typical photoassimilatory accumulation products. While the red algal species synthesize a rather specific heteroside, 2-O-D-glycerol-α-D-galactopyranoside (= floridoside), not encountered in the other species analyzed, blue-green algae accumulate fructose, glucose, and sucrose, while the cryptomonads accumulate only glucose and. to a lesser extent, fructose. Cyanidium synthesizes neither disaccharides, nor a heteroside, but shows rapid 14C-labelling of fructose and glucose. These results are compared with further biochemical and structural findings and are discussed with emphasis on chemotaxonomic implications. Cyanidium caldarium is proposed as an endocyanome consisting of a single endocyanella providing the functions of a chromatophore in a colourless (apoplastidal algal?) host cell. © 2015 Verlag der Zeitschrift für Naturforschung.
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The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
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To classify an organism is to assign it to a group. Classification, which is part of the science of systematics, is the essential concern of taxonomy. Taxonomy is the branch of biological science involved with identifying, naming, and classifying organisms into a formal hierarchical system. Systematics is the science that deals with the relationships of organisms as approached through their form and function, their genetic systems, their fossil histories, and the understanding of the evolutionary process from which they arose.
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The phylogeny of the rather diverse and varied forms of organisms called the Fungi has been a hotbed of debate among mycologists for several decades. Until the late 1950s, almost all phylogenetic schemes of the fungi were based on morphological criteria. But, in the absence of reliable fossil records, all phylogenetic trees proposed had to remain hypothetical since it could not be proven unequivocally whether a particular morphological homology between taxa developed through convergent or parallel evolution.
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This chapter will argue that modern biologists, in spite of social pressures and historical precedents, need to replace the traditional two-kingdom animal-plant distinction, which has outlived its usefulness, with a multikingdom classification of living organisms. For reasons discussed below, based on recent discoveries from a variety of disciplines, it seems that Whittaker’s five-kingdom system (Whittaker, 1969) is the most logical and consistent yet devised. Whittaker’s system is expanded below the phylum level and slightly modified on the basis of cell evolutionary considerations; suggestions for its adoption by zoologists, botanists, and microbiologists are made.*
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Summary A variety of schemes are employed currently for the classification of plants into higher taxa. The two most widely used schemes, the traditional kingdom Plantae with subkingdoms Thallophyta and Embryophyta, and the Whittaker five-kingdom system with plants in the kingdoms Monera, Protista, Fungi and Plantae, rely on nineteenth century morphological criteria for delimitation of taxa that result in polyphyletic assemblages of organisms. It is proposed that plants be assigned to seven kingdoms, subordinate to the superkingdoms Procaryota and Eucaryota which are based on the procaryotic and eucaryotic types of cellular organization. The distribution of accessory chlorophylls is used as a major taxonomic criterion for classifying photosynthetic organisms at the kingdom level. This results in a single kingdom, the Cyanochlorobionta for photosynthetic plants containing chlorophyll a only within the superkingdom Procaryota. Photosynthetic plants within the superkingdom Eucaryota have been divided into three groups, the kingdom Erythrobionta for organisms with no accessory chlorophyll or occasionally chlorophyll d (and lacking flagella), the kingdom Chlorobionta for organisms with accessory chlorophyll b, and the Ochrobionta for those organisms with accessory chlorophyll c. Vascular plants have been assigned to a single division, the Tracheophyta, since in addition to having a similar biochemistry (chlorophylls a and b, similar carotenoids, starch as a reserve food product) they possess also a basic morphological groundplan - a vascular system containing xylem and phloem, and a life history consisting of an alternation of generations. The fungi have been assigned three kingdoms as opposed to most extant schemes of classification in which they are allocated to a single polyphyletic assemblage. The true fungi have been divided into kingdoms Fungi I and Fungi 2 since it is thought that they have evolved from the Chlorobionta and Ochrobionta, respectively; the myxomycetes have been placed in a third kingdom, the Myxobionta. A perusal of eighteen botanical books published in the U.S.A. during the last decade has revealed a considerable lack of uniformity in the usage of the higher categories of classification: five used the traditional two kingdom system of organisms with the kingdom Plantae for plants and the subkingdoms Thallophyta and Embryophyta; three employed the recently proposed five kingdom organismic system of Whittaker (1969) with plants in the kingdoms Monera, Protista, Plantae and Fungi; six began their treatment at the division level, presumably due to lack of satisfaction with existing schemes; and two proposed new systems for the subdivision of the traditional kingdom Plantae, Bold (1973), who has been followed subsequently by two authors, established the subkingdoms Prokaryonta, Chloronta, and Achloronta, and Neushul (1974) the subkingdoms Prokaryonta and Eukaryonta. In the last few decades a tremendous accumulation of cytological and biochemical data has occurred (Klein and Cronquist, 1967), but these have not been adequately utilized in classification. With the recent publication of compendia
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Dodson, E. O. (Dept. Biology, Univ. Ottawa, Ottawa, Out. KIN6N5). 1971. The Kingdoms of Organisms. Syst. Zool. 20:265–281.—Traditionally, all organisms have been assigned to the Plant and Animal Kingdoms. Higher members of these assemblages differ so clearly in so many ways that no confusion arises even in those cases in which members of one kingdom show some characteristic of the other, for example, insectivorous plants, or cellulose producing tunicates. Among primitive organisms, especially among flagellates and fungi, however, application of the ordinary criteria for differentiation of plants and animals leads only to confusion. Most biologists have ignored this problem, but for over a century a few have tried to resolve it by erecting additional kingdoms for these primitive organisms. While such systems have expressed a widespread professional malaise, they have not achieved general acceptance because of logical difficulties of these systems and the relative unfamiliarity of the key groups to most biologists. Recently, however, it has been shown that the bacteria and blue-green algae (procaryotes) contrast with all higher organisms (eucaryotes) so sharply in an extensive array of nuclear and cytoplasmic characteristics that the procaryotes must be regarded as a separate kingdom of life, the Kingdom Mychota. The major cytoplasmic organelles of eucaryotes, i.e., chloroplasts, flagella and other 9 + 2 organelles, and mitochondria, are all missing from procaryotes. A long series of observations, culminating in exact biochemical comparisons, indicates that these organelles originated as intracellular symbionts. Thus, the eucaryotes arose from a large, amoeboid, anaerobic procaryote given to ingestion of smaller procaryotes, some of which became established as intracellular symbionts. Aerobic symbionts were integrated into the host as mitochondria, while flagellate procaryotes with the 9 + 2 structure became flagella and a whole series of other 9 + 2 organelles. Mitosis and meiosis then evolved, and the eucaryote cell was complete. There is a nexus of relationships among the eucaryotes which makes it infeasible to separate the problematical groups of primitive eucaryotes into a kingdom apart. Thus, the present paper supports a basic taxonomy of three kingdoms Mychota, Animalia, and Plantae. The intergrades between the latter two are treated not as defects of the classification but rather as the inevitable result of common ancestry and separation by a process of evolution.
Article
It is generally agreed that the first organisms were prokaryotic in nature. However, opinions differ as to the mechanism responsible for the origin of the eukaryotic cell -- whether it arose by direct filiation from an ancestral blue-green alga or by a series of symbioses. The timing of the emergence of photosynthesis in eukaryotes has largely been based on evidence from Precambrian palaeontology. For this reason attention is drawn to recent reassessments of the Precambrian fossil record, which have suggested that a number of structures previously considered to be remnants of eukaryotic nuclei and organelles may instead have been artifacts that formed in certain blue-green algae during their lithification. Evidence regarding the mechanism responsible for the origin of chloroplasts may be sought in the molecular fossil record. Studies employing the techniques of DNA-RNA hybridization and RNA sequencing (oligonucleotide cataloguing) have established the prokaryotic nature of chloroplast ribosomal RNAs. In addition, a close phylogenetic relationship between the blue-green alga Aphanocapsa 6308 and the chloroplasts of Euglena gracilis has been indicated. By contrast, the sequence resemblance of prokaryotic and chloroplast 16 S rRNAs to eukaryotic 18 S rRNAs is revealed to be no greater than that expected between completely unrelated molecules. However, the size differences which exist between 16 S and 18 S rRNAs raise doubts as to whether these RNA species are in fact directly comparable. On the other hand, all known examples of mature 5 S rRNA are approximately 120 nucleotides in length, and thus this RNA would appear to bridge the evolutionary discontinuity between prokaryotes and eukaryotes in an almost unambiguous manner. The identification of 5 S rRNA in chloroplast ribosomes has therefore prompted a number of investigations designed to establish the prokaryotic or eukaryotic affinities of this RNA species. These have confirmed the prokaryotic nature of chloroplast 5 S rRNAs, and have indicated the sequence dissimilarity of these species to the cytoplasmic 5 S rRNAs of eukaryotes. However, it is pointed out that such results can only provide conclusive support for the endosymbiotic hypothesis, if rates of change in homologous RNAs have remained approximately constant in all lines. Combined evidence suggests that nucleotide substitutions in cytoplasmic ribosomal RNAs have occurred more frequently during the evolution of flowering plants, Gramineae in particular, than during the evolution of yeast or vertebrates. By contrast, chloroplast ribosomal RNAs are shown to be very strongly conserved. Moreover, considerable disparities are also noted in the relative amounts of change in prokaryotic and eukaryotic 5 S rRNAs. Although undoubtedly associated with their different architectures and functional roles, it is suggested that the primary explanation for this phenomenon lies in the fact that the cytoplasmic 5 S rRNAs of eukaryotes are not derived from that of the protoeukaryote host, but rather, from that of the protomitochondrion. The cytoplasmic 5.8 rRNAs are now considered to be the extant descendants of the original protoeukaryote 5 S rRNA these species having increased in size in a similar manner to the other cytoplasmic ribosomal RNAs of eukaryotes. Because the rates of nucleotide substitution in homologous prokaryotic and eukaryotic ribosomal RNAs are non-identical, consideration is given to derived character states. The late methylated sequence -Gm2 6Am2 6AC- has been identified in the 16 S rRNAs of many prokaryotic microorganisms and may possibly be universal in the 18 S rRNAs of eukaryotes. Although its presence has been indicated in the 18 S rRNA of Euglena gracilis, it is absent from the chloroplast 16 S rRNA of this protist, as well as from the 16 S rRNAs of Aphanocapsa 6308 and many other blue-green algae. Direct filiation would seem unable to provide a satisfactory explanation for this phenomenon. As a result it is concluded that chloroplasts, and most probably mitochondria also, are of endosymbiotic origin.
Article
The division of living organisms into Plantae and Animalia fails to recognise the major evolutionary discontinuity between prokaryotes and eukaryotes. In addition, fungi and "plant-animal" unicells lie uncomfortably in such a two-kingdom system. Systems have been proposed which separate prokaryotes from eukaryotes and divide the latter into several kingdoms. These schemes share two limitations. The "low" eukaryote kingdom (Protoctista or Protista) contains phyla more closely related to phyla of the "higher" kingdoms than to other phyla in the same kingdom. Secondly, the higher kingdoms are polyphyletic to a disturbing degree. Can one make broad classifications without these limitations? A Prokaryota/Eukaryota two-kingdom scheme is one possibility; another is a four-kingdom scheme in which the protistan level is absorbed into the eukaryote kingdoms; a third possibility is a system in which phylum and phylogeny units stand as monophyletic kingdoms; such a multikingdom scheme provides fruitful scope for discussion. The Prokaryota/Eukaryota and multikingdom schemes allow flexibility for incorporation of new information on relationships, but may be thought too fragmentary for practical taxonomy. If so, various four- or five-kingdom schemes are available.
Article
Zusammenfassung Die Morphologie und Feinstruktur (einschließlich Pellicula, Geißelapparat, Mitose und Cytokinese) von Cyanophora paradoxa, Gloeochaete wittrockiana und Glaucocystis nostochinearum, drei apoplastidalen Algen mit blaugrünen Endosymbionten (Cyanellen), wurde vergleichend untersucht. Gloeochaete und Glaucocystis sind in allen systematisch bedeutsamen Merkmalen gleich, während Cyanophora insbesondere durch seine andersartige Struktur der Geißelwurzeln abweicht. Die bei Gloeochaete und Glaucocystis vorkommende Kombination von Merkmalen, in geringerem Maße gilt das auch für Cyanophora, ist bei keiner anderen Klasse der Algen vorhanden. Es wird vorgeschlagen, Gloeochaete und Glaucocystis (und mit gewissen Einschränkungen auch Cyanophora) als Glaucophyceen zu führen, wie das bereits Skuja (1954) vorgeschlagen hat.
Article
The photosynthetic performance of the blue-green endosymbiotes (cyanelles) in four apoplastidal algae, Cyanophora paradoxa, Gloeocbaete wittrockiana, Glaucosphaera vacuolata, and Glaucocystis nostochinearum, has comparatively been investigated. All cyanelles exhibit rates of light dependent carbon assimilation comparable to other algal species. Dark carbon fixation is negligibly low. Kinetics of 14C-labelling of intermediary photosynthates indicate that the reductive pentose phosphate cycle is operational in all cyanelles. The pattern of 14C-labelled low-molecular weight photosynthetic products is very similar in all endocyanomes investigated. It differs considerably from 14C-assimilate patterns of the Rhodophyta (and Chlorophyta). Sucrose is not 14C-labelled in the cyanomes, whereas glucose, maltose, and fructose are the most intensely labelled compounds encountered. The comparison of the intact association Cyanophora paradoxa and its isolated cyanelles as well as the results from feeding experiments with 14C-glucose suggest that glucose is transferred from the cyanelles to the host cells and there converted into disaccharides (maltose) and/or polyglucans. The results are discussed with emphasis on the symbiotic status of the cyanelles.
Article
Evolutionary relations are better represented by new classifications than by the traditional two kingdoms.
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Evidence for the presence of silica in the costae of Stephanoeca diplocostata Ellis has been provided by a combination of light and electron microscopy. The solubility of costae in hydrofluoric acid has been demonstrated. The presence of silicon in the costae has been strongly confirmed by means of the X-ray analytical electron microscope (EMMA) but tests for a crystalline substructure by means of electron diffraction were negative; it is concluded that silicon is present in a crystallographically amorphous form. Preliminary observations on other biological aspects of the organism include the presence of a sac-like membrane between the lorica and protoplast, the presence of immature costal strips within the cytoplasm and the nature of ingested food. The phyletic position of the group is briefly discussed with special reference to mitochondrial substructure.
Article
SYNOPSIS. Information relating to the ultrastructure of 4 organellar systems of flagellates—nuclei (including mitosis), flagella, mitochondria and chloroplasts—is examined for bearing on the probable phylogeny of the principal flagellate groups, first considered singly and then in combination. The mitotic mechanism has not proved to be as conservative a character as might be hoped, but still remains characteristic for the average condition in many of the groups. Flagellar features are useful if allowance is made for the reduction or multiplication of the basic pair, and the loss of lateral and terminal hairs seems to have occurred independently several times. The presence of paraxial rods within flagella may be a useful indication of affinity. Rootlet systems are not dealt with in detail here, although the possible similarity between axial microtubular sheets in axostylar flagellates and some members of the green algae containing “manchettes” is noted. The basic patterns of chloroplast internal structure are summarized and their general agreement with other characters is affirmed, noting however that cryptomonads may be closer to the green flagellates (including euglenoids) than is generally accepted. Attention is drawn to the potential value of internal mitochondrial morphology as an indicator of large assemblages. Finally, a “tree” based on multiple cell organizational features is presented and discussed.
Article
The ustilaginaceous fungi, traditionally synonymous with the smuts, now include recent taxa derived from the yeasts. Although generally placed next to the rusts, these fungi only superficially resemble the Uredinales-the resistant cell, here termed a ustospore, is not a teliospore and its one or more germ hyphae bear somatic sporidia, not meiotically derived basidiospores. Examination of the ultrastructure of a number of species shows the septa to be basidiomycetously layered but with pores lacking a dolipore/parenthesome complex. Further, inLeucosporidium andRhodosporidium, in which the clamps also have simple pores, the electron microscopic observations admit the interpretation that the ustospore is an encysted proascus. Because the characteristics of these fungi do not allow them to be satisfactorily included among either the Ascomycota or the Basidiomycota, it is proposed to accommodate them in a new taxon of equal rank, the Division Ustomycota.
Article
An electron-dense helix is the most conspicuous structure in the flagellar transition region of members of the algal class Chrysophyceae. This “transitional helix” (TH) lies immediately distal to a partition across the flagellar axoneme which occurs exactly at the level at which the flagellum enters the cell body. The helix surrounds the central axonemal pair and lies at a distance of 10 nm from the 9 peripheral doublets. From the new data presented and a survey of published observations on the structure of the transition region of all the chlorophyll c-containing classes of algae, it is shown that a TH characteristic of the Chrysophyceae, Xanthophyceae and Eustigmatophyceae. The number of TH gyres varies from 3 to 6 in the Xanthophyceae and from 1 to 8 in the Chrysophyceae. In any one species, however, the TH is the same size in both the long flagellum which bears tubular mastigonemes and in the short smooth flagellum, though in some chrysophytes where the short flagellum is vestigial the number is fewer than in the normal flagellum. A TH appears to be absent from the Rhaphidophyceae and zoids of the Bacillariophyceae and Phaeophyceae though the structure of the transition region in these groups otherwise resembles that of the Chrysophyceae, Xanthophyceae and Eustigmatophyceae.
Article
Mitosis is defined as all those types of nuclear division that produce two, or rarely more, daughter nuclei, each containing a chromosome complement approximately similar to that of the original nucleus. The greatest range of variations by which mitosis is accomplished, occurs in the protistan and fungal kingdoms, some members of which are probably most similar to the ancestors of higher plants and animals. The variations in the higher organisms are secondarily derived from the division patterns of typical plants and animals. This chapter discusses the characteristics and evolution of mitosis. The efficiency of mitosis consists of two basic components; the frequency with which each daughter nucleus receives the necessary complete genome complement (genetic efficiency) and the amount of energy and materials expended in the synthesis and operation of the mitotic apparatus. The chapter also discusses the use of mitosis as a phylogenetic marker. It is applicable to all eukaryotic cells and thus is valuable across boundaries where other structures are absent on one side and present in various forms on the other side.