This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

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The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

In this volume John Murray investigates the ecological processes that control the distribution, abundance, and species diversity of benthic foraminifera in environments ranging from marsh to the deepest ocean. To interpret the fossil record it is necessary to have an understanding of the ecology of modern foraminifera and the processes operating after death leading to burial and fossilisation. This book presents the ecological background required to explain how fossil forms are used in dating rocks and reconstructing past environmental features including changes of sea level. It demonstrates how living foraminifera can be used to monitor modern-day environmental change. Ecology and Applications of Benthic Foraminifera presents a comprehensive and global coverage of the subject using all the available literature. It is supported by a website hosting a large database of additional ecological information (www.cambridge.org/0521828392) and will form an important reference for academic researchers and graduate students in Earth and Environmental Sciences.

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Ecology and Applications of Benthic Foraminifera

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.2012.00644.x

The revised classification of eukaryotes

1. Introduction.- 2. Taxonomy and Species Features.- 2.1 Introduction.- 2.2 Species List.- 2.2.1 Spinose Planktonic Foraminifera.- 2.2.2 Non-spinose Planktonic Foraminifera.- 3. Collecting and Culture Methods.- 3.1 Introduction.- 3.2 Collection for Ecological Studies.- 3.3 Fixation and Storing of Samples.- 3.4 Laboratory Preparations.- 3.5 Collection for Physiological and Ecological Studies.- 3.5.1 Net Collection.- 3.5.2 SCUBA Collection.- 3.6 Isolation and Preparation for Maintenance Culture.- 3.7 Maintenance Cultures.- 3.8 Monitoring Vitality and Growth of the Cultures.- 3.9 Feeding Techniques.- 3.9.1 Algal Prey.- 3.9.2 Animal Prey.- 3.10 Cataloguing and Storing Shells.- 3.11 Summary.- 4. Cellular Ultrastructure.- 4.1 Introduction.- 4.2 Fixation of Planktonic Foraminifera for Fine Structure Analysis.- 4.3 Cytoplasmic Streaming.- 4.4 Peripheral Cytoplasm and Rhizopodial Morphology.- 4.4.1 Cytoskeletal Structures.- 4.4.2 Filaments.- 4.5 Fine Structure of Cytoplasmic Organelles.- 4.5.1 Nucleus.- 4.5.2 Mitochondria.- 4.5.3 Peroxisomes.- 4.5.4 Endoplasmic Reticulum, Golgi Complex, and Vacuolar System.- 4.5.5 Fibrillar Bodies.- 4.5.6 Lipids and Various Cytoplasmic Inclusions.- 4.6 Comparative Fine Structure Data of Benthic and Planktonic Species.- 4.7 Comparative Fine Structure of Planktonic Foraminifera and Radiolaria.- 4.8 Summary.- 5. Host and Symbiont Relationships.- 5.1 Introduction.- 5.2 Symbiosis, Commensalism and Parasitism.- 5.3 Symbiont Morphology and Structural Association with Host.- 5.3.1 Dinoflagellate Symbiont Fine Structure.- 5.3.2 Chrysophycophyte Symbiont Fine Structure.- 5.4 Symbiont and Host Physiological Interactions.- 5.5 Origin of Symbionts.- 5.6 Major Features of Algal Symbionts.- 5.7 Summary.- 6. Trophic Activity and Nutrition.- 6.1 Introduction.- 6.2 Natural Prey.- 6.3 Laboratory Studies of Trophic Activity.- 6.3.1 Prey Acceptance and Rate of Digestion.- 6.3.2 Cannibalism.- 6.3.3 Fine Structure Studies of Prey Capture and Digestion.- 6.3.4 Trophic Activity and Longevity.- 6.3.5 Laboratory Studies of Omnivorous Feeding.- 6.4 Prey Abundance and Foraminiferal Distribution.- 6.5 Predators on Planktonic Foraminifera.- 6.6 Comparative Data with Benthic Foraminifera and Radiolaria.- 6.7 Summary.- 7. Reproduction.- 7.1 Introduction.- 7.2 Gametogenesis.- 7.2.1 Light Microscopic Data.- 7.2.2 Fine Structure Data.- 7.3 Morphological Changes during Gametogenesis.- 7.4 Reproductive Cycles.- 7.5 Comparisons with Benthic Foraminifera and Radiolaria.- 7.6 Summary.- 8. Shell Ontogeny.- 8.1 Introduction.- 8.2 Ontogenetic Concept for Spinose Species.- 8.2.1 Five Stage Concept.- 8.2.2 Ontogeny of Globigerinoides sacculifer.- 8.3 Variations in Developmental Morphology of Spinose Species.- 8.4 Variations in Developmental Morphology of Non-spinose Species.- 8.5 Quantitative Ontogeny.- 8.6 Coiling Directions.- 8.7 Taxonomic Applications.- 8.8 Summary.- 9. Shell Architecture.- 9.1 Introduction.- 9.2 Chamber Deposition and Pore Formation.- 9.2.1 Chamber Formation in Non-spinose Species.- 9.2.2 Pore Formation and Wall Thickening.- 9.2.3 Keel Development.- 9.2.4 Pustule Formation.- 9.3 Chamber Formation in Spinose Species.- 9.3.1 Spine Types.- 9.4 Wall Thickening and Gametogenic Calcification.- 9.5 Physiological Mechanism and Rates of Calcification.- 9.6 Organic Composition of the Calcitic Wall.- 9.7 Resorption and Repair Processes.- 9.8 Abnormal Shell Growth.- 9.9 Summary.- 10. Ecology.- 10.1 Introduction.- 10.2 Statistical Treatment and the Transfer Function.- 10.3 Stable Isotopes.- 10.4 Distributional Pattern of Planktonic Foraminifera.- 10.4.1 Horizontal Distribution.- 10.4.2 Seasonal Distribution.- 10.4.3 Vertical Distribution.- 10.4.4 Patchiness and Daily Vertical Migration.- 10.4.5 General Sea Surface Temperature in the Past.- 10.5 Population Dynamics.- 10.5.1 Reproductive Strategies.- 10.5.1.1 Lunar Periodicity.- 10.5.1.2 Annual Periodicity.- 10.5.2 Water Mass Boundary Effects.- 10.6 Experimental Studies.- 10.7 Summary.- 11. Sedimentation - Settlement of Shells.- 11.1 Introduction.- 11.2 Shells Released by Reproduction and Juvenile Mortality.- 11.3 Aggregates - Sedimentation.- 11.4 Predation.- 11.5 Residence Time and Sinking Velocity.- 11.6 Seasonal Fluctuations in the Settlement.- 11.7 Dissolution in the Deep Water.- 11.8 Summary.- 12. Concluding Remarks.- 12.1 Effects Influencing the Isotopic Signal.- 12.1.1 Temperature Effect.- 12.1.2 GlacialEffect.- 12.1.3 Water Mass Effect.- 12.1.4 VitalEffect.- 12.1.5 Selective Production.- 12.1.6 Differential Dissolution.- 12.2 Carbon Isotopes.- 12.3 Summative Perspective.- 13. References.- 14. Glossary.- 15. Index.

Modern Planktonic Foraminifera

The community structure and ecological function of contemporary marine ecosystems are critically dependent on eukaryotic phytoplankton. Although numerically inferior to cyanobacteria, these organisms are responsible for the majority of the flux of organic matter to higher trophic levels and the ocean interior. Photosynthetic eukaryotes evolved more than 1.5 billion years ago in the Proterozoic oceans. However, it was not until the Mesozoic Era (251 to 65 million years ago) that the three principal phytoplankton clades that would come to dominate the modern seas rose to ecological prominence. In contrast to their pioneering predecessors, the dinoflagellates, coccolithophores, and diatoms all contain plastids derived from an ancestral red alga by secondary symbiosis. Here we examine the geological, geochemical, and biological processes that contributed to the rise of these three, distantly related, phytoplankton groups.

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The Evolution of Modern Eukaryotic Phytoplankton

Systematic descriptions Family group taxa based on genera of uncertain status Unavailable family-group names used for foraminifera Cladegroups, category not recognized by ICZN Unavailable generic names used for foraminifera Generic and family group taxa appearing too late for inclusion Apparently described genera for which reference not seen Generic taxa erroneously regarded as foraminifers

Foraminiferal Genera and Their Classification

The Paleobiology of Plant Protists

Sarcodina : chiefly "Thecamoebians" and Foraminiferida

Late Osagean to Meramecian Platycrinites and Eucladocrinus from Illinois, Iowa, and Missouri are redescribed and redefined from study of type material. Three of the oldest species were incorrectly synonymized with P. sarae, and this correction leads to a realignment of species systematics within Platycrinites. Accordingly, six species of Platycrinites and one species of Eucladocrinus are considered valid in the Keokuk Limestone through St. Louis Limestone of the stratotype area. Valid species include Platycrinites saffordi (Hall), P. sarae (Hall), P. georgii (Hall), P. pumilus (Hall), P. brevinodus (Hall), P. niotensis (Meek and Worthen), and Eucladocrinus millebrachiatus Wahsmuth and Springer. Nomenclatoral changes include the following: 1) P. sarae is redescribed and all junior synonyms are removed; 2) P. georgii is a valid senior synonym of P. bonoensis (White), P. aeternalis (Miller), P. boonvillensis (Miller), and P. cauducus; 3) P. pentagonus (Miller) is a junior synonym of P. niotensis; 4) P. pumilus is a valid senior synonym of P. prattenanus (Meek and Worthen), and P. monroensis (Worthen); 5) P. bloomfieldensis (Miller) is designated as a nomen dubium; and 6) Eucladocrinus millebrachiatus immaturus is a junior synonym of E. millebrachiatus.The evoluton of new species in Platycrinites was by a combination of cladogenesis and possibly anagenesis. Platycrinites sarae evolved from P. saffordi possibly through anagenesis, P. pumilus evolved from P. niotensis through cladogenesis, and P. hemisphaericus evolved through cladogenesis from P. brevinodus, although P. hemisphaericus does not occur in the geographic area of this study.

Foraminiferal evolution, diversification, and extinction

A revised classification is presented for the Foraminiferida, combining the results of our research with various partial or more inclusive reclassifications that have appeared during the past two decades. The total 591 suprageneric taxa used herein for the Order Foraminiferida include 12 suborders, 63 superfamilies, 253 families and 263 subfamilies. Brief definitions are given herein for all recognized suprageneric taxa within the Foraminiferida. The synonymy listed for these suprageneric taxa includes only those taxa based on included genera. An index to recognized suprageneric taxa is included.

Helen Tappan

Papers

Foraminiferal Genera and Their Classification

The Paleobiology of Plant Protists

Sarcodina : chiefly "Thecamoebians" and Foraminiferida

Foraminiferal evolution, diversification, and extinction

Suprageneric classification of the foraminiferida protozoa