Overview Of The Tree

Most eukaryotes can be assigned to one of eight major groups, six of which can be further grouped to make three supergroups (see Figure 1). Opisthokonts include animals, fungi, and several primitively single-celled lineages. Amoebozoa consists mostly of naked amoebae with lobose pseudopo-dia plus the social amoebas. Together, Amoebozoa and Opisthokonta form the supergroup "unikonts," probably the only major group of eukaryotes to be ancestrally uniflagellate (Richards and Cavalier-Smith 2005). Rhizaria are mostly testate (shelled) amoebas with fine, anastomosing pseu-dopodia. The Archaeplastida (formerly

Archaeplastida

Archaeplastida

Overview The Tree

FIGURE 1. Consensus phylogeny of eukaryotes showing the distribution of photosynthesis among the major groups. The tree shown is a consensus phylogeny of eukaryotes based on a combination of molecular phylogenetic and ultrastructural data. The tree is further annotated to indicate the distribution of photosynthesis across the tree. Groups harboring endosymbiotic organelles are indicated by schematic plastids with variable numbers of membranes and chlorophyll composition, as indicated in the key to the lower right of the figure. Groups with members harboring transient algal endosymbionts are indicated by stars. Taxa classified as Radiolaria are indicated by an "r" following their names, and former "Heliozoa" are indicated by an "h." (See color plate.)

FIGURE 1. Consensus phylogeny of eukaryotes showing the distribution of photosynthesis among the major groups. The tree shown is a consensus phylogeny of eukaryotes based on a combination of molecular phylogenetic and ultrastructural data. The tree is further annotated to indicate the distribution of photosynthesis across the tree. Groups harboring endosymbiotic organelles are indicated by schematic plastids with variable numbers of membranes and chlorophyll composition, as indicated in the key to the lower right of the figure. Groups with members harboring transient algal endosymbionts are indicated by stars. Taxa classified as Radiolaria are indicated by an "r" following their names, and former "Heliozoa" are indicated by an "h." (See color plate.)

Plantae) are the group in which eukaryotic photosynthesis first arose. Chromalveolates (alveolates + stramenopiles + cryptophytes + haptophytes) include all major groups of marine algae. Finally, the excavates (dis-cicristates + amitochondrial excavates) is a tenuous grouping of extremely diverse unicellular taxa. The main treatments of the higher level classification of eukaryotes are by Adl et al. (2005) and Cavalier-Smith (2004). Detailed organismal descriptions can be found in Lee et al. (2000) and Haus-man and Hulsmann (1996). There are many recent reviews of higher-level classification (Baldauf 2003; Cavalier-Smith, 2004; Simpson and Roger 2004; Keeling et al. 2005). Especially useful websites include the Tree of Life site (http://tolweb.org/tree/), and David Patterson's Micro*scope, which contains a wealth of protist images and much more (http://starcentral.mbl.edu/ microscope).

A. Opisthokonts

The sisterhood of animals and fungi is supported by all large, broadly taxonomi-cally sampled molecular datasets (Baldauf et al. 2000), and, most importantly, all large multigene trees (Baldauf et al. 2000; Moreira et al. 2000; Bapteste et al. 2002; Lang et al. 2002; Steenkamp et al. 2006). Nonetheless, the validity of the taxon continues to be debated (Loytynoja and Milinkovitch 2001; Philip et al. 2005). Animals and fungi together also possess the unique combination of flattened mitochondrial cristae, and, when flagellate, a single basal flagellum on reproductive cells (Cavalier-Smith 1998, 2002). These flagella also have unique similarities in their anchorage systems (Patterson 1999). However, none of these characters is universally present in all animals and fungi or uniquely absent in all other eukaryotes (Steenkamp and Baldauf 2004). The only universal synapomor-phy for animals and fungi is a 9-17 amino acid insertion in protein synthesis elongation factor 1A (EF1A; Baldauf and Palmer 1993; Steenkamp et al. 2006), although some choanoflagellates appear to have lost this gene and the insertion may have evolved a second time independently (Atkinson and Baldauf unpublished; Keeling and Inagaki 2005).

One reason for the lack of phenotypic j ustification for opisthokonts is probably that animals and fungi are such highly morphologically derived lineages. They have independently invented very different types of multicellularity, as indicated by the fact that the earliest branches in both lineages are single-celled taxa (Steenkamp et al. 2006). Therefore, it is perhaps among these single-celled lineages that additional opisthokont synapomorphies may be found. Recent molecular phylogenetic data have identified several primitively unicellular lineages specifically allied with either animals or fungi (ministeriids, choanoflagellates, and mesomycetozoa; Steenkamp et al. 2006, and references therein).

Possibly the closest sister taxon to animals is Ministeria vibrans, the only currently cultured member of its genus. It is a stalked uni-cell, the body of which is surrounded by stiff radiating arms of unknown composition, and with flattened mitochondrial cristae (Cavalier-Smith and Chao 2003). However, support for M. vibrans as the sister taxon to animals is not unambiguous (Cavalier-Smith and Chao 2003; Steenkamp et al. 2006), and it may just be an unusual choanoflagellate with fast-evolving sequences (Steenkamp et al. 2006). On the other hand, there is now very strong support for choanoflagellates as the next closest relatives to animals (Lang et al. 2002; Medina et al. 2005; Steenkamp et al. 2006). These aquatic uniflagellates with flattened mitochondrial cristae have long been noted for their resemblance to the collar cells of sponges. The next deepest branch leading to animals is the Mesomyceto-zoa (Lang et al. 2002; Mendozoa et al. 2002; Steenkamp et al. 2006). These are a grab bag of obligate intracellular parasites of aquatic animals, whose relationship to each other is only obvious in molecular trees (Ragan et al. 1996). The enigmatic taxon Capsaspora prow-ozekei may also be a mesomycetozoan, or it may, as some now believe, form an even deeper branch, making it the deepest branch of the entire holozoa (Lang et al. 2002; Ruiz-Trillo et al. 2004). It is an amoeba with filose pseudopodia, formerly classified as a nucle-ariid. This is particularly intriguing, as most of the rest of the nucleariids appear to be the sister group to the fungi (Medina et al. 2005; Steenkamp et al. 2006).

Within fungi, the earliest major branches are chytrids, which may be paraphyletic with respect to the rest of the fungi (Keeling et al., 2000; James et al. 2006). These unicells form pseudo-hyphae and have zoospores with a single basal flagellum. Thus, chytrids are the only known flagellated members of the fungi. The first branch of multicellular fungi is the Zygomycetes, followed by the Glomales (Schufiler et al. 2001). The latter are the arbuscular mycorrhizal fungi, which form symbioses with the vast majority of land plants. Their hyphae invade plant roots where they proliferate, exchanging mineral nutrients for host photosynthate. So far, no reproductive stage is known. The Ascomyc-etes and Basidiomycetes form the remaining two major groups of fungi. Both appear to be monophyletic and each other's sister taxon. It has long been suspected, and has now been confirmed by ciPCR survey that a vast diversity of fungi remain undescribed (Vandenkoornhuyse et al. 2002).

Deep relationships within the metazoa have proven much harder to resolve. This may be due to explosive radiation (Rokas et al. 2006) or to multiple genome duplications and differential gene loss such that orthologous genes are difficult to identify (Wolfe 2001). The limited amount of data currently available suggest that sponges are paraphyletic, with the glass sponges (Hex-actinellida) branching off first, followed by the group of Calcarea + Demospongiae (Borchiellini et al. 2001). These appear to be followed by various branches of diploblasts, such as comb jellies (Ctenophora) and corals and jellyfish (Hydrozoa) (Halanych 2004). For the "higher" animals, current consensus is that they form three separate groups. The Deuterostomes include echinoderms and chordates, and their sister group is the Ecdysozoa + Lophotrochozoa. Ecdysozoa include the molting animals such as nema-todes and arthropods, and Lophotrochozoa include most platyhelminthes, brachiopods, annelids, mollusks, and others (Wolf et al. 2004; Philippe and Telford 2006).

B. Amoebozoa

The Amoebozoa include several subdivisions of free-living amoebae, a group of amitochondriate amoeba/amoeboflagellates (Archamoebae), and the social amoebas (Mycetozoa or slime molds). Together with Rhizaria, they are molecularly the least well-characterized major group of eukaryotes, including many species of uncertain affinity. Amoebozoa have lobose or tubelike pseu-dopods, often a single nucleus, and tubular branched mitochondrial cristae (Adl et al. 2005). They range in size from a few microns to several millimeters, and many smaller forms probably remain to be discovered. Cyst formation to survive desiccation or to invade hosts is common. Most taxa are free-living and cosmopolitan in distribution, and they are important as major bacterial predators. In addition, the group includes some animal commensals and opportunistic pathogens.

1. Lobose Amoebae

The lobose amoebae are probably para-phyletic and include the most basal branches of Amoebozoa. They can be roughly divided into two classes: the Tubulinea and Flabellinea (Smirnov et al. 2005). There are also many species of uncertain affinity, which branch at the base of the amoebozoan tree. The Tubulinea share the ability to adopt a monopodial locomotive form with monoaxial cytoplasmic flow. The taxon also includes the arcellinids, the only lobose amoebae to form tests, which they construct from organic material. The Flabellinea are flattened naked amoebae having polyaxial cytoplasmic flow (Smirnov et al. 2005). Among the other lobose amoebae the most distinctive group are Acanthopodida, which differ from other amoebae in having cytoplasmic microtubule-organizing centers (MTOC) and a specific pseudopodial network. The genus Acanthamoeba is very important medically as causative agent of amoebic keratitis, a chronic eye infection (Marciano-Cabral et al. 2000).

2. Archamoebae

The Archamoebae are a tentative grouping of pelobionts and entamoebas (Bapteste et al. 2002; Cavalier-Smith et al. 2004). Most live in low-oxygen environments, and all lack mitochondria (Bap-teste et al. 2002; Cavalier-Smith et al. 2004; Smirnov et al. 2005). Instead of mitochondria they have mitosomes, which are small mitochondrial-derived organelles of unknown function (Tovar et al. 1999). Pelobionts are amoeboflagellates, that is, they can assume amoeboid or flagellate forms, the latter with one or many flagella. They vary widely in size; Pelomyxa can be up to 3 mm long with several nonmotile flagella in its tail region. Entamoebae are small nonflagellates and mostly commensals or parasites of animals. Several species live in the mouth and intestinal tract of humans. Entamoeba histolytica causes amoebic dysentery, sometimes invading the liver with more severe consequences. Recent completion of the E. histolytica genome sequence shows that substantial amounts of its novel metabolic repertoire were acquired from bacteria by lateral gene transfer (LGT) (Loftus et al. 2005).

3. Mycetozoa

These are also called Eumycetozoa or social amoebas. They include the plasmodial (myxogastrid), cellular (dictyostelid), and protostelid slime molds, which have strikingly different trophic stage morphologies (Olive and Stoianovitch 1975). However, all possess an amoeboid stage with pointed, smoothly moving pseudopods, and they form similar fruiting bodies consisting of a cellulosic stalk supporting spore-bearing sori. Dictyostelids and myxogastrids have been variously classified as plants, animals, or fungi in the ~150 years since they were first described, and there has been a long running debate as to whether they are even related to each other. However, molecular data confirm that they form a group (Baldauf and Doolittle 1997), and recent evidence suggests that their closest relatives may be the Archamoebae (Nikolaev et al. 2006).

The myxogastrids are also referred to as plasmodial, true, or acellular slime molds, or simply "giant amoebas." The best known is the model organism Physarum polycepha-lum. Myxogastrids are amoeboflagellates, switching between amoeboid and flagellate forms early in their life cycle before maturing into large plasmodia. The latter can grow to a meter or more in diameter and have tens of thousands of synchronously dividing nuclei but no internal cell walls. Plasmodia are mobile and can move substantial distances at rates of ~1 cm per hour, propelled by means of cytoplasmic pulses. Eventually, the plasmodium breaks down to form numerous, often colorful and ornate fruiting bodies (Olive and Stoiano-vitch 1975).

In contrast, the dictyostelids spend most of their life cycle as single-celled amoebae, foraging for bacteria among detritus or in the soil. Under appropriate conditions, tens of thousands of these amoebae will come together to form a "slug." This is a mobile, macroscopic (2-5 mm) organism surrounded by an outer sheath and with defined head and body regions. Cell fate is determined in the slug such that when it metamorphoses into a fruiting body, the cells in the head of the slug will die during formation of the cellulosic stalk (Strmecki et al. 2005). Much less is known about the almost exclusively microscopic protostel-ids, which can be either amoeboflagellate or strictly amoeboid and form simple fruiting bodies (Olive and Stoianovitch 1975). They include the sister group to the dictyostel-ids and myxogastrids (Baldauf and Doolittle 1997) and may be paraphyletic (Spiegel et al. 1995).

C. Rhizaria (Formerly Cercozoa)

The Rhizaria consist largely of testate (shell-forming) amoeboid protists with typically thin finely pointed (filose) pseudopo-dia. However, the group is morphologically and ecologically very diverse and includes also a number of flagellate or biflagellate species, some naked amoebae, and plasmo-dial parasites. Rhizarian tests are built from a variety of materials, and the amoebae reside within them through most of their life cycle. The group includes the foraminif-erans, the radiolarians, some heliozoans, the euglyphid amoebas, the plasmodio-phorids, the chlorarachniophytes, and more. Rhizaria has been defined based exclusively on molecular characters, including phy-logenetic analysis of actin, ribosomal RNA, and RNA polymerase II gene sequences (Keeling 2001; Berney and Pawlowski 2003; Longet et al. 2003; Nikolaev et al. 2004) and the presence of a specific insertion in the polyubiquitin gene (Archibald et al. 2003; Bass et al. 2005).

1. Qroup 1 (Radiolaria)

This group includes two classes of radi-olarians, Acantharea and Polycystinea, and one former heliozoan group, Taxopodida. Radiolarians are identified by the combined presence of an internal mineralized "skeleton" and axopodia, which are long, radiating, unbranched processes stiffened by microtubular arrays. All are marine and pelagic, and they can be solitary or colonial. Radiolarians traditionally consist of three divisions—Acantharea, Polycystinea, and Phaeodarea, but Phaeodarea appear to be more closely related to Cercozoa (Polet et al. 2004), a different section of Rhizaria (see Section IV.C.). Acantharea have delicate skeletons with radial spicules. These tests are composed of strontium sulfate, joined at the center of the cell and emerging from the cell surface in a regular pattern. Polycystinea have silicious skeletons varying from simple spicules to complex helmet-shaped structures. Taxopodida consist of a single genus, Sticholonche, which are large heart-shaped protists with rows of oarlike pseudopodia that it uses for locomotion. The body is covered with silicious spicules and spines, giving the overall appearance of a star (Chachon and Chachon 1977).

2. Group 2 (Foraminifera)

This group includes the foraminiferans and their relatives, the haplosporidians and gromiids. Foraminiferans are a well-studied group with 940 modern genera and a rich fossil record (Lee et al. 2000). They are widely distributed in all types of marine environments, and some also occur in freshwater and terrestrial habitats (Pawlowski et al. 1999; Meisterfeld et al. 2001). They have finely granular reticulated pseudopods with bidirectional cytoplasmic flow. Most foraminif-erans possess tests, which may be organic, agglutinated or calcareous, and composed of single or multiple chambers. Many also have complex life cycles consisting of alternating sexual and asexual generations (Lee et al. 2000). Haplosporidians are endoparasites that form large multinucleate plasmodia in freshwater and marine invertebrates. The gromiids are widespread marine protists with filose pseudopodia, a large (up to 5 mm) spherical to ovoid organic test with a characteristic layer of honeycomb membranes and a complex life cycle. They appear to be the sister group to foraminiferans or foraminiferans + haplosporidians (Longet et al. 2003).

3. Group 3 (Cercozoa)

This large heterogenous assemblage includes cercomonads, chlorarachniophytes, filose testate amoebae, some former helio-zoans (desmothoracids) and radiolarians (Phaeodaria), and plasmodial parasites (Nikolaev et al. 2004). Chlorarachniophytes are photosynthetic marine protists with anastomosing, network-like (reticulate) pseudopods and a uniflagellate dispersal stage. They acquired photosynthesis by capturing a green alga, and they retain both the plastid of the green alga and a remnant of its nucleus (nucleomorph), essentially a cell within a cell (McFadden 2001; Hackett et al., Chapter 7, this volume). Chlorarachni-ophytes are closely related to cercomonads, which are common heterotrophic amoebo-flagellates (Keeling 2001). Euglyphid testate amoebae, which build their tests from silica scales, are common in freshwater and in mosses. Plasmodiophorids (Phytomyxea) are endoparasites of plants or heterokont algae. They form multinucleated plasmo-dia, have a distinctive cruciform nuclear division, and have bi- or tetra-flagellate zoospores (Adl et al. 2005). Phaeodaria have siliceous skeletons, usually made of hollow radial spines, and a characteristic thick capsular membrane. Desmothoracids (Nucleo-helea) are amoeboflagellates. The trophic amoeboid stage tends to be stalked with a perforated lorica through which multiple long thin pseudopodia protrude, giving it a starlike appearance.

4. Fossils

Both foraminiferan and radiolarian skeletons contribute substantially to the microfossil record in marine sediments extending back to the Cambrian. Their fossilized tests are used in micropaleontology as biostratigraphic markers and as paleoceanographic indicators to determine ancient water temperature, ocean depths, circulation patterns, and the age of water masses.

D. Archaeplastida

Archaeplastida (formerly Plantae) consist of the Rhodophyta (red algae), Glauco-phyta, and Chloroplastida (green algae + land plants) (O'Kelly, Chapter 13, this volume). This is almost certainly the group in which eukaryotic plastids arose, by direct acquisition of a cyanobacterium (primary endosymbiosis). This cyanobacterium was converted into a plastid by massive restructuring of its genome, with roughly 95% of its genes being either lost or transferred to the host nucleus (Martin et al. 1998). As a result, ~90% of chloroplast proteins are encoded in the nucleus, synthesized in the cytosol, and posttranslationally imported into the plastid (Steiner et al. 2005). Thus, one of the primary events in plastid endo-symbiosis would have been the evolution of a protein-import machinery (McFadden and van Dooren 2004).

The debate on whether there were one or more origins of eukaryotic photosynthesis is a long running one. Much of this hinges on evidence for the monophyly of (1) Archaeplastida and (2) their plastids. Strong support for the monophyly of these plastids includes the fact that their genomes have a similar derived gene order and composition (Douglas 1998). In addition, all the plastids in this group have only two membranes, whereas all other eukaryote plastids have three or more (Archibald and Keeling 2002; Hackett et al., Chapter 7, this volume). Evidence for the monophyly of archae-plastid nuclear genomes has been slower in coming. However, there is now strong evidence for this from comparative genom-ics of red and green plants (McFadden and van Dooren 2004) and from multigene datasets, which also place glaucophytes as the first major branch in the group (Rodrigues-Ezpeleta et al. 2005).

1. Qlaucophyta

The morphology of glaucophytes varies from biflagellates to coccoid nonflagellates to palmelloid forms (nonmotile cells in a mucilaginous matrix). All are small unicells whose light-harvesting complexes share similarities with red algae in that they use only chlorophyll (chl) a, which is attached to phycobiliproteins, and their thylakoids are unstacked. One of the most remarkable features of these taxa is their plastids, or "cyanelles." These have a bacterial-like peptidoglycan cell wall in between the inner and outer plastid membranes (Steiner et al. 2005). Genera include Cyanophora, Glauco-cystis, and Gloeochaete.

2. Rhodophyta

Rhodophytes vary from large seaweeds to crustose mats that look more like rocks than living plants. Their plastids have two membranes and unstacked thylakoids. Light is harvested primarily with chl a and phycoerythrins conjugated to phycobilipro-teins. Two major subgroups are recognized, Bangiophyceae and Florideophyceae; the former appears to be older and may have given rise to the latter. However, the taxonomy of the group requires major revision, and many, if not all, of the traditional major divisions may be invalid (Adl et al. 2005).

3. Chloroplastida

Chloroplastida include the green algae and the land plants, which were derived from the charaphyte branch of green algae. Thus, members of the Chlorophyta vary from single-celled flagellates to large marine filaments to redwoods. Their plas-tids have two membranes and stacked thy-lakoids, and they harvest light with chls a and b attached to chla/b-binding proteins. For a detailed discussion of Chloroplastida and the origin of land plants, see O'Kelly (Chapter 13, this volume; also Bhattacharya and Medlin 1998; Karol et al. 2001).

E. Chromalveolates

Chromalveolates are a large group and morphologically and ecologically extremely diverse. They consist of the alveolates (cili-ates, dinoflagellates, and apicomplexans), the stramenopiles (heterokonts), and possibly also the cryptophytes and haptophytes (Cavalier-Smith 2000, but see Hackett et al., Chapter 7, this volume). Secondary endo-symbiosis is widespread in the group, and the source in all cases appears to be red algae (Yoon et al. 2002b; Hackett et al, Chapter 7, this volume). Dinoflagellates in particular have a tendency to acquire extra plastids on a regular basis (Yoon et al. 2002a; Delwiche, Chapter 10, this volume). In cryptophytes, a remnant of the red alga nucleus persists in the form of a nucleomorph, similar to the situation in chlorarachniophytes (see Section II.C.).

1. Stramenopiles

The stramenopiles are morphologically and ecologically one of the most diverse groups of eukaryotes. Nonetheless, they have strong molecular phylogenetic support and phenotypic justification. All major divisions of the group include organisms with a "tinsillated" flagellum, and most have a second, shorter, smooth flagellum (hence the commonly used alternate name "heter-okont"). The shorter flagellum is posteriorly directed and often associated with an eye-spot. The tinsillated flagellum is anteriorly directed and bears two rows of stiff, tripartite hairs (stramenopiles) along its length. These hairs reverse the flow around the flagellum so that the cell is dragged forward, rather than pushed along. Environmental sampling shows that there may be additional major divisions of the group, so far known only as uncultured ultra-small species (Moreira and Lopez-Garcia 2002; Massana et al. 2006). In fact, there appears to be a huge diversity of very small free-swimming phototrophic, mixotrophic, and heterotrophic strameno-piles in most planktonic systems (Moreira and Lopez-Garcia 2002).

a. Nonphotosynthetic Stramenopiles

Stramenopiles include a wide diversity of nonphotosynthetic lineages. They are not a monophyletic group and are only presented together here for convenience. Oomycetes are the water molds and downy mildews; they include important plant parasites such as Phytophthora infestans, the cause of potato blight. Once classed as fungi, they are now clearly assigned to stramenopiles (Gajad-har et al. 1991). The bicosoecids are small heterotrophic biflagellates, such as Cafeteria, possibly the world's most abundant predator (Moreira and Lopez-Garcia 2002). Laby-rinthulids or slime nets form filamentous networks and were once thought to be close relatives of slime molds (see Section III.C.; Olive and Stoianovitch 1975). Opalinids, which have cell bodies covered with stra-menopile bearing flagella, and the taxo-nomically enigmatic Blastocystis are both commensals in the guts of cold-blooded animals. Although lacking a plastid, recent sequence data suggest that at least some of these taxa may have once been photosyn-thetic because they retain genes of apparent cyanobacterial origin in their nuclear genomes (Andersson and Roger 2002).

b. Photosynthetic Stramenopiles

Eleven major divisions of photosynthetic stramenopiles are recognized (Adl et al. 2005). These are Bacillariophyceae (diatoms), Chrysophyceae, Dictyochophyceae, Eustig-matales, Pelagophyceae, Phaeothamnio-phyceae (brown algae), Pinguiochrysidales, Raphidophyceae, Schizocladia, Synurales, and Xanthophyceae. Many are purely unicells, but there are also massive multicellular forms, such as the giant kelps. Various extracellular structures are found, such as scales or loricas.

Diatoms are ubiquitous and often the dominant marine photoautotroph. They reside in lidded boxes made of silica (see chapters by Kooistra et al, Chapter 11, and by Hamm and Smetacek, Chapter 14, this volume). There are ~11,000 recognized species, and millions of undescribed ones by some estimates (Norton et al. 1996). Phaeophytes are particularly widespread in temperate intertidal and subtidal zones. Some of them have true parenchyma and build "forests" in near-shore environments that support complex ecosystems including fish and marine mammals. The xanthophytes, or yellow-green algae, include primarily freshwater algae. Most of them are unicellular, but a substantial number are colonial and live as naked cells in a gelatinous envelope. The Eustigmatales represent small unicellular coccoid algae, some of which have a very short flagellum and a large orange eyespot that is located outside the plastid. Raphidophytes are relatively large flagellates with the typical stramenopile flagella. They are naked but can bear trichocysts and usually have a variety of brown or green plastids.

2. Haptophytes

Haptophytes get their name from the presence of a unique anterior appendage, the hap-tonema, used for adhesion and capturing prey. The group includes the coccolithophorids, which build external coverings of calcium carbonate scales (coccoliths) and tend to dominate open oceanic waters worldwide. Emiliania huxleyi, in particular, has received considerable attention (see de Vargas et al, Chapter 12, this volume). This is because of its role as a major carbon sink and because its massive blooms affect the temperature and optical qualities of ocean waters and play an important role in cloud production through dimethyl sulfoxide release (Buitenhuis et al. 1996). Coccoliths from dead cells accumulate as limestone deposits on the ocean floor, contributing to the largest inorganic reservoirs of carbon on Earth. Noncancerous haptophyte genera, Chrysochromulina and Prymnesium, are an important source of toxic blooms.

3. Cryptophytes

The cryptophytes are, perhaps, the least well known of the chromists, being rela tively small (mostly 2-10 |im diameter) unicells and particularly good competitors in low light conditions in a wide variety of habitats (Gillot 1989). The group has received considerable attention because of its importance in unraveling the process of secondary endosymbiosis by retaining an intermediate stage in the process. Similar to chlorarachniophytes (see Section II.C.), cryptophyte plastids are accompanied by a remnant of their primary host nucleus (nucleomorph) that still encodes some of the proteins required for plastid function. Analysis of the nucleomorph genome (e.g., Douglas et al. 1999, 2001) provided the first phylogenetic evidence for the chimeric nature of algal cells by confirming the red algal origin of the cryptophyte plastid (see Hackett et al., Chapter 7, this volume).

4. Alveolates

The alveolates are another large assemblage of protists with strong molecular and ultrastructural justification. The group includes the dinoflagellates (see Delwiche, Chapter 10, this volume), many of which are algae, the parasitic apicomplexans, and the ciliates (Adl et al. 2005). Cortical alveoli, which are saclike structures that lie immediately beneath the plasma membrane, are widely present, although sometimes lost. The alveoli form the pellicle in cili-ates, surround the peripheral armor plates in dinoflagellates, and form the pellicular membrane in apicomplexans.

a. Ciliates

Ciliates appear to be the sister group to dino-flagellates + Apicomplexa. They are mostly free-living aquatic unicells characterized by an abundance of flagella (cilia) on their body surface (Hausmann and Hulsmann 1996). Ciliates are also noted for their nuclear dualism, where all cells have one or more of two very different types of nuclei. The smaller micronucleus contains the diploid germ nucleus, and the second much larger macronucleus contains thousands of copies of only the physiologically active genes. Ciliate nuclear genome organization can be truly remarkable; genes may not only be fragmented by introns and often numerous short intervening sequences, but the order of the gene fragments themselves may be scrambled. Therefore, extensive editing is required during generation of the macronucleus in order to produce the active working copy of the gene, and the mechanism by which this occurs is still unknown (Prescott 2000; Dalby and Prescott 2004).

b. Dinoflagellates

Dinoflagellates are a diverse, predominantly unicellular group, characterized by having one transverse and one longitudinal flagellum, resulting in a unique rotatory swimming motion. Many are also covered by often elaborate plates or armor. Although the group was probably primitively photosyn-thetic, only about half of the extant species still are, and many of these are mixotrophs (Stoecker 1999). The latter ingest bacteria and other eukaryotes, sometimes retaining algae or their plastids for varying lengths of time (Jakobsen et al. 2000; Tamura et al. 2005). The group includes the only known example of tertiary endosymbiosis involving the secondary endosymbiosis of a secondary endosymbiont (Yoon et al. 2002a; Delwiche, Chapter 10, this volume). Symbiodinium species are endosymbionts of corals and other invertebrates and occasionally other protists. Some dinoflagellates are a common source of phosphorescence in marine waters. Dino-flagellates are an important component of marine ecosystems as primary producers as well as parasites, symbionts, and micro-grazers. They also produce some of the most potent toxins known and are the main source of toxic red tides and other forms of fish and shellfish poisoning.

c. Apicomplexa

Apicomplexa are the sister group to the dinoflagellates and include some of the most important protozoan disease agents of both invertebrates and vertebrates. All but the co/podellids are obligate and mostly intracellular parasites, and they include the causative agents of malaria and toxoplasmosis. They are characterized by the presence of an intricate apical complex, a system of organelles and micro-tubules situated at the posterior of the cell that functions in the attachment and initial penetration of the host. Parasitic apicomplexa have complex life cycles that are completed entirely within the host, and they exist outside it only as spores or oocysts. The group appears to have been derived from photosynthetic ancestors. It retains a vestigial plastid (apicoplast), most likely of red algal origin (Fast et al. 2001) that may be required for heme, lipid, and/or isoprenoid biosynthesis (Waller and McFadden 2005).

F. Excavates

This is easily the most enigmatic of the major groups of eukaryotes, and, in fact, molecular phylogenetic support for the group as a whole is weak at best. All are single-celled organisms, and many possess some type of conspicuous "excavated" ventral feeding groove (Simpson and Patterson 1999; Cavalier-Smith 2002). There are two recognized subdivisions within the "group." The discicristates include two well-defined subgroups, the Euglenozoa and the Heterolobosea, and possibly also some "jakobid" flagellates (Simpson et al. 2006). The latter lack the disc-shaped mitochondrial cristae (O'Kelly 1993) that were originally identified as a unifying character for the group along with strong molecular phylogenetic evidence (Baldauf et al. 2000). The second division of excavates, which, for lack of a better name will be referred to here as amitochondriate excavates, is a grab bag of taxa, many of which are largely known as obligate symbionts or parasites. Thus, they tend to have structurally simple cells and fast-evolving gene sequences and appear as the earliest branches in molecular trees

(Sogin et al. 1989; Cavalier-Smith and Chao 1996). Although many now consider the latter an artifact (Philippe and Germot, 2000), it seems to be quite a consistent one (Bap-teste et al. 2002; Hedges et al. 2004; Ciccarelli et al. 2006).

1. Discicristates

The discicristates include the Eugleno-zoa and the Heterolobosea. They may also include some of the species known as jakobids, which have bacterial-like mitochondrial genomes (Lang et al. 1997). Euglenozoa include kinetoplastids and euglenids. Kine-toplastids are small uniflagellated or biflag-ellated cells, including the causative agents of sleeping sickness, Chagas' disease, and leishmaniasis. They are also famous for their bizarre mitochondrial genomes, where the genes are essentially encoded in a highly abbreviated shorthand. As a result, oligonu-cleotide fragments must be posttranscription-ally inserted into the initial messenger RNAs so that they can be properly decoded into protein (Sollner-Webb 1996).

a. Euglenozoa

Euglenids are usually free-living uni- or biflagellate cells enclosed by a thickened pellicle made of proteinaceous strips. Most euglenids are free-living osmotrophs, or phagotrophs, some of which are capable of ingesting whole eukaryotic cells. This is probably how photosynthetic forms, such as Euglena, acquired their chloroplasts, through secondary endosymbiosis of a green alga. Euglena has an unusual chloro-plast genome, particularly the presence of twintrons. These are self-splicing introns within introns, where the inner intron must be spliced out before the outer intron can assume the correct structure for its own splicing (Hallick et al. 1993).

b. Heterolobosea

The Heterolobosea are mostly amoebae, although many have flagellate phases in their life cycles (Patterson et al. 2000a).

These naked amoebae differ from lobosean amoebae in that their pseudopods develop and move in a sporadic, "eruptive" manner. Most are soil or freshwater bacterivores, although one, Naegleria fowleri, is a rare but often fatal facultative human pathogen. The acrasid "slime molds" have been reassigned to this group based on molecular trees (Roger et al. 1996; Baldauf et al. 2000), which fits with the morphology of their heterolobosean-like pseudopodia (Olive and Stoianovitch 1975).

c. Jakobids

Discicristates probably also include some of the unicells referred to as jakobids (Simpson et al. 2006). These are small free-living bacterivores, noted for their bacteria-like mitochondrial genomes. Although most eukaryotes have fewer than 20 genes remaining in their mitochondrial genomes, jakobids retain more than 100. Also, unlike other eukaryotes, these genes are arranged in bacteria-like operons (Lang et al. 1997), consistent with the alpha-proteobacterial ancestry of mitochondria (Andersson et al. 2003).

2. Amitochondriate Excavates

The true or amitochondriate excavates are a grab bag of unicells, including some real morphological oddities. Many are obligate parasites, and all lack mitochondria. This led to the suggestion that they represented very early branches in the eukaryote tree, preceding the origin of mitochondria (Cavalier-Smith and Chao 1996). However, genes of mitochondrial origin have now been found in excavate nuclear genomes (Roger 1999; Tachezy et al. 2001), and some, perhaps even all, have what appear to be mitochondrially derived organelles (Dyall and Johnson 2000; Tovar et al. 2003).

The diplomonads typically exhibit a "doubled" morphology, with duplicate nuclei, sets of flagella, and cytoskeletons arranged back-to-back in each cell. The intestinal parasite Giardia intestinalis is a major human diarrheal agent, and Spironu-cleus includes some serious fish parasites. Most diplomonads are parasites, and the few free-living species are found only in low-oxygen habitats (Bernard et al. 2000). Retor-tamonads are broadly similar to diplomonads but have a single nucleus, flagellar cluster, and feeding groove per cell (Silberman et al. 2002). Most are intestinal commensals. Oxy-monads are flagellated symbionts from the intestinal tracts of animals, mostly termites.

Parabasalids are mostly parasites and symbionts that are defined by the presence of a parabasalar apparatus, which is a complex of Golgi stacks and striated cytoskeletal elements. They include hyper-mastigids and trichomonads. Hypermas-tigids are huge multiflagellated cells, hundreds of micrometers long and covered in ectosymbiotic bacteria. They are found only in the hindgut of termites, itself a complex ecosystem, and are essential for the breakdown of cellulose. Trichomon-ads are small teardrop-shaped cells with four to six flagella that cause trichomo-niasis, the most common human sexually transmitted protozoan infection (Embley and Hirt 1998).

G. Incertae Sedis

In 1999, Patterson identified 230 protists of uncertain affinity (Patterson 1999). In 2005, this number had only decreased to 204 (Adl et al. 2005), so much remains to be done. Most of these are small free-living heterotrophic flagellates or amoebae or are parasites of various kinds. Many, if not most, will undoubtedly turn out to fall within one or more of the groups described previously. Environmental surveys further suggest the existence of major undiscovered eukaryotic lineages (Amaral Zettler et al. 2002; Dawson and Pace 2002; Moreira and Lopez-Garcia 2002). These "nanoeukaryotes," cells less than 2-3 pm in diameter, have previously escaped detection because they are all but indistinguishable from bacteria under the light microscope.

Some of the new taxa appear to represent major new subdivisions of established groups (e.g., alveolates and stramenopiles, Section II.E.), including major components of marine ecosystems (Massana et al. 2006). Others, however, appear to represent known lineages for which DNA sequences were not previously available (Berney et al. 2004; Guil-lou et al. 2004).

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