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habitats (e.g., Halteria , Meseres ). Furthermore, there are ecologically significant differences in growth rates and responses to tem- perature between geographically distant isolates of species of Uronema (Pérez-Uz, 1995) and Urotricha (Weisse & Montagnes, 1998; Weisse et al., 2001), and even among clones of planktonic Coleps and Rimostrombidium species (Weisse & Rammer, 2006). Dini and Nyberg (1999) have shown that ecological differentiation of genotypes occurs at all levels among species of Euplotes \u2013 at 4.2 Life History and Ecology 103 104 4. Phylum CILIOPHORA \u2013 Conjugating, Ciliated Protists with Nuclear Dualism the morphospecies level, breeding system level, breeding group level, and stock level. Thus, we must put pragmatism aside if we are to advance our understanding of the interactions between the ecological factors and the evolutionary forces shaping ciliate diversity , and we must also move beyond the concept of morphospecies. A major first step would be to consider models for specia- tion other than the allopatric one, which is clearly inappropriate in its classical interpretation. 4.3 Somatic Structures The surface of ciliates is covered by a plasma membrane underlain by cortical alveoli (Figs. 4.9B, 4.10A, 4.10B). In some nassophoreans, the alveoli can extend into the cortex as the so-called alveolo- cysts (Fig. 4.10G). The plasma membrane is char- acterized by a variety of intramembranous particles (Allen, 1978; Bardele, 1983; Hufnagel, 1992). The surface membranes are sites of ion channels that enable ciliates to sense mechanical, chemical, and temperature stimuli (Machemer & Teunis, 1996). The alveoli can be the sites of Ca 2+ ion storage in some ciliates, thus playing a role in modulat- ing locomotion (Mohamed et al., 2003; Plattner, Diehl, Husser, & Hentschel, 2006; Stelly, Halpern, Nicolas, Fragu, & Adoutte, 1995). All these inputs to the cell are \u201ctranslated\u201d into complex behavioral sequences that Ricci (1990, 1996) has described as an ethogram \u2013 a quantitative description of the behavioral repertoire of a species. At various points on the cell surface, typically associated with the emergence of cilia, parasomal sacs or coated pits extend into the cytoplasm (Fig. 4.10E). These sacs can be the sites of pinocytosis (Nilsson & Van Deurs, 1983). The membranous junctions of neighboring alveoli or fibrous compo- nents associated with these boundaries (Fig. 4.10E) form characteristic patterned networks that are revealed upon silver-staining \u2013 the so-called argy- rome (Foissner & Simonsberger, 1975a, 1975b). Underlying the alveoli is a fibrous or filamentous layer called the epiplasm , which is constructed, in part, by specific proteins called epiplasmins and articulins (Figs. 4.9B, 4.9C, 4.10B) (Coffe, Le Caer, Lima, & Adoutte, 1996; Huttenlauch & Stick, 2003; Huttenlauch, Peck, Plessmann, Weber, & Stick, 1998b; de Puytorac, 1984a). Genetic interference with some of these \u201ccortical\u201d genes can influence cell shape (Williams, 2004). The most prominent features of the somatic surface of the vast majority of ciliates are the cilia . Membranous particles are also distributed in cili- ary membranes, and undoubtedly function in the movement of Ca 2+ ions influencing the ciliary beat pattern (Machemer & Teunis, 1996; Plattner, 1975; Plattner et al., 2006), and these patterns of intram- embranous particles on the cilia may characterize different groups of ciliates (Bardele, 1981). The cilia beat with a straight effective stroke and a curved recovery stroke, typically moving the cili- ate through the medium, whether it be the water of an ocean or pond or the digestive contents of the intestine of a sea urchin (Sleigh & Barlow, 1982). The often thousands of cilia on the cell surface are coordinated by a hydrodynamic coupling that is manifested in the metachronal waves observed passing along the cell\u2019s surface (Guirao & Joanny, 2007; Sleigh, 1984, 1989). The ciliary axoneme with its 9 + 2 arrangement of microtubules underlies the ciliary membrane. The major force for the ciliary beat derives from active sliding of the nine peripheral doublet micro- tubules driven by dynein motors and ATP (Satir & Barkalow, 1996). The central pair of microtubules may rotate in a counterclockwise direction, viewed from the outside of the cell, making a complete rotation with every beat cycle (Omoto & Kung, 1980). Furthermore, this defined directional rota- tion, if true, means that when a patch of cortex is rotated, as sometimes happens following conjuga- tion of Paramecium when the two cells separate, the cilia on the reversed patch beat in the opposite direction to the surrounding cortex that has a normal polarity (Tamm, Sonneborn, & Dippell, 1975). The central-pair microtubules are anchored in the axo- some , which lies in a region of extreme complexity \u2013 the transition zone \u2013 between the ciliary axoneme and the basal body or kinetosome (Dute & Kung, 1978). In reviews, Fokin (1994, 1995) has demon- strated a considerable diversity in transition zone structures in ciliates, and suggested that transition- zone types may characterize some of the major clades of ciliates. The axonemal microtubules arise out of the kinetosome , which is composed in most ciliates of nine sets of microtubular triplets. Associated with the ciliate kinetosome are three fibrillar associates \u2013 the striated kinetodesmal fibril , the transverse microtubular ribbon , and the postciliary microtubu- lar ribbon (Fig. 4.10C, 4.10F, 4.10H\u2013K). All these elements together \u2013 cilium, kinetosome, fibrillar associates \u2013 form the kinetid . Theoretical calcula- tions support the notion that these fibrous struc- tures function as anchors for the kinetid (Sleigh & Silvester, 1983). These fibrillar systems have diversified in form and pattern as ciliate lineages have evolved, providing a variety of patterns that have proved useful in characterizing major clades (Fig. 4.7; see Taxonomic Structure above). The fibrillar associates extend in a various directions, depending upon the ciliate, and form an elaborate cortical cytoskeleton (Figs. 4.10D, 4.11). This cytoskeleton functions both to \u201cpassively\u201d support the cortex, since disassembly of the microtubules changes the form of the cell (Lynn & Zimmerman, 1981), and to \u201cactively\u201d change cell shape, since active sliding of postciliary microtubular ribbons in the heterotrich Stentor extends the body after con- traction (Huang & Pitelka, 1973). Electron micro- Fig. 4.9. Ultrastructural features of ciliates. A Longitudinal section of the colpodean Colpoda steinii . Note the anterior oral cavity ( OC ), macronucleus ( MA ) with its large nucleolus ( N ), and food vacuoles ( FV ) filled with bacteria ( B ). B Section through two cortical alveoli ( A ) of the colpodean Colpoda cavicola . Note the thin epiplasmic layer (arrow) in this small ciliate. C Section through the pellicle of the colpodean Colpoda magna . Note the much thicker epiplas- mic layer (arrow) in this large colpodid and the mitochondrion ( M ) with tubular cristae. D A mucocyst in the cortex of the colpodean Bresslaua insidiatrix 4.3 Somatic Structures 105 Fig. 4.10. Ultrastructural features of the somatic cortex of ciliates. A Section through a cortical alveolus (A) of the colpo- dean Colpoda cavicola . Note the epiplasm underlain by overlapping ribbons of cortical microtubules. B Section through the pellicle of the colpodean Colpoda magna showing microtubules underlying the thicker epiplasm ( Ep ). C Cross-section of the somatic dikinetid of the heterotrichean Climacostomum virens , showing the transverse microtubular ribbon ( T), kinetodesmal fibril ( Kd ), and postciliary microtubular ribbon ( Pc ) (from Peck, Pelvat, Bolivar, & Haller, 1975). D Section through