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as lakes (Beaver & Crisman, 1982, 1989a; Esteban, Finlay, Olmo, & Tyler, 2000; Taylor & Heynen, 1987), freshwater ponds (Finlay & Maberly, 2000; Taylor & Berger, 1976), rivers (Balazi & Matis, 2002; El Serehy & Sleigh, 1993; Foissner, 1997b), and streams (Madoni & Ghetti, 1980; Taylor, 1983a), and hypersaline lagoons and lakes (García & Niell, 1993; Post, Borowitzka, Borowitzka, Mackay, & Moulton, 1983; Yasindi, Lynn, & Taylor, 2002). Ciliates are also recorded from terrestrial habitats,primarily soils and mosses (Buitkamp, 1977; Foissner, 1998a; Ryan et al., 1989). Along with their association with mosses, ciliates can also be found in the liquid in pitcher plants leaves (Addicott, 1974; Rojo-Herguedas & Olmo, 1999) and in the axils of tropical plants, such as bromeliads (Foissner, Strüder-Kypke, van der Staay, Moon-van der Staay, & Hackstein, 2003). The species composition and diversity of ciliates have been used as bioindicators of the state of eco- systems (e.g., Foissner, 1988a, 1997b, 1997e). How have ciliates come to be distributed as we now see them? Bamforth (1981) reviewed the factors that, in his view, explained the biogeography of both free-living and symbiotic species. For free-living species, these included characteristics of the autecology of the species and environmental conditions, such as wind patterns and ocean currents. For example, a variety of species are distributed by wind currents (Maguire, 1963b). The distribution of tintinnids in the Adriatic Sea , for example, is strongly influenced by ocean currents: still certain tintinnid species, despite the absence of vertical bar- riers to migration, can be characterized as surface, mesopelagic, or deep-sea forms (Krsinic & Grbec, 2006). Symbiotic ciliates have a biogeography that is influenced by the historical biogeography of their hosts. However, even species that we do not nor- mally imagine as symbiotic, such as Paramecium , can be transported in tropical snails from flower to flower (Maguire & Belk, 1967)! Humans may have also played a role in dispersing species as a variety of taxa has been observed in the ballast tanks of ocean-going vessels (Galil & Hülsmann, 1997). Nevertheless, the opinions on how the diversity of free-living ciliates is geographically distributed have become polarized into two major views. On one hand, ciliates are considered ubiquitous and cosmo- politan , and on the other, many ciliates are considered moderately endemic . Some of the controversy cent- ers around semantics. Finlay, Esteban, and Fenchel (2004) have offered the following definitions to focus debate. They suggested that ubiquitous refer to the process of continuous, worldwide dispersal of organisms while cosmopolitan should refer to species that thrive wherever their habitat is found worldwide. Endemic refers to organisms of low dispersal ability and restricted distribution. Many years ago, Beijerinck (1913) made the argument for bacterial species that \u201ceverything is everywhere, the environment selects\u201d. Finlay and Clarke (1999) and Finlay and Fenchel (1999) have taken up this argument for protists, emphasizing that the typically small size and extremely high abundances of protist species, including most ciliates, should permit them to defy barriers to migration, making allopatric speciation almost impossible. While it is undoubt- edly impossible that everything be everywhere, cosmopolitan species, as defined above, have been observed. For example, similar freshwater species assemblages have been found in the northern and southern hemispheres (Esteban et al., 2000); marine ciliates have been recorded in inland saline envi- ronments (Esteban & Finlay, 2004); and allegedly endemic \u201cflagship\u201d ciliates may be more broadly distributed than previously thought (Esteban, Finlay, Charubhun, & Charubhun, 2001). Moreover, there is now genetic evidence to suggest that the effec- tive population sizes of ciliates might be quite large (Snoke, Berendon, Barth, & Lynch, 2006), although there is debate on how large (Katz, Snoeyenbos- West, & Doerder, 2006). On the other side, Foissner (1999c) takes the view that many species show limited geographical distributions and low dispersal abilities. For exam- ple, the large tropical peniculine Neobursaridium gigas , a \u201c flagship \u201d tropical freshwater species , was described over 60 years ago in Africa, and yet it has only been recorded in the Southern Hemisphere des- pite intensive sampling of Northern Hemisphere habitats. Foissner (2005a) has described two large, scaled trachelophyllid haptorians that he describes as new \u201cflagship\u201d species from the Southern Hemisphere , to which can be added large-bodied species of the nassophorean Frontonia and the stichotrichian Gigantothrix (Foissner, 2006). Thus, he argued that endemism and a biogeography may be properties of a much larger subset of species than currently reported, perhaps up to one-third. This proportion has been supported by a more extensive analysis of over 300 soil samples from five continents (Chao, Li, Agatha, & Foissner, 2006), but a contrary view was provided by Finlay, Esteban, Clarke, and Olmo (2001) who found no evidence for geographic restriction of species across local and global scales. The debate has important implications, as pointed out by Mitchell and Meisterfeld (2005). If species have global distributions, then overall diversity will be low; if species have more restricted distributions, not just due to narrow niche breadths, then overall diversity will be high. For ciliates, Finlay, Corliss, Esteban, and Fenchel (1996) concluded that there may only be 3,000 morphospecies of free-living ciliates. On the other hand, Foissner (1999c) argued that the number could be considerably higher, per- haps two or three times as many, since up to 80% of the morphospecies at some sites were new in his global studies of soil ciliate species diversity. New species are being discovered even in regions of Central Europe , which have been intensively investigated (Foissner, Berger, Xu, & Zechmeister- Boltenstern, 2005b). Of crucial importance to this debate is one\u2019s conception of a species: \u201csplitters\u201d might conclude that there are high rates of ende- mism while \u201clumpers\u201d might conclude just the opposite (Mitchell & Meisterfeld). Finlay et al. (1996) concluded that a pragmatic approach to ciliate biodiversity should be to recognize the \u201cmorphospecies\u201d as the operational unit for ana- lyses of biodiversity. They defined a morphospecies as \u201ca collection of forms that all fit into a defined range of morphological variation \u2013 forms that, so far as we can tell, occupy the same ecological niche\u201d (p. 232, Finlay et al.; see also Esteban & Finlay, 2004). Given the broad physicochemical tolerances of many ciliates species, they suggested that niche breadths are probably broad, and so morphospe- cies provide us a reasonable understanding of the functional role of ciliate biodiversity in ecosystems. There are certainly a number of studies that suggest that subunits of morphospecies, such as sibling species and particular genotypes, are not geographically restricted (e.g., Ammerman, Schlegel, & Hellmer, 1989; Bowers, Kroll, & Pratt, 1998; Przybos & Fokin, 2000; Stoeck, Przybos, & Schmidt, 1998; Stoeck, Przybos, Kusch, & Schmidt, 2000a). In contrast, however, there is preliminary evidence that some genotypes may have restricted ranges (Stoeck et al., 1998) or appear at particular seasons of the year (Doerder, Gates, Eberhardt, & Arslanyolu, 1995; Doerder et al., 1996). Katz et al. (2005) have presented convincing evidence that gene flow was high and diversity was low in planktonic spirotrichs that inhabit open coastal waters (e.g., Laboea ), while gene flow was high and diversity was also high in oligotrichs that inhabit ephemeral