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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 “everything is everywhere, 
the environment selects”. 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 “flagship” 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 “ flagship ” 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 “flagship” 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’s conception of a species: “splitters” 
might conclude that there are high rates of ende-
mism while “lumpers” might conclude just the 
opposite (Mitchell & Meisterfeld). 
 Finlay et al. (1996) concluded that a pragmatic 
approach to ciliate biodiversity should be to recognize 
the “morphospecies” as the operational unit for ana-
lyses of biodiversity. They defined a morphospecies 
as “a collection of forms that all fit into a defined 
range of morphological variation – forms that, so far 
as we can tell, occupy the same ecological niche” 
(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