Molecular Ecology (2005) 14, 2991–3004 doi: 10.1111/j.1365-294X.2005.02583.x © 2005 Blackwell Publishing Ltd Blackwell Publishing, Ltd. Ice age cloning – comparison of the Quaternary evolutionary histories of sexual and clonal forms of spiny loaches (Cobitis; Teleostei) using the analysis of mitochondrial DNA variation K. JANKO,* M. A. CULLING,† P. RÁB *‡ and P. KOTLÍK * *Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Libechov, Czech Republic, †School of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, NR4 7TJ, UK, ‡ Joint Laboratory of Genetics, Physiology and Reproduction of Fishes of IAPG CAS, Lib e chov, and RIFH USB, Vod - any Abstract Recent advances in population history reconstruction offered a powerful tool for comparisons of the abilities of sexual and clonal forms to respond to Quaternary climatic oscillations, ultimately leading to inferences about the advantages and disadvantages of a given mode of reproduction. We reconstructed the Quaternary historical biogeography of the sexual parental species and clonal hybrid lineages within the Europe-wide hybrid complex of Cobitis spiny loaches. Cobitis elongatoides and Cobitis taenia recolonizing Europe from separated refuges met in central Europe and the Pontic region giving rise to hybrid lineages during the Holocene. Cobitis elongatoides due to its long-term reproductive contact with the remaining parental species of the complex — C. tanaitica and C. spec. — gave rise to two clonal hybrid lineages probably during the last interglacial or even earlier, which survived the Würmian glaciation with C. elongatoides. These lineages followed C. elongatoides post- glacial expansion and probably decreased its dispersal rate. Our data indicate the frequent origins of asexuality irrespective of the parental populations involved and the comparable dispersal potential of diploid and triploid lineages. Keywords: asexuality, Cobitis, glacial refuges, hybridization, phylogeography Received 29 November 2004; revision accepted 14 March 2005 Introduction More than a century after the introduction of the ‘paradox of sex’ (Weissman 1889), there is little disagreement that strict asexuality among higher organisms generally repres- ents an evolutionary dead end due to the inability of clones to escape mutation or parasite loads or to cope with the changing environment (Felsenstein 1974; Hamilton 1980; Howard & Lively 1998). Yet, recent findings contrasting traditional assumptions in some model groups (Vrijenhoek 1993; Judson & Normark 1996; Alves et al . 1998) together with a growing amount of discovered asexual complexes (Vrijenhoek et al . 1989; for review of later described cases see Alves et al . 2001) suggest that we are far from understanding the roles of sex and the asexual reproductive mode in evolution. Theoretical predictions have been tested on suitable animal, plant and fungi model organisms, among which vertebrates occupy a privileged position, due to relatively easy sampling and rather well-developed methodological approaches. Since the discovery of the first clonal verte- brate, Poecilia formosa (Hubbs & Hubbs 1932), significant research effort led to some conclusions about asexuality among metazoans in general and among vertebrates in particular. Generally, asexual lineages are recent offshoots of extant Mendelian taxa, although some lineages have apparently persisted without sex for longer (Quattro et al . 1992a; Spolsky et al . 1992; Judson & Normark 1996) than predicted by mutation-accumulation models (Lynch et al . 1993). Clonal vertebrates studied so far apparently have Correspondence: K. Janko, Fax: + 420 315639510; E-mail: janko@iapg.cas.cz