Acta Chiropterologica, 10(2): 193–206, 2008 PL ISSN 1508-1109 © Museum and Institute of Zoology PAS doi: 10.3161/150811008X414782 Variation of mitochondrial DNA in the Hipposideros caffer complex (Chiroptera: Hipposideridae) and its taxonomic implications PETER V ALLO 1, 2, 7 , ANTONIO GUILLÉN-SERVENT 3 , PETR BENDA 4, 5 , DEBRA B. PIRES 6 , and PETR KOUBEK 1 1 Institute of Vertebrate Biology, v. v. i., Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic 2 Institute of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic 3 Instituto de Ecología, A.C., km 2.5 Ctra. Antigua a Coatepec #351, Congregación el Haya, 91070 Xalapa, Veracruz, México 4 Department of Zoology, National Museum (Natural History), Václavské náměstí 68, 115 79 Praha 1, Czech Republic 5 Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44 Praha 2, Czech Republic 6 Department of Life Sciences, University of California, 621 Charles E. Young Drive South, Los Angeles, California 90095–1606, USA 7 Corresponding author: E-mail: vallo@ivb.cz The Afrotropical leaf-nosed bat Hipposideros caffer has been traditionally regarded as a complex of populations, currently pertaining to two recognized cryptic species, H. caffer and H. ruber. Extent of distribution and morphological variation of these bats has raised concerns over whether the current perception of the complex reflects true phylogenetic relationships and taxonomic diversity. Our phylogenetic analysis of nucleotide sequences of the mitochondrial cytochrome b gene challenged the hypothesis of two cryptic species. Instead of the two reciprocally monophyletic lineages expected, corresponding to the two species, we recovered four distinct lineages with deep internal divergences. Two sister clades within a lineage of bats of H. caffer represent respectively the nominotypical form H. c. caffer, restricted to Southern Africa, and H. c. tephrus, inhabiting the Maghreb, West Africa and the Arabian Peninsula. Geographical isolation and deep genetic divergence suggest species status of both the forms. Another lineage comprises specimens of both morphotypes from West and East Africa. It probably represents a distinct species but its taxonomic assignation remains obscure. A Central African lineage of H. ruber comprises two sister clades, which become sympatric in Cameroon. Their status has to be clarified with additional evidence, since nuclear gene flow might be taking place. A further divergent lineage with H. ruber morphotype, most probably representing another distinct species, is restricted to West Africa. Although all three genetic forms of H. ruber may correspond to named taxa, their proper taxonomic assignation has to be assessed by comparison with type material. Key words: Africa, Hipposideros caffer, H. ruber, leaf-nosed bats, cryptic species, cytochrome b, molecular systematics, phylogeny INTRODUCTION Flight and echolocation constrain bat morpholo- gy in a way that parallel and convergent evolution can be widespread among species that use similar ecological niches (Norberg, 1994; Ruedi and Mayer, 2001). This may make taxonomy difficult, since species evolutionarily related and ecologically simi- lar may lack conspicuous morphological characters useful to discriminate among them. Genetic data may be fundamental in these cases, allowing the identification of deeply divergent lineages that may represent evolutionary independent units (Bradley and Baker, 2001). Molecular phylogenetic methods have been used extensively in recent years to reveal many new cryptic forms of bats within traditionally recognized species. The recent increase of about 20% in the number of species of the European fau- na of bats, probably the best known Chiropteran fau- na in the World, is an illuminating example of the utility of the genetic data to discover hidden taxo- nomic diversity within bats (Mayer and von Helver- sen, 2001; Ibáñez et al., 2006; Mayer et al., 2007). The genus Hipposideros Gray, 1831, the largest in the Palaeotropical family of the leaf-nosed bats, Hipposideridae, has traditionally had a difficult ta- xonomy due to the extreme morphological similari- ty of many of its members (Hill, 1963; Bogdano- wicz and Owen, 1998). This morphological similar- ity suggests that cryptic species might be particular- ly common among these bats. Systematic biologists have so far paid most attention to the Southeast