Cryptic lineages of little free-tailed bats, Chaerephon pumilus (Chiroptera: Molossidae) from southern Africa and the western Indian Ocean islands Peter John Taylor 1 * , Jennifer Lamb 2 , Devendran Reddy 2 , Theshnie Naidoo 2 , Fanja Ratrimomanarivo 3 & Steven M. Goodman 3,4 1 Durban Natural Science Museum, P.O. Box 4085, Durban, 4000 South Africa 2 School of Biological and Conservation Sciences, George Campbell Building, University of KwaZulu-Natal, King George V Avenue, Durban, 4041 South Africa 3 Vahatra, BP 3972, Antananarivo (101), Madagascar 4 Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois 60605, U.S.A. Received 14 July 2008. Accepted 27 January 2009 We investigate mitochondrial DNA and craniometric variation in southern African and Malagasy populations of the small and morphologically variable, house-roosting molossid bat, Chaerephon pumilus in relation to Malagasy populations of the related, smaller-sized species, C. leucogaster. Both cytochrome b and D-loop sequences show C. leucogaster to be nested within C. pumilus sensu lato, with Malagasy C. pumilus forming a sister group to African C. pumilus and Malagasy C. leucogaster. Four distinct D-loop clades are found in southern African populations, all of which occur sympatrically in the greater Durban area of KwaZulu-Natal Province, whilst two of the Durban clades also characterize 1) northern KwaZulu-Natal and low-lying (<600 m) areas of Swaziland, and 2) ‘inland’ populations comprising the Kruger National Park and higher-lying (>600 m) areas of Swaziland. Clades from low-lying areas show evidence of historical demographic expansion around 3300–13 000 years ago (KwaZulu-Natal coastal clade, Clade A1) to 14 700–60 000 years ago (Durban clade, Clade B1), whilst the inland clade (Clade B2a) was demographically more stable. The origin of these clades can be explained by sea level and vegetation changes hypothesized to follow the Last Glacial Maximum (LGM) after 18 000 years ago. Sympatric clades are shown to differ significantly in the proportional width of the braincase, and ongoing work will test evidence for acoustic and other morphological differences between them. Key words: Chiroptera, mitochondrial, DNA D-loop, cytochrome b, phylogeography, population genetics, morphometrics, taxonomy. INTRODUCTION The little free-tailed bat Chaerephon pumilus (Cretzschmar, 1830–31), a small, common, house- roosting molossid bat (forearm length c. 37 mm; mass c. 10 g), is characterized by extreme pheno- typic variation throughout its broad distribution (confined mostly to altitudes <600 m: Fig. 1) in Africa and Madagascar (Peterson et al. 1995; Taylor 1999a; Simmons 2005). The species was described from Massawe, Eritrea, and currently includes nine synonyms (Simmons 2005). The often recognized form limbata from central and east Africa is notice- ably white-winged (usually also with greater extent of white ventral body markings) compared with the dark-winged forms found elsewhere across this species’ range. Jacobs et al. (2004) showed that cytochrome b haplotypes from dark-winged southern African and white-winged east and central African (Tanzania and Zambia) forms of pumilus exhibited 0.9% divergence. Distinct but genetically similar haplotypes also character- ized the southern (several localities in Durban and surrounds) and northern (a single locality, Hell’s Gate, bordering Lake St Lucia) regions of KwaZulu-Natal Province of South Africa (Jacobs et al. 2004). Taylor (1999a) demonstrated that populations of C. pumilus from eastern South Africa and Swazi- land revealed polymorphism in diagnostic charac- ters such as body size, pelage coloration, the degree of development of the male aural crest and African Zoology 44(1): 55–70 (April 2009) *Author for correspondence. Email: taylorpeter@durban.gov.za