Biol. Rev. (2002), 77, pp. 223–259  Cambridge Philosophical Society DOI : 10.1017S1464793101005899 Printed in the United Kingdom 223 A phylogenetic supertree of the bats (Mammalia : Chiroptera) KATE E. JONES , *, ANDY PURVIS, ANN MacLARNON, OLAF R. P. BININDA-EMONDS and NANCY B. SIMMONS  Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire, SL5 7PY, UK  School of Life Sciences, University of Surrey Roehampton, West Hill, London SW15 3SN, UK  Institute of Evolutionary and Ecological Sciences, Leiden University, Kaiserstraat 63, P.O. Box 9516, 2300 RA Leiden, The Netherlands  Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History, New York, New York 10024, USA (Received 28 June 2001 ; revised 21 November 2001 ; accepted 12 December 2001) ABSTRACT We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats (Mammalia : Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have focused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades : overall resolution is poor (46.4 % of a fully bifurcating solution) but reaches 100 % in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats. Key words : bats, evolution, matrix representation, parsimony, phylogeny, supertree construction. CONTENTS I. Introduction ............................................................................................................................ 224 II. Chiropteran phylogeny : a general review ............................................................................... 224 III. Study goals .............................................................................................................................. 226 IV. Materials and methods ............................................................................................................ 227 (1) Data ................................................................................................................................ 227 (2) Matrix construction......................................................................................................... 228 (3) Analysis ........................................................................................................................... 228 V. Results and Discussion ............................................................................................................. 229 (1) Taxonomic coverage and resolution................................................................................ 229 * Author to whom correspondence should be addressed. Present address : Department of Biology, University of Virginia, Charlottesville, Virginia 22904-4328, USA (e-mail : kate.jonesvirginia.edu).