Molecular phylogeny of New World sheath-tailed bats (Emballonuridae: Diclidurini) based on loci from the four genetic transmission systems in mammals BURTON K. LIM 1 *, MARK D. ENGSTROM 1 , JOHN W. BICKHAM 2 † and JOHN C. PATTON 2 † 1 Department of Natural History, Royal Ontario Museum, Toronto, Ontario, M5S 2C6, Canada 2 Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, 77843-2258, USA Received 3 December 2006; accepted for publication 16 March 2007 Multiple unlinked loci are surveyed in a methodological approach for mammalian systematics that uses genes from the four pathways of genetic transmission: mitochondrial, autosomal, and X and Y sex chromosomes. Each of these components has different properties, such as effective population size, mutation rate, and recombination, that result in a robust hypothesis of evolutionary history. The utility of this experimental design is tested with bats in the family Emballonuridae and the hypothesis that the New World taxa are monophyletic. Parsimony and Bayesian analyses of the individual data sets give generally congruent topologies with high bootstrap proportions and posterior probabilities for monophyletic clades representing species and genera. The mitochondrial gene has significantly faster rates of substitution, higher levels of homoplasy, and a greater degree of saturation than the nuclear genes that contributed to the loss of phylogenetic signal at deeper branches of the tree. However, there is better resolution and support for the more slowly evolving nuclear introns including a New World clade, indicating a single origin of emballonurid bats in the Neotropics (tribe Diclidurini). One novel subtribe has a hard basal polytomy that is unresolved for all of the nuclear partitions, suggesting a rapid burst of evolution during the diversification of genera. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 189–209. ADDITIONAL KEYWORDS: Bayesian inference – Chd1 – Cytb – Dby – Neotropics – parsimony – phyloge- netic analysis – Usp9x. INTRODUCTION There has been a general pattern of loci-use in sys- tematic research as genetic techniques have devel- oped and matured. Early molecular studies commonly used a mitochondrial gene because of the reliability of polymerase chain reaction (PCR) amplification asso- ciated with this multiple copy genome (Irwin, Kocher & Wilson, 1991). To ensure the recovery of a more robust species tree, as opposed to a gene tree, later phylogenetic reconstructions used a digenomic ap- proach by also incorporating loci from the nuclear genome because of the linked nature of mitochondrial genes (Palumbi & Baker, 1994; Moore, 1995; Baker et al., 2003). More recent analyses have selected molecular markers based on the distinction of modes of inheritance by incorporating a paternally inherited gene, such as from the Y sex chromosome in mammals, in addition to a maternally inherited mito- chondrial gene and biparentally inherited autosomal chromosome gene (Lundrigan, Jansa & Tucker, 2002; Tosi, Morales & Melnick, 2003). A natural extension of this approach is to use loci from the four genomic components as defined by transmission genetics. For mammals, this would include the mitochondrial genome, and the autosomal, and Y and X sex chro- mosomes of the nuclear genome. Each of these genetic systems has different biological properties, such as *Corresponding author. E-mail: burtonl@rom.on.ca †Current address: Center for the Environment, Purdue University, West Lafayette, Indiana, 47907-2966, USA. Biological Journal of the Linnean Society, 2008, 93, 189–209. With 7 figures © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 189–209 189