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VII. REFERENCES

  • Alfaro, M. E., Zoller, S. & Lutzoni, F. (2003). Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20, 255266.
  • Anthony, N. M., Clifford, S. L., Bawe-Johnson, M., Abernethy, K. A., Bruford, M. W. & Wickings, E. J. (2007). Distinguishing gorilla mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases. Molecular Phylogenetics and Evolution 43, 553566.
  • Antunes, A., Pontius, J., Ramos, M. J., O’Brien, S. J. & Johnson, W. E. (2007). Mitochondrial introgressions into the nuclear genome of the domestic cat. Journal of Heredity 98, 414420.
  • Baker, R. J., Porter, C. A., Hoofer, S. R. & Van Den Bussche, R. A. (2003). Diversification among New World leaf-nosed bats: an evolutionary hypothesis and classification inferred from digenomic congruence of DNA sequence. Occasional Papers, Museum of Texas Tech University 230, 132.
  • Baker, R. J., Porter, C. A., Patton, J. C. & Van Den Bussche, R. A. (2000). Systematics of bats of the family Phyllostomidae based on RAG2 DNA sequences. Occasional Papers, Museum of Texas Tech University 202, 116.
  • Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R. L. & Doolittle, W. F. (2005). Do orthologous gene phylogenies really support tree-thinking?. BMC Evolutionary Biology 5, 33.
  • Baurain, D., Brinkmann, H. & Philippe, H. (2007). Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors? Molecular Biology and Evolution 24, 69.
  • Bell, G. P. & Fenton, M. B. (1986). Visual acuity, sensitivity and binocularity in a gleaning insectivorous bat, Macrotus californicus (Chiroptera: Phyllostomidae). Animal Behaviour 34, 409414.
  • Bensasson, D., Feldman, M. W. & Petrov, D. A. (2003). Rates of DNA duplication and mitochondrial DNA insertion in the human genome. Journal of Molecular Evolution 57, 343354.
  • Berthier, P., Excoffier, L. & Ruedi, M. (2006). Recurrent replacement of mtDNA and cryptic hybridization between two sibling bat species Myotis myotis and Myotis blythii. Proceedings of the Royal Society of London Series B: Biological Sciences 273, 31013109.
  • Bharathan, G., Goliber, T. E., Moore, C., Kessler, S., Pham, T. & Sinha, N. R. (2002). Homologies in leaf form inferred from KNOXI gene expression during development. Science 296, 18581860.
  • Bielawski, J. P. & Yang, Z. (2003). Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of Structural and Functional Genomics 3, 201212.
  • Bielawski, J. P. & Yang, Z. (2004). A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. Journal of Molecular Evolution 59, 121132.
  • Bininda-Emonds, O. R. P. (2005). TransAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 6, 156.
  • Brumfield, R. T., Liu, L., Lum, D. E. & Edwards, S. V. (2008). Comparison of species tree methods for reconstructing the phylogeny of Bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Systematic Biology 57, 719731.
  • Buckley, T. R., Simon, C. & Chambers, G. K. (2001). Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Systematic Biology 50, 6786.
  • Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L. & Waddell, P. J. (1993). Partitioning and combining data in phylogenetic analysis. Systematic Biology 42, 384397.
  • Burk, A., Douzery, E. J. P. & Springer, M. S. (2002). The secondary structure of mammalian mitochondrial 16S rRNA molecules: refinements based on a comparative phylogenetic approach. Journal of Mammalian Evolution 9, 225252.
  • Burnham, K. P. & Anderson, D. R. (2002). Model Selection and Multimodel Inference . Springer-Verlag, New York.
  • Canback, B., Tamas, I. & Andersson, S. G. E. (2004). A phylogenomic study of endosymbiotic bacteria. Molecular Biology and Evolution 21, 11101122.
  • Carstens, B. C., Lundrigan, B. L. & Myers, P. (2002). A phylogeny of the neotropical nectar-feeding bats (Chiroptera: Phyllostomidae) based on morphological and molecular data. Journal of Mammalian Evolution 9, 2353.
  • de Carvalho, M., Bockmann, F., Amorim, D. & Brandão, C. (2008). Systematics must embrace comparative biology and evolution, not speed and automation. Evolutionary Biology 35, 150157.
  • Castoe, T. A., de Koning, A. P. J., Kim, H.-M., Gu, W., Noonan, B. P., Naylor, G., Jiang, Z. J., Parkinson, C. L. & Pollock, D. D. (2009). Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences of the United States of America 106, 89868991.
  • Clamp, M., Cuff, J., Searle, S. M. & Barton, G. J. (2004). The Jalview java alignment editor. Bioinformatics 20, 426427.
  • Clare, E. L., Lim, B. K., Engstrom, M. D., Eger, J. L. & Hebert, P. D. N. (2007). DNA barcoding of neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes 7, 184190.
  • Coelho, D. C. & Marinho-Filho, J. (2002). Diet and activity of Lonchophylla dekeyseri (Chiroptera, Phyllostomidae) in the Federal District, Brazil. Mammalia 66, 319330.
  • Corneo, B., Moshous, D., Güngör, T., Wulffraat, N., Philippet, P., Deist, F. O. L., Fischer, A. & de Villartay, J.-P. (2001). Identical mutations in RAG1 or RAG2 genes leading to defective V(D)J recombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome. Blood 97, 27722776.
  • Cramer, W. A., Zhang, H., Yan, J., Kurisu, G. & Smith, J. L. (2006). Transmembrane traffic in the cytochrome b 6 f complex. Annual Review of Biochemistry 75, 769790.
  • Datzmann, T., von Helversen, O. & Mayer, F. (2010). Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia). BMC Evolutionary Biology 10, 165.
  • Daubin, V., Moran, N. A. & Ochman, H. (2003). Phylogenetics and the cohesion of bacterial genomes. Science 301, 829832.
  • Dávalos, L. M. (2005). Molecular phylogeny of Funnel-eared bats (Chiroptera: Natalidae), with notes on biogeography and conservation. Molecular Phylogenetics and Evolution 37, 91103.
  • Dávalos, L. M. (2007). Short-faced bats (Phyllostomidae: Stenodermatina): a Caribbean radiation of strict frugivores. Journal of Biogeography 34, 364375.
  • Dávalos, L. M. & Jansa, S. A. (2004). Phylogeny of the lonchophyllini (Chiroptera: Phyllostomidae). Journal of Mammalogy 85, 404413.
  • Dávalos, L. M. & Perkins, S. L. (2008). Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics 91, 433442.
  • Dávalos, L. M. & Porzecanski, A. L. (2009). Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria. Molecular Phylogenetics and Evolution 53, 234248.
  • Davis, B. W., Li, G. & Murphy, W. J. (2010). Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). Molecular Phylogenetics and Evolution 56, 6476.
  • Degnan, J. H. & Rosenberg, N. A. (2006). Discordance of species trees with their most likely gene trees. PLoS Genetics 2, e68.
  • Delsuc, F., Brinkmann, H., Chourrout, D. & Philippe, H. (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965968.
  • Delsuc, F., Catzeflis, F. M., Stanhope, M. J. & Douzery, E. J. P. (2001). The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua. Proceedings of the Royal Society of London Series B: Biological Sciences 268, 16051615.
  • Donoghue, M. J. & Ree, R. H. (2000). Homoplasy and developmental constraint: a model and an example from plants. American Zoologist 40, 759769.
  • Dumont, E. R., Dávalos, L. M., Goldberg, A., Voigt, C. C., Rex, K. & Santana, S. E. (2012). Morphological innovation, diversification and the invasion of a new adaptive zone. Proceedings of the Royal Society Series B: Biological Sciences 279, 17971805.
  • Eckert, A. J. & Carstens, B. C. (2008). Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Molecular Phylogenetics and Evolution 49, 832842.
  • Esposti, M. D., De Vries, S., Crimi, M., Ghelli, A., Patarnello, T. & Meyer, A. (1993). Mitochondrial cytochrome b: evolution and structure of the protein. Biochimica et Biophysica Acta: Bioenergetics 1143, 243271.
  • Farris, J. S. (1989a). The retention index and homoplasy excess. Systematic Zoology 38, 406407.
  • Farris, J. S. (1989b). The retention index and the rescaled consistency index. Cladistics 5, 417419.
  • Fawcett, J. A., Maere, S. & Van de Peer, Y. (2009). Plants with double genomes might have had a better chance to survive the Cretaceous—Tertiary extinction event. Proceedings of the National Academy of Sciences of the United States of America 106, 57375742.
  • Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27, 401410.
  • Freeman, P.-W. (1995). Nectarivorous feeding mechanisms in bats. Biological Journal of the Linnean Society 56, 439463.
  • Freeman, P. W. (2000). Macroevolution in microchiroptera: recoupling morphology and ecology with phylogeny. Evolutionary Ecology Research 2, 317335.
  • Gatesy, J., Hayashi, C., Cronin, M. A. & Arctander, P. (1996). Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls. Molecular Biology and Evolution 13, 954963.
  • Gaubert, P., Wozencraft, W. C., Cordeiro-Estrela, P. & Veron, G. r. (2005). Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran? Systematic Biology 54, 865894.
  • Geeta, R., Dávalos, L. M., Levy, A., Bohs, L., Lavin, M., Mummenhoff, K., Sinha, N. & Wojciechowski, M. F. (2012). Keeping it simple: flowering plants tend to retain, and revert to, simple leaves. New Phytologist 193, 481493.
  • Gibson, A., Gowri-Shankar, V., Higgs, P. G. & Rattray, M. (2005). A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Molecular Biology and Evolution 22, 251264.
  • Graybeal, A. (1998). Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology 47, 917.
  • Griffiths, T. A. (1982). Systematics of the New World nectar-feeding bats (Mammalia, Phyllostomidae), based on the morphology of the hyoid and lingual regions. American Museum Novitates 2742, 145.
  • Griffiths, T. A. (1983). On the phylogeny of the glossophaginae and the proper use of outgroup analysis. Systematic Zoology 32, 283285.
  • Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696704.
  • Hailer, F. & Leonard, J. A. (2008). Hybridization among three native North American Canis species in a region of natural sympatry. PLoS ONE 3, e3333.
  • Handcock, M. S. & Morris, M. (1999). Relative Distribution Methods in the Social Sciences . Springer, New York.
  • Hasegawa, M., Kishino, H. & Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22, 160174.
  • Hazkani-Covo, E. & Graur, D. (2007). A comparative analysis of numt evolution in human and chimpanzee. Molecular Biology and Evolution 24, 1318.
  • Heckman, K. L., Mariani, C. L., Rasoloarison, R. & Yoder, A. D. (2007). Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus). Molecular Phylogenetics and Evolution 43, 353367.
  • Hedtke, S. M., Townsend, T. M. & Hillis, D. M. (2006). Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Systematic Biology 55, 522529.
  • Henry, M. l. & Kalko, E. K. V. (2007). Foraging strategy and breeding constraints of Rhinophylla pumilio (Phyllostomidae) in the Amazon lowlands. Journal of Mammalogy 88, 8193.
  • Hoffmann, F. G. & Baker, R. J. (2001). Systematics of bats of the genus Glossophaga (Chiroptera: Phyllostomidae) and phylogeography in G. soricina based on the cytochrome b gene. Journal of Mammalogy 82, 10921101.
  • Hoofer, S. R. & Baker, R. J. (2006). Molecular systematics of vampyressine bats (Phyllostomidae: Stenodermatinae) with comparison of direct and indirect surveys of mitochondrial DNA variation. Molecular Phylogenetics and Evolution 39, 424438.
  • Hotopp, J. C. D., Clark, M. E., Oliveira, D. C. S. G., Foster, J. M., Fischer, P., Torres, M. C. M., Giebel, J. D., Kumar, N., Ishmael, N., Wang, S., Ingram, J., Nene, R. V., Shepard, J., Tomkins, J., Richards, S., Spiro, D. J., Ghedin, E., Slatko, B. E., Tettelin, H. & Werren, J. H. (2007). Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317, 17531756.
  • Huelsenbeck, J. P. (1997). Is the Felsenstein zone a fly trap? Systematic Biology 46, 6974.
  • Hunter, J. P. & Jernvall, J. (1995). The hypocone as a key innovation in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America 92, 1071810722.
  • Ingman, M. & Gyllensten, U. (2007). Rate variation between mitochondrial domains and adaptive evolution in humans. Human Molecular Genetics 16, 22812287.
  • Iwata, S., Lee, J. W., Okada, K., Lee, J. K., Iwata, M., Rasmussen, B., Link, T. A., Ramaswamy, S. & Jap, B. K. (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. Science 281, 6471.
  • Jeffroy, O., Brinkmann, H., Delsuc, F. & Philippe, H. (2006). Phylogenomics: the beginning of incongruence? Trends in Genetics 22, 225231.
  • Jones, K. E., Purvis, A., MacLarnon, A., Bininda-Emonds, O. R. P. & Simmons, N. B. (2002). A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biological Reviews 77, 223259.
  • Kalka, M. & Kalko, E. K. V. (2006). Gleaning bats as underestimated predators of herbivorous insects: diet of Micronycteris microtis (Phyllostomidae) in Panama. Journal of Tropical Ecology 22, 110.
  • Katoh, K. & Toh, H. (2008a). Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9, 212.
  • Katoh, K. & Toh, H. (2008b). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9, 286298.
  • Keightley, J. A., Anitori, R., Burton, M. D., Quan, F., Buist, N. R. & Kennaway, N. G. (2000). Mitochondrial encephalomyopathy and complex III deficiency associated with a stop-codon mutation in the cytochrome b gene. American Journal of Human Genetics 67, 14001410.
  • Kelm, D. H., Simon, R., Kuhlow, D., Voigt, C. C. & Ristow, M. (2011). High activity enables life on a high-sugar diet: blood glucose regulation in nectar-feeding bats. Proceedings of the Royal Society Series B: Biological Sciences 278, 34903496.
  • Lartillot, N., Brinkmann, H. & Philippe, H. (2007). Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evolutionary Biology 7 (Suppl 1), S4.
  • Lee, T. E. Jr., Hoofer, S. R. & Van Den Bussche, R. A. (2002). Molecular phylogenetics and taxonomic revision of the genus Tonatia (Chiroptera: Phyllostomidae). Journal of Mammalogy 83, 4957.
  • Lee, M. S. Y. & Hugall, A. F. (2003). Partitioned likelihood support and the evaluation of data set conflict. Systematic Biology 52, 1522.
  • Leebens-Mack, J., Raubeson, L. A., Cui, L., Kuehl, J. V., Fourcade, M. H., Chumley, T. W., Boore, J. L., Jansen, R. K. & dePamphilis, C. W. (2005). Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 22, 19481963.
  • Lerat, E., Daubin, V. & Moran, N. A. (2003). From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biology 1, e19.
  • Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50, 913925.
  • Li, Y., Liu, Z., Shi, P. & Zhang, J. (2010). The hearing gene Prestin unites echolocating bats and whales. Current Biology 20, R55R56.
  • Li, G., Wang, J., Rossiter, S. J., Jones, G., Cotton, J. A. & Zhang, S. (2008). The hearing gene Prestin reunites echolocating bats. Proceedings of the National Academy of Sciences of the United States of America 105, 1395913964.
  • Li, G., Wang, J., Rossiter, S. J., Jones, G. & Zhang, S. (2007). Accelerated Foxp2 evolution in echolocating bats. PLoS ONE 2, e900.
  • Liu, Y., Cotton, J. A., Shen, B., Han, X., Rossiter, S. J. & Zhang, S. (2010). Convergent sequence evolution between echolocating bats and dolphins. Current Biology 20, R53R54.
  • Liu, L., Pearl, D. K., Brumfield, R. T. & Edwards, S. V. (2008). Estimating species trees using multiple-allele DNA sequence data. Evolution 62, 20802091.
  • Liu, L., Yu, L., Kubatko, L., Pearl, D. K. & Edwards, S. V. (2009). Coalescent methods for estimating phylogenetic trees. Molecular Phylogenetics and Evolution 53, 320328.
  • Maddison, D. R. & Maddison, W. P. (2003). Macclade 4: Analysis of Phylogeny and Character Evolution . Sinauer Associates, Inc., Sunderland.
  • Mann, H. B. & Whitney, D. R. (1947). On a test of whether one of two random variables is stochastically larger than the other. Annals of Mathematical Statistics 18, 5060.
  • Mao, X., Zhang, J., Zhang, S. & Rossiter, S. J. (2010). Historical male-mediated introgression in Horseshoe bats revealed by multilocus DNA sequence data. Molecular Ecology 19, 13521366.
  • Market, E. & Papavasiliou, F. N. (2003). V(D)J recombination and the evolution of the adaptive immune system. PLoS Biology 1, e16.
  • Massey, F. J. Jr. (1951). The Kolmogorov-Smirnov test for goodness of fit. Journal of the American Statistical Association 46, 6878.
  • Masters, J. C. (2007). Taking phylogenetics beyond pattern analysis: can models of genome dynamics guide predictions about homoplasy in morphological and behavioral data sets? Journal of Human Evolution 52, 522535.
  • McGuire, J. A., Witt, C. C., Altshuler, D. L. & Remsen, J. V., Jr. (2007). Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Systematic Biology 56, 837856.
  • Minin, V., Abdo, Z., Joyce, P. & Sullivan, J. (2003). Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology 52, 673683.
  • Mitchell, P. (1975). The protonmotive Q cycle: a general formulation. FEBS Letters 59, 137139.
  • Moran, N. A. (1996). Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proceedings of the National Academy of Sciences of the United States of America 93, 28732878.
  • Morell, V. (1993). Treebase: the roots of phylogeny. Science 273, 569.
  • Muggeo, V. M. R. (2008). Segmented: an R package to fit regression models with broken-line relationships. R News 8, 2025.
  • Nylander, J. A. A. (2004). MrAIC.pl . Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University, Uppsala.
  • Oettinger, M. A., Schatz, D. G., Gorka, C. & Baltimore, D. (1990). RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248, 15171523.
  • Olson, L. E. & Yoder, A. D. (2002). Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. Molecular Biology and Evolution 19, 93100.
  • Owen, R. D. (1991). The systematic status of Dermanura concolor (Peters, 1865) (Chiroptera: Phyllostomidae), with description of a new genus. Bulletin of the American Museum of Natural History 206, 1825.
  • Patterson, C. (1988). Homology in classical and molecular biology. Molecular Biology and Evolution 5, 603625.
  • Philippe, H., Lartillot, N. & Brinkmann, H. (2005). Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Molecular Biology and Evolution 22, 12461253.
  • Phillips, M. J., Delsuc, F. & Penny, D. (2004). Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution 21, 14551458.
  • Pollard, D. A., Iyer, V. N., Moses, A. M. & Eisen, M. B. (2006). Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genetics 2, e173.
  • Porter, C. A. & Baker, R. J. (2004). Systematics of Vampyressa and related genera of phyllostomid bats as determined by cytochrome-b sequences. Journal of Mammalogy 85, 126132.
  • Porter, C. A., Hoofer, S. R., Cline, C. A., Hoffmann, F. G. & Baker, R. J. (2007). Molecular phylogenetics of the phyllostomid bat genus Micronycteris with descriptions of two new subgenera. Journal of Mammalogy 88, 12051215.
  • Posada, D. & Buckley, T. R. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53, 793808.
  • Pumo, D.-E., Finamore, P.-S., Franek, W.-R., Phillips, C.-J., Tarzami, S. & Balzarano, D. (1998). Complete mitochondrial genome of a neotropical fruit bat, Artibeus jamaicensis, and a new hypothesis of the relationships of bats to other eutherian mammals. Journal of Molecular Evolution 47, 709717.
  • di Rago, J.-P., Macadre, C., Lazowska, J. & Slonimski, P. P. (1993). The C-terminal domain of yeast cytochromeb is essential for a correct assembly of the mitochondrial cytochrome bc1 complex. FEBS Letters 328, 153158.
  • Ragsdale, E. J. & Baldwin, J. G. (2010). Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda. Proceedings of the Royal Society Series B: Biological Sciences 277, 12991307.
  • R Development Core Team (2010). R: A Language and Environment for Statistical Computing . R Foundation for Statistical Computing, Vienna.
  • Reiss, K.-Z. (2001). Using phylogenies to study convergence: the case of the ant-eating mammals. American Zoologist 41, 507525.
  • Rieppel, O. & Kearney, M. (2002). Similarity. Biological Journal of the Linnean Society 75, 5982.
  • van Rij, R. P., Worobey, M., Visser, J. A. & Schuitemaker, H. (2003). Evolution of R5 and X4 human immunodeficiency virus type 1 gag sequences in vivo: evidence for recombination. Virology 314, 451459.
  • Rodríguez-Ezpeleta, N., Brinkmann, H., Roure, B., Lartillot, N., Lang, B. F. & Philippe, H. (2007). Detecting and overcoming systematic errors in genome-scale phylogenies. Systematic Biology 56, 389399.
  • Rojas, D., Vale, Á., Ferrero, V. & Navarro, L. (2011). When did plants become important to leaf-nosed bats? Diversification of feeding habits in the family Phyllostomidae. Molecular Ecology 20, 22172228.
  • Rokas, A., Williams, B. L., King, N. & Carroll, S. B. (2003). Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798804.
  • Ronquist, F. & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 15721574.
  • Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kidd, K. K., Zhivotovsky, L. A. & Feldman, M. W. (2002). Genetic structure of human populations. Science 298, 23812385.
  • Ruedi, M. & Mayer, F. (2001). Molecular systematics of bats of the genus Myotis (Vespertilionidae) suggests deterministic ecomorphological convergences. Molecular Phylogenetics and Evolution 21, 436448.
  • Russell, A., Cox, M., Brown, V. & McCracken, G. (2011). Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity. BMC Evolutionary Biology 11, 88.
  • Russell, A. L., Goodman, S. M., Fiorentino, I. & Yoder, A. D. (2008). Population genetic analysis of Myzopoda (Chiroptera: Myzopodidae) in Madagascar. Journal of Mammalogy 89, 209221.
  • Sadofsky, M. J. (2004). Recombination-activating gene proteins: more regulation, please. Immunological Reviews 200, 8389.
  • Salzberg, S. L., White, O., Peterson, J. & Eisen, J. A. (2001). Microbial genes in the human genome: lateral transfer or gene loss? Science 292, 19031906.
  • Sanderson, M. J. & Donoghue, M. J. (1989). Patterns of variation in levels of homoplasy. Evolution 43, 17811795.
  • Sanderson, M. J., Wojciechowski, M. F., Hu, J. M., Khan, T. S. & Brady, S. G. (2000). Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants. Molecular Biology and Evolution 17, 782797.
  • Santana, S. E. & Dumont, E. R. (2009). Connecting behaviour and performance: the evolution of biting behaviour and bite performance in bats. Journal of Evolutionary Biology 22, 21312145.
  • Schluter, S. F., Bernstein, R. M., Bernstein, H. & Marchalonis, J. J. (1999). ’Big bang’ emergence of the combinatorial immune system. Developmental and Comparative Immunology 23, 107111.
  • Schultz, T. R. & Churchill, G. A. (1999). The role of subjectivity in reconstructing ancestral character states: a Bayesian approach to unknown rates, states, and transformation asymmetries. Systematic Biology 48, 651664.
  • Shimodaira, H. (2002). An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51, 492508.
  • Shimodaira, H. & Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16, 11141116.
  • Shimodaira, H. & Hasegawa, M. (2001). Consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 12461247.
  • Simmons, N. B. (1993). The importance of methods: archontan phylogeny and cladistic analysis of morphological data. In Primates and Their Relative in Phylogenetic Perspective (ed. R. D. E. MacPhee), pp. 161. Plenum Press, New York.
  • Simmons, N. B. (2005). Order chiroptera. In Mammal Species of the World: A Taxonomic and Geographic Reference (eds D. E. Wilson and D. M. Reeder), pp. 313529. Johns Hopkins University Press, Baltimore.
  • Simmons, N. B. & Conway, T. M. (2001). Phylogenetic relationships of mormoopid bats (Chiroptera: Mormoopidae) based on morphological data. Bulletin of the American Museum of Natural History 258, 197.
  • Smith, S., Beaulieu, J. & Donoghue, M. (2009). Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evolutionary Biology 9, 37.
  • Smith, J. D. & Hood, C. S. (1984). Genealogy of the New World nectar-feeding bats reexamined: a reply to Griffiths. Systematic Zoology 33, 435460.
  • Springer, M. S., Burk-Herrick, A., Meredith, R., Eizirik, E., Teeling, E., O’Brien, S. J. & Murphy, W. J. (2007). The adequacy of morphology for reconstructing the early history of placental mammals. Systematic Biology 56, 673684.
  • Springer, M. S. & Douzery, E. J. P. (1996). Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. Journal of Molecular Evolution 43, 357573.
  • Stamatakis, A. (2006a). Phylogenetic models of rate heterogeneity: a high performance computing perspective. In Proceedings of the 20th Internationational Parallel and Distributed Processing Symposium, Rhodos.
  • Stamatakis, A. (2006b). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 26882690.
  • Stamatakis, A., Hoover, P. & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57, 758771.
  • Swofford, D. L. (2002). PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods) . Sinauer Associates, Inc, Sunderland.
  • Tavaré, S. (1986). Some probabilistic and statistical problems on the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17, 5786.
  • Tavares, V. D. C. (2008). Systematic Revision of the Vampyressa Complex . City University of New York, New York.
  • Teeling, E. C., Madsen, O., Murphy, W. J., Springer, M. S. & O’Brien, S. J. (2003). Nuclear gene sequences confirm an ancient link between New Zealand's Short-tailed bat and South American noctilionoid bats. Molecular Phylogenetics and Evolution 28, 308319.
  • Teeling, E. C., Springer, M. S., Madsen, O., Bates, P., O’Brien, S. J. & Murphy, W. J. (2005). A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307, 580584.
  • Thies, W., Kalko, E. K. V. & Schnitzler, H.-U. (1998). The roles of echolocation and olfaction in two neotropical fruit-eating bats, Carollia perspicillata and C. castanea, feeding on Piper. Behavioral Ecology and Sociobiology 42, 397409.
  • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research 22, 46734680.
  • Trumpower, B. L. & Gennis, R. B. (1994). Energy transduction by cytochrome complexes in mitochondrial and bacterial respiration: the enzymology of coupling electron transfer reactions to transmembrane proton translocation. Annual Review of Biochemistry 63, 675716.
  • Van Den Bussche, R. A. & Hoofer, S. R. (2004). Phylogenetic relationships among recent chiropteran families and the importance of choosing appropriate out-group taxa. Journal of Mammalogy 85, 321.
  • Van Den Bussche, R. A., Hudgeons, J. L. & Baker, R. J. (1998). Phylogenetic accuracy, stability, and congruence: relationships within and among the new world bat genera Artibeus, Dermanura, and Koopmania. In Bats: Phylogeny, Morphology, Echolocation, and Conservation Biology (eds T. H. Kunz and P. A. Racey), pp. 5971. Smithsonian Institution Press, Washington.
  • Velazco, P. & Patterson, B. D. (2008). Phylogenetics and biogeography of the Broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae). Molecular Phylogenetics and Evolution 49, 749759.
  • Voigt, C. C. & Speakman, J. R. (2007). Nectar-feeding bats fuel their high metabolism directly with exogenous carbohydrates. Functional Ecology 21, 913921.
  • Waddell, P. J., Cao, Y., Hauf, J. & Hasegawa, M. (1999). Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Systematic Biology 48, 3153.
  • Wagner, P. J. (2000). Exhaustion of morphologic character states among fossil taxa. Evolution 54, 365386.
  • Wagner, P. J. (2012). Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates. Biology Letters 8, 112114.
  • Wake, D. B. (1991). Homoplasy: the result of natural selection, or evidence of design limitations? American Naturalist 138, 543567.
  • Wetterer, A. L., Rockman, M. V. & Simmons, N. B. (2000). Phylogeny of phyllostomid bats (Mammalia: Chiroptera): data from diverse morphological systems, sex chromosomes, and restriction sites. Bulletin of the American Museum of Natural History 248, 1200.
  • Wiens, J. J. (2000). Coding morphological variation within species and higher taxa for phylogenetic analysis. In Phylogenetic Analysis of Morphological Data (ed. J. J. Wiens), pp. 115145. Smithsonian Institute Press, Washington.
  • Wiens, J. J. (2005). Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Systematic Biology 54, 731742.
  • Wiens, J. J. (2009). Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa? Systematic Biology 58, 8799.
  • Wiens, J. J., Chippindale, P. T. & Hillis, D. M. (2003). When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders. Systematic Biology 52, 501514.
  • Wilkinson, M. (1995). A comparison of two methods of character construction. Cladistics 11, 297308.
  • Winter, Y. (1998). In vivo measurement of near maximal rates of nutrient absorption in a mammal. Comparative Biochemistry and Physiology 119, 853859.
  • Wright, A. J., Van Den Bussche, R. A., Lim, B. K., Engstrom, M. D. & Baker, R. J. (1999). Systematics of the genera Carollia and Rhinophylla based on the cytochrome b gene. Journal of Mammalogy 80, 12021213.
  • Xu, J., Mahowald, M. A., Ley, R. E., Lozupone, C. A., Hamady, M., Martens, E. C., Henrissat, B., Coutinho, P. M., Minx, P., Latreille, P., Cordum, H., Van Brunt, A., Kim, K., Fulton, R. S., Fulton, L. A., Clifton, S. W., Wilson, R. K., Knight, R. D. & Gordon, J. I. (2007). Evolution of symbiotic bacteria in the distal human intestine. PLoS Biology 5, e156.
  • Yang, Z. (1996). Maximum-likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution 42, 587596.
  • Yang, Z. (2007a). Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics. Molecular Biology and Evolution 24, 16391655.
  • Yang, Z. (2007b). Paml 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24, 15861591.
  • Yang, Z. (2008). Empirical evaluation of a prior for Bayesian phylogenetic inference. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 363, 40314039.
  • Yang, Z., Nielsen, R. & Hasegawa, M. (1998). Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution 15, 16001611.
  • Yang, Z. & Rannala, B. (2005). Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology 54, 455470.
  • Zhao, H., Zhou, Y., Pinto, C. M., Charles-Dominique, P., Galindo- González, J., Zhang, S. & Zhang, J. (2010). Evolution of the sweet taste receptor gene Tas1r2 in bats. Molecular Biology and Evolution 27, 26422650.
  • Zortea, M. (2003). Reproductive patterns and feeding habits of three nectarivorous bats (Phyllostomidae: Glossophaginae) from the brazilian cerrado. Brazilian Journal of Biology 63, 159168.
  • Zwickl, D. J. & Hillis, D. M. (2002). Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51, 588598.