29 Evidences for Macroevolution

Abel, O. (1908) "Die Morphologie der Huftbeinrudimente der Cetaceen." Denkschr. Math. Naturw. Klasse Kaiserl. Aka. Wiss. Vol. 81.

Acharya, K. R., D. I. Stuart, et al. (1989) "Refined structure of baboon alpha-lactalbumin at 1.7 Å resolution - comparison with c-type lysozyme." Journal of Molecular Biology 208: 99-127.

Adami, C., C. Ofria, et al. (2000) "Evolution of biological complexity." PNAS 97: 4463-4468.

Andren, C., M. Marden, et al. (1989) "Tolerance to low pH in a population of moor frogs, Rana arvalis from an acid and a neutral environment : a possible test case of rapid evolutionary response to acidification." Oikos 56: 215-223.

Andrews, R.C. (1921) "A remarkable case of external hind limbs in a humpback whale." Amer. Mus. Novitates. No. 9.

Aravind, L. and E. V. Koonin (1999) "DNA polymerase beta-like nucleotidyl transferase superfamily: identification of three new families, classification, and evolutionary history." Nucleic Acids Research 27: 1609.

Archie, J. W. (1989) "A randomization test for phylogenetic information in systematic data." Systematic Zoology 38: 219-252.

Atchely, W. R. and W. M. Fitch (1991) "Gene trees and the origins of inbred strains of mice." Science 254: 554-558.

Avery, O. T., MacLeod, C. M. and M. McCarty. (1944) "Studies on the chemical nature of the substance inducing transformation of pneumococcal types." J. Exp. Med. 79:137-158.

Avise, J.C., and Wollenberg, K. (1997) "Phylogenetics and the origin of species." PNAS 94: 7748Ð7755.

Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., and Doolittle, W.F. (2000) "A kingdom-level phylogeny of eukaryotes based on combined protein data." Science 290: 972-7.

Ban, N., P. Nissen, et al. (1999) "Placement of protien and RNA structures in a 5 Å resolution map of the 50S ribosomal subunit." Nature 400: 841-847.

Barrell, B. G., et al. (1996) "Life with 6000 genes." Science 274: 546-567.

Barsh, G. S. (1996) "The genetics of pigmentation: from fancy genes to complex traits." Trends in Genetics 12: 299-305.

Barton, N. H. and R. S. Gale (1993) "Genetic analysis of hybrid zones." Hybrid Zones and the Evolutionary Process. New York, Oxford University Press: 12-45.

Behe, M. (1996) Darwin's Black Box. New York, Touchstone.

Belzberg, A.J., Myles, S.T., and C.L. Trevenen. "The human tail and spinal dysraphism." J Pediatr Surg (1991) 26: 1243-1245.

Bennett, A. F., R. E. Lenski, et al. (1992) "Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment." Evolution 46: 16-30.

Benton, M. J. (1998) "Molecular and morphological phylogenies of mammals: Congruence with stratigraphic data." Molecular Phylogenetics and Evolution 9: 398-407.

Benton, M. J. and Hitchin, R. (1996) "Testing the quality of the fossil record by groups and by major habitats." Historical Biol. 12: 111-157.

Benton, M. J. and Hitchin, R. (1997) "Congruence between phylogenetic and stratigraphic data on the history of life." Proc. R. Soc. Lond. B. 264: 885-890.

Benton, M. J., Hitchin, R., and Wills, M. A. (1999) "Assessing congruence between cladistic and stratigraphic data." Syst. Biol. 48: 581Ð596.

Benton, M. J. and Storrs, G. W. (1994) "Testing the quality of the fossil record: paleontological knowledge is improving." Geology 22: 111-114.

Benton, M. J., Wills, M. A., and Hitchin R. (2000) "Quality of the fossil record through time." Nature 403: 534-537.

Bergman, J. (2000) "Is the inverted human eye a poor design?" Perspectives on Science and Christian Faith 52: 18-30.

Berzin, A.A. (1972) The Sperm Whale. Pacific Scientific Research Institute of Fisheries and Oceanography. Israel Program for Scientific Translations, Jerusalem. Available from the U.S. Dept. of Commerce, national Technical Information Service. Springfield, VA.

Bishop, J. A. (1981) "A neo-Darwinian approach to resistance: Examples from mammals." Genetic Consequences of Man Made Change. J. A. Bishop and L. M. Cook. London, Academic Press.

Bohossian, H.B., Skaletsky, H., Page, D.C. (2000) "Unexpectedly similar rates of nucleotide substitution found in male and female hominids." Nature. 406: 622-5.

Bonner, T. I., C. O'Connell, et al. (1982) "Cloned endogenous retroviral sequences from human DNA." PNAS 79: 4709.

Brenner, S. (1957) "On the impossibility of all overlapping triplet codes in information transfer from nucleic acid to proteins." PNAS 43:687-694.

Britton-Davidian, J., J. Catalan, et al. (2000) "Rapid chromosomal evolution in island mice." Nature 403: 158.

Brooks, D. R. and D. A. McLennon (1991) Phylogeny, ecology, and behavior. Chicago, University of Chicago Press.

Brown, J. H., and M. V. Lomolino. (1998) Biogeography. Second edition. Boston, MA: Sunderland.

Buell, J. and V. Ahearn, Eds. (1994) Darwinism, Science or Philosophy?

Bunn, H. F. and E. G. Forget (1986) Hemoglobin: Molecular, Genetic, and Clinical Aspects, Saunders.

Bush, R. M., C. A. Bender, et al. (1999) "Predicting the evolution of human influenza A." Science 286: 1921-1925.

Carpenter, M. A. and S. J. O'Brien (1995) "Coadaptation and immunodeficiency virus: lessons from the Felidae." Current Opinion in Genetics and Development 5: 739-745.

Carroll, R. L. (1988) Vertebrate Paleontology and Evolution. New York, W.H. Freeman and Co.

Carroll, R. L. (1997) Patterns and Processes of Vertebrate Evolution. Cambridge, Cambridge University Press.

Carter, G. S. (1954) Animal Evolution. London, Sidgwick and Jackson.

Cech, T. R., A. J. Zaug, et al. (1981) "In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence." Cell 27: 487- 496.

Chalmers, A. F. (1982) What is this thing called Science? Queensland, Australia, University of Queensland Press.

Chaterjee, S. (1997) The Rise of Birds: 225 million years of evolution. Baltimore, MD, Johns Hopkins University Press.

Chen, P.-j., Z.-m. Dong, et al. (1998) "An exceptionally well- preserved theropod dinosaur from the Yixian formation of China." Nature 391: 147-152.

Chervitz, S. A., et al. (1998) "Comparison of the complete protein sets of worm and yeast: Orthology and divergence." Science 282: 2022- 2028.

Clements, J.M., O'Connell, L.I., Tsunasawa, S., and Sherman, F. (1989) "Expression and activity of a gene encoding rat cytochrome c in the yeast Saccharomyces cerevisiae." Gene 83: 1-14.

Clemons, W. M., J. L. C. May, et al. (1999) "Structure of a bacterial 30S ribosomal subunit at 5.5. Å resolution." Nature 400: 833-840.

Clyde, W.C. and Fisher, D.C. (1997) "Compaing the fit of stratigraphic and morphologic data in phylogenetic analysis." Paleobiology 23: 1-19.

Consortium, C. e. S. (1998) "Genome sequence of the nematode C. elegans: A platform for investigating biology." Science 282: 2012-2018.

Copley, S.C. (2000) "Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach." TIBS 25: 261-265.

Crick, F. H. C. (1968) "The origin of the genetic code." Journal of Molecular Biology 38: 367-379.

Crick, F.H.C., Barnett, L., Brenner, S., and R.J. Watts-Tobin. (1961) "General nature of the genetic code for proteins." Nature 192:1227-1232.

Crowe, J. F. (1993) "Mutation, fitness, and genetic load." Oxford Survey of Evolutionary Biology 9: 3-42.

Cummins, R. (1975) "Functional Analysis." Journal of Philosophy 72: 741-765.

Dao, A.H., and M.G. Netsky (1984) "Human tails and pseudotails." Human Pathology 15: 449-453.

Dangel, A. W., B. J. Baker, et al. (1995) "Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution." Immunogenetics 42: 41-52.

Darwin, C. (1871) The Descent of Man. Amherst, New York, Prometheus Books.

Darwin, C. (1872) On the Origin of Species. New York, Random House.

Davies, J. C. I., R. J. Almassey, et al. (1994) "2.3 Å crystal structure of the catalytic domain of DNA polymerase beta." Cell 76: 1123-1133.

Dawkins, R. (1996) The Blind Watchmaker. New York, Norton.

Dawkins, R. (1999) The Extended Phenotype. Oxford, Oxford University Press.

Diamond, J. M. (1984) "Historic extinctions: A Rosetta Stone for understanding pre-historic extinctions." Quaternary Extinctions: A Prehistoric Revolution. P. S. Martin and R. G. Klein. Tucson, University of Arizona Press: 824-862.

Diamond, J. M. (1984) "Normal" extinctions of isolated populations. Extinctions. M. Nitecki. Chicago, University of Chicago Press: 191-246.

Dickerson, R. E. (1972) Scientific American. 226: 58-72.

Dickerson, R. E. and R. Timkovich (1975) cytochrome c. The Enzymes. P. D. Boyer. New York, Academic Press. 11: 397-547.

Dodson, E. O. (1960) Evolution: Process and Product. New York, Reinhold Publishers.

Doolittle, W. F. (1999) "Phylogenetic Classification and the Universal Tree." Science 284: 2124.

Doolittle, W. F. (2000) "The nature of the universal ancestor and the evolution of the proteome." Current Opinion in Structural Biology 10: 355Ð358.

Dowson, C.G., Coffey, T.J., Spratt, B.G. (1994) "Origin and molecular epidemiology of penicillin-binding-protein-mediated resistance to beta-lactam antibiotics." Trends Microbiol 2: 361-66.

Dubrow, T. J., Wackym, P. A., and m. A. Lesavoy. (1988) "Detailing the human tail." Annals of Plastic Surgery 20:340-344.

Eldredge, N. and S. J. Gould (1972) "Punctuated equilibrium: An alternative to phyletic gradualism." In Models in Paleobiology. Ed. T. J. M. Schopf. San Francisco, CA, Freeman, Cooper, and Company: 82-115.

Endler, J. A. (1986) Natural Selection in the Wild. Princeton, NJ, Princeton University Press.

Faith, D. P., and Cranston, P. S. (1991) "Could a cladogram this short have arisen by chance alone?: on permutation tests for cladistic structure." Cladistics 7: 1-28.

Fara, M. (1977) "Coccygeal ('tail') projection with cartilage content." Acta Chir. Plast. 19: 50-55.

Farris, J.S. (1989) "The retention index and the rescaled consistency index." Cladistics 5:417-419.

Felsenstein, J. (1982) "Numerical methods for inferring evolutionary trees." Quart. Rev. Biol. 57: 379-404.

Felsenstein, J. (1985) "Confidence limits on phylogenies: an approach using the bootstrap." Evolution 39: 783-791.

Ffrench-Constant, R. H., N. Anthony, et al. (2000) "Cyclodiene insecticide resistance: from molecular to population genetics." Annual Review of Entymology 45: 449-466.

Fisher, R. A. (1942) The Design of Experiments. Edinburgh, Oliver and Boyd.

Freitag, J., G. Ludwig, et al. (1998) "Olfactory receptors in aquatic and terrestrial vertebrates." Journal of Comparative Physiology 183: 635-650.

Futuyma, D. (1998) Evolutionary Biology. Third edition. Sunderland, Mass., Sinauer Associates.

Galili, U. and K. Swanson (1991) "Gene sequences suggest inactivation of alpha-1,3-galactosyltransferase in catarrhines after the divergence of apes from monkeys." PNAS 88: 7401-7404.

Garavelli, J. S., Hou, Z., et al. (2001) "The RESID Database of protein structure modifications and the NRL-3D SequenceÐStructure Database." Nucleic Acids Research 29: 199-201. http://www.ncifcrf.gov/RESID/

Garstang, W. (1922) "The theory of recapitulation: a critical restatement of the biogenetic law." The Journal of the Linnean Society of London. Zoology 35: 81-101.

Gilbert, S. F., Opitz, J.M. and Raff, R.A. (1996) "Resynthesizing evolutionary and developmental biology." Developmental Biology 173: 357-372.

Gilbert, S. F. (1997) Developmental Biology. Fifth edition. Sinauer Associates.

Gilbert, W. (1986) "The RNA World." Nature 319: 618.

Gingerich, P. D. (1983) "Rates of evolution: Effects of time and temporal scaling." Science 222: 159-161.

Gish, D. T. (1978) Evolution? The Fossils Say No! Public School Edition, San Diego: Creation-Life Publishers.

Gish, D. T. (1983) "Evolution and the human tail." ICR Impact No. 117

Goldsmith, T. H. (1990) "Optimization, constraint, and history in the evolution of eyes." Quarterly Review of Biology 65: 281-322.

Goodman, M., B. F. Koop, et al. (1989) "Molecular phylogeny of the family of apes and humans." Genome 31(316-335)

Gould, S. J. (1990) "An earful of jaw." Natural History 3: 12-23.

Gould, S. J. and N. Eldredge (1977) "Punctuated equilibria: The tempo and mode of evolution reconsidered." Paleobiology 3: 115-151.

Gregory, W.K. (1951) Evolution Emerging: A survey of changing patterns from primeval life to man. Volume I. The Macmillan Co., New York.

Groves, C.P. (2000) "The genus Cheirogaleus: Unrecognized biodiversity in dwarf lemurs." International Journal of Primatology. 21(6): 943-962.

Gura, T. (2000) "Bones, molecules ... or both?" Nature 406: 230-233.

Haag, F., F. Koch-Nolte, et al. (1994) "Premature stop codons inactivate the RT6 genes of the human and chimpanzee species." Journal of Molecular Biology 243: 537-546.

Haeckel, E. (1898) The Last Link. Adam and Charles Black, London.

Hairston, N. G., Jr. (1990) "Fluctuating selection and response in a population of freshwater copepods." Evolution 44: 1796-1805.

Hall, B. G. (1982) "Evolution on a petri dish: The evolved b- galactosidase system as a model for studying acquisitive evolution in the laboratory." Evolutionary Biology 15: 85-150.

Hall, B.K. (1984) "Developmental mechanisms underlying the formation of atavisms." Biol. Rev. 59: 89-124.

Hall, B.K. (1995) "Atavisms and atavistic mutations." Nature Genetics 10: 126-127.

Hampsey, D. M., Das, G., and Sherman F. (1986) "Amino acid replacements in yeast iso-1-cytochrome c." Journal of Biological Chemistry 261: 3259-71.

Hampsey, D. M., Das, G., and Sherman F. (1988) "Yeast iso-1- cytochrome c: genetic analysis of structural requirements." FEBS Letters 231: 275-83.

Harris, J. I., F. Sanger, et al. (1956) "Species differences in insulin." Archives of Biochemistry and Biophysics 65: 427-438.

Harris, T. E. (1989) The Theory of Branching Processes. New York, Dover.

Hastings, M.L. and Krainer, A.R. (2001) "Pre-mRNA splicing in the new millennium." Curr Opin Cell Biol 13: 302-309.

Hedges, S.B. (1994) "Molecular evidence for the origin of birds." PNAS 91: 2621-2624.

Hedges, S.B. and Poling, L.L. (1999) "A molecular phylogeny of reptiles." Science 283: 998-1001.

Hendy, M. D., Little, C. H. C., and Penny, D. (1984) "Comparing trees with pendant vertices labelled." SIAM J. Appl. Math. 44: 1054-1065.

Hennig, W. (1966) Phylogenetic Systematics. Urbana, University of Illinios Press.

Hickey, D.R., Jayaraman, K., Goodhue, C.T., Shah,J., Fingar, S.A., Clements, J.M., Hosokawa, Y., Tsunasawa, S., and Sherman, F. (1991) "Synthesis and expression of genes encoding tuna, pigeon, and horse cytochromes c in the yeast Saccharomyces cerevisiae." Gene105: 73-81.

Hill, W.C.O. (1974) Primates: Comparative Anatomy and Taxonomy. VII. Cyropithecinae: Cercocebus, Maccaca, Cynopithecus. New York, Halstead Press, John Wiley and Sons.

Hillis, D. M., J. J. Bull, et al. (1992) "Experimental phylogenetics: Generation of a known phylogeny." Science 255: 589-592.

Hillis, D. M., J. P. Huelsenbeck, et al. (1994) "Application and accuracy of molecular phylogenies." Science 264: 671-677.

Hillis, D. M., C. Moritz, et al., Eds. (1996) Molecular systematics. Sunderland, MA, Sinauer Associates.

Hindmarsh, P. and J. Leis. (1999) "Retroviral DNA Integration." Microbiology and Molecular Biology Reviews 63: 836-843.

Hinegardner, T.T. and J. Engelberg. (1963) "Rationale for a Universal Genetic Code." Science 142: 1083-1085.

Hitchin, R. and Benton, M.J. (1997) "Congruence between parsimony and stratigraphy: comparisons of three indices." Paleobiology 23: 20-32.

Hooten, E. A. (1947) Up From the Ape. Second edition. New York: Macmillan.

Houde, A. E. (1988) "Genetic differences in female choice between two guppy populations." Animal Behavior 36: 510-516.

Hutter, H. e. a. (2000) "Conservation and novelty in the evolution of cell adhesion and extracellular matrix genes." Science 287: 989-994.

Huttley, G.A., Jakobsen, I.B., Wilson, S.R., Easteal, S. (2000) "How important is DNA replication for mutagenesis?" Mol Biol Evol. 17: 929-37.

Huxley, T. H. (1900) Life and letters of Thomas Henry Huxley. London, MacMillan.

International Human Genome Sequencing Consortium (2001) "Initial sequencing and analysis of the human genome." Nature 409: 860-921.

Johnston, R. F. and R. K. Selander (1973) "Evolution in the house sparrow. III. Variation in size and sexual dimorphism in Europe and North and South America." American Naturalist 107: 373-390.

Joyce, G. F. (1999) "Appendix 3: Reactions catalyzed by RNA and DNA enzymes." In The RNA World. R. F. Gesteland, T. R. Cech and J. F. Atkins. Cold Spring Harbor, New York, Cold Spring Harbor Lab Press: 687-690.

Joyce, G. F. and L. Orgel (1999) "Prospects for Understanding the Origin of the RNA World." In The RNA World. R. F. Gesteland, T. R. Cech and J. F. Atkins. Cold Spring Harbor, New York, Cold Spring Harbor Lab Press: 49-77.

Judson, H. F. (1996) The Eighth Day of Creation: Makers of the Revolution in Biology. Expanded edition. Cold Spring Harbor Press.

Kardong, K. V. (2002) Vertebrates: Comparative Anatomy, Function, Evolution. Third ed. New York: McGraw Hill.

Kawaguchi, H., C. O'hUigin, et al. (1992) "Evolutionary origin of mutations in the primate cytochrome P450c21 gene." American Journal of Human Genetics 50: 766-780.

Kazazian, H. H., C. Wong, et al. (1988) "Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man." Nature 332: 164.

Kemp, J. S. (1982) Mammal-like reptiles and the origin of mammals.

Kestenbaum, D. (1998) "Gravity Measurements Close in on Big G." Science 282: 2180-2181.

King, M. C. and A. C. Wilson (1975) "Evolution at two levels in humans and chimpanzees." Science 188: 107-116.

Kjellman, C., H. O. Sjogren, et al. (1999) "HERV-F, a new group of human endogenous retrovirus sequences." Journal of General Virology 80: 2383.

Klassen, G.J., Mooi, R.D., and A. Locke. (1991) "Consistency indices and random data." Syst. Zool. 40:446-457.

Koshy, T.I., Luntz, T.L., Garber, E.A., and Margoliash, E. (1992) "Expression of recombinant cytochromes c from various species in Saccharomyces cerevisiae: post-translational modifications." Protein Expr. Purif. 3: 441-52.

Kuhn, T. (1970) The Structure of Scientific Revolutions.

Kumar, S. and S. Subramanian (2002) "Mutation rates in mammalian genomes." Proc Natl Acad Sci 99: 803-808.

Lakatos, I. (1974) Falsification and the Methodology of Scientific Research Progammes. Criticism and the Growth of Knowledge. I. Lakatos and A. Musgrave. Cambridge, Cambridge University Press: 91-196.

Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and E. D. Sverdlov. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

Lederberg, J. and E. M. Lederberg (1952) "Replica plating and indirect selection of bacterial mutants." Journal of Bacteriology 63: 399-406.

Ledley, F. D. (1982) "Evolution and the human tail." New Eng. J. Med. 306: 1212-1215.

Lee, S. G., B. D. Yoon, et al. (1998) "Isolation of a novel pentachlorophenol-degrading bacterium, Pseudomonas sp. Bu34." Journal of Applied Microbiology 85: 1-8.

Lehman, N. (2001) "Please release me, genetic code." Current Biology 11: R63-R66.

Lewin, B. (1999) Genes VII. New York, Oxford University Press.

Li, W.-H. (1997) Molecular Evolution. Sunderland, MA, Sinauer Associates.

Lundberg, G. D., and R. W. Parsons. (1962) "A case of human tail." Am. J. Dis. Child 104: 72.

Luria, S. and M. Delbruck (1943) "Mutations of bacteria from virus sensitivity to virus resistance." Genetics 28: 491-511.

Lyons-Weiler, J., Hoeker, G. A., and Tausch, R. J. (1996) "Relative Apparent Synapomorphy Analysis (RASA) I: The Statistical Measurement of Phylogenetic Signal." Mol. Biol. Evol. 13: 749-757.

MacFadden, B. J. (1992) Fossil Horses: Systematics, Paleobiology, and Evolution of the Family Equidae. New York, Cambridge University Press.

Maddison, W. P. and D. R. Maddison (1992) MacClade: Analysis of Phylogeny and Character Evolution. Sunderland, Massachusetts, Sinauer.

Maizels, N. and A. M. Weiner (1999) "The Genomic Tag Hypothesis: What Molecular Fossils Tell Us about the Evolution of tRNA." In The RNA World. R. F. Gesteland, T. R. Cech and J. F. Atkins. Cold Spring Harbor, New York, Cold Spring Harbor Lab Press: 79-111.

Maley, L.E. and Marshall, C. R. (1998) "The coming age of molecular systematics." Science 279: 505-506.

Matsuo, T., Koga, H., Moriyama, T., Yamashita, H., Imazato, K., and M. Kondo (1993) "[A case of true human tail accompanied with spinal lipoma.]" No Shinkei Geka 21: 925-929.

Matthews, B.W. (1996) "Structural and genetic analysis of the folding and function of T4 lysozyme." FASEB J. 10: 35-41.

Mayo, D. (1996) Error and the Growth of Experimental Knowledge. Chicago, University of Chicago Press.

Mayr, E. (1942) Systematics and the Origin of Species. New York, Columbia University Press.

Mayr, E. (1991) One Long Argument. Cambridge, Harvard University Press.

Mayr, E. a. P. D. A. (1990) Principles of Systematic Zoology.

McLaughlin, P. J. and M. O. Dayhoff (1973) "Eukaryote evolution: a view based on cytochrome c sequence data." Journal of Molecular Evolution 2(99-116)

Mighell, A.J., Smith N.R., Robinson P.A., and A.F. Markham (2000) "Vertebrate pseudogenes." FEBS Lett. 468: 109-114.

Millikan, R. (1989) "In defence of proper functions." Philosophy of Science 56: 288-302.

Mohrenweiser, H. (1994) "Impact of the molecular spectrum of mutational lesions on estimates of germinal gene-mutation rates." Mutation Research 304: 119-137.

Moore, G. R. and G. W. Pettigrew (1990) Cytochromes c: Evolutionary, Structural and Physicochemical Aspects. Berlin, Springer-Verlag.

Moritz, C., C. J. Schneider, et al. (1982) "Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation." Systematic Biology 41: 273-291.

Morton, E. S. (1990) "Habitat segregation by sex in the hooded warbler: Experiments on proximate causation and discussion of its evolution." American Naturalist 135: 319-333.

Negoro, S., Kato, K., Fujiyama, K., Okada, H. (1994) "The nylon oligomer biodegradation system of Flavobacterium and Pseudomonas." Biodegradation. 5: 185-194.

Nemoto, T. (1963) "New records of sperm whales with protruded rudimentary hind limbs." Sci. Rep. Whales Res. Inst. No. 17.

Nishikimi, M., R. Fukuyama, et al. (1994) "Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man." Journal of Biological Chemistry 269: 13685-13688.

Nishikimi, M., T. Kawai, et al. (1992) "Guinea pigs possess a highly mutated gene for L-gulono-gamma-lactone oxidase, the key enzyme for L-ascorbic acid biosynthesis missing in this species." Journal of Biological Chemistry 267: 21967-21972.

Noller, H. F. (1999) "On the Origin of the Ribosome: Coevolution of Subdomains of tRNA dn rRNA." In The RNA World. R. F. Gesteland, T. R. Cech and J. F. Atkins. Cold Spring Harbor, New York, Cold Spring Harbor Lab Press: 197-219.

Noller, H. F., B. Hoffarth, et al. (1992) "Unusual resistance of peptidyl transferase activity to protein extraction methods." Science 256: 1416-1419.

Norell, M. A. and Novacek, M. J. (1992) "Congruence between superpositional and phylogenetic patterns: Comparing cladistic patterns with fossil records." Cladistics 8: 319-337.

Norell, M. A. and Novacek, M. J. (1992b) "The fossil record and evolution: Comparing cladistic and paleontologic evidence for vertebrate history." Science 255: 1690-93.

Norris, J. R. (1997) Markov Chains. Cambridge, Cambridge University Press.

Ochman, H., Lawrence, J.G., Groisman, E.A. (2000) "Lateral gene transfer and the nature of bacterial innovation." Nature 405: 299-304.

Oetting, W. S., O. C. Stine, et al. (1993) "Evolution of the tyrosinase related gene (TYRL) in primates." Pigment Cell Research 6: 171-177.

Ogawa, R. and T.A. Kamiya. (1957) "Case of the cachalot with protruded rudimentary hind limbs." Sci. Rep. Whales Res. Inst. No. 12.

Ohno, S. (1984) "Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence." PNAS 81: 2421-5.

Ohta, T. (1993) "An examination of the generation-time effect on molecular evolution." PNAS 90: 10676-10680.

Okada, H., Negoro, S., Kimura, H., and S. Nakamura (1983) "Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers." Nature 306: 203-6.

Orser, C. S. and C. C. Lange (1994) "Molecular analysis of pentachlorophenol degradation." Biodegradation 5: 277-288.

Osborn, H.F. (1918) The Origin and Evolution of Life. Charles Scribner's Sons, New York.

Ostertag, E.M. and H.H. Kazazian. (2001) "Biology of mammalian L1 retrotransposons." Annu. Rev. Genet. 35: 501-538.

Ostrom, J. H. (1973) "The ancestry of birds." Nature 242: 136.

Patterson, C., Williams, D., and Humphries, C. (1993) "Congruence between molecular and morphological phylogenies." Annual Review of Ecology and Systematics 24: 153-188.

Pei, M. (1949) The Story of Language. Philadelphia, Lippincott.

Penny, D. and Hendy M. D. (1986) "Estimating the reliability of phylogenetic trees." Mol. Biol. Evol. 3: 403-417.

Penny, D., Foulds, L. R., and Hendy, M. D. (1982) "Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences." Nature 297: 197-200.

Penny, D., Hendy, M. D., and Steel, M. A. (1991) "Testing the theory of descent." In Phylogenetic Analysis of DNA Sequences, eds. Miyamoto, M. and Cracraft, J., Oxford University Press, New York. pp. 155-183.

Piccirilli, J. A., T. S. McConnell, et al. (1992) "Aminoacyl esterase activity of the Tetrahymena ribozyme." Science 256: 1420-1424.

Popper, K. R. (1968) The Logic of Scientific Discovery. London, Hutchinson.

Prager, E. M. and A. C. Wilson (1988) "Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences." Journal of Molecular Evolution 27: 326-335.

Prijambada, I.D., Negoro, S., Yomo, T., Urabe, I. (1995) "Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution." Appl Environ Microbiol. 61: 2020-2022.

Ptitsyn, O. B. (1998) "Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes." Journal of Molecular Biology 278: 655.

Qasba, P. K. and S. Kumar (1997) "Molecular divergence of lysozymes and alpha lactalbumin." Critical Review of Biochemistry and Molecular Biology 32: 255-306.

Qiang, J., P. J. Currie, et al. (1998) "Two feathered dinosaurs from northeastern China." Nature 393: 753-761.

Rasoloarison, R.M., Goodman, S.M., and Ganzhorn, J.U. (2000) "Taxonomic revision of mouse lemurs (Microcebus) in the western portions of Madagascar." International Journal of Primatology. 21(6): 963-1019.

Raymond, M., Berticat, C., Weill, M., Pasteur, N., Chevillon, C. (2001) "Insecticide resistance in the mosquito culex pipiens: what have we learned about adaptation?" Genetica 112-113:287-296.

Reeve, H. K. and P. W. Sherman (1993) "Adaptation and the goals of evolutionary success." Quarterly Review of Biology 68: 1-32.

Reznick, D. N. (1997) "Evaluation of the rate of evolution in natural populations of guppies (Poecilia ieticulata)" Science 275: 1934-1937.

Rhodes, F. H. T. (1983) "Gradualism, punctuated equilibria, and the origin of species." Nature 305: 269-272.

Richter, T. E. and P. C. Ronald (2000) "The evolution of disease resistance genes." Plant Molecular Biology 42: 195-204.

Ridley, M., Ed. (1997) Evolution. Oxford, Oxford University Press.

Rightmire, G. P. (1985) "The tempo of change in the evolution of mid- Pleistocene Homo." In Ancestors: the Hard Evidence. E. Delson. New York, Alan R. Liss: pp. 255-264.

Ringe, D., (1999) "Language classification: scientific and unscientific methods." in The Human Inheritance, ed. B. Sykes. Oxford: Oxford University Press, 45Ð74.

Roth, V. L. (1984) "On homology." Biological Journal of the Linnaean Society 22: 13-29.

Rouquier, S., A. Blancher, et al. (2000) "The olfactory receptor gene repertoire in primates and mouse: Evidence for reduction of the functional fraction in primates." PNAS 97: 2870-2874.

Rozenski, J., P. F. Crain, et al. (1999) "The RNA Modification Database: 1999 update." Nucleic Acids Research 27: 196-197. http://medlib.med.utah.edu/RNAmods/

Salamone, P.R., Kavakli, I.H., Slattery, C.J., Okita, T.W. (2002) "Directed molecular evolution of ADP-glucose pyrophosphorylase." Proc Natl Acad Sci 99: 1070-1075.

Salmon, W. (1990) "Rationality and Objectivity in Science, or Tom Kuhn meets Tom Bayes." In Scientific Theories. C. W. Savage. Minneapolis, University of Minnesota Press. 14.

Sawada, I., C. Willard, et al. (1985) "Evolution of Alu family repeats since the divergence of human and chimpanzee." Journal of Molecular Evolution 22(316)

Scarpulla, R.C., and Nye, S.H. (1986) "Functional expression of rat cytochrome c in Saccharomyces cerevisiae." Proc Natl Acad Sci 83: 6352-6.

Sereno, P. C. (1999) "The Evolution of Dinosaurs." Science 284: 2137-2147.

Shimamura, M., et al. (1997) "Molecular evidence from retroposons that whales form a clade within even-toed ungulates." Nature 388: 666.

Sleptsov, M.M. "On the asymmetry of the skull of Odontoceti." Zoologicheskii Zhurnal 18(3)

Smit, A. F. A. (1996) "The origin of interspersed repeats in the human genome." Current Opinion in Genetics and Development 6: 743-748.

Smith, J. M. (1993) The Theory of Evolution. Cambridge, Cambridge University Press.

Spiegelmann, R. Schinder, E. Mintz, M., and A. Blakstein. (1985) "The human tail: a benign stigma." J. Neurosurgery 63:461-462.

Standfast, A. L. (1992) "The human tail." New York State Journal of Medicine. 92: 116.

Stanley, S. (1993) Earth and Life Through Time. New York, W.H. Freeman.

Steel, M.A. and D. Penny. (1993) "Distributions of tree comparison metrics - some new results." Systematic Biology 42: 126-141.

Stewart, C. B. and T. R. Disotell (1998) "Primate evolution - in and out of Africa." Current Biology 8: R582-588.

Svensson, A. C., N. Setterblad, et al. (1995) "Primate DRB genes from the DR3 and DR8 haplotypes contain ERV9 LTR elements at identical positions." Immunogenetics 41: 74.

Sverdlov, E. D. (2000) "Retroviruses and primate evolution." BioEssays 22: 161-171.

Swofford, D. L., Olsen, G. J., Waddell, P. J., and Hillis, D. M. (1996) "Phylogenetic inference." In Molecular Systematics, pp 407-514. Hillis, D. M., Moritiz, C. and Mable, B. K. eds., Sinauer, Sunderland, Massachusetts.

Tanaka, Y., Ashikari, T., Shibano, Y., Amachi, T., Yoshizumi, H., and Matsubara, H. (1988a) "Amino acid replacement studies of human cytochrome c by a complementation system using CYC1 deficient yeast." J Biochem (Tokyo) Sep;104: 477-80.

Tanaka, Y., Ashikari, T., Shibano, Y., Amachi, T., Yoshizumi, H., and Matsubara, H. (1988b) "Construction of a human cytochrome c gene and its functional expression in Saccharomyces cerevisiae." J Biochem (Tokyo) 103: 954-61.

Tarrusova, N. B., G. M. Jacovleva, et al. (1981) "Synthesis of an unnatural P-N bond catalyzed with Escherichia coli ribosomes." FEBS Letters 130: 85-87.

Thalmann, U. and Geissmann, T. (2000) "Distribution and geographic variation in the western woolly lemur (Avahi occidentalis) with description of a new species (A. unicolor)" International Journal of Primatology. 21(6): 915-941.

Thornhill, R. H. and D. W. Ussery (2000) "A classification of possible routes of Darwinian evolution." Journal of Theoretical Biology 203: 111-116.

Unrau, P. D. and D. P. Bartel (1998) "RNA-catalyzed nucleotide synthesis." Nature 395: 260-263.

Urnovitz, H.B., and W.H. Murphy (1996) "Human endogenous retroviruses: nature, occurrence, and clinical implications in human disease." Clin Microbiol Rev 9: 72-99.

van Roosmalen, M.G.M., van Roosmalen, T., Mittermeier, R. A. and Rylands, A. B. (2000) "Two new species of marmoset, genus Callithrix Erxleben, 1777 (Callitrichidae, Primates), from the Tapajos/Madeira interfluvium, south central Amazonia." Neotropical Primates 8(1): 2-18.

Voet, D. and Voet, J. (1995) Biochemistry. New York, John Wiley and Sons.

von Ahsen, U. and H. F. Noller (1995) "Antibiotic inhibition of group I ribozyme function." Nature 353: 368-370.

von Fraassen, B. C. (1980) The Scientific Image. Oxford, Clarendon Press.

Wallace, C.J. and Tanaka, Y. (1994) "Improving cytochrome c function by protein engineering?: studies of site-directed mutants of the human protein." J. Biochem. (Tokyo) 115: 693-700.

Wallace, M. R., L. B. Andersen, et al. (1991) "A de novo Alu insertion results in neurofibromatosis type 1." Nature 353: 864-866.

White III, H. B. (1976) "Coenzymes as fossils of an earlier metabolic state." Journal of Molecular Evolution 7: 101-104.

Widdowson, C.A., Adrian, P.V., Klugman, K.P. (2000) "Acquisition of chloramphenicol resistance by the linearization and integration of the entire staphylococcal plasmid pC194 into the chromosome of Streptococcus pneumoniae." Antimicrob Agents Chemother 44: 393-95.

Williams, G. C. (1992) Natural Selection: Domains, Levels, and Challenges. New York, Oxford University Press.

Wills, M. A. (1999) "The gap excess ratio, randomization tests, and the goodness of fit of trees to stratigraphy." Syst. Biol. 48: 559-580.

Wilson, E. O. (1992) The Diversity of Life. Cambridge, MA, Harvard University Press.

Wise, K. P. (1994) "The Origin of Life's Major Groups." In The Creation Hypothesis, pp. 211-234. Moreland, J.P. ed., InterVarsity Press, Downers Grove, IL.

Woese, C. (1967) The Genetic Code: The Molecular Basis for Genetic Expression. New York, Harper and Row: 179-195.

Woese, C. (1998) "The universal ancestor." PNAS 95: 6854Ð6859.

Woodburne, M. O. and J. A. Case (1996) "Dispersal, vicariance, and the Late Cretaceous to Early Tertiary land mammal biogeography from South America to Australia." Journal of Mammalian Evolution 3: 121-161.

Wright, L. (1973) "Functions." Philosophical Review 82: 139- 168.

Yockey, H. P. (1992) Information Theory and Molecular Biology. New York, Cambridge University Press.

Yoder, A.D., Rasoloarison, R.M., Goodman, S.M., Irwin, J.A., Atsalis, S., Ravosa, M.J., and Ganzhorn, J.U. (2000) "Remarkable species diversity in Malagasy mouse lemurs (primates, Microcebus)" Proc Natl Acad Sci 97(21): 11325-30.

Zembskii, V.A. and A. A. Berzin. (1961) "On the rare phenomenon of atavism in the sperm whale." Nauchnye Doklady Vysshei Shkoly. Series "Biologicheskie Nauki."

Zhu, T., B. Korber, et al. (1998) "An African HIV-1 sequence from 1959 and implications for the origin of the epidemic." Nature 391: 594- 597.