[I} A . C.vVilson, R.L. Cann, S . .\;1. Carr, J. George, KB. Gyllensten, K..\;L Helm bychowski, R.G. Higuchi, S.R. Palumbi, E.::\1. Prager, R.D. Sage, and ::\1. Stoneking. ::vritochondrial DKA and two perspectives on evolutionary genetics. Biol. J. Linn. Soc. , 26:375 400, 1 985.
[2} R.A. AIm and 22 others. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori . Nature, 397: 176
180, 1999.
[3] H .-J. Bandelt. Phylogenetic networks. Verhandl. Naturwiss Vereins Hamburg,
34:51--71, 1994.
[4] H.-J. Bandelt and A.vV.::vr. Dress. A canonical decomposition theory for met rics on a finite set. Adv. Math . , 92:47 105, 1990.
[5] H.-J. Bandelt and A.vV.::vr. D ress. Split decomposition: A new and useful approach to phylogenetic analysis of distance data. Mol. Phyl. Evol. , 1 : 242 252, 1992.
[6] H.-J. Bandelt, P. Forster, and A. Roh!. ::vredian-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. , 16:37- 48, 1 999.
[7] H.-J. Bandelt, P. Forster, B.C. Sykes, and M.B. Richards. Mitochondrial portraits of human populations using median networks. Genetics, 141:743-- 753, 1 995.
148 B I B L IO G RA P HY
[8] H .-J. Bandelt, V . Macaulay, and M. Richards. "Median networks:speedy con struction and greedy reduction, one simulation, and two case studies from human mtDl\"A. Mol. Phyl. Evol. , 16:8-28, 2000.
[9] C.VV. Birky. Cniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc. Natl. Acad. Sci., 92: 1 1 331 1 1 338, 1 995. [101 P.L. Bollyky, A. Rambaut, P.H . Harvey, and E.C. Holmes. Recombination
between sequences of Hepatitis B virus from different genotypes. J. Mol. Evol. , 42:97-102, 1996.
[1 1] W . .J. Bruno and A.L. Halpern. Topological bias and inconsistency of maxi mum likelihood using wrong models. Mol. Bioi. Evol. , 1 6:564- 566, 1 999. [12] P. Buneman. The recovery of trees from measures of dissimilarity. In Math
ematics in the A rchaeological and Historical Sciences, pages 387 -395. Edin burgh Cniversity Press, 1971 .
[13] S. Campbell, A. Fraser, B. Holliss, J . Schmid, and P. VV. O'Toole. Evidence for ethnic tropism of Helicobacter pylori . Infect. Immun. , 65:3708 -371 2 , 1997. [14] M.A. Charleston. Factors affecting the performance of phylogenetic methods.
PhD thesis, Massey Cniversity, 1994.
[15] M.A. Charleston, M.D. Hendy, and D. Penny. The effects of sequence length, tree topology, and number of taxa on the performance of phylogenetic meth ods. J. Comp. Bio. , 1 : 1 33-151, 1994.
[16] B. Chor, .\i.D. H endy, B.R. Holland, and D . Penny. Multiple maxima of likelihood in phylogenetic trees: An analytic approach. Mol. BioI. Evol. ,
17:1 529--154 1 , 2000.
[17] A. Cooper and D. Penny. Mass survival of birds across the Cretaceous Tertiary boundary: Molecular evidence. Science, 275:1109-1 1 13, 1 997.
[18] Z. Debyser, E.v. vVijngaerden, Kv. Laethem, K Beuselinck, :\11. Reynders, E.D. Clerq, J. Desmyter, and A.M. Vandame. Failure to quantify viral load with two of the three commercial methods in a pregnant woman harboring a HIV type 1 subtype G strain. AIDS Research and Httman Retrovirtt8es,
14:453 459, 1998.
[19] A. Dress. Statistische geometrie von konfigurationen und deren evolution in sequenz-diumen - definitionen und probleme. ein programmvorschlag. In Die Bedentttng der von Berlin att8 gehenden Mathematik in Vergangenheit und Gegenwar·t. Kolloquium-Verlag, Berlin. , 1988.
[20] A. Dress, B. Holland, KT. Huber, J.H. Koolen, V . Moulton, and J. Weyer .\1enkoff. r5 additive and r5 ultra-additive maps, Gromov's trees, and the Farris transform. submitted to Discrete Applied Math., 200 1 .
[21] A. Dress, D. Huson, and V. :\Iloulton. Analyzing and visualizing sequence and distance data using SplitsTree. Disc. Appl. Math. , 71 :95 1 09, 1 996. [22] A. Drummond, G.K. :Kicholls, A.G. Rodrigo, and W. Solomon. Estimating
mutation rate, population history, substitution model and genealogy simul taneously from temporally spaced sequence data. Unpttblished, 200 1 .
[23] A. Drummond and A . G . Rodrigo. Reconstructing genealogies of serial sam ples under the assumption of a molecular clock using serial sample ePG MA
(
sC'PGMA)
. Mol. Bioi. Evol. , 17:1807 1815, 2000.[24] E.S. Edgington. Randomization Test8. Marcel Dekker, Inc., 3rd edition, 1 995. [25] B. Efron. The Jackknife, the Boot8tmp and other re8ampling plans. Dept. of
Statistics Stanford C'niversity, 1982.
[26] B. Efron, E. Halloran, and S. Holmes. Bootstrap confidence levels for phylo genetic trees. Proc. Natl. Acad. Sd. , 93:13429�13434, 1 996.
1 50 B I BLIO G RA P HY
[27] B. Efron and R J . Tibshirani. An introduction to the bootstrap. Chapman and Hall, 1 993.
[28] :\1. Eigen and R vVinkler-Oswatitsch. Statistical geometry on sequence space.
Methods in Enzymology, 183:505-530, 1 990.
[29] :VI. Eigen, R. vVinkler-Oswatitsch, and A. Dress. Statistical geometry in sequence space: a method of quantitative sequence analysis. Proc. Natl. Acad. Sci. , 85:5913-5917, 1988.
[30] B .S. Everitt. Cluster Analysis. Edward Arnold, 3rd edition, 1 993.
[31] J .S. Farris. A probability model for inferring evolutionary trees. Syst. Zool. ,
22:250 256, 1973.
[32] J. Felsenstein. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. , 27:401 - 410, 1 978.
[33] J. Felsenstein. Evolutionary trees from DI\A sequences: A maximum likeli hood approach. J. Mol. Evol. , 1 7:368-376, 1 98 1 .
[34] J. Felsenstein. PHYLIP (Phylogeny Inference Package) version 3. 5c. Depart ment of Genetics, Cniversity of Washington, Seattle, 1993. Distributed by the author.
[35] W.�1. Fitch. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. , 20:406-416, 1 971 .
[36] M.R Garey and D.S. Johnson. Computers and intractability: A guide to the theory of NP-completeness. W.H. Freeman and Company, 1 979.
[37] A.D. Gordon. Classification: methods for exploratory analysis of multivariate data. Chapman and Hall, 1981 .
[38] Y. Graser, M. Volovsek, J. Arrington, G. Schonian, VV. Presber, T.G. Mitchell, and R. Vilgalys. Molecular markers reveal that population struc ture of the human pathogen Candida albicans exhibits both clonality and recombination. Pmc. Nat. Acad. Sci. , 93: 1 2473 1 2477, 1996.
[39] K.C. Grassly and E.C. Holmes. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. BioI. Evol. ,
14:239 247, 1997.
[40] :\i. Gromov. Hyperbolic groups. In Essays zn gmup theo'f'Y. , volume 8. Springer-Verlag, 1988.
[41] :\1. Hasegawa, H. Kishino, and T. Yano. Dating of the human-ape splitting by a molecular clock of mitochondrial DKA. J. Mol. Evol. , 21 :160 1 74, 1 985. [42] J.c. Heine and T.W. Speir. Ornithogenic soils of the Cape Bird Adelie pen
guin rookeries, Antarctica. Geology, 22:23--26, 1994.
[43] "Y1.D. Hendy and D. Penny. A framework for the quantitative study of evo lutionary trees. Syst. Zool. , 38:297 309, 1989.
[44] :\1.D. Hendy and D . Penny. Spectral analysis of phylogenetic data. J. Class. ,
10:5-24, 1993.
[45] :\i.D. Hendy, D. Penny, and :\i.A. Steel. A discrete fourier analysis for evolu tionary trees. Pmc. Natl. Acad. Sci. , 91 :3339-3343, 1994.
[46] D.M. Hillis, J.P. Huelsenbeck, and C.W. Cunningham. Application and ac curacy of molecular phylogenies. Science, 264:671-677, 1 994.
[47] E.C. Holmes, M. vVorobey, and A. Rambaut. Phylogenetic evidence for re combination in Dengue virus. Mol. BioI. Evol. , 16:405-409, 1999.
1 52 B I B L I O G RA P HY
[48] "M . Hoss, P. Jaruga, T. Zastawny, �1. Dizdaroglu, and S . Piiiibo. DNA dam age and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. ,
24: 1304--1307, 1996.
[49] D. Huson. Splits Tree verswn 2.4, 1997. Available from ftp:/ /ftp.uni bielefeld.de/pub/mat h/splits/splitstree2.
[50
J
D . Huson. SplitsTree: a program for analyzing and visualizing evolutionary data. Bioinformatics, 14:68-73, 1 998.[51] "M. \11. Jensen and D.N. Wright. Introduction to microbiology for the health sciences. Prentice Hall, 3rd edition, 1993.
[52] J. Kim. Improving the accuracy of phylogenetic estimation by combining different methods. Syst. Bio!. , 42:331 -340, 1993.
[53] J. Kim. Slicing hyperdimensional oranges: the geometry of phylogenetic estimation. Mol. Phyl. Evol. , 17:58- 75, 2000.
[54] "M. Kimura. Estimation of evolutionary sequences between homologous nu cleotide sequences. Proc. Nat!. Acad. Sci. , 78:454-458, 1 981 .
[55] J.F.C. Kingman. The coalescent. Stochastic Processes and their Applications,
13:235-248, 1982.
[56] J.F.C. Kingman. On the genealogy of large populations. J. Appl. Prob.,
1 9A:27-43, 1982.
[57] S. Kumar , K. Tamura, and M. Nei. MEGA : Molecular Evolutionary Genetics Analysis, version 1 . 01. The Pennsylvania State University, University Park, PA 16802, 1993.
[58] D."M. Lambert, P.A. Ritchie, C.D. M ill ar , B. Holland, A. Drummond, and C. Baroni. Evolution in action: Ancient DNA from frozen Adelie penguin bones in Antarctica. Submitted to Nature, 2001 .
[59] T. Lindahl. Instability and decay of the primary structure of DKA. Natu r'e,
362:709 715, 1993.
[60] P.J. Lockhart and S.A. Cameron. Trees for bees. Trends in Eco . and Evol. ,
16:84 88, 2001 .
[61] J. Lyons--Weiler, G.A. Hoelzer, and R.J. Tausch. Relative Apparent Synapo morphy Analysis (RASA) I: The statistical measurement of phylogenetic sig nal. Mol. BioI. Evol. , 13:749 757, 1 996.
[62] .1. Lyons-Weiler, G.A. Hoelzer, and R.J. Tausch. Optimal outgroup analysis.
Bioi. J. Linn. Soc., 64:493 5 1 1 , 1 998.
[63] S. :\1archant and P.J. Higgins. Handbook of Australia) New Zealand and Antarctic Birds. Oxford Cniversity Press, :YIelbourne, 1990.
[64] G. :\1cGuire, F. Wright, and . .1. Prentice. A graphical method for detecting recombination in phylogenetic data sets. Mol. BioI. Evol. , 14: 1 1 25 1 131, 1997. [65] S. :\1eyer, G. Weiss, and A.v. Haeseler. Patterns of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtD I\ A .
Genetics, 1 52:1 103 1 1 10, 1999.
[66] M . C . :\1ilinkovitch. Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious. Mol. Phyl Evol. , 9:348- 357, 1997. [67] D .P. 11indell, :\1.0. Sorenson, D.E. Dimcheff, :\1. Hasegawa, J.C. Ast, and
T . Yuri. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. BioI. , 48:1 38--152, 1 999.
[68] K. Kieselt-Struwe and A. von Haeseler. Quartet-mapping, a generalization of the likelihood mapping procedure. Mol. BioI. Evol. , 18: 1204�1 219, 2001. [69] E.W. Koreen. Computer intensive method8 for testing hypotheses: An intro
154 B I B L I O G R A P HY
[70] F.G. Odds. Candida and Candidosis. Bailliere Tindall, 2nd edition, 1 988. [71] S. paabo. Ancient DKA:Extraction, characterization, molecular cloning, and
enzymatic amplification. PIOC. Natl. Acad. Sci., 86: 1 939- 1 943, 1 989.
[72] D . Penny and �1. Hasegawa. The platypus put in its place. Nature, 387:549- 550, 1 997.
[73] D. Penny, M.D. Hendy, P.J. Lockhart, and :'\1.A. Steel. Corrected parsimony, minimum evolution, and Hadarnard conjugations. SY8t. Biol. , 45:596 606, 1996.
[74] D . Penny, ).I1.D. Hendy, and M.A. Steel. Testing the theory of descent. In
Phylogenetic analysis of DNA sequences, pages 155-1 83. Oxford University Press, Inc. , 199 1 .
[75] D . Posada and K . A . Crandall. Simple (wrong) models for complex trees: a case from retroviridae. Mol. Biol. Evol. , 1 8:271-275, 200 1 .
[76] C. Pujol, J. Reynes, F . Renaud, M . Raymond, M. Tibayrenc, F . J . Ayala, F . Janbon, :VI. Mallie, and J. Bastide. The yeast Candida albicans has a clonal mode of reproduction in a population of infected human immunodeficiency virus-positive patients. Proc. Nat. Acad. Sci. , 90:9456-9459, 1 993.
[77] Y. Qui, J. Lee, F. Bernasconi-Quadroni, D.E. Soltis, P.S. Soltis, M. Zanis, E.A. Zimmer, Z. Chen, V. Savolainen, and M.W. Chase. The earliest an giosperms: evidence from mitochondrial, plastid and nuclear genomes. N a ture, 402:404-407, 1999.
[78] T.W. Quinn. The genetic legacy of Mother Goose - phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages. Mol. Ecol. , 1 :1 05-11 7, 1992.
[79] A. Rambaut. Estimating the rate of molecular evolution: incorporating non contemporaneous sequences into maximum likelihood phylogenies. Bioinfor matics, 16:395- 399, 2000.
[80] A.E. Rambaut and K.C. Grassly. Treevolve version 1 .3. Available from http://evolve.zoo.ox.ac. uk.
[81] A.E. Rambaut and K .C. Grassly. Seq-Gen: An application for the ::vIonte Carlo simulation of DKA sequence evolution along phylogenetic trees. Com put. Appl. Biosci. , 1 997.
[82] P. Ritchie. The evolution of the mitochondrial DNA control region in the Adetie penguins of Antarctica. PhD thesis, :\IIassey Cniversity, Kew Zealand, 2001.
[83] K. Saitou and T. Imanishi. Relative efficiencies of the fitch- margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. BioI. Evol. , 6:514 525, 1989.
[84J K. Saitou and ::vI. Kei. The Keighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. BioI. Evol. , 4:406 - 425, 1 987.
[85] T. Al Samarrai, K. Zhang, L Lamont, J. Kolbe, ::vI. Wilsher, A. J . :\I!or
ris, and J. Schmid. A fast, highly discriminating and inexpensive method for computer-assisted typing of Pseudomonas aeruginosa. KZ:\IlS meeting, Dunedin, New Zealand, 1 999.
[86] J. Schmid, S. Herd, P.R. Hunter, R.D. Cannon, and ::vI. Salleh. Evidence for a general-purpose genotype in Candida albicans , highly prevalent in multi ple geographical regions, patient types and types of infection. Microbiology,
156 B IB LIO G RA P HY [87] S. Siguroard6ttir, A. Helgason, J.R. Gulcher, K . Stefansson, and P. Donnelly.
The mutation rate in the human mtDNA control region. Am. J. Hum. Genet. , 66:1599-1609, 2000.
[88] A.B. Smith. Rooting molecular trees: problems and strategies. Bioi. J. Linn. Soc., 5 1 :279-292, 1 994.
[89J R.R. Sokal and C.D. :Michener. A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bul. , 38:1 409 1 438, 1 958.
[90J P.S. Soltis, D .E. Soltis, and ),1.W. Chase. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature, 402:402 404, 1 999.
[9 1J J. Sourdis and C. Krimbas. Accuracy of phylogenetic trees estimated from DNA sequence data. Mol. Bioi. Evol. , 4:159-166 , 1 987.
[92J J. Sourdis and M. Kei. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol. BioI. Evol. , 5:298- 3 1 1 , 1 988.
[93] M.A. Steel, M.D. Hendy, and D. Penny. Parsimony can be consistent! Syst. BioI. , 42:581 -587, 1 993.
[94] C.K. Stover and 30 others. Complete genome sequence of Pseudomonas aerug inosa PA01 , an opportunistic pathogen. Nature, 406:959-964, 2000.
[95J K. Strimmer and A. von Haesler. Likelihood-mapping: a simple method to visualize phylogenetic content of sequence alignment. Proc. Natl. A cad. Sci.
USA, 94:68 1 5-6819, 1997.
[96J D. Swofford, G. Olsen, P. Waddell, and D . Hillis. Phylogenetic inference. In
[97] D.L. Swofford. PA UP * Phylogenetic Analysis Using Par'simony (*and Other Methods), 1 998. Version 4. Sinauer Associates, Sunderland, Mass.
[98] F. Tajima. Unbiased estimation of evolutionary distance between nucleotide sequences. Mol. BioI. Evol. , 10:677 688, 1 993.
[99] K . Talaro and A . Talaro. Foundations in microbiology. Dubuque, lA, 1 996. [100J Y. Tateno, I\. Takezaki, and M. Kei. Relative efficiencies of the maximum
likelihood, neighbour joining and maximum parsimony methods when substi tution rates varies with site. Mol. BioI. Evol. , 1 1 : 261 277, 1994.
[101] M. Tibayrenc. Are Candida albicans natural populations subdivided? Trends in Microbiology, 5: 253 257, 1997.
[102] J.-F. Tomb and 41 others. The complete genomic sequence of the gastric pathogen Helicobacter pylori . Nature, 388:539 547, 1997.
[103] P.J. vVaddell, Y. Cao, J. Hauf, and M. Hasegawa. Csing novel phylogenetic methods to evaluate mammalian mtDKA, including amino acid-invariant sites-Iogdet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Syst. Bioi. , 48:31 53, 1 999.
[104] P.J. vVaddell, D . Penny, M .D. Hendy, and G. Arnold. The sampling dis tributions and covariance matrix of phylogenetic spectra. Mol. Bioi. Evol,
1 1 :630-642, 1994.
[105] P. J. vVaddell, D. Penny, and T. Moore. Hadamard conjugations and modelling sequence evolution with unequal rates across sites. Mol. Phyl. Evol, 8:33�-50, 1 997.
[106] E.B. Watson. Threads from the past: A genetic study of African ethnic groUp8 and human origins. PhD thesis, Massey University, Kew Zealand, 1996.
1 58 B IB LI O G RA P HY
[1 07] G.F. vVeiller. Phylogenetic profiles: A graphical method for detecting genetic recombinations in homologous sequences. Mol. Evol. Sys . , 1 5:326-335, 1998. [108] B.S. vVeir. Genetic Data Analysis II. Sinauer Associates Inc., 2nd edition,
1 996.
[109] T.D. vVilliams. The Penguins: Spheniscidae. Oxford Cniversity Press, Ox ford, 1 995.
[ 1 1 0] Z. Yang. How often do wrong models produce better phylogenies? Mol. Biol. Evol. , 14:105-108, 1997.