• Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A. and Lake, J. A.(1997) Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature,387,489493.
  • Blanchette, M., Kunisawa, T. and Sankoff, D.(1999) Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Molec. Evoln,49,193203.
  • Boore, J.(2001)Mitochondrial Gene Arrangement Source Guide, Version 6.0. Department of the Environment Joint Genome Institute, Walnut Creek. (Available from
  • Boore, J. L. and Brown, W. M.(1998)Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Devlpmnt,8,668674.
  • — (2000)Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molec. Biol. Evoln,17,87106.
  • De Rosa, R.(2001)Molecular data indicate the protostome affinity of brachiopods. Syst. Biol.,50,848859.
  • Felsenstein, J.(1978)The number of evolutionary trees. Syst. Zool.,27,2733.
  • — (1981)Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Molec. Biol.,17,368376.
  • — (1983)Statistical inference of phylogenies (with discussion). J. R. Statist. Soc. A,146,246272.
  • Halanych, K. M., Bacheller, J. D., Aguinaldo, A. M. A., Liva, S. M., Hillis, D. M. and Lake, J. A.(1995)Evidence from 18S ribosomal DNA that lophophorates are protostome animals. Science,267,16411643.
  • Hastings, W. K.(1970)Monte Carlo sampling methods using Markov chains and their applications. Biometrika,57,97109.
  • Helfenbein, K. G., Brown, W. M. and Boore, J. L.(2001)The complete mitochondrial genome of the articulate brachiopod. Molec. Biol. Evoln,18,17341744.
  • Huelsenbeck, J. P., Ronquist, F., Nielsen, R. and Bollback, J.(2001)Bayesian inference of phylogeny and its impact on evolutionary biology. Science,294,23102314.
  • Hyman, L. H.(1940)The Invertebrates. New York: McGraw-Hill.
  • Kaplan, H., Shamir, R. and Tarjan, R.(1999)Faster and simpler algorithm for sorting signed permutations by reversals. SIAM J. Comput.,29,880892.
  • Larget, B. and Simon, D. L.(1999)Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molec. Biol. Evoln,16,750759.
  • Li, S., Doss, H. and Pearl, D.(2000)Phylogenetic tree reconstruction using Markov chain Monte Carlo. J. Am. Statist. Ass.,95,493508.
  • Mau, B., Newton, M. A. and Larget, B.(1999)Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics,55,112.
  • Metropolis, N., Rosenbluth, A., Rosenbluth, M., Teller, A. and Teller, E.(1953)Equation of state calculations by fast computing machines. J. Chem. Phys.,21,10871092.
  • Newton, M., Mau, B. and Larget, B.(1999)Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences. IMS Lect. Notes Monogr. Ser.,33,143162.
  • Pevzner, P.(2000)Computational Molecular Biology—an Algorithmic Approach,ch. 10. Cambridge: MIT Press.
  • Rannala, B. and Yang, Z.(1996)Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Molec. Evoln,43,304311.
  • Sankoff, D. and Blanchette, M.(1998)Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol.,5,555570.
  • — (1999)Phylogentic invariants for genome rearrangements. J. Comput. Biol.,6,431445.
  • Simon, D. L. and Larget, B.(2001)Phylogenetic inference from mitochondrial genome arrangement data. Lect. Notes Comput. Sci.,2074,10221028.
  • Swofford, D., Olsen, G., Waddell, P. and Hillis, D.(1996)Phylogenetic inference.InMolecular Systematics(eds D. M. Hillis, C. Moritz and B. K. Mable). Sunderland: Sinauer.
  • Yang, Z. and Rannala, B.(1997)Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Molec. Biol. Evoln,14,717724.