David Bryant's Publications

Submitted/  
Bryant, D, Nies, A. and Tupper, P. 2016. A diversity analogue of the Urysohn metric space. Submitted
Mehta, R., Bryant, D., Rosenberg, N. The probability of monophyly of a sample of gene lineages on a species tree. Invited manuscript, PNAS. Submitted.  
Balvocuite, M., Bryant, D., Spillner, A. 2016. When can splits be drawn in the plane? SIAM journal on Discrete Mathematics (accepted subject to revision)
Published / In press  

Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F., Lockhart, P.J., Bryant, D., Hazkani-Covo, E., McInerney, J., Landan, G., Martin, W. 2015. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524: 427-432.

Leigh, J. and Bryant, D. 2015. Popart: full‐feature software for haplotype network construction. Methods in Ecology and Evolution 6(9): 1110-1116.

 
Leigh, J. and Bryant, D. 2015. Monte Carlo Strategies for Selecting Parameter Values in Simulation Experiments. Systematic Biology 64(5):741-51.  

Scornavacca, C., van Iersel, L., Kelk, S. Bryant, D. 2014. The agreement problem for unrooted phylogenetic trees is FPT. J. Graph Algorithms and Applications. 18(3): 385-392.

 
Joly, S., Bryant, D. and Lockhart, P.J. 2014. Flexible methods for estimating genetic distances from single nucleotide polymorphisms. Methods in Ecology and Evolution. 6(8):938--948.  
Nelson-Sathi, S., F.L.Sousa, M. Röttger, N. Lozada-Chávez, T. Thiergart, A. Janssen, D. Bryant, G. Landan, P. Schönheit, P. Siebers, J. McInerney and W.F. Martin. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:77-80.  
Bryant, D. 2014. Statistical flaws undermine pre-Columbian chicken debate. PNAS (letter to editor). doi:10.1073/pnas.1410797111
Bryant, D. and Tupper, P. Diversities and the Geometry of Hypergraphs. 2014. Discrete Mathematics and Theoretical Computer Science 16:2 1-20.
Bryant, D. and Kydd, J. 2013. Forty years of model-based phylogeography. in Chauve, C., El-Mabrouk, N. and Tannier (eds), Models and Algorithms for Genome Evolution. Springer.
Holder, M. T., Lewis, P. O., Swofford, D. L., and Bryant, D. 2013. Variable tree topology stepping-stone marginal likelihood estimation. In: Chen, M.-H., Kuo, L., and Lewis, P. O. (eds.), Bayesian phylogenetics: methods, algorithms, and applications. Chapman & Hall, New York.  
Davies, T. and Bryant, D. 2013. On Circulant Embedding for Gaussian Random Fields in R. Journal of Statistical Software 55(9)
White, D.J., Bryant, D. and Gemmell, N.J. 2013. How good are indirect tests at detecting recombination in human mtDNA? Genes, Genomes and Genetics, 3 (7), 1095-1104.
Heled, J., Bryant, D. and Drummond, A. 2013. Simulating gene trees under the multispecies coalescent and time-dependent migration. BMC Evolutionary Biology. in press.
Bryant, D. and Tupper, P. 2012. Hyperconvexity and tight span theory for diversities.Advances in Mathematics. 231:3172-3198.
Atheer A. Matroud, Christopher P. Tuffley, D. Bryant, Michael D. Hendy. 2012. A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats. BSB 2012. LNCS 7409, 37-48  
Storey, A, J Stephen Athens, David Bryant, Mike Carson, Kitty Emery, Charles Higham, Leon Huynen, Michiko Intoh, Sharyn Jones, Patrick V Kirch, Thegn Ladefoged, Patrick McCoy, Arturo Morales-Muñiz, Daniel Quiroz, Elizabeth Reitz, Judith Robins, Richard Walter, Elizabeth Matisoo-Smith. 2012. Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures. PLoS One 7(7) e39171.
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N., RoyChoudhury, A. 2012 Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 19(8):1917-1932
Bryant, D. and Steel, M. 'Bureaucratic' set systems, and their role in phylogenetics. 2012Applied Mathematics Letters (in press)

Siekmann, I., Wagner, L.E., Yule, D., Fox, C., Bryant, D., Crampin, E., and Sneyd, J. 2011. MCMC Estimation of Markov Models for Ion Channels. Biophysical Journal 100:1919-1929.

Bryant, D., and Klaere, S. 2011. The link between segregation and phylogenetic diversity. Journal of Mathematical Biology.

Sangaralingam, A., Susko, E., Bryant, D., Spencer, M. On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations. 2010 BMC Evolutionary Biology 10:343
Dagan, T, Roettger, M. Bryant, D. and Martin, W. 2010. Genome network roots the tree of life between prokaryotic domains. Genome Biology and Evolution. 2:379-392.
Gray, R.D., Greenhill, S.J., and Bryant, D. 2010. On the shape and fabric of human history. Philosophical Transactions of The Royal Society London 365:3923-3933
Bryant, D. and Steel, M. 2009. Computing the Distribution of a Tree Metric. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6, 420-426.
Meudt, H. and Lockhart, P. and Bryant, D. 2009. Species delimitation and phylogeny of a New Zealand plant species radiation. BMC Evolutionary Biology. 9, 111.
Degnan, J., DeGiorgio, M., Bryant, D. and Rosenberg, N. 2009. Properties of consensus methods for inferring species trees from gene trees. Systematic Biology, 58:35-54.
Bryant, D. 2009. Hadamard phylogenetic methods and the n-taxon process. Bull Math Biol, 71.339-351.
Thierer, T., Bryant, D. and Steel, M. 2008. Counting ancestral reconstructions in a fixed phylogeny. Annals Combinatorics, 12.123-132.
Bruen, T. and Bryant, D. 2008. Parsimony via consensus. Systematic Biology, 57.251-256
Bruen, T. and Bryant, D. 2008. A subdivision approach to maximum parsimony. Annals of Combinatorics, 12:45-51
Spencer, M., Bryant, D., Susko, E 2007. Conditioned Genome Reconstruction: How to Avoid Choosing the Conditioning Genome. Systematic Biology 56(1):25-43.
Bevan, R., Bryant, D., Lang, F. 2007. Accounting for gene rate heterogeneity in phylogenetic inference. Systematic Biology 56, 194-205
Bryant, D. and Dress, A. 2007. Linearly independent split systems. European J. Combin. 28, 1814-1831.
Lepage, T., Bryant, D., Philippe, H. and Lartillot, N. 2007. A general comparison of relaxed molecular clock models. Molecular Biology and Evolution, 24.2669-2680
Bryant, D. and Moulton, V. and Spillner, A. 2007. Consistency of the NeighborNet algorithm. Algorithms in Molecular Biology, 2,8
Bruen, T., Philiipe, H. and Bryant, D. 2006. A quick and robust statistical test to detect the presence of recombination. Genetics 172, 2665--2681
Bryant, D. and Lagergren, J. 2006. Compatibility of unrooted trees is FPT. Theoretical Computer Science 351 (3), 296-302.
Huson, D. and Bryant, D. 2006. Application of Phylogenetic Networks in Evolutionary Studies. Molecular Biology and Evolution 23(2) 254-267.
Lepage, T., Lawi, S., Tupper, P. and Bryant, D. 2006. Continuous and Tractable Models for the Variation of Evolutionary Rates. Mathematical Biosciences 199(2) 216-233.
Bryant, D. 2006. Radiation and network breaking in Polynesian Language Evolution. in Forster, P. and Renfrew, C. (eds)Phylogenetics and the Prehistory of Languages.
Bryant, D. 2005. Extending tree models to split networks. in Pachter, L. and Sturmfels, B. Algebraic statistics for computational biology. Cambridge University Press. 322-334.
Bevan, R., Franz Lang, B. and Bryant, D. 2005. Calculating the Evolutionary Rates of Different Genes: A Fast, Accurate Estimator with Applications to Maximum Likelihood Phylogenetic Analysis. Systematic Biology 54(6):900-915.
Bryant, D. 2005. On the uniqueness of the selection criterion in Neighbor-joining. Journal of Classification. 22(1):3--15.
Winkworth, R., Bryant, D., Lockhart, P. and Moulton, V. 2005. Biogeographic interpretation of split graphs: studying Quaternary plant diversification. Systematic Biology 54(1):56-65.
Rodrique, N., Lartillot, N., Bryant, D., and Philippe, H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 207-217
Bryant, D., Filimon, F. and Gray, R. 2005. Untangling our past: Languages, trees, splits and networks. in R. Mace, C. Holden, S. Shennan. (eds) The Evolution of Cultural Diversity: Phylogenetic Approaches. UCL Press. 67-84
Bryant, D., Galtier, N. and Poursat, M.A. 2004. Likelihood calculation in molecular phylogenetics. in Gascuel, O. (ed) Mathematics of Evolution and Phylogeny Oxford University Press.
Bryant, D., Semple, C and Steel, M. 2004. Supertrees with ancestral divergence times. in Bininda-Emonds (ed) Phylogenetic Supertrees: Combining information to reveal the tree of life Kluwer. pp. 129-150.
Esser, C., Ahmadinejad, N. Wiegand, C. Rotte, C. Sebastiani, F., Gelius-Dietrich, G., Henzel, K. Kretschmann, E., Richly, E. Leister, D., Bryant, D., Steel, M., Lockhart, P., Penny, D., and Martin, W. 2004. A genome phylogeny for mitochondria among alpha-proteo bacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Molecular Biology and Evolution. 21: 1643 - 1660
Bryant, D. and Moulton, V. 2004. NeighborNet: an agglomerative algorithm for the construction of phylogenetic networks. Molecular Biology and Evolution 21(2):255-265. Errata
Lapointe, F.J., Wilkinson M. and Bryant D. 2004. Matrix Representations with Parsimony or with Distances? A Tale of Two Consensus Approaches. Systematic Biology 52(6): 865-869
Bryant, D. 2004. The splits in the neighbourhood of a tree. Annals of Combinatorics 8(1):1-11. Errata
Bryant, D. 2004. A lower bound for the breakpoint phylogeny problem. J. Discrete Algorithms 2(2): 229--255. (first submitted June 2000)
Bryant, D. Huson, D., Kloepper, T. and Nieselt-Struwe, K. 2003. Distance corrections on recombinant sequences WABI (Workshop on Algorithms in Bioinformatics) 2003 LNCS 2812:271-286.
Bryant, D. 2003. A classification of consensus methods for phylogenies. in Janowitz, M., Lapointe, F.-J., McMorris, F.R., Mirkin, B., Roberts, F.S. (eds) BioConsensus, DIMACS. AMS. 163--184.
Bryant, D., Steel, M., and MacKenzie, A.. 2003. The size of a maximum agreement subtree for random binary trees. in Janowitz, M., Lapointe, F.-J., McMorris, F.R., Mirkin, B., Roberts, F.S. (eds) BioConsensus, DIMACS. AMS. 55--66.
Bryant, D. and Berry, V. 2001. A family of clustering and tree construction methods. Advances in Applied Mathematics 27(4), 705--732.
Gascuel, O., Bryant, D., and Denis, F. 2001. Theoretical limitations of the minimum evolution principle. Systematic Biology 50(5), 621-627.
Bryant, D. Optimal agreement supertrees. 2001. First Int. Conference on Biology, Informatics, and Mathematics (JOBIM 2000) Lecture notes in computer science 2066, Springer-verlag, 24--31.
Bryant, D. 2001. The complexity of calculating exemplar distances. in Sankoff, D. and Nadeau, J.H. (eds) Comparative Genomics Kluwer, 207--212.
Bryant, D. and Steel, M. 2001. Constructing optimal trees from quartets. Journal of Algorithms (An extended version of Bryant and Steel 1999). 38(1) 237--259.
Sankoff, D., Parent, M.N., and Bryant, D.. 2000. Accuracy and robustness of analyses based on numbers of genes in observed segments. in Sankoff, D. and Nadeau, J.H. (eds) Comparative Genomics , Kluwer, 299--306.  
Sankoff, D. Deneault, M., Bryant, D., Lemieuex, C. and Turmel, M. 2001. Chloroplast gene order and the divergence of plants and algae, from the normalised number of induced breakpoints. in Sankoff, D. and Nadeau, J.H. (eds) Comparative Genomics Kluwer, 89--98.
Böcker, S., Bryant, D., Dress, A., and Steel, M. 2000. Algorithmic aspects of tree amalgamation. Journal of Algorithms, 37(2), 522--537.
Sankoff, D., Bryant, D., Denault, M., Lang, B.F., and Burger, G. 2000. Early eukaryote evolution based on mitochondrial gene order breakpoints. Journal of Computational Biology 7(3) 521--536.
Bryant, D., Tsang, J., Kearney, P., and Li, M. 2000. Computing the quartet distance between evolutionary trees. Proc. ACM-SIAM Symposium on Discrete Algorithms
Berry, V., Bryant, D., Kearney, P., Li, M., Jiang, T., Wareham, T. and Zhang, H. 1999. A practical algorithm for recovering the best supported edges in an evolutionary tree. Proc. ACM-SIAM Symposium on Discrete Algorithms.
El-Mabrouk, N., Bryant, D. and Sankoff, D. 2000. Reconstructing the pre-doubling genome. Proc. 3rd international conference on comp. mol. biol. (RECOMB) 3, 154-163.  
Berry, V. and Bryant, D. Faster reliable phylogenetic analysis. 1999. Proc. 3rd international conference on comp. mol. biol. (RECOMB) 3, 59-69. Winner of the best paper by a young scientist award.
Bryant, D. and Steel, M. 1999. Fast algorithms for constructing optimal trees from quartets. Proc. ACM-SIAM Symposium on Discrete Algorithms 10, 147-155.  
Bryant, D. and Moulton, V. 1999. A polynomial time algorithm for the refined Buneman tree. Applied Mathematics Letters 12, 51-56.
Bryant, D. The complexity of the breakpoint median problem. 1998. Tech. report CRM-2579. Centre de recherches mathématiques, Université de Montréal.
Bryant, D. and Waddell, P. 1997. Rapid evaluation of least squares and minimum evolution criteria on phylogenetic trees. Molecular Biology and Evolution 15(10), 1346-1359.
Bryant, D. Hunting for trees, building trees and comparing trees: theory and method in phylogenetic analysis. Ph.D. thesis, Dept. Mathematics, University of Canterbury.
Bryant, D. 1996. Hunting for trees in binary character sets. Journal of Computational Biology 3(2), 275-288.
Bryant, D. and Steel, M. 1995. Extension operations on sets of leaf-labelled trees. Advances in Applied Mathematics 16, 425-453.
Krishnan, P. and Bryant, D. 1994. A digraph model for extended event structures. Technical report 1/94, Dept. Computer Science, University of Canterbury.