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Professor David Bryant

(PhD)David Bryant image (2023)

Director of Computational Modelling (COMO)
Vice-president of the New Zealand Mathematical Society
Fellow of the Royal Society of NZ

Office: Science III, room 515
Tel +64 3 479 7889
Email david.bryant@otago.ac.nz

About

David Bryant is a world leader in the development of mathematical tools for inferring evolutionary relationships among biological organisms. He has made significant theoretical and practical contributions to phylogenetics — the field of biology studying the reconstruction of evolutionary history. His research has been highly cited and applied to a diverse range of different areas, including early bacterial evolution, plant ecology, rapid identification of pathogens and even the origins of the fairy tales! He was joint winner of the 2016 New Zealand Mathematics Society Research Award.

Prior to coming to Otago, David was an associate professor at McGill University, Montreal, and then at the University of Auckland.

Teaching responsibilities

His teaching responsibilities include:

Research Interests

  • Evolutionary Biology, phylogenetics and population genetics
  • Metric geometry and mathematical diversities
  • Computational Bayesian statistics

See David Bryant's Google Scholar profile for more details.

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Publications

Stoltz, M., Stoltz, G., Obara, K., Wang, T., & Bryant, D. (2021). Acceleration of hidden Markov model fitting using graphical processing units, with application to low-frequency tremor classification. Computers & Geosciences, 156(104902). doi: 10.1016/j.cageo.2021.104902

Stoltz, M., Baeumer, B., Bouckaert, R., Fox, C., Hiscott, G., & Bryant, D. (2021). Bayesian inference of species trees using diffusion models. Systematic Biology, 70(1), 145-161. doi: 10.1093/sysbio/syaa051

Collienne, L., Elmes, K., Fischer, M., Bryant, D., & Gavryushkin, A. (2021). Discrete coalescent trees. Journal of Mathematical Biology, 83, 60. doi: 10.1007/s00285-021-01685-0

Bryant, D., Cioica-Licht, P., Clark, L., & Young, R. (2021). Inner products for convex bodies. Journal of Convex Analysis. Advance online publication.

Bryant, D., Nies, A., & Tupper, P. (2021). Fraïssé limits for relational metric structures. Journal of Symbolic Logic, 86(3), 913-934. doi: 10.1017/jsl.2021.65

Stoltz, M., Stoltz, G., Obara, K., Wang, T., & Bryant, D. (2021). Acceleration of hidden Markov model fitting using graphical processing units, with application to low-frequency tremor classification. Computers & Geosciences, 156(104902). doi: 10.1016/j.cageo.2021.104902

Journal - Research Article

Stoltz, M., Baeumer, B., Bouckaert, R., Fox, C., Hiscott, G., & Bryant, D. (2021). Bayesian inference of species trees using diffusion models. Systematic Biology, 70(1), 145-161. doi: 10.1093/sysbio/syaa051

Journal - Research Article

Collienne, L., Elmes, K., Fischer, M., Bryant, D., & Gavryushkin, A. (2021). Discrete coalescent trees. Journal of Mathematical Biology, 83, 60. doi: 10.1007/s00285-021-01685-0

Journal - Research Article

Bryant, D., Cioica-Licht, P., Clark, L., & Young, R. (2021). Inner products for convex bodies. Journal of Convex Analysis. Advance online publication.

Journal - Research Article

Bryant, D., Nies, A., & Tupper, P. (2021). Fraïssé limits for relational metric structures. Journal of Symbolic Logic, 86(3), 913-934. doi: 10.1017/jsl.2021.65

Journal - Research Article

Wu, P., Bryant, D., & Tupper, P. (2021). Negative-type diversities, a multi-dimensional analogue of negative-type metrics. Journal of Geometric Analysis, 31, 1703-1720. doi: 10.1007/s12220-019-00321-0

Journal - Research Article

Bryant, D., & Scornvacca, C. (2019). An O(n log n) time algorithm for computing the path-length distance between trees. Algorithmica, 81, 3692-3706. doi: 10.1007/s00453-019-00594-5

Journal - Research Article

Kapust, N., Nelson-Sathi, S., Schönfeld, B., Hazkani-Covo, E., Bryant, D., Lockhart, P. J., … Martin, W. F. (2018). Failure to recover major events of gene flux in real biological data due to method misapplication. Genome Biology & Evolution, 10(5), 1198-1209. doi: 10.1093/gbe/evy080

Journal - Research Article

Larcombe, M. J., Jordan, G. J., Bryant, D., & Higgins, S. I. (2018). The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification. Nature Communications, 9, 4258. doi: 10.1038/s41467-018-06732-x

Journal - Research Article

Balvočiūtė, M., Bryant, D., & Spillner, A. (2017). When can splits be drawn in the plane? SIAM Journal on Discrete Mathematics, 31(2), 839-856. doi: 10.1137/15M1040852

Journal - Research Article

Bryant, D., Nies, A., & Tupper, P. (2017). A universal separable diversity. Analysis & Geometry in Metric Spaces, 5, 138-151. doi: 10.1515/agms-2017-0008

Journal - Research Article

Hiscott, G., Fox, C., Parry, M., & Bryant, D. (2016). Efficient recycled algorithms for quantitative trait models on phylogenies. Genome Biology & Evolution, 8(5), 1338-1350. doi: 10.1093/gbe/evw064

Journal - Research Article

Mehta, R. S., Bryant, D., & Rosenberg, N. A. (2016). The probability of monophyly of a sample of gene lineages on a species tree. PNAS, 113(29), 8002-8009. doi: 10.1073/pnas.1601074113

Journal - Research Article

Nelson-Sathi, S., Sousa, F. L., Roettger, M., Lozada-Chávez, N., Thiergart, T., Janssen, A., Bryant, D., … Martin, W. F. (2015). Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature, 517(7532), 77-80. doi: 10.1038/nature13805

Journal - Research Article

Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F. L., Lockhart, P. J., Bryant, D., … Martin, W. F. (2015). Endosymbiotic origin and differential loss of eukaryotic genes. Nature, 524, 427-432. doi: 10.1038/nature14963

Journal - Research Article

Leigh, J. W., & Bryant, D. (2015). Monte Carlo strategies for selecting parameter values in simulation experiments. Systematic Biology, 64(5), 741-751. doi: 10.1093/sysbio/syv030

Journal - Research Article

Leigh, J. W., & Bryant, D. (2015). POPART: Full-feature software for haplotype network construction. Methods in Ecology & Evolution, 6(9), 1110-1116. doi: 10.1111/2041-210X.12410

Journal - Research Article

Holder, M. T., Lewis, P. O., Swofford, D. L., & Bryant, D. (2014). Variable tree topology stepping-stone marginal likelihood estimation. In M.-H. Chen, L. Kuo & P. O. Lewis (Eds.), Bayesian phylogenetics: Methods, algorithms, and applications. Boca Raton, FL: CRC Press.

Chapter in Book - Research

Bryant, D., & Tupper, P. F. (2014). Diversities and the geometry of hypergraphs. Discrete Mathematics & Theoretical Computer Science, 16(2), 1-20.

Journal - Research Article

Bryant, D. (2014). Statistical flaws undermine pre-Columbian chicken debate. PNAS, 111(35), E3584. doi: 10.1073/pnas.1410797111

Journal - Research Other

Bryant, D., & Kydd, J. (2013). Forty years of model-based phylogeography. In C. Chauve, N. El Mabrouk & E. Tannier (Eds.), Models and algorithms for genome evolution (Computational Biology Vol. 19). (pp. 17-28). London, UK: Springer. doi: 10.1007/978-1-4471-5298-9

Chapter in Book - Research

White, D. J., Bryant, D. J., & Gemmell, N. J. (2013). How good are indirect tests at detecting recombination in human mtDNA? Genes Genomes Genetics, 3(7), 1095-1104. doi: 10.1534/g3.113.006510

Journal - Research Article

Bryant, D., & Tupper, P. F. (2012). Hyperconvexity and tight-span theory for diversities. Advances in Mathematics, 231(6), 3172-3198. doi: 10.1016/j.aim.2012.08.008

Journal - Research Article

Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & Choudhury, A. R. (2012). Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Molecular Biology & Evolution, 29(8), 1917-1932. doi: 10.1093/molbev/mss086

Journal - Research Article

Storey, A. A., Athens, J. S., Bryant, D., Carson, M., Emery, K., deFrance, S., Higham, C., … Walter, R., & Matisoo-Smith, E. (2012). Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures. PLoS ONE, 7(7), e39171. doi: 10.1371/journal.pone.0039171

Journal - Research Article

Bryant, D., & Klaere, S. (2012). The link between segregation and phylogenetic diversity. Journal of Mathematical Biology, 64(1-2), 149-162. doi: 10.1007/s00285-011-0409-5

Journal - Research Article

Siekmann, I., Wagner, L. E., Yule, D., Fox, C., Bryant, D., Crampin, E. J., & Sneyd, J. (2011). MCMC estimation of Markov models for ion channels. Biophysical Journal, 100(8), 1919-1929. doi: 10.1016/j.bpj.2011.02.059

Journal - Research Article

Dagan, T., Roettger, M., Bryant, D., & Martin, W. (2010). Genome networks root the tree of life between prokaryotic domains. Genome Biology & Evolution, 2, 379-392. doi: 10.1093/gbe/evq025

Journal - Research Article

Gray, R. D., Bryant, D., & Greenhill, S. J. (2010). On the shape and fabric of human history. Philosophical Transactions of the Royal Society B, 365(1559), 3923-3933. doi: 10.1098/rstb.2010.0162

Journal - Research Article

Bryant, D., & Steel, M. (2009). Computing the distribution of a tree metric. IEEE/ACM Transactions on Computational Biology & Bioinformatics, 6(3), 420-426. doi: 10.1109/tcbb.2009.32

Journal - Research Article

Bryant, D. (2009). Hadamard phylogenetic methods and the n-taxon process. Bulletin of Mathematical Biology, 71(2), 339-351. doi: 10.1007/s11538-008-9364-8

Journal - Research Article

Bryant, D., Moulton, V., & Spillner, A. (2007). Consistency of the Neighbor-Net algorithm. Algorithms for Molecular Biology, 2, 8. doi: 10.1186/1748-7188-2-8

Journal - Research Article

Bryant, D., & Dress, A. (2007). Linearly independent split systems. European Journal of Combinatorics, 28(6), 1814-1831. doi: 10.1016/j.ejc.2006.04.007

Journal - Research Article

Bruen, T. C., Philippe, H., & Bryant, D. (2006). A simple and robust statistical test for detecting the presence of recombination. Genetics, 172(4), 2665-2681. doi: 10.1534/genetics.105.048975

Journal - Research Article

Huson, D. H., & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology & Evolution, 23(2), 254-267. doi: 10.1093/molbev/msj030

Journal - Research Article

Bryant, D., & Lagergren, J. (2006). Compatibility of unrooted phylogenetic trees is FPT. Theoretical Computer Science, 351(3), 296-302. doi: 10.1016/j.tcs.2005.10.033

Journal - Research Article

Lepage, T., Lawi, S., Tupper, P., & Bryant, D. (2006). Continuous and tractable models for the variation of evolutionary rates. Mathematical Biosciences, 199(2), 216-233. doi: 10.1016/j.mbs.2005.11.002

Journal - Research Article

More publications...