UC Spark

Dr James Degnan

Mathematics and Statistics

Fields of Research

  • phylogenetics
  • population genetics

Researcher Summary

My research has focused on applying statistics to problems in evolutionary biology.  My biggest contributions have been at the intersection of population genetics, which typically models single populations, and phylogenetics, in which the goal is to infer evolutionary trees describing multiple populations or species.

Subject Area: Disciplines

Research Groups

Affiliations

Publications


Journal Article
  • Degnan, J.H., Rosenberg, N.A. and Stadler, T. (2012) A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(6): 1558-1568. http://dx.doi.org/10.1109/TCBB.2012.110.
  • Stadler, T. and Degnan, J.H. (2012) A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. Algorithms for Molecular Biology 7: 7. http://dx.doi.org/10.1186/1748-7188-7-7.
  • Ramanathan, A.K., Nowacki, J., Hoffman, H., Mclaughlin, K., Kelly, P. and Degnan, J.H. (2012) An Ode to Cimino. The Journal of Vascular Access 13(3): 180-186. http://dx.doi.org/10.5301/jva.5000023.
  • Eldon, B. and Degnan, J.H. (2012) Multiple merger gene genealogies in two species: Monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents. Theoretical Population Biology 82(2): 117-130. http://dx.doi.org/10.1016/j.tpb.2012.05.001.
  • Yu, Y., Degnan, J.H. and Nakhleh, L. (2012) The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics 8(4): e1002660. http://dx.doi.org/10.1371/journal.pgen.1002660.
  • Yu, Y., Than, C., Degnan, J.H. and Nakhleh, L. (2011) Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60(4): 138-149. http://dx.doi.org/10.1093/sysbio/syq084.
  • Allman, E.S., Degnan, J.H. and Rhodes, J.A. (2011) Determining species tree topologies from clade probabilities under the coalescent. Journal of Theoretical Biology 289: 96-106. http://dx.doi.org/10.1016/j.jtbi.2011.08.006.
  • Allman, E.S., Degnan, J.H. and Rhodes, J.A. (2011) Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. Journal of Mathematical Biology 62(6): 833-862. http://dx.doi.org/10.1007/s00285-010-0355-7.
  • Wang, Y. and Degnan, J.H. (2011) Performance of Matrix Representation with Parsimony for Inferring Species from Gene Trees. Statistical Applications in Genetics and Molecular Biology 10(1): Article 21. http://dx.doi.org/10.2202/1544-6115.1611.
  • Wang, C., Szpiech, Z.A., Degnan, J.H., Jakobsson, M., Pemberton, T.J., Hardy, J.A., Singleton, A.B. and Rosenberg, N.A. (2010) Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis. Statistical Applications in Genetics and Molecular Biology 9(1): 1-20. http://dx.doi.org/10.2202/1544-6115.1493.
  • DeGiorgio, M. and Degnan, J.H. (2010) Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples. Molecular Biology and Evolution 27(3): 552-569. http://dx.doi.org/10.1093/molbev/msp250.
  • Degnan, J.H., DeGiorgio, M., Bryant, D. and Rosenberg, N.A. (2009) Properties of Consensus Methods for Inferring Species Trees from Gene Trees. Systematic Biology 58(1): 35-54. http://dx.doi.org/10.1093/sysbio/syp008.
  • Degnan, J.H., Lasky-Su, J., Raby, B.A., Xu, M., Molony, C., Schadt, E.E. and Lange, C. (2008) Genomics and genome-wide association studies: An integrative approach for expression QTL mapping. Genomics 92: 129-133. http://dx.doi.org/10.1016/j.ygeno.2008.05.012.
  • Jackobsson, M., Scholz, S.W., Scheet, P., Gibbs, J.R., VanLiere, J.M., Fung, H-C., Spiezch, J.A., Degnan, J.H., Wang, K., Guerreiro, R., Bras, J.M., Schymick, J.C., Hernandez, D.G., Traynor, B.J., Simon-Sanchez, J., Matarin, M., Britton, A., van de Leemput, J., Rafferty, I., Bucan, M., Cann, H.M., Hardy, J.A., Rosenberg, N.A. and Singleton, A.B. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003. http://dx.doi.org/10.1038/nature06472.
Conference Contribution - Poster presentation
  • DeGiorgio, M. and Degnan, J.H. (2009) Rescuing concatenation with maximum likelihood using supermatrix rooted triples. Philadelphia, PA, USA: 9th Workshop on Algorithms in Bioinformatics (WABI 2009), 12-13 Sep 2009.
  • Degnan, J. and Kubatko, L. (2008) Distributions of gene tree branch lengths under coalescence. Barcelona, Spain: Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 08), 5-8 Jun 2008.
Additional Publications
  • DeGiorgio, M., Jakobsson, M., Degnan, J.H. and Rosenberg, N.A. (2010) Explaining patterns of human genetic variation rising coalescent-based models of human origins. Albuquerque, NM, USA: 79th Annual Meeting of the American-Association-of-Physical-Anthropologists, 14-17 Apr 2010. In American Journal of Physical Anthropology 141(S50) 93.
  • Degnan, J.H. (2010) Probabilities of gene trees topologies with intraspecific sampling given a species tree. In L.L. Knowles and L.S. Kubatko (Ed.), Estimating Species Trees: Practical and Theoretical Aspects: 53-77. Hoboken, NJ: Wiley-Blackwell.
  • Degnan, J.H., DeGiorgio, M., Bryant, D. and Rosenberg, N.A. (2007) Coalescent consequences for consensus cladograms. San Diego, CA, USA: Fifth Annual RECOMB Satellite Workshop on Comparative Genomics, 16-18 Sep 2007.