Publications
Submitted papers
T Stadler, JH Degnan. A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree.
B Eldon, JH Degnan. Multiple merger gene genealogies in two species: monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents.
Book Chapters
2010. JH Degnan. Probabilities of gene trees with intraspecific sampling given a species tree. LL Knowles and LS Kubatko (eds), Estimating Species Trees: Practical and Theoretical Aspects. Wiley-Blackwell, pp. 53-78. ISBN 0470526858
Journal articles
2012. JH Degnan, NA Rosenberg, T Stadler. The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235: 45-55
AK Ramanathan, J Nowacki, H Hoffman, K Mclaughlin, P Kelly, JH Degnan. Ode to Cimino. Accepted for J. Vascular Access DOI:10.5301/jva.5000023
2011. M DeGiorgio, JH Degnan, NA Rosenberg. Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics 189: 579-593
2011. ES Allman, JH Degnan, JA Rhodes. Determining species tree topologies from clade probabilities under the coalescent. Determining species tree topologies from clade probabilities under the coalescent. J. Theoretical Biology 289:96-106.
2011. Y Wang and JH Degnan. Performance of matrix represenation with parsimony for inferring species trees from gene trees. Statistical Applications in Genetics and Molecular Biology. Volume 10: Issue 1, Article 21
2011. Y Yu, C Than, JH Degnan, L Nakhleh. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60:138-149.
2011. S Zhu, JH Degnan, and M Steel. Clades, clans and reciprocal monophyly under neutral evolutionary models. Theoretical Population Biology 79:220-227 arXiv:1101.1311
2011. ES Allman, JH Degnan, JA Rhodes. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. J. Mathematical Biology 62: 833-862[arXiv:0912.4472]
2010. C Wang, ZA Szpiech, JH Degnan, M Jakobsson, TJ Pemberton, JA Hardy, AB Singleton, and NA Rosenberg. Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology Volume 9: Issue 1, Article 13.
2010. NA Rosenberg and JH Degnan. Coalescent histories for discordant gene trees and species trees. Theoretical Population Biology 77: 145-151
2010. M DeGiorgio and JH Degnan. Fast and consistent estimation of species trees using supermatrix rooted triples. Molecular Biology and Evolution 27(3):552-569. [author's preprint with supplement, 1.1MB]
2009. JH Degnan and NA Rosenberg. Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends in Ecology and Evolution 24:332-340.
2009. JH Degnan, M DeGiorgio, D Bryant, and NA Rosenberg. Properties of consensus methods for inferring species trees from gene trees. Systematic Biology 58:35-54.
2008. JH Degnan, J Lasky-Su, BA Raby, M Xu, C Molony, EE Schadt, and C Lange. Genomics and genome-wide association studies: An integrative approach to expression QTL mapping. Genomics 92: 129-133.
2008. M Jakobsson, SW Scholz, P Scheet, JR Gibbs, JM VanLiere, HC Fung, ZA Szpiech, JH Degnan, K Wang, R Guerreiro, JM Bras, JC Schymick, DG Hernandez, BJ Traynor, J Simon-Sanchez, M Matarin, A Britton, J van de Leemput, I Rafferty, M Bucan, HM Cann, JA Hardy, NA Rosenberg, and AB Singleton. Genotype, haplotype and copy-number variation in worldwide human populations Nature 451: 998-1003.
2007. K Schneiter, JH Degnan, C Corcoran, X Xu, N Laird. EFBAT: exact family-based association tests. BMC Genetics. 8:86. [software link]
2007. LS Kubatko and JH Degnan. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56:17-24.
2006. JH Degnan and NA Rosenberg. Discordance of species trees with their most likely gene trees. PLoS Genetics 3:762-768.
2005. JH Degnan and LA Salter. Gene tree distributions under the coalescent process. Evolution 59:24-37.[software link]