Home Page of James Degnan
Dr. James Degnan
Department of Mathematics and Statistics
The University of New Mexico
Albuquerque, NM  87131
Office: SMLC 342
Phone: NULL
E-Mail: jamdeg@unm.edu

Education Information :

PhD, University of New Mexico, 2005

Software links :

RTIST by Gleb Zhelezov, computes the exact optimal and sub-optimal median trees to infer species trees using rooted triples. See Zhelezov and Degnan (2022), Bioinformatics.

PRANC by Anastasiia Kim, computes ranked and unranked gene tree topology probabilities, and can infer species trees from ranked gene tree probabilities. See Kim, Rosenberg, Degnan (2020), Molecular Biology and Evolution, and Kim and Degnan (2020), Bioinformatics

hybrid-Lambda (by Sha Zhu, replaces COAL functionality for simulating gene trees in species trees, plus allows simulating in hybridization networks and/or Lambda-coalescent models)

Paper for hybrid-Lambda

hybrid-coal (by Sha Zhu, replaces COAL functionality for computing gene tree probabilities in species trees or species networks), see Zhu and Degnan (2017) Systematic Biology

COAL files (unzip and type "make" at a linux/Mac OS X prompt. I've had trouble running this on Mac recently.)

Poe Presentation

Teaching Schedule:

Office hours: James 1pm-3pm Wednesdays

Email: jamdeg@unm.edu

STAT453/STAT553 (Spring 2023)

Previous courses:

Summer 2014, MCTP: coalescent R tutorial, Biology notes, Probability notes, align565.txt, temptrees.txt, drift.r, wf.r, data.zip (includes alignment files)

Spring 2014: STAT579, Statistics in Genetics, TR 9:30, ASM-1064


My research focuses on statistical applications in genetics and evolutionary biology. Particular areas have included coalescent theory and its applications, phylogenetics, and human genetics.


Current Students at University of New Mexico

Jaimasan Sutton, MS student

Mary Hopkins, MS student, Modeling trait evolution

Karen Shore, PhD student, missingness in longitudinal data

Former Students at University of New Mexico, (what they did next...)

Md Rashidul Hasan, PhD student, probabilistic models of social networks

Jonathan Odumegwu, Ph.D. Summer 2022, Gene Tree Heterogeneity (Visiting Assistant Professor, New York University)

Sarah Alver, Ph.D. Spring 2022, Measurement Error Modeling Applied to Phylogenetic Inference and Parametric Bootstrap Approach to Multifactor ANOVA Models with Unequal Variances and Unbalanced Data (Postdoc, Fred Hutchinson Cancer Center)

Cristina Murray-Krezan, Ph.D., Spring 2021, Extension of the Two-Step Approach for Informative Dropout in Survival Analysis (Assistant Professor, Univeristy of Pittsburgh)

Anastasiia Kim, Ph.D., Summer 2020, Maximum likelihood estimation of speciestrees and anomaly zone detection usingranked gene trees (Postdoc at Los Alamos National Labs)

Huan Jiang, Ph.D. Spring 2017, Thesis: Modeling trait evolutionary processes with more than one gene, (biostatistician for DCI Dialysis Clinic, Inc)

Ayed Alanzi, Ph.D., Spring 2017, Thesis: Inferring rooted species trees from unrooted species trees (faculty member, Majmaah University, Saudi Arabia)

Xingya Ma, MS student, COVID-19 modeling

Nichole Fluke, M.S. student, COVID-19 modeling

Morris Goodrich, M.S., Summer 2022, Neural Network Algorithms as Nonparametric Regression

Xingya Ma, M.S., Summer 2022, Mitigation impact of statewide non-pharmaceutical policies on COVID-19: An application of infectious disease transmission model and partially observed Markov process to New Mexico

Tabytha Perez, M.S. Summer 2022, Effect of phylogeny misestimation on estimating trait evolution parameters

Aaron Segura, M.S. Spring 2022, Machine Learning Model Comparison and ARMA Simulation of Exhaled Breath Signals Classifying COVID-19 Patients

Rick Haaker, M.S., Spring 2022, Predictive Model for Radium-226 Concentrations

Eunice Choi, M.S., Spring 2019, Assessing the efficacy of Home-Based Renal Care using Propensity Scores (Biostatistician and UNM Health Sciences)

Mina Lee, M.S., Summer 2016, Application of Model Selection Techniques and Measures of Agreement to Advertising Data (Compliance Analyst, Fidelity Investments)

Bibiana Seng, B.S. Honors student, Spring 2019, A Comparison of Clustering Algorithms and1Identification Methods on Genomic Variants to Compare Modern Dogs and Wolves (PhD student, Penn State University)

Kyle Laktasic, B.S., CTSP summer 2019, project for analyzing text data, 2019

Andrew Hollis, B.S. Honors, Spring 2018, Clustering and Summarization of Large Document Sets, (PhD student, NC State)

Former Students at University of Canterbury

Joe Zhu, Phd, 2013 (postdoc at Oxford Univeristy)

Sam Ramsay, Summer student, 2012-2013

Fiona Morrison, Honours, 2011

James Cho, Summer scholarship, 2010-2011

Yuancheng Wang, MS, 2010 (PhD student, Massey University, New Zealand)

Joe Zhu, Summer scholarship, 2009-2010 (PhD student, University of Canterbury)

Joe Zhu, Honours, 2009


Book Chapters

2016. JH Degnan. Consensus Methods, Phylogenetic. Encyclopedia of Evolutionary Biology 1, 341-346. Oxford: Academic Press

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

Refereed Conference Proceedings

2013. JH Degnan. Evaluating variations on the STAR algorithm for relative efficiency and sample sizes needed to reconstruct species trees. Pacific Symposium in Biocomputing 18:262-272

2021. MR Hasan, D Saha, FA Chowdhury, J Degnan, A Mueen. DiffuScope: inferring post-specific diffusion network. Proceedings of the 2021 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, 407-415.

Journal articles

2024. B Wagner, TS Ing, M-E Roumelioti, Raminam , CP Argyropoulos, SQ Lew, ML Unruh, RI Dorin, JH Degnan, AH Tzamaloukas. Hypernatremia in Hyperglycemia: Clinical Features and Relationship to Fractional Changes in Body Water and Monovalent Cations during Its Development. J. Clinical Medicine 13:1957.

2023. J DeAguero, T Howard, D Kusewitt, A Brearley, A-M Ali, JH Degnan, S Jett, J Watt, GP Escobar, K Dokladny, B Wagner. The onset of rare earth metallosis begins with renal gadolinium-rich nanoparticles from magnetic resonance imaging contrast agent exposure. Scientific Reports 13: 2025.

2022. G Zhelezov, JH Degnan. Trying out a million genes to find the perfect pair with RTIST. Bioinformatics doi:10.1093/bioinformatics/btac349

2021. ARA Alanzi, JH Degnan. Statistical inconsistency of the unrooted minimize deep coalescence criterion. PLOS ONE 10.1371/journal.pone.0251107

2021. A Kim, JH Degnan. Heuristics for unrooted, unranked, and ranked anomaly zones under birth-death models. Molecular Phylogenetics and Evolution 161, doi:10.1016/j.ympev.2021.107162

2020. A Kim, JH Degnan. PRANC: ML species tree estimation from the ranked gene trees under coalescence. Bioinformatics 36, 4819-4821.

2020. A Kim, NA Rosenberg, JH Degnan. Probabilities of unranked and ranked anomaly zones under birth-death models. Molecular biology and evolution 37, 1480-1494.

2020. MZ S Gerlach, C Mermier, L Kravitz, J Degnan, L Dalleck. Comparison of treadmill and cycle ergometer exercise during cardiac rehabilitation: a meta-analysis. Archives of Physical Medicine and Rehabilitation 101, 690-699.

2020. HC Palm, JH Degnan, SD Biefeld, AL Reese, E Espey, LG Hofler. An initiative to implement immediate postpartum long-acting reversible contraception in rural New Mexico. American Journal of Obstetrics and Gynecology 222, S911.e1-7.

2020. JH Degnan. Meng and Kubatko (2009): Modeling hybridization with coalescence. Theoretical Population Biology 133, 36-37.

2018. JH Degnan. Modeling hybridization under the network multispecies coalescent. Systematic Biology 67, 786-799.

2018. ES Allman, JH Degnan, JA Rhodes. Species tree inference from gene splits by Unrooted STAR methods. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15, 337-342.

2018. ES Allman, JH Degnan, and JA Rhodes. Split probabilities and species tree inference under the multispecies coalescent model. Bulletin of Mathematical Biology 80 (1), 64-103.

2017. ARA Alanzi and JH Degnan. Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation. In press at Molecular Phylogenetics and Evolution. 116, 13-24.

2017. S Zhu and JH Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. Systematic Biology , 66, 283-298.

2016. T Stadler, JH Degnan, NA Rosenberg. Does gene tree discordance explain the mismatch between macroevolutionary models and empirical patterns of tree shape and branching times? Systematic Biology 65, 628-639.

2015. JH Degnan, JA Rhodes. There are no caterpillars in a wicked forest. Theoretical Population Biology 105, 17-23.

2015. S Zhu, JH Degnan, SJ Goldstien, B Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. BMC Bioinformatics 16, 292.

2014. M DeGiorgio and JH Degnan. Robustness to divergence time underestimation when inferring species trees from estimated gene trees. Systematic Biology 63: 66-82.

2013. JH Degnan. Anomalous unrooted gene trees. Systematic Biology 62, 574-590. doi:10.1093/sysbio/syt023 Supplemental files

2013. ES Allman, JH Degnan, JA Rhodes. Species tree inference by the STAR method and its generalizations. J. Computational Biology 20, 50-61. doi:10.1089/cmb.2012.0101.

2012. JH Degnan, NA Rosenberg, T Stadler. A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9, 1558-1568

2012. T Stadler, JH Degnan. A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. Algorithms for Molecular Biology 7:7 arXiv:1203.0204

2012. B Eldon, JH Degnan. Multiple merger gene genealogies in two species: monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents. Theoretical Population Biology 82, 117-130, doi:10.1016/j/tpb.2012.05.001

2012. Y Yu, JH Degnan, L Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics 8:e1002660

2012. JH Degnan, NA Rosenberg, T Stadler. The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235, 45-55

2012. AK Ramanathan, J Nowacki, H Hoffman, K Mclaughlin, P Kelly, JH Degnan. Ode to Cimino. J. Vascular Access 13, 180-186. 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]

Department of Mathematics and Statistics       University of New Mexico      Humanities 415     Albuquerque     NM     87131