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 :

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

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)

Teaching Schedule:

Spring, 2017: STAT474/574: Biostatistics


Week 1 notes (includes first hw at end of slides)

Week 2 notes (new slides added for Friday, uploaded 1/26/17)

Week 3 notes uploaded 1/31/17

small data set

leukemia data

Week 4 notes uploaded 2/7/17

Week 6 notes uploaded 2/24/17

Week 7 notes uploaded 2/27/17

Homework 3, due Wednesday, 3/8/2017

recidivism data

Week 8 notes uploaded 3/5/17

P-Value Statement from ASA

Week 9 notes uploaded 3/20/17

Week 11 notes uploaded 4/5/17

Week 12 notes uploaded 4/10/17

Week 13 notes uploaded 4/14/17 (this will be added to)

Week 14

Spring 2017: STAT453/553: Statistical Inference


Homework 1, due Monday, 1/30/2017 (ignore the due date on the pdf)

Homework 2, due Wednesday, 2/8/2017. This homework includes some work in R. If you have not used R, get started early to make sure the R coding won't cause problems.

R code to illustrate plotting a theoretical density over a histogram

Homework 3, due Friday, 3/2/2017 (ignore the due date on the pdf)

Homework 4, due Friday, due 3/22/2017

Homework 5, due Friday, due 4/17/2017

R code for Rao-Blackwell example

Fall, 2016: Math 441/STAT461/STAT561: Probability

Syllabus for Math441/Stat461/Stat561

Probability HW1 due 8/31/16 (HW1 Solution)

Probability HW2 due 9/9/16 (HW2 Solution)

Probability HW3 due 9/19/16 (HW3 Solution)

Probability HW4 due 9/28/16 (HW4 Solution)

Formula sheet for Probability TEST 1, 9/30/16

Practice Test (Hastily made solutions at 1am, updated at 1:30pm, Thursday--email me if there are more typos!)

Probability HW5 due 10/17/16 (HW5 Solution)

Probability HW6 due 10/25/16 (Solutions)

Probability HW7 due 11/9/16 (Solutions)

REMINDER: TEST 2 on 11/11/16

Practice Test (Solutions that probably have typos...)

R code to illustrate plotting a theoretical density over a histogram

Probability HW8 due 11/23/16

Probability HW9 due 12/7/16

Fall, 2016: STAT579: Statistical Phylongenetics

Syllabus for STAT579: Statistical Phylogenetics

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

Anastasiia Kim, PhD student, working on ranked gene trees

Huan Jiang, PhD student, Thesis: Modeling trait evolutionary processes with more than one gene

Ayed Alanzi, PhD student, Thesis: Inferring rooted species trees from unrooted species trees

Former Students at University of New Mexico

Mina Lee, MS student, thesis completed summer 2016 (Compliance Analyst, Fidelity Investments)

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

Journal articles

2016. S Zhu and JH Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In press, Systematic Biology , doi: 10.1093/sysbio/syw097.

2016. ES Allman, JH Degnan, JA Rhodes. Species tree inference from gene splits by Unrooted STAR methods. In press, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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]

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