About

John Huelsenbeck is a Professor of Integrative Biology at the Center for Computational Biology. His research interests include biostatistics and statistics, clinical data analysis, evolutionary biology and phylogenetics, genomics and genetics, machine learning and algorithms, and population genetics. Huelsenbeck is particularly interested in the phylogeny problem, which involves reconstructing the genealogical history of life from comparison of DNA sequences. His work also encompasses the genetics of adaptation, computational biology, and evolutionary biology, contributing to the understanding of evolutionary processes through computational and statistical methods.

Research topics

• Biology
• Evolutionary biology
• Computer science
• Statistics
• Computational biology

Selected publications

• Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process

  Zenodo (CERN European Organization for Nuclear Research) · 2026-01-16

  otherOpen access

  Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model—called the birth-death-shift (BDS) process—in which diversification rates may vary across both extant and extinct (and/or unsampled) lineages. We estimate the parameters of this model in a Bayesian framework from phylogenies of exclusively extant species. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical (primates) dataset, which reveals that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a mathematically coherent model.

  PublisherDOI

• Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process

  Zenodo (CERN European Organization for Nuclear Research) · 2026-01-16

  otherOpen access

  Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model—called the birth-death-shift (BDS) process—in which diversification rates may vary across both extant and extinct (and/or unsampled) lineages. We estimate the parameters of this model in a Bayesian framework from phylogenies of exclusively extant species. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical (primates) dataset, which reveals that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a mathematically coherent model.

  PublisherDOI

• Inferring Branch-Specific Rates of Lineage Diversification Under the Birth–Death-Shift Process

  Systematic Biology · 2026-01-23 · 1 citations

  articleOpen access

  Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model-called the birth-death-shift (BDS) process-in which diversification rates may vary across both extant and extinct and unsampled lineages. We estimate the parameters of this model in a Bayesian statistical framework from phylogenies of exclusively extant lineages. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical primates dataset, which reveal that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a statistically coherent model.

  PublisherDOI

• Phylogenetic inference from cognate word forms

  Journal of Language Evolution · 2026-01-01

  articleOpen accessSenior author

  Abstract Linguistic phylogenies are commonly inferred from abstract cognate classifications that encode relationships among lexemes. Although widespread, this practice has well-recognized limitations: it discards the phylogenetic signal contained in segmental word forms; restricts the range of evolutionary questions that can be addressed; and treats cognacy judgments, which are hypotheses, as observed data. We introduce a comparative framework that addresses these limitations by modeling the evolution of aligned cognate word forms directly. Our approach adapts the TKF91 model of molecular evolution, originally developed to account for insertion and deletion events in DNA sequences, to the domain of linguistic data. By operating on segmental strings rather than abstract character codings, the framework enables phylogenetic inference from observable word forms and supports quantitative investigation of sound change. We demonstrate its utility through analyses that illuminate patterns of segmental stability and the evolution of phonological inventories.

  PublisherDOI

• Simulated Phylogenies for: Inferring branch-specific rates of lineage diversification under the birth-death-shift process

  Open MIND · 2025-12-09

  dataset

  Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model—called the birth-death-shift (BDS) process—in which diversification rates may vary across both extant and extinct (and/or unsampled) lineages. We estimate the parameters of this model in a Bayesian framework from phylogenies of exclusively extant species. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical (primates) dataset, which reveals that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a mathematically coherent model.

  DOI

• Principal Components Analysis fails to recover phylogenetic structure in hominins

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-31

  preprintOpen accessSenior author

  Abstract Objectives Paleoanthropologists often utilize geometric morphometrics and principal components analysis (PCA) to interpret shape variation within the hominin fossil record. It is common practice to interpret proximity in principal components (PC) space among taxa as indicative of not just morphological, but also phylogenetic affinity. This interpretation, however, has not been directly evaluated for hominins. Materials and Methods First, we inferred the posterior distribution of hominin phylogenetic trees and subsampled trees from this distribution. On these phylogenies, we simulated 2D and 3D geometric morphometric datasets and traditional morphological datasets, containing traits analogous to measurements of size or length, with varying numbers of landmarks or traits and evolutionary rates. On each dataset, we conducted a PCA and used neighbor-joining to infer evolutionary relationships from the PC scores of each taxon. We measure the difference between the PCA tree and sampled tree with subtree pruning and regrafting distance and Robinson-Foulds distance. Results PCA trees inferred from traditional morphometric data were identical to the sampled tree in 0.11% of datasets when we only considered PC axes 1 and 2, and in 2.9% of datasets when we considered all axes. No PCA tree inferred from any of the 2,400,000 shape datasets was identical to the sampled tree, regardless of the number of axes. Discussion Phylogenetic interpretations of the hominin fossil record based on proximity in PC space are inherently flawed and likely to be erroneous. Arguments in the hominin systematics literature based on PCA should therefore be reevaluated using phylogenetically-informed alternatives.

  PublisherOA PDFDOI

• Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics

  PeerJ · 2021-11-02 · 21 citations

  articleOpen accessSenior author

  In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.

  PublisherDOI

• A COMPARATIVE ANALYSIS OF DE NOVO TRANSCRIPTOME ASSEMBLY TO UNDERSTAND THE ABIOTIC STRESS ADAPTATION OF DESERT PLANTS IN SAUDI ARABIA

  Applied Ecology and Environmental Research · 2021-01-01 · 8 citations

  articleOpen accessSenior author

  Rhazya stricta, Senna italica, and Zygophyllum simplex are important desert plants of Saudi Arabia with great economic and medicinal value. However, their tolerance and survival mechanisms under combined abiotic stresses such as high temperature, high salinity, and drought are not well understood. In order to investigate the potential molecule mechanism of abiotic stress tolerance in these plants, we used de novo transcriptome assembly and their comparative analysis. This study used leaf tissues to construct three cDNA libraries of these plants and then generated RNA-seq data by the Illumina HiSeq2000 platform. Sequencing reads were de novo assembled to generate: (a) 71,116 unigenes in R. stricta; (b) 59,274 unigenes in S. italica; (c) 70,300 unigenes in Z. simplex. Furthermore, the unigenes from these plants were annotated and analyzed with different databases. A comparative analysis of KEGG pathways identified several common pathways induced in these plants, including "Plant-pathogen interaction", "Plant hormone signal transduction", "Spliceosome", "RNA transport", and "Protein processing in endoplasmic reticulum", which may play an important role in combined abiotic drought, heat, and salinity stress. Finally, a comparative analysis of transcriptional regulators identified C2H2, C3H, CCHC(Zn), MYB-HB-like, PHD, WD40-like, and bHLH as common Transcription Factors responsible for abiotic stress tolerance in these plants. Our study revealed key factors involved in abiotic stress tolerance, which could be applied to develop high-yield transgenic crops capable of growing under combined abiotic stresses in the field.

  PublisherDOI

• DIVERSITY PROFILING OF ASSOCIATED BACTERIA FROM THE SOILS OF STRESS TOLERANT PLANTS FROM SEACOAST OF JEDDAH, SAUDI ARABIA

  Applied Ecology and Environmental Research · 2020-01-01 · 7 citations

  articleOpen accessSenior author

  Soils associated with halophytic plants naturally contain a number of ubiquitous microbial communities facing limited nutrients and harsh environmental conditions including salinity and drought. In the present study, metagenomic sequencing of 16S rRNA was used to analyze and classify bacterial communities of the soil associated with halophytic plants Halopeplis perfoliata and Zygophyllum album collected from various soil samples located in the seacoast of Jeddah province, Saudi Arabia. Analysis of the 16S rRNA sequences at the taxonomic phylum-level revealed that bacterial communities in the soil samples belonged to nineteen phyla, and the most abundant were highlighted for further analysis. Results indicated that the most common phyla were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Deinococcus-Thermus, Gemmatimonadetes, and an unclassified phyla. At the taxonomic genus-level, the most abundant ones were highlighted for further analysis which include Marinicauda, Altererythrobacter, Maricurvus, Marinobacter, Porticoccus, Salicola, and three unclassified genera were found belonging to Proteobacteria. Actinopolyspora, Geodermatophilus, Propionibacterium, Euzebya and four unclassified ones were found associated with Actinobacteria.

  PublisherOA PDFDOI

• Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics

  Archives of Microbiology · 2020-11-24 · 6 citations

  articleSenior author
  PublisherDOI

Recent grants

• Developing a platform for Bayesian inference of phylogeny

  NSF · $357k · 2009–2013

• Extending Bayesian Phylogenetic Analysis

  NIH · $2.1M · 2004–2014

• Model Choice and Model Averaging in Molecular Phylogenetics

  NSF · $207k · 2006–2009

Frequent coauthors

• Michael J. Landis

  Washington University in St. Louis

  85 shared

• Tracy A. Heath

  82 shared

• Bastien Boussau

  Laboratoire de Biométrie et Biologie Evolutive

  81 shared

• Sebastian Höhna

  Ludwig-Maximilians-Universität München

  79 shared

• Fredrik Ronquist

  Swedish Museum of Natural History

  64 shared

• Fredrik Ronquist

  Stockholm University

  25 shared

• Rasmus Nielsen

  University of Copenhagen

  20 shared

• Brian R. Moore

  Children's Medical Center

  18 shared

Education

• Ph.D., Zoology

  University of Texas at Austin

  1995

• M.A., Geology

  University of Texas at Austin

  1992

• B.A., Paleontology

  University of California Berkeley

  1988