Research

Broadly, our research leverages a variety of genomic (e.g., genome, transcriptome, microbiome) and observational (e.g., social interaction and association) data, and uses computational approaches to understand the processes shaping organismal diversity. Our major research projects all aim to investigate one or more of the following topics: (1) the forces for shaping evolutionary processes, especially speciation, adaptation, and lineage-specific demographic history; (2) modern and historical aspects of behavioral ecology and social organization, especially those that relate to sex-biased demography and fission-fusion societies; and (3) sex chromosome evolution. We primarily study these phenomena in nonhuman primates, but we also work with a variety of nonprimates, particularly reptiles. In addition, we are engaged in method development to improve the accuracy of genomic analyses and enable high-quality genomic investigations in wild populations. Finally, while most of our research is computational, we both conduct fieldwork and collaborate with other field biologists.

Highlighted

Human Ancestors Interbred with Two Distinct Populations of Distant Relatives

Alan R. Rogers, Md Touhidul Islam, Colin M. Brand, Timothy H. Webster

bioRxiv  ·  23 Mar 2026  ·  doi:10.64898/2026.03.22.713509

introgression ancient-dna genomics

All

2026

Human Ancestors Interbred with Two Distinct Populations of Distant Relatives

Alan R. Rogers, Md Touhidul Islam, Colin M. Brand, Timothy H. Webster

bioRxiv  ·  23 Mar 2026  ·  doi:10.64898/2026.03.22.713509

introgression ancient-dna genomics

2025

Climate, diet, and nutrition drive gut microbiome variation in a fruit-specialist primate

Nina Beeby, Lahitsara Jean Pierre, Razafindraibe Faustin Jean Guy, Rakotonjatovo Justin, Tombotiana Aimé Victor, …, Lotte van den Hout, Jessica M. Rothman, Katherine R. Amato, Timothy H. Webster, Andrea L. Baden

Scientific Reports  ·  01 Jul 2025  ·  doi:10.1038/s41598-025-07399-3

microbiome diet ecology behavior lemurs

Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises

N. Jade Mellor, Timothy H. Webster, Hazel Byrne, Avery S. Williams, Taylor Edwards, Dale F. DeNardo, Melissa A. Wilson, Kenro Kusumi, Greer A. Dolby

Molecular Ecology  ·  01 Jan 2025  ·  doi:10.1111/mec.17600

genomics speciation reptiles adaptation tortoises

2024

Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees

Colin M Brand, Shuzhen Kuang, Erin N Gilbertson, Evonne McArthur, Katherine S Pollard, Timothy H Webster, John A Capra

Genome Biology and Evolution  ·  09 Oct 2024  ·  doi:10.1093/gbe/evae210

genomics speciation chimpanzees-and-bonobos

Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly

Timothy H Webster, Annika Vannan, Brendan J Pinto, Grant Denbrock, Matheo Morales, Greer A Dolby, Ian T Fiddes, Dale F DeNardo, Melissa A Wilson

Genome Biology and Evolution  ·  06 Feb 2024  ·  doi:10.1093/gbe/evae018

genomics reptiles sex-chromosomes

2023

Characterizing fungal communities on Mojave desert tortoises (Gopherus agassizii) in Arizona to uncover potential pathogens

Daniel R. Kollath, Greer A. Dolby, Timothy H. Webster, Bridget M. Barker

Journal of Arid Environments  ·  01 Dec 2023  ·  doi:10.1016/j.jaridenv.2023.105089

microbiome reptiles tortoises pathogens

Genomic and demographic processes differentially influence genetic variation across the human X chromosome

Daniel J. Cotter, Timothy H. Webster, Melissa A. Wilson

PLOS ONE  ·  01 Nov 2023  ·  doi:10.1371/journal.pone.0287609

genomics sex-chromosomes

2022

Estimating bonobo ( Pan paniscus ) and chimpanzee ( Pan troglodytes ) evolutionary history from nucleotide site patterns

Colin M. Brand, Frances J. White, Alan R. Rogers, Timothy H. Webster

Proceedings of the National Academy of Sciences  ·  22 Apr 2022  ·  doi:10.1073/pnas.2200858119

Estimating Pan evolutionary history from nucleotide site patterns

Colin M. Brand, Frances J. White, Alan R. Rogers, Timothy H. Webster

openRxiv  ·  09 Jan 2022  ·  doi:10.1101/2022.01.07.475438

2021

Signatures of adaptive evolution in platyrrhine primate genomes

Hazel Byrne, Timothy H. Webster, Sarah F. Brosnan, Patrícia Izar, Jessica W. Lynch

openRxiv  ·  20 Aug 2021  ·  doi:10.1101/2021.08.19.456368

Comparative genomic analysis of sifakas ( Propithecus ) reveals selection for folivory and high heterozygosity despite endangered status

Elaine E. Guevara, Timothy H. Webster, Richard R. Lawler, Brenda J. Bradley, Lydia K. Greene, …, Daniel S. T. Hughes, Donna M. Muzny, Anne D. Yoder, Kim C. Worley, Jeffrey Rogers

Science Advances  ·  23 Apr 2021  ·  doi:10.1126/sciadv.abd2274

Genomic and demographic processes differentially influence genetic variation across the X chromosome

Daniel J. Cotter, Timothy H. Webster, Melissa A. Wilson

openRxiv  ·  01 Feb 2021  ·  doi:10.1101/2021.01.31.429027

2020

Soft sweeps predominate recent positive selection in bonobos ( Pan paniscus ) and chimpanzees ( Pan troglodytes )

Colin M. Brand, Frances J. White, Nelson Ting, Timothy H. Webster

openRxiv  ·  14 Dec 2020  ·  doi:10.1101/2020.12.14.422788

High-throughput phenotyping methods for quantifying hair fiber morphology

Tina Lasisi, Arslan A. Zaidi, Timothy Harding Webster, Nicholas Bradley Stephens, Kendall Routch, Nina Grace Jablonski, Mark David Shriver

openRxiv  ·  24 Nov 2020  ·  doi:10.1101/2020.11.24.392191

Urine as a high‐quality source of host genomic DNA from wild populations

Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca S. Nockerts, Michael L. Wilson, Anne E. Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

Molecular Ecology Resources  ·  17 Oct 2020  ·  doi:10.1111/1755-0998.13260

Genetic relatedness cannot explain social preferences in black-and-white ruffed lemurs, Varecia variegata

Andrea L. Baden, Timothy H. Webster, Brenda J. Bradley

Animal Behaviour  ·  01 Jun 2020  ·  doi:10.1016/j.anbehav.2020.04.003

Urine as a high-quality source of host genomic DNA from wild populations

Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca S. Nockerts, Michael L. Wilson, Anne E. Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

openRxiv  ·  20 Feb 2020  ·  doi:10.1101/2020.02.18.955377

Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Greer A Dolby, Matheo Morales, Timothy H Webster, Dale F DeNardo, Melissa A Wilson, Kenro Kusumi

Genome Biology and Evolution  ·  01 Feb 2020  ·  doi:10.1093/gbe/evaa016

Virus Discovery in Desert Tortoise Fecal Samples: Novel Circular Single-Stranded DNA Viruses

Joseph P. Orton, Matheo Morales, Rafaela S. Fontenele, Kara Schmidlin, Simona Kraberger, …, Timothy H. Webster, Melissa A. Wilson, Kenro Kusumi, Greer A. Dolby, Arvind Varsani

Viruses  ·  26 Jan 2020  ·  doi:10.3390/v12020143

2019

Genetic relatedness cannot explain social preferences in black-and-white ruffed lemurs ( Varecia variegata )

Andrea L Baden, Timothy H Webster, Brenda J Bradley

openRxiv  ·  10 Oct 2019  ·  doi:10.1101/799825

Positively selected variants in functionally important regions of TLR7 in Alouatta guariba clamitans with yellow fever virus exposure in Northern Argentina

Nicole S. Torosin, Timothy H. Webster, Hernan Argibay, Hebe Ferreyra, Marcela Uhart, Ilaria Agostini, Leslie A. Knapp

openRxiv  ·  05 Aug 2019  ·  doi:10.1101/725333

Comparing the selective landscape of TLR7 and TLR8 across primates reveals unique sites under positive selection in Alouatta

Nicole S. Torosin, Hernan Argibay, Timothy H. Webster, Patrice Showers Corneli, Leslie A. Knapp

openRxiv  ·  19 Jul 2019  ·  doi:10.1101/708008

Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data

Timothy H Webster, Madeline Couse, Bruno M Grande, Eric Karlins, Tanya N Phung, Phillip A Richmond, Whitney Whitford, Melissa A Wilson

GigaScience  ·  01 Jul 2019  ·  doi:10.1093/gigascience/giz074

XYalign: Version 1.1.6

Timothy H. Webster, Madeline Couse, Bruno M. Grande, Eric Karlins, Tanya N. Phung, Phillip A. Richmond, Whitney Whitford, Melissa A. Wilson

Zenodo  ·  10 Apr 2019  ·  doi:10.5281/zenodo.2635885

2018

Successful exome capture and sequencing in lemurs using human baits

Timothy H. Webster, Elaine E. Guevara, Richard R. Lawler, Brenda J. Bradley

openRxiv  ·  18 Dec 2018  ·  doi:10.1101/490839

Bioconda: sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster

Nature Methods  ·  01 Jul 2018  ·  doi:10.1038/s41592-018-0046-7

Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data

Timothy H. Webster, Madeline Couse, Bruno M. Grande, Eric Karlins, Tanya N. Phung, Phillip A. Richmond, Whitney Whitford, Melissa A. Wilson Sayres

openRxiv  ·  14 Jun 2018  ·  doi:10.1101/346940

Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii , version 1.1

Timothy H Webster, Greer A Dolby, Melissa A Wilson Sayres, Kenro Kusumi

PeerJ  ·  31 Jan 2018  ·  doi:10.7287/peerj.preprints.3266v4

2017

EvSex16: Evolutionary Genomics of Sex

Kimberly C Olney, Pooja Narang, Angela M Taravella, Timothy H Webster, Melissa A Wilson Sayres

Journal of Heredity  ·  01 Oct 2017  ·  doi:10.1093/jhered/esx084

Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii , version 1.1

Timothy H Webster, Greer A. Dolby, Melissa Wilson Sayres, Kenro Kusumi

PeerJ  ·  19 Sep 2017  ·  doi:10.7287/peerj.preprints.3266v3

2016

Genomic signatures of sex-biased demography: progress and prospects

Timothy H Webster, Melissa A Wilson Sayres

Current Opinion in Genetics & Development  ·  01 Dec 2016  ·  doi:10.1016/j.gde.2016.08.002

Evolution of dosage compensation in Anolis carolinensis , a reptile with XX/XY chromosomal sex determination

Shawn M. Rupp, Timothy H. Webster, Kimberly C. Olney, Elizabeth D. Hutchins, Kenro Kusumi, Melissa A. Wilson Sayres

Genome Biology and Evolution  ·  09 Nov 2016  ·  doi:10.1093/gbe/evw263

Coprophagy by the semi-habituated chimpanzees of Semliki, Uganda.

Pan Africa News  ·  24 Feb 2016  ·  [no id info]

Grooming hand-clasp by chimpanzees of the Mugiri community, Toro-Semliki Wildlife Reserve, Uganda

Pan Africa News  ·  24 Feb 2016  ·  [no id info]

Chimpanzees at Semliki ignore oil palms

Pan Africa News  ·  24 Feb 2016  ·  [no id info]

Well digging by Semliki chimpanzees: new data on laterality and hydrology

Pan Africa News  ·  24 Feb 2016  ·  [no id info]

2015

Resource seasonality and reproduction predict fission–fusion dynamics in black‐and‐white ruffed lemurs (Varecia variegata)

Andrea L. Baden, Timothy H. Webster, Jason M. Kamilar

American Journal of Primatology  ·  25 Nov 2015  ·  doi:10.1002/ajp.22507

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Allison Y Hsiang, Daniel J Field, Timothy H Webster, Adam DB Behlke, Matthew B Davis, Rachel A Racicot, Jacques A Gauthier

BMC Evolutionary Biology  ·  20 May 2015  ·  doi:10.1186/s12862-015-0358-5

2014

Selective insectivory at Toro-Semliki, Uganda: Comparative analyses suggest no ‘savanna’ chimpanzee pattern

Timothy H. Webster, William C. McGrew, Linda F. Marchant, Charlotte L.R. Payne, Kevin D. Hunt

Journal of Human Evolution  ·  01 Jun 2014  ·  doi:10.1016/j.jhevol.2014.02.005

AVPR1A Variation in Chimpanzees (Pan troglodytes): Population Differences and Association with Behavioral Style

Stephanie F. Anestis, Timothy H. Webster, Jason M. Kamilar, M. Babette Fontenot, David P. Watts, Brenda J. Bradley

International Journal of Primatology  ·  11 Jan 2014  ·  doi:10.1007/s10764-013-9747-z

2012

The Apolipoprotein E (APOE) Gene Appears Functionally Monomorphic in Chimpanzees (Pan troglodytes)

Annick M. McIntosh, Calvin Bennett, Dara Dickson, Stephanie F. Anestis, David P. Watts, Timothy H. Webster, M. Babette Fontenot, Brenda J. Bradley

PLoS ONE  ·  24 Oct 2012  ·  doi:10.1371/journal.pone.0047760