Publications

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) 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 primates

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

Signatures of adaptive evolution in platyrrhine primate genomes

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

Proceedings of the National Academy of Sciences  ·  22 Aug 2022  ·  doi:10.1073/pnas.2116681119

genomics adaptation primates

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

genomics chimpanzees-and-bonobos introgression primates speciation

2021

High-throughput phenotyping methods for quantifying hair fiber morphology

Tina Lasisi, Arslan A. Zaidi, Timothy H. Webster, Nicholas B. Stephens, Kendall Routch, Nina G. Jablonski, Mark D. Shriver

Scientific Reports  ·  01 Jun 2021  ·  doi:10.1038/s41598-021-90409-x

methods hair

Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity

Tanya N. Phung, Timothy H. Webster, Elizabeth Lenkiewicz, Smriti Malasi, Mariacarla Andreozzi, Ann E. McCullough, Karen S. Anderson, Barbara A. Pockaj, Melissa A. Wilson, Michael T. Barrett

Scientific Reports  ·  19 May 2021  ·  doi:10.1038/s41598-021-90170-1

genomics cancer

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

genomics adaptation primates lemurs diet ecology

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  ·  01 Jan 2021  ·  doi:10.1111/1755-0998.13260

genomics methods chimpanzees-and-bonobos primate

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

bioRxiv  ·  14 Dec 2020  ·  doi:10.1101/2020.12.14.422788

genomics primates adaptation chimpanzees-and-bonobos speciation

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

Molecular Phylogenetics and Evolution  ·  01 Nov 2020  ·  doi:10.1016/j.ympev.2020.106920

genomics primates adaptation pathogens sex-chromosomes

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, Hernán Argibay, Candelaria Sanchez Fernandez, Hebe Ferreyra, Marcela Uhart, Ilaria Agostini, Leslie A. Knapp

American Journal of Physical Anthropology  ·  25 Jun 2020  ·  doi:10.1002/ajpa.24086

genomics primates adaptation pathogens sex-chromosomes

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

lemurs fission-fusion behavior primates

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

genomics tortoises reptiles

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

tortoises reptiles microbiome pathogens

2019

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

methods genomics sex-chromosomes

2018

Successful exome capture and sequencing in lemurs using human baits

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

bioRxiv  ·  18 Dec 2018  ·  doi:10.1101/490839

genomics methods primates lemurs

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

methods genomics

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

genomics reptiles tortoises

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

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  ·  01 Jan 2017  ·  doi:10.1093/gbe/evw263

genomics sex-chromosomes reptiles

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

review genomics sex-chromosomes

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]

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  ·  01 Feb 2016  ·  doi:10.1002/ajp.22507

fission-fusion behavior primates lemurs

2015

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

reptiles

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

primates behavior culture chimpanzees-and-bonobos diet

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

primates behavior chimpanzees-and-bonobos genetics

2013

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

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

Pan Africa News  ·  01 Jun 2013  ·  [no id info]

primates behavior culture chimpanzees-and-bonobos

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

primates chimpanzees-and-bonobos genetics

2010

Chimpanzees at Semliki ignore oil palms

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

Pan Africa News  ·  01 Dec 2010  ·  [no id info]

primates behavior culture chimpanzees-and-bonobos diet

2009

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

Timothy H. Webster, Phineas R. Hodson, Kevin D. Hunt

Pan Africa News  ·  01 Jul 2009  ·  [no id info]

primates behavior culture chimpanzees-and-bonobos

2008

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

Charlotte L. R. Payne, Timothy H. Webster, Kevin D. Hunt

Pan Africa News  ·  01 Dec 2008  ·  [no id info]

primates behavior culture chimpanzees-and-bonobos diet