THE Applied Phylogenetics Lab at USC


We’re a diverse group of people, with a diverse set of backgrounds, interests, and expertise. We are united by a shared passion for applying rigorous quantitative reasoning and evolutionary principles to understand biological phenomena. We are located in the University of Southern California’s Department of Quantitative and Computational Biology, the oldest, and one of the most recognized, computational biology groups in the US. And we live, work, and play in Los Angeles, the most interesting city in the world.

Dr. Matt Pennell

Associate Professor

Dr. Matt Pennell is an Associate Professor of Quantitative and Computational Biology and Associate Professor of Biological Sciences at the University of Southern California. He earned his Ph.D. in Bioinformatics and Computational Biology from the University of Idaho, where he worked under the supervision of Dr. Luke Harmon. He then moved to the University of British Columbia to be a Izaak Killam/NSERC Postdoctoral Fellow, working with Dr. Sally Otto, and subsequently, a faculty member in the Department of Zoology from 2016-2022. In his research, he uses phylogenetic trees, graphical depictions of historical relationships, to study evolution at multiple scales—from the grandest (e.g., the origin of major groups of organisms) to the smallest (e.g., the transmission of viruses and the development of the adaptive immune system within an individual) of scales. While superficially disparate, these projects all revolve around a few common themes: he aims to define the outer boundaries of our knowledge and understand what we can and cannot learn about evolution from different types of data. In recognition of his contributions, he was awarded the Theodosius Dobzhansky Prize from the Society for the Study of Evolution, the Jasper Loftus-Hills Young Investigator Prize from the American Society of Naturalists, and a Canada Research Chair from the Government of Canada.

Current Lab members

Dr. Josh Schraiber

Lab Member

Dr. Schraiber is working on mathematical models at the intersection of macroevolution and population genetics

Dr. Daohan “Rex” Jiang

Lab Member

Dr. Jiang combines simulations and empirical analyses to understand evolutionary variation in transcription and translation

Dr. Alex Cope

Lab Member

Dr. Cope is developing new approaches for analyzing comparative transcriptomic and proteomic data

Rituparna Banerjee

Lab Member

Rituparna (UBC BIOINF.) is developing new mathematical models to understand the co-evolution of viruses and B-cells

Kat Voss

Lab Member

Kat (USC CBB) is applying evolutionary approaches to understand variation in immunoglobulins

Yixin Zhu

Lab Member

Yixin (USC CBB) is applying evolutionary approaches to understand variation in immunoglobulins

Lab Alumni

Dr. Chris Muir

Lab Alumni

Dr. Muir studied the evolutionary processes that generate diversity in plant ecophysiology

Dr. Ailene MacPherson

Lab Alumni

Dr. Ailene MacPherson derived mathematical models that predicted phylogenetic tree shape from epidemiological process.

Dr. Francisco Henao Diaz

Lab Alumni

Dr. Henao Diaz (Ph.D., 2022, UBC) investigated the footprint of diversification dynamics on phylogenetic trees and biodiversity gradients.

Dr. Katrina Kaur

Lab Alumni

Dr. Kaur (Ph.D., 2022, UBC) investigated the influence of species interactions on diversification dynamics.

Fiel Dimayacyac

Lab Alumni

Fiel (M.Sc. 2022, UBC) assessed the performance of phylogenetic models for describing the evolutionary dynamics of gene expression.

Barbara Neto-Bradley

Lab Alumni

Barbara (M.Sc. 2020, UBC) studied the evolution of photosynthetic capacity across angiosperms using a ‘macroevolutionary common garden’.

Mauro Sugawara

Lab Alumni

Mauro investigated how eco-evolutionary dynamics shaped patterns of biodiversity, using both theoretical and empirical approaches.

Join the lab

We do not have any specific openings for postdoctoral fellows but as our lab is still partially funded by startup funds, we have some flexibility to consider hires if there is an exceptional fit. If you are interested in joining our lab as a postdoctoral fellow, please contact Dr. Pennell directly.

Computational Biology and Bioinformatics

Most of the students in the lab will be enrolled in the Computational Biology and Bioinformatics (CBB) Ph.D. program.

The next admission deadline is Dec. 15, 2023. Interested students may, but do not need to, contact me prior to submitting an application. Students are admitted by the program and do not need to have decided on a lab prior to applying; there are many other excellent research groups affiliated with the Department of Quantitative and Computational Biology and I would advise interested students to check these groups out as well. 

Unlike many other programs at other universities, the CBB program does not discriminate between domestic and international applicants. We have a long tradition of training researchers from all around the world.


Marine and Environmental Biology

Our lab is also part of the Marine and Environmental Biology section of the Biological Sciences Department at USC. And we can take students enrolled in Marine and Environmental Biology Ph.D. program. If you are interested in being admitted through this program, please contact please contact Dr. Pennell directly. directly to discuss this option.

We welcome undergraduate students (and high school students) interested in joining a research lab. Many, if not most, of the ongoing projects in the lab could use additional researchers; Dr. Pennell is also interested in supervising independent research projects if the student is exceptionally driven and if there is a good match between their interests and the interests of the rest of the lab. (Previously, we’ve even had undergraduate researchers publish their independent projects in peer reviewed scientific journals.)

Our lab is exclusively a ‘dry lab’, meaning that all our work is computational. Undergraduates interested in conducting research in our group need to have a serious interest in programming. We welcome folks with minimal programming backgrounds – we are happy to help you learn! – but you need to be motivated to learn. Please reach out to Dr. Pennell if you are interested.