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Indiana University Bloomington

Department of Biology

Graduate Studies

Genetics, Cellular & Molecular Sciences Training Grant

Trainee Profile

Gregg Thomas

Photo of Gregg Thomas
Research Image(s)
Example diagram of how erroneous base calls can affect downstream phylogenetic analyses

Erroneous base calls can affect downstream phylogenetic analyses in many ways. For example, The incorrectly assembled base shown in red above can lead to the inference of a mutation where none actually occurs.

“Hominoid slowdown” diagram

The difference in observed mutation rates between humans and other great apes is known as the "Hominoid slowdown" and is a classic example of rate variation between species. Mutation rates are now being inferred at the molecular level and can be affected by sequencing error.

Graduate Student
Contact Information
By telephone: 812-856-7016 (lab)
JH 249
Hahn Lab website
School of Informatics (Bioinformatics)
B.S., Biology, 2010, Purdue University
M.S., Bioinformatics, 2013, Indiana University
Sandy Ostroy Undergraduate Summer Internship, Purdue University, 2009
Research Description

Mutation is the main source of variation between organisms and is relevant to many human diseases. One fascinating aspect of mutation is the mutation rate itself. Mutation rates evolve and vary between species and I am interested in explaining this variation, particularly in the context of humans and other primates. 

However, one major issue that plagues our understanding of mutation rates in the context of modern genomics is the presence of base-calling errors within genome assemblies. I previously demonstrated that genome assembly and annotation errors led to higher estimated rates of gene family evolution, and I helped to devise a method to estimate this error. Similarly, base-calling errors are carried into downstream phylogenetic analyses and can lead to an inflated estimate of the mutation rate across a phylogeny and inaccurate signals of convergent evolution, so correcting these errors is imperative for phylogenetics.

To solve this problem, my future research goal is to develop a method to probabilistically model base-calling errors in genome assembly and correct for them in downstream analyses. I aim to use the method to correct genome assemblies and more accurately study mutation rate variation between species and convergent evolution.

Select Publications
Han MV, Thomas GWC, Lugo-Martinez J, and Hahn MW. (2013) Estimating gene gain and loss rates in the presence of genome assembly and annotation error using CAFE 3. Molecular Biology and Evolution. 30:1987-1997.
Thomas GWC. and Hahn MW (2014) The human mutation rate is increasing, even as it slows. Molecular Biology and Evolution. 31:253-257.
Select Presentations
Convergent evolution of the genomes of marine mammals. Society for Molecular Biology and Evolution, 2014.

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