Publication Date

Summer 7-14-2022


Biologists are interested in estimating trait evolution models from phylogenies. However, phylogenies are imperfectly estimated, generally from DNA sequence data. In this study, true phylogenies are simulated to understand whether errors in phylogeny estimation affect inference of the trait evolution model. Given the tree, DNA sequences as well as traits are then simulated from the true phylogeny; both are simulated independently from the other. After the simulation, the DNA sequences were used to estimate trees using the UPGMA method without utilizing the trait information. The estimated trees combined with the traits are used to infer the evolutionary trait models, specifically the Brownian motion and the OU model. These results were also compared with estimating parameters of trait models from the true tree. Here we found the estimated evolutionary rates approach the true evolutionary rates as DNA sequence lengths and the number of taxa increase, but fluctuation occurs between different DNA sequence lengths greater than 500. Here, we found that estimates of trait evolution parameters were not very sensitive to errors in the gene tree when DNA sequences had length 500 or more.

Degree Name


Level of Degree


Department Name

Mathematics & Statistics

First Committee Member (Chair)

James Degnan

Second Committee Member

Fletcher G. W. Christensen

Third Committee Member

Steven Poe



Document Type