Publication Date

Spring 5-12-2017


Methods for inferring species trees from gene trees motivated by incomplete lineage

sorting typically use either rooted gene trees to infer a rooted species tree, or use

unrooted gene trees to infer an unrooted species tree, which is then typically rooted

using one or more outgroups. Theoretically, however, it has been known since 2011

that it is possible to infer the root of the species tree directly from unrooted gene

trees without assuming an outgroup. The present work is the first that we know of

which attempts to infer the root of a species tree using unrooted gene trees as the

input data and without assuming an outgroup. It is hoped that this approach will

be useful in cases where an appropriate outgroup is difficult to find and gene trees do

not follow a molecular clock. The method uses Approximate Bayesian Computation

(ABC), and could also be useful when there is prior information that makes a small

number of root locations plausible in an unrooted species tree. This study also uses

the MLE method to compute the maximum value of the correct tree, which also uses

bootstrapping to support the MLE results. Also, this study makes a comparison

between using rooted gene trees and unrooted gene trees, both with and without

DNA sequences, for five and eight taxa. Finally, an original method developed in

this work is applied in an empirical study to data from Xi et al. (2014), and which

uses their hypothesis as part of the prior in the present study.

Degree Name


Level of Degree


Department Name

Mathematics & Statistics

First Committee Member (Chair)

James Degnan

Second Committee Member

Gabriel Huerta

Third Committee Member

Erik Barry Erhardt

Fourth Committee Member

Christopher Witt




multispecies coalescent, outgroup, midpoint rooting, molecular clock, identifiability, sufficiency, MLE, bootstrapping, DNA sequences.

Document Type