Publication Date

Summer 7-5-2022

Abstract

Multilocus phylogenetic studies often show a high degree of gene tree heterogeneity —gene trees that have different topologies from each other as well as from the species tree topology. In some cases, this can lead to studies with hundreds of loci having distinct gene tree topologies. The degree of heterogeneity is expected to increase when there is a high degree of incomplete lineage sorting due to short branches (as measured in coalescent units) in the species tree. Other potential sources of heterogeneity include other biological processes such as introgression, recombination within genes, ancestral population structure, gene duplication and loss, and horizontal gene transfer, as well as gene tree estimation error due to short DNA sequences or inadequate substitution models. Here we examine the relationships between speciation and extinction rates and gene tree heterogeneity with both gene tree estimation error and no gene tree estimation error. In particular, higher speciation rates lead to shorter branches in the species tree and, therefore, higher levels of incomplete lineage sorting. In many cases, it might not be surprising that every gene tree has a unique topology, even for data sets with 1000 gene trees. We also propose using the average pairwise Robinson-Foulds (RF) distance between gene trees as a measure of heterogeneity as opposed to using the average RF distance between gene trees and the true species tree. Further, methods of inferring birth-death parameters (speciation and extinction rates) have involved using species trees estimated from gene trees or concatenation of DNA sequences. We infer these parameters using gene trees instead of species trees in this work. The method uses Approximate Bayesian Computation (ABC), which is useful when the maximum likelihood method is intractable, as in the case of gene trees given a species tree with a large number of taxa.

Degree Name

Statistics

Level of Degree

Doctoral

Department Name

Mathematics & Statistics

First Committee Member (Chair)

James Degnan

Second Committee Member

Yan Lu

Third Committee Member

Helen Wearing

Fourth Committee Member

Joseph Cook

Language

English

Document Type

Dissertation

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