Undergraduate Honors Theses

Thesis Defended

Fall 2015

Document Type


Type of Thesis

Departmental Honors


Ecology and Evolutionary Biology

First Advisor

Nolan Kane

Second Advisor

Barbara Demmig-Adams

Third Advisor

Robin Dowell


Chloroplast DNA (cpDNA) is a traditional workhorse for reconstructing evolutionary relationships among angiosperms. The frequent use of cpDNA in such analyses is predicated on the apparent simplicity of its inheritance: uniparental through the maternal line, and lacking biparental recombination. In hybrid zones, where reproductive barriers between sympatric species may not be fully developed, infrequent leakage of divergent male cytoplasm into hybrid offspring may result in at least transient heteroplasmy. Heteroplasmy provides the potential for detectable recombination between maternal and paternal chloroplast genomes to occur. Despite the widespread occurrence of paternal leakage of organelles and heteroplasmy in higher plants, no documented examples of cpDNA recombination in natural angiosperm populations are known. This study presents evidence for the recombination of chloroplast DNA in the Andean subtribe Iochrominae (Solanaceae), of which several species are believed to be interspecific or intergeneric hybrids. Recombination was detected by seven distinct methods and verified by approximately unbiased (AU) and Shimodaira-Hasegawa (SH) tests for tree incongruence. The results of this study suggest that a single bifurcating evolutionary history of the plastome cannot be assumed in all lineages. The importance of recombination in angiosperm chloroplasts has broad implications across several fields, ranging from the compromise of phylogenetic reconstruction and the application of molecular clocks to the optimization of agricultural productivity.