Date of Award

Spring 1-1-2015

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Ecology & Evolutionary Biology

First Advisor

Nolan C. Kane

Second Advisor

Noah Fierer

Third Advisor

Andy Martin

Fourth Advisor

Erin Tripp

Fifth Advisor

Diana Nemergut

Abstract

Recent and ongoing advances in DNA sequencing, coupled with computational developments, have opened new frontiers for understanding the structure and function of biological diversity. For my dissertation, I first addressed questions related to a low diversity community of un-cultured Atacama Desert bacteria, using a variety of sequencing approaches. The principal goal was to infer what metabolic traits these bacteria possess, which allows them to survive harsh desert conditions that other bacteria could not. Through detailed genome assembly, annotation and comparative analyses I developed a working hypothesis that trace gas metabolism (H2, CO and several organic C1 compounds) may sustain these microorganisms in their habitat, although many aspects of their metabolic capacity remain undetermined. In the second component of my dissertation, I used whole genome sequencing of diverse Cannabis accessions to infer the phylogenetic lineages of this genus. These findings show support for at least one major clade of hemp and two clades of drug-type Cannabis, as well as hybrid origins of many commercially available modern drug-type cultivars. The levels of divergence among these clades suggest multiple independent domestication events may have occurred, though extensive breeding for hemp and drug-type strains from a single domestication origin cannot be ruled out at present, due to the lack of known true wild populations. This work has relevance for future cultivar development, but also reflects long forgotten events that have occurred during 6,000 years of the Cannabis-human relationship. Together, my dissertation demonstrates several ways that DNA sequencing technology and analytical approaches can address questions in ecology and evolutionary biology, but also highlights the limitations of these methods and underscores the importance of complementary non-sequencing approaches.

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