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Publication Date


First Advisor

Sara Mathieson

Document Type

Honors Project

Degree Name

Bachelor of Arts


Biological Sciences


Selective sweep, Evolution, Agriculture, Selective pressures, Crops-Evolution, Genomics, Adaptations (Biology)


Genetic diversity within a population can be understood by looking at polymorphisms in the genome. When selection occurs, linkage of those polymorphisms reveals the pattern of a selective sweep. When a beneficial mutation is selected for, linked regions of the genome will also rise in frequency within the population.

Humans began to take advantage of their ability to influence selection with the advent of agriculture. Agricultural domesticates serve as a long term study of the impacts of selective pressures. Agricultural practice has led to coevolution between people and the species that they were dependent on. This has resulted in genotypic varieties between human populations such that a ‘healthy’ diet is specific to a person’s genotype. Agriculture allowed for the rapid expansion of the human population, and our modern population is responsible for a variety of selective pressures that threaten the diversity of different species around the globe. Our population is expected to continue growing over the next 50 years, magnifying the impact of our behaviors.

To understand how crops can adapt to environmental changes, it is necessary to understand how these species have been evolving. Many of the studies identifying recent evolutionary adaptations as a response to climate change rely on phenotypic evidence to describe proposed genotypic changes, though phenotype can shift without any evolutionary change occurring.

The recent advancements in sequencing technologies could serve to change that trend in research. Plant genome sequencing focuses primarily on food crops. Tomatoes have been focused on in sequencing projects as a model species for the nightshade family. In this project, I explore methods for identifying patterns consistent with selection in the model genomes of several tomato varieties. The pipeline established here could be used on a variety of crops as those sequences become available.




59 pages : color illustrations. Includes bibliographical references (pages 54-59)