DOI

10.17077/etd.dkah-rfvq

Document Type

Dissertation

Date of Degree

Fall 2018

Access Restrictions

Access restricted until 01/31/2021

Degree Name

PhD (Doctor of Philosophy)

Degree In

Genetics

First Advisor

Comeron, Josep M.

First Committee Member

Kwitek, Anne E.

Second Committee Member

Llopar, Ana

Third Committee Member

Manak, John R.

Fourth Committee Member

Grobe, Justin L.

Abstract

Under most conditions, meiotic recombination is essential for ensuring that organisms adapt to ever changing biotic and abiotic conditions and, as such, it shapes evolutionary change within and between species. The interplay between selection and recombination plays a role shaping levels diversity within populations. Remarkably, recombination is itself an evolving trait that varies at many levels: between distant species of eukaryotes, between closely related species and among populations (and individuals) of the same species. Recombination rates also vary across genomes. Most of the causes and mechanisms of this plasticity in recombination rates and distribution are not clearly understood. Also, our understanding of how this variability in recombination rates influences levels of diversity within populations and across genomes is incomplete.

Here, I present a study combining molecular genetics with bioinformatic techniques to characterize recombination landscapes in Drosophila melanogaster. I present a model that accounts for a significant fraction of the variation in crossover rates across the genome of Drosophila melanogaster. Our predictive model suggests that crossover distribution is influenced by both meiosis-specific chromatin dynamics and very local constitutively open chromatin associated with DNA motifs that prevent nucleosome stabilization. I also present a novel method for genomic scans to identify recent events of adaptation in using nucleotide diversity data. In addition, I characterized variability in recombination rates in different populations of D. melanogaster and detected that the highest degree of variability in recombination rates across the genome is associated with intermediate genomic scales, and that this intermediate scale also plays a major role in explaining differences in recombination among populations. Our report is the first linking variation in recombination rates across genomes (genomic) and among populations (evolutionary), possibly suggesting a common mechanistic/genomic cause. Finally, I present preliminary data of the first large-scale project to study the effects of multiple environmental conditions in recombination rates at genome-wide level. In conclusion, these studies provide a new framework to investigate variation in recombination rates and to understand the genomic causes and evolutionary consequences.

Keywords

adaptive events, Drosophila melanogaster, motifs, open chromatin, recombination, wavelet

Pages

xiii, 158 pages

Bibliography

Includes bibliographical references.

Comments

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Copyright

Copyright © 2018 Johnny Cruz Corchado

Available for download on Sunday, January 31, 2021

Included in

Genetics Commons

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