Genomic and Regulatory Divergence between Sister Species of Daphnia

Doctoral Dissertation


In this doctoral thesis, I overview the empirical and theoretical consequences of evolution by drift and/or natural selection, as it acts upon lineages during ecological speciation. Then, I outline the evolutionary divergence between two such lineages. To address my questions empirically, I utilize genomic and transcriptomic data applied to a taxon (Daphnia; Crustacea : Cladocera) which serves presently more as an ecological model than a genetic one. I am fortunate to have undertaken the necessary research at the present time and place, where high throughput next-generation sequence data could be generated for and meaningfully applied by a doctoral student for novel purposes. I have had a lot of help.

What follows in this text are an introductory chapter, three data chapters, and a conclusion, concerning the diversity and divergence among North American Daphnia pulex and Daphnia pulicaria. In the second chapter, I use novel data to address their genomic divergence; in the third, their regulatory divergence; and in the fourth, their ongoing hybridization and admixture. Each chapter is written to be submitted as a stand-alone manuscript for publication in a peer-reviewed scientific journal. Herein, their content is presented as a dissertation for the partial fulfillment of the requirements for the degree of Doctor of Philosophy from the University of Notre Dame. Finally, I offer my concluding remarks upon completion of this research, concerning the state of biology as a field, and the immense opportunities that exist going forward.


Attribute NameValues
Author Benjamin J. Clifford
Contributor Dr. Stuart Jones, Committee Member
Contributor Dr. Jeanne Romero-Severson, Committee Member
Contributor Dr. Michael Ferdig, Committee Member
Contributor Dr. Jeffrey Feder, Committee Member
Contributor Dr. Michael Pfrender, Research Director
Degree Level Doctoral Dissertation
Degree Discipline Biological Sciences
Degree Name Doctor of Philosophy
Defense Date
  • 2016-03-16

Submission Date 2016-04-12
  • mesocosm

  • Microarray

  • lactate dehydrogenase

  • Speciation

  • Natural selection

  • crustacean

  • Evolution

  • Differential expression

  • Population Genetics

  • pond

  • Taxonomy

  • Restriction-site Associated DNA (RAD)-Sequencing

  • population structure

  • Gene expression

  • Genomics

  • hybrid inviability

  • ecological speciation

  • Daphnia

  • apomixis

  • meiosis

  • Hybrid

  • Biology

  • Ecological Genomics

  • Asexual reproduction

  • Regulatory divergence

  • Genome Scan

  • Ecology

  • cis-regulation

  • meiotic cohesin protein

  • hybrid vigor

  • GATK

  • β-tubulin folding cofactor D

  • parthenogenesis

  • Divergence

  • PCA

  • Daphnia pulicaria

  • D. pulex × pulicaria hybrids

  • R

  • trans-regulation

  • reproductive isolation

  • Fastq

  • Reference Genome

  • ggplot2

  • habitat

  • lake

  • Admixture

  • Daphnia pulex

  • arthropod

  • gene ontology

  • orthology

  • vernal pond

  • Fst

  • Rec8

  • VCF

  • English

Record Visibility Public
Content License
  • All rights reserved

Departments and Units

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