Year of Award

2025

Document Type

Dissertation

Degree Type

Doctor of Philosophy (PhD)

Degree Name

Ecology and Evolution

Department or School/College

Division of Biological Sciences

Committee Chair

Jeffrey M. Good

Commitee Members

Zachary A. Cheviron, Brandon S. Cooper, Lila Fishman, Polly Campbell

Keywords

Genomic conflict, Junctional zone, Labyrinth zone, Maternal Decidua, trophoblast interface

Abstract

Understanding the origin and diversification of reproductive traits is a central goal in evolutionary biology. In mammals, the placenta represents a key evolutionary innovation that reshaped developmental strategies and enabled the ecological success of the clade. Yet despite its importance, the genetic mechanisms and selective pressures driving placental evolution remain poorly understood, due in part to methodological challenges and the limited phylogenetic and genomic scope of prior studies. This dissertation research addresses these gaps by integrating comparative genomics, transcriptomics, and new analytical tools to investigate placental gene regulation across closely related rodent species. Chapter one presents an extensive comparison of gene expression and genomic imprinting across placental layers in multiple lineages of house mice (Mus). This work reveals a strong association between imprinting and the labyrinth zone (the compartment specialized in nutrient exchange), extensive conservation of imprinting across species, and increased expression divergence in the endocrine layer of the placenta. Chapter two extends this framework to two species of dwarf hamsters (Phodopus) and their reciprocal hybrids, combining new chromosome-scale genome assemblies with histology and layer-enriched transcriptomes. These analyses uncover parallels in layer-specific imprinting patterns between mice and hamsters and identify hybrid disruption of pathways involved in trophoblast invasion. Chapter three details the development of new bioinformatic tools for allele-specific expression and gene expression modeling, demonstrating their broad applicability. Chapter four examines placental expression specificity across hamsters, mice, and deer mice, revealing how gene family expansions and sex chromosome contributions generate expression novelty across placental compartments. Together, these studies illuminate the evolutionary forces shaping placental diversity in rodents and provide a framework for understanding the emergence of reproductive innovation and incompatibility in mammals.

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© Copyright 2025 Luis Fernando Rodriguez Caro