Macroevolution of Gene Expression in Passerine Birds

Abstract

A key objective of evolutionary biology is to decipher the molecular mechanisms driving phenotypic diver- sity. Whereas genomes provide the informational foundation of life, gene expression compromises how that information is used to define the biology of an organism. As part of the biological cascade from information to function, gene expression dynamics play a critical role in influencing the evolutionary trajectory of diver- sity. It is therefore crucial to the understanding of evolutionary processes that we investigate how gene ex- pression evolves on a macroevolutionary level and what role it plays in life history variation. Advancements in technologies such as RNA-Seq and evolving computational tools have enabled comparative transcriptomics research to blossom in recent years with studies steadily gaining in species count and tissue scope. To elucidate the role of gene expression in macroevolutionary dynamics, my dissertation investigates interspecific differ- ences in gene expression and their connection to life history trait evolution using passerine birds as a focal system. I provide a review of the historical progression of transcriptomic technology, the challenges facing tran- scriptomic researchers, and the current landscape of comparative transcriptomics. I discuss the vital role of RNA preservation in museum collections and provide an original analysis of over 300 museum-preserved tissue samples demonstrating that RNA quality was not significantly affected by preservation method, col- lection method, or tissue type, underscoring the suitability of these samples for transcriptomic research. I further discuss recent technological developments, such as single cell sequencing and multi-omic data integra- tion, which I expect to impact the future directions of comparative transcriptomic research. Empirically, I investigate the macroevolutionary dynamics of gene expression in the two major clades of passerines: oscines and suboscines. For this analysis, I sequenced 327 transcriptomes from six key tissues (heart, pectoralis major, liver, brain, eye, and testis) across 22 passerine species and two outgroup species. Using this dataset, I ask which macroevolutionary models – specifically the Brownian motion and Ornstein– Uhlenbeck process – best fit the patterns of gene expression observed in these clades and what genes are dif- ferentially expressed between oscines and suboscines. My findings indicate that most genes’ expression are best fit by a Brownian motion model of evolution with only a small selection best fit by the Ornstein Uhlen- beck process indicating the strong role of phylogenetic structure or drift in between-clade gene expression evolution dynamics. I further find that differential expression between avian clades is enriched for genes with broad, systemic roles rather than tissue-specific functions. Expanding on this, I examine the relationship between gene expression evolution and life history traits by interrogating the correlation of differential expression with the key avian traits of diet and migration. My results from evolutionary model fit analyses indicate that migratory strategy significantly influences gene expression in the brain whereas diet had a broader impact across multiple tissues, strongly shaping gene ex- pression in the brain, heart, liver, and pectoralis major. Similarly, the results from a differential expression analyses indicated that, of the tissues studied, gonad and muscle were most heavily impacted by migratory strategy whereas brain and eye were most heavily associated with diet. Similar to the between clade analysis, GO term enrichment revealed consistent terms across tissue types indicating an important role in differential expression of broad, systematic roles. The findings from my dissertation enhance our understanding of gene expression evolution and provide valuable insights into how life history traits correlate with gene expression across species.