UCLA

This doctoral dissertation focuses on genomic approaches to study evolution and adaptation in birds. Recent advances in next-generation sequencing (NGS) technology and analytical tools are making the production of genomic data more accessible than ever before. As such, the accumulation of genomic data is occurring at an ever-increasing pace. This genomic data harbors a trove of information waiting to be unlocked. For birds, an initiative called the Bird 10,000 Genomes Project strives to produce genomes for all living species of birds. This growing availability of bird genomes is fueling our ability to understand the genetic architecture underlying evolutionary and adaptative processes. In my dissertation, I use genomic data and analytical tools to understand color evolution and genomic signals of climate adaptation in birds. My first two chapters explore color and visual system evolution in birds. In the first chapter, I introduce the R package, charisma, for categorizing color from digital images for high-throughput analyses of color evolution. Current color categorization of digital images often entails manual classification of color for each image or a single estimate of colors for the entire group. I present charisma a novel efficient and standardized method to identify biologically relevant colors in thousands of images. In the second chapter, I explore the evolution of avian visual system sensitivity. I align and trim SWS1 opsin sequences to predict the visual sensitivity of 418 bird species across the bird tree of life. I estimate rates and reconstruct ancestral states of visual system sensitivity. I found that a violet-sensitive visual system is ancestral in birds and that an ultraviolet-sensitive visual system has evolved at least 18 times across the bird tree of life. In the last two chapters of my dissertation, I present a reference genome and investigate climate adaptation in Yellow Warblers, Setophaga petechia. In my third chapter, I present a highly contiguous reference genome assembly for Yellow Warbler using HiFi long-read and Hi-C proximity sequencing technologies. I generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This high-quality reference provides a key resource for understanding gene flow, divergence, and local adaptation and informing conservation management. In my fourth chapter, I investigate genomic signals of climate adaptation in Yellow Warblers in California. Climate change is an ongoing threat to biodiversity and species are being forced to respond or face extinction. This response is dependent on their ability to adapt to rapidly changing environments. I use a whole genome sequencing approach to examine genomic signals of local adaptation in California breeding Yellow Warblers to identify populations most vulnerable to climate change. Despite low genetic structure in Yellow Warblers breeding in California, I identified unique genotype-environment associations and 2,972 putatively adaptive single-nucleotide polymorphisms across 137 individuals. This study highlights the importance of understanding neutral and adaptive genetic variation in bird populations.