Genomics and Population History of Black-headed Bulbul (Brachypodius atriceps) Color Morphs

Intraspecific polymorphism in birds, especially color polymorphism, is an area of active research in evolutionary biology. In this dissertation, I applied WGS to uncover the potential genetic underpinnings of color polymorphism in the Black-headed Bulbul (Brachypodius atriceps) of Southeast Asia. This species was selected because of the heterogeneous dispersion of two morphs across its range: a yellow form predominating on mainland Asia and the Greater Sunda Islands and a gray morph on two islands—Bawean and Maratua. I approached this project from three angles. First, I reconstructed the phylogeny of the bulbul family, Pycnonotidae, to examine patterns of coloration among all species and infer the commonality of color changes relevant to B. atriceps. To build the phylogenetic tree, I used a super-matrix approach, which allowed the inclusion of 121 of the 130 known species of bulbuls. Using the tree, I determined the most appropriate outgroups for comparison with B. atriceps in subsequent genomic study. Next, I generated a high-quality reference genome of a yellow individual of B. atriceps and, subsequently, sequenced low-coverage genomes of multiple gray and yellow individuals, and three outgroup taxa. I compared Fst values between genomes of gray and yellow individuals to locate peaks of divergence and identify potential candidate loci for the color polymorphism. I also tested the protein-coding genes between yellow and gray birds for signs of selection. Among genes potentially responsible for the color polymorphism, several involved in lipid uptake, transport, and deposition—processes fundamental to carotenoid expression. In the final chapter, I assessed characteristics among B. atriceps populations across the species range in Sundaland with an emphasis on Bawean and Maratua islands. The Bawean population was barely discernable genetically from that on mainland Borneo. The Maratua population, however, was notably divergent from the mainland Bornean and other populations. Therefore, I modelled its demographic parameters and used the information to gain a better idea of the historical processes that have led to its unique, singular coloration. The Maratua population was originally isolated from other Sundaic populations c. 1.9 Ma, but c. 1000 years ago began to experience a small amount of gene flow