Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Forestry and Natural Resources

Committee Chair

J. Andrew DeWoody

Committee Member 1

Mark Christie

Committee Member 2

J. Barny Dunning

Committee Member 3

Robert Ricklefs


A key goal of evolutionary biology is understanding the complex mechanisms underlying adaptive evolution, and the study of the co-evolution of hosts and parasites is a primary tool. The work in this dissertation involves exploring the evolution of avian immune genes in the context of phylogeny and malarial parasitic infection using next generation sequencing approaches. The bananaquit (Coereba flaveola) is a Caribbean passerine bird and a common host of haemosporidian parasites which cause avian malaria (Plasmodium spp. and Haemoproteus spp.). The genes of a host’s immune system, including those of the Major Histocompatability Complex (MHC) of the adaptive immune system and Toll-like receptor (TLR) family of the innate immune system, are related to its susceptibility to disease, and are targets for natural selection driven by parasites. In Chapter 1 we created genomic tools to study avian genomics and immune gene evolution by the de novo sequencing, assembling, and annotating of a new avian whole genome genome sequence (the bananaquit), and characterization of target immune genes (MHC and TLR). In Chapter 2 we used a pooled amplicon sequencing approach to assess MHC and TLR allelic associations with resistance/susceptibility to parasitic infection in a bananaquit population with different infection statuses. We found that allele frequencies are associated with infection status in the immune loci sequenced, showing that the infected groups have more alleles at lower frequencies and harbor unique alleles compared to the uninfected groups. These results support the theory of selection favoring particular alleles or numbers of alleles for resistance while maintaining overall genetic diversity in the population. This has been demonstrated previously as one mechanism driving evolution in MHC, but has been understudied in TLRs. In Chapter 3 we explored interspecific immunogenetic divergence and signatures of selection by utilizing publicly available avian MHC and TLR sequences. We found evidence of episodic diversifying positive selection in the immune gene-wide phylogenies, at specific sites within each gene, and in particular lineages, including the bananaquit. We also demonstrated differential strengths of selection at these genes among the three main clades of birds (Paleognathae, Galloanseres, and Neoves). Ultimately this work contributed a new avian genome assembly with applications to the study of host-parasite co-evolution, and explored both inter-and intra-specific avian immunogenetic diversity. Our analyses have provided new insights into evolutionary processes which shape the avian immunogenetic repertoire.