Doctor of Philosophy (PhD)


Biological Sciences

Document Type



Observations of phenotypic diversity among closely-related organisms, especially those preserved as museum specimens, have driven the fields of systematics, taxonomy, and evolutionary biology for hundreds of years. In this dissertation, I used genomic data from modern and historical specimens to investigate the evolutionary processes that have generated phenotypic and genetic diversity in a highly polytypic group of birds, the New World quails (Odontophoridae), with a focus on the most phenotypically diverse member of this family: Northern Bobwhites (Colinus virginianus). To facilitate this work, I began by generating a highly contiguous reference genome assembly for Northern Bobwhites, which is reported in Chapter 2.

In Chapter 3, I used enrichment of ultraconserved elements from modern tissues and historical specimens to assess the subspecies-level relationships in Odontophoridae, which comprises 10 genera, 33 species, and 131 subspecies. Historical samples initially caused a variety of problems with standard phylogenetic analyses of this group, but I identified strategies for resolving many of the inconsistencies observed, resulting in well-supported topologies that were concordant across analytical paradigms.

In Chapter 4, I investigated the origin of Cuban bobwhites (C. v. cubanensis), the only Northern Bobwhite subspecies considered endemic to the Caribbean. How and when bobwhites arrived to Cuba has long been debated, and several hypotheses explaining their origin have been suggested in prior work. I used a combination of RAD-seq and target capture approaches to sequence single nucleotide polymorphisms (SNPs) from historical bobwhite specimens collected in Cuba, the USA, and Mexico, and I used these SNP data to reconstruct the complex human-mediated demographic history of Cuban bobwhites.

In Chapter 5, I leveraged a unique series of historical museum specimens to investigate the genetic basis of a rare, naturally occurring erythristic color morph in Northern Bobwhites. This phenotype was the subject of breeding experiments during the 1930s, which produced a series of specimens from F1, F2, and backcross individuals. I used whole genome resequencing data to investigate the genetic basis of erythrism using 32 individuals representing seven historical crosses as well as modern samples, and I identified candidate genes potentially involved in producing the erythristic phenotype.



Committee Chair

Faircloth, Brant C.



Available for download on Monday, October 28, 2024

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