Balakrishnan, Christopher N.Lansverk, Allison L.2017-08-092019-02-262017-082017-07-18August 201http://hdl.handle.net/10342/6368Zebra finches (Taeniopygia guttata) have been the subject of extensive neurological and behavioral research having served as the dominant model for vocal learning over half a century. Learned vocal communication, or vocal learning, is a trait that is shared by humans and songbirds but is rare or less well developed in other animals. Unlike innate communication, learned vocalizations are acquired early on by juveniles listening and copying what they hear from adults. Little, however, has been done to characterize the intraspecific variation in song behavior in the zebra finch model system. Other systems, such as the lab mouse, Mus musculus, have begun to take advantage of inbred and natural populations to assess genetic variation and to link genotype and behavior. The opportunity exists to do the same in the zebra finch. The first step to better able study song learning in a genetics context is to define trait variation within and among populations. The majority of research conducted on these birds relies on domesticated populations of Taeniopygia guttata castanotis (T. g. castanotis), but wild populations are also available for study, as is a second subspecies, T. g. guttata. With the sequencing of the zebra finch genome a decade ago, zebra finches have risen in importance in the field of population genomics so there is an opportunity to investigate the genetic variation in this system as well. I compared patterns genetic and song variation among these populations to examine how these features have diverged during the early stages of domestication as well as during divergence in allopatry. When comparing the wild and domesticated populations, I find that overall levels of genetic differentiation are low (FST = ~0.02); I also find evidence of selection acting on portions of the genome. Genetic drift also appears to have played a role in shaping patterns of genetic variation. While genetic drift has led to reduced diversity and a loss of rare alleles in domestic populations, it has also done so in the island subspecies, T. g. guttata: I found further support for a dramatic bottleneck in the island subspecies as the two subspecies have diverged, as there is an overall reduction in diversity. Among the most highly diverged regions of the genome are two genes associated with color. I have identified fixed differences in two well-known pigmentation genes, SLC45A2 and CDKN2A that may contribute to plumage color differences between subspecies. In addition to genetic divergence, I also characterized divergence in song behavior among populations. I find that the island subspecies shows less variation in song among individuals than the mainland birds. Though the island subspecies, T. g. guttata, shows a reduction in variation in song among individuals possibly due to the bottleneck during speciation, the domestication process has actually led to increased variability in song structure in domesticated birds. It is possible that domesticated birds have been freed from the constraints on song structure imposed by mate choice and the need for accurate species recognition. Finally, in order to differentiate between genetic or cultural controls of this difference in variation, I cross-fostered both subspecies to the Bengalese finch, Lonchura striata domestica, to test for differences in song copying behavior. I cannot reject the null hypothesis that zebra finch subspecies copy tutor songs equally well, but it does appear that the high variability in song structure in T. g. castanotis remains following controlled tutoring. Overall, I have begun to characterize the intraspecific behavioral and genetic variation in zebra finches, which has the potential to further our ability to study gene-environment influences on behavior, particularly with regards to the genetic contributions to song copying ability.application/pdfendomesticationspeciationbottleneckpigmentationsong productioncross-fosteringZebra finchSound production by animalsDivergence (Biology)Animal genetics--VariationDoctoral Dissertation2017-08-07