Person: Kay, Emily Ho
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Emily Ho
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Kay, Emily Ho
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Publication Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species(Public Library of Science (PLoS), 2012) Peterson, Brant K.; Weber, Jesse N.; Kay, Emily Ho; Fisher, Heidi; Hoekstra, HopiThe ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via ‘‘SNP chip’’ microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotype-phenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.Publication Rodents(Elsevier BV, 2008) Kay, Emily Ho; Hoekstra, HopiPublication The role of sexual imprinting in speciation: lessons from deer mice (genus Peromyscus)(2014-10-21) Kay, Emily Ho; Hoekstra, Hopi E.; Mallet, James; Edwards, ScottSexual imprinting, the process of learning mate preferences at a young age, could promote speciation by reducing attraction to individuals from divergent populations or species, consequently creating or maintaining reproductive isolation. Yet, despite the documentation of sexual imprinting in many taxa, its connection to speciation has been understudied. I chose to explore the potential link between sexual imprinting and reproductive isolation and in two North American rodents--the white-footed mouse (Peromyscus leucopus) and its sister species, the cotton mouse (Peromyscus gossypinus). These species have overlapping distributions in nature, possibly allowing interbreeding and admixture. In Chapter 1, I used double-digest restriction-associated DNA sequencing to test for hybridization in sympatric natural populations and found that 1.5% of sampled individuals showed evidence of admixture yet the species have maintained genetic distinctness in sympatry. In the lab, the species hybridize when given no choice of mates but mate more readily with conspecifics, suggesting that mating preferences may prevent hybridization in the wild. In Chapter 2, I tested whether mating preferences create significant reproductive isolation. I measured mating preferences in controlled laboratory conditions and found that both species and sexes preferred conspecific to heterospecific mates in 85% of trials. I then raised offspring with foster parents of the opposite species and found that P. leucopus has a genetically-determined preference while P. gossypinus learns its preference. In Chapter 3, I tested whether sexual imprinting on parental diet could generate assortative mating within a species. I tested this hypothesis by feeding P. gossypinus parents either orange- or garlic-flavored water, thereby exposing their offspring to these flavors through their parents until weaning. I tested the preferences of these offspring as adults and found that P. gossypinus, especially females, had strong assortative mating preferences. This implies that at least females learn parental dietary information and that assortative mating could evolve within a single generation. Together, my results confirm that sexual imprinting on parental traits--possibly mediated through dietary differences--can create assortative mating capable of generating sexual isolation and reducing gene flow between species. My research supports the importance of mating preferences and learning in speciation.Publication Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani(BioMed Central, 2010) Hull, Joshua M; Mindell, David P; Talbot, Sandra L; Kay, Emily Ho; Hoekstra, Hopi; Ernest, Holly BBackground: Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. Results: To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor (Mc1r) to investigate molecular genetic differentiation among three B. jamaicensis subspecies (B. j. borealis, B. j. calurus, B. j. harlani). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis. Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus, and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus, suggesting that Mc1r does not play a significant role in B. jamaicensis melanism. Conclusions: These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.