Nathan Kilian

Date Approved


Date Posted


Degree Type

Campus Only Senior Honors Thesis

Department or School


First Advisor

David Kass

Second Advisor

Aaron Liepman


Mammalian genomes contain thousands to over a million copies of retrotransposons. These "jumping genes" are transcribed into RNA, copied to DNA, and stably integrated into new genomic sites. These integration events can contribute to a "molecular fossil record" that can be used to trace the evolutionary history of different organisms. Short interspersed DNA elements (SINEs) are non-autonomous retrotransposons. This investigation analyzes presumptively "younger" individual elements of the Bl, B2, and ID rodent SINE families to address recent questions regarding the evolutionary relationships of various Peromyscus species (deer mouse and relatives). Shared integrations of individual elements suggest common ancestry, because these are homoplasy-free markers. We have identified nineteen elements of which seventeen integrations were shared among the members of the P. leucopus / P. maniculatus clade, eight integrated more recently, and one element was found in all Peromyscus species analyzed. Six integrations were limited to one or more subspecies of P. maniculatus. Therefore, the findings of this study support the potential of identifying relatively recent SINE integrations among numerous copies within Peromyscus genomes, as well as their use in elucidating the phylogenetic relationships of the species within this genus.