#1 - Alu-Derived Orthologous Chromosome Classification for the Primate Order

Orthologous chromosomes between any family of related species have been difficult thus far to obtain, often requiring substantial biochemical testing and computationally-intensive genomic analysis. By employing computational strategies on repeated non-coding DNA, numerous advantages to accurately determining orthologous chromosomes between species can be ascertained. Throughout the primate genome, the Alu repeated element covers 10% of the genome among higher order primates, spanning across each chromosome. These non-protein-coding sequences replicate themselves repeatedly, with each iteration allowed to mutate more than their protein-coding counterparts. Therefore, upon examining the genetic sequences of such “junk” DNA, increasingly specific distinctions can be made between any two compared primate genomes. We propose a novel strategy of matching known Alu repeats by subfamily between two species, thereby ascertaining the not only the frequency of specific Alu elements conserved, but also which where each matched pair is located on the species’ chromosomes. By collecting Alu-identified primate genomes the University of California Santa Cruz Table Browser, this methodology was applied to 12 species-specific genomes. After comparing the Alu elements between each of the primates and subsequent frequency analysis, we were able to accurately highlight what chromosomes were conserved across members of the Order Primate. In addition, we were able to use our alignment with currently accepted literature to produce orthologous chromosomes for numerous species previously not compared against one another. In conclusion, we propose a far less computationally and resource intensive solution to determining conserved chromosomal relationships among primates

#11 - Sequence Analysis of Alu Repeated Elements for Primate Phylogenetic Tree Construction

Phylogenetic tree construction can be a particularly challenging and time-intensive process. This study employs a novel computational approach to phylogenetic tree construction, using the Alu repeating element, a SINE. Repetitive elements including Short and Long Interspersed Nuclear Elements (SINEs/LINEs) have successfully been applied as accurate tools for phylogenetic analysis, as they are predominately unidirectional and homoplasy-free. However, previous analysis of phylogenetic relationships using these repeating elements has been limited to a small number of isolated repeats among relatively few organisms. As a highly repetitive sequence, the Alu element and its associated subfamilies can provide detailed analysis on evolutionary divergence among species in the Order Primates. This study identified shared sequences as Alu repeating elements that were conserved in both location and base-pair sequence between the primate genomes of interest. These shared sequences, derived from the Genome Library at the University of California San Diego, were analyzed to construct individual phylogenetic trees for each of the 49 Alu subfamilies. As this method solely requires the sequence analysis of available primate genomes, this serves as a cheaper and more time-efficient approach to phylogenetic tree construction for the Order Primates relative to biochemical and anatomical analysis