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Sequence Analysis of Homologous Alu Elements: A Novel Methodology for Primate Phylogenetic Tree Construction
Author(s) -
Sood Nitish,
Mehra Mehul,
Mittal Anav,
Bates Christopher
Publication year - 2020
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2020.34.s1.09578
Subject(s) - phylogenetic tree , alu element , biology , phylogenetics , evolutionary biology , genome , phylogenetic network , tree (set theory) , genetics , computational biology , human genome , gene , mathematics , mathematical analysis
Non‐human primates are essential model organisms across a broad spectrum of biomedical research, from drug discovery & development to insights into immunological responses. The study of phylogeny enhances understanding of the particular experimental advantages of each model organism. Despite considerable efforts invested into developing currently accepted practices of phylogenetic analysis, these strategies often involve significant expenditures of time and resources. To address these concerns, we developed a novel computational approach to primate phylogenetic tree construction using the Alu transposable element. Short Interspersed Nuclear Elements such as Alu have previously been validated as accurate tools for phylogenetic analysis, as they predominantly evolve in a unidirectional and homoplasy‐free manner. However, previous Alu‐based investigations into phylogenetic relationships have been limited to detecting specific Alu insertion polymorphisms as a proxy for evolutionary divergence. Here, we present a novel methodology for primate phylogenetic analysis using genetic diversity in homologous Alu sequences. Alu elements for 11 primate genomes, classified by subfamily, were extracted from the University of California Santa Cruz’s Genome Table Browser. Subsequently, multiple sequence alignments were performed to identify which Alu sequences were homologous among the 11 primates. Following identification, phylogenetic trees for each of 22 conserved subfamilies were constructed. These trees were then compared to randomly generated phylogenetic trees and found to be significantly (p < 1e‐10) more accurate on all tree distance metrics calculated (Robinson‐Foulds, Path difference, Subtree Pruning and Regrafting, Hamming distance, and Penny Hendy). The Alu‐based trees were then compared to published primate phylogenetic trees to confirm the validity of this technique. No significant difference in accuracy was found for the most accurate Alu subfamily tested, demonstrating its validity. We therefore propose that our approach of comparing homologous Alu sequences can serve as a supplement or alternative to current primate phylogenetic tree construction.