Presentation Type

Poster

Faculty Mentor’s Full Name

Travis Wheeler

Faculty Mentor’s Department

Computer Science

Abstract

Plants in Southeast Asia are historically understudied, and their evolutionary relationships are poorly understood. This lack of an evolutionary history has proven to be an obstacle to further investigation of these species, so this research seeks to create a phylogeny, or evolutionary tree, of these plants using molecular data and computational tools. To accomplish this, I downloaded amino acid and DNA sequences from respected databases. I determined which sequences are best recorded in the species of interest, and utilized a blend of pre-existing tools and scripts written in the Perl programming language to eliminate sequences that could lead to inaccurate results. I fed these “filtered” sequences into programs that create alignments of protein or DNA sequences (MAFFT and Opal). These sequence alignments are used to infer likely relationships among these sequences and, therefore, relationships among the species they were obtained from. The resulting alignments were used to compute the most probable phylogeny, using the inference tool, FastTree. The resulting evolutionary tree will assist in filling a significant gap in our knowledge of the evolutionary history of the plants of Southeast Asia. It will also be directly applicable to the research of our Biology Department’s Dr. Jedediah Brodie, who is investigating how interactions with marsupials and mammals has shaped the evolution of these plant species.

Category

Life Sciences

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Apr 27th, 3:00 PM Apr 27th, 4:00 PM

Branching Out: Generating an Evolutionary Tree of Southeast Asian Plants with Computational Tools

UC South Ballroom

Plants in Southeast Asia are historically understudied, and their evolutionary relationships are poorly understood. This lack of an evolutionary history has proven to be an obstacle to further investigation of these species, so this research seeks to create a phylogeny, or evolutionary tree, of these plants using molecular data and computational tools. To accomplish this, I downloaded amino acid and DNA sequences from respected databases. I determined which sequences are best recorded in the species of interest, and utilized a blend of pre-existing tools and scripts written in the Perl programming language to eliminate sequences that could lead to inaccurate results. I fed these “filtered” sequences into programs that create alignments of protein or DNA sequences (MAFFT and Opal). These sequence alignments are used to infer likely relationships among these sequences and, therefore, relationships among the species they were obtained from. The resulting alignments were used to compute the most probable phylogeny, using the inference tool, FastTree. The resulting evolutionary tree will assist in filling a significant gap in our knowledge of the evolutionary history of the plants of Southeast Asia. It will also be directly applicable to the research of our Biology Department’s Dr. Jedediah Brodie, who is investigating how interactions with marsupials and mammals has shaped the evolution of these plant species.