Vanesa Robledo

Comparative Genomics of Mosquitos Using Orthofinder

This was my part of the final project for BIOL 469 Comparative Genomics. I used the Python-based command line tool Orthofinder for three mosquito species, then analyzed the results with the help of a Python script written by my group member to map the identified orthogroups and proteins to Gene Ontology (GO terms) in the Uniprot database. I processed the results using the dplyr and ggplot packages in R to discuss significant findings from Orthofinder.

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Phylogenetic Analysis of Brown Recluse Spider Venom

Sphingomyelinase D (SMase D) is the protein responsible for the pathological effects of the venom found in brown recluse spiders, Loxosceles. This assignment attempted to analyze the evolutionary history of SMase D found in Loxosceles species and its homologs by constructing phylogenetic trees from homologs of SMase D. One phylogenetic tree was constructed with a set of sequences from different species, and the second was constructed focusing on homologs within spiders (Aranae). The first tree was constructed using Seaview, and the second tree using the phangorn package in R. This assignment hypothesized that SMase D emerged in Loxosceles from a gene duplication event.

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Comparison of Environmental DNA Metabarcoding & Conventional Methods for Measuring Species Richness of Fish

BIOL-ERSC-4030H: Data Design & Data Analysis (Trent University)

This research paper replicates the methods of measuring species richness in fish using R.

Abstract: Environmental DNA (eDNA) metabarcoding is a biomonitoring tool that can rapidly assess species richness in a variety of environments. It is important that this is calibrated with current, conventional standards of measuring species richness, as currently there is a lack of general understanding of how these methods compare. A dataset containing 121 sites in freshwater and marine systems measuring species richness of bony fish was analyzed using Lin's Concordance Coefficient (CCC) and Bland-Altman analyses to determine agreement in methods. This analysis found that there was significant agreement between these methods up to a species richness of around 75-100 species in freshwater systems, but not in marine systems. This suggests eDNA metabarcoding methods and conventional methods serve best as complements when measuring species richness of an area.

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DNA Analysis of Unknown Hair Samples Presentation

FRSC-3111H: Non-Human DNA Forensics (Trent University)

This is a PowerPoint presentation of my case study of an unknown, non-human hair sample. I extracted the DNA using appropriate techniques, submitted them for microsatellite analysis, and reported the results in a scientific manner. I was able to determine species, sex, and probability of an individual with the same DNA profile. The species was determined using a BLAST search of the extracted sequence. The likelihood of the sample coming from the same source as the suspected sample was calculated using known allele frequencies in moose populations.

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Wildlife CSI: Ivory Trade

ERSC-3501H: Environmental Communication (Trent University)

This is a video describing the harmful ivory industry and how expert scientists are using genetics to track ivory poachers and saving elephants. With DNA, wildlife forensic scientists can find where most of the poaching happens, help convict poachers, and prevent future poaching through prediction of where poachers strike next.

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How can we use DNA to conserve a species?

ERSC-3501H: Environmental Communication (Trent University)

This is a video about how eDNA can be used for conservation purposes geared towards a general, non-expert audience. eDNA is an easy, effective, and cruelty-free method to track species. It can indicate where killer whale populations are without ever having to disturb them. Scientists can find where killer whales are or have been just by checking for killer whale DNA in different areas.

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