Fish do grow on trees: Analysis of deep-sea anglerfish adaptive immunogenomics using phylogenetic trees
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Horn, Kristin Rebecca
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With an ever-growing concern for our environment, scientists look to new tools and techniques to learn as much as they can to understand our Earth and prevent further environmental harm. In their journey to explore the sea armed with the increased versatility of genomics and bioinformatic tools, researchers are finding previously studied animals to be more complex than originally anticipated. This thesis looks at the anglerfish and their immunogenomics to see how their transition to the deep-sea has paralleled changes in their genes. This research uses the MEGA software to align orthologous amino acid sequences from 11 genes within 13 anglerfish species. The PAML CODE-ML software application was used to complete evolutionary modeling by means of branch-site likelihood ratio tests for positive selection on the branches of phylogenetic trees. An existing data set was used to observe and compare changes in specific genes of six families of deep-sea anglerfish species while using three shallow water species, including a species from Chaunacidae, the living sister lineage to deep-sea anglerfish (Ceratioidei), as outgroup comparisons. Analysis of the trees from the sampled genes determined that there was potential evidence of adaptive change in the form of lineage-specific non-silent substitutions of amino acids at shared sites in gene-specific alignments which was used as a proxy to indicate positive selection and describe differences between the studied genes in shallow and deep-sea anglerfish. Additionally, the author noted several interesting trends with regards to the genes and sexual parasitism which were also discussed.