COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES
As knowledge of evolutionary processes has expanded over the years, we havedeepened our understanding about how they drive organismal, cellular, and molecular biology and the factors beyond natural selection that are involved. Nevertheless, selection maintains a role in fixing and maintaining succes...
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fttempleuniv:oai:scholarshare.temple.edu:20.500.12613/4753 2023-05-15T15:13:12+02:00 COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES Northover, David orcid:0000-0003-2889-1098 Liberles, David A. 2020 94 pages https://hdl.handle.net/20.500.12613/4753 eng eng Temple University. Libraries http://dx.doi.org/10.34944/dspace/4735 Theses and Dissertations 14312 http://hdl.handle.net/20.500.12613/4753 IN COPYRIGHT- This Rights Statement can be used for an Item that is in copyright. Using this statement implies that the organization making this Item available has determined that the Item is in copyright and either is the rights-holder, has obtained permission from the rights-holder(s) to make their Work(s) available, or makes the Item available under an exception or limitation to copyright (including Fair Use) that entitles it to make the Item available. http://rightsstatements.org/vocab/InC/1.0/ Biology Bioinformatics Thesis/Dissertation Text 2020 fttempleuniv https://doi.org/20.500.12613/4753 https://doi.org/10.34944/dspace/4735 2021-08-26T18:59:42Z As knowledge of evolutionary processes has expanded over the years, we havedeepened our understanding about how they drive organismal, cellular, and molecular biology and the factors beyond natural selection that are involved. Nevertheless, selection maintains a role in fixing and maintaining successful adaptations to new niches, whether from environmental change or organismal migration. Adaptation should not be considered solely on the level of individual genes and point substitutions as selection occurs on multiple levels. Examination on these multiple levels can further aid in understanding the constraints on evolution and how organisms can attain a phenotype. Here we present two packages of tools for the examination of selection on the levels of protein structure and genetic pathways as well as on the individual gene and sequence levels., followed by examples of potential applications. First, we present a package of Application Programming Interface (API) tools that simplifies use of The Adaptive Evolutionary Database. Second, we present a package of tools implemented in the Rust programming language for fast and reliable analysis of phylogenetic data. Then we describe the phenotypic data and methodology for use of these tools to analyze evolution on multiple levels, where genomic data is available. A broad scale analysis of the protein structural properties of evolutionary genetic changes in proteins is developed and described. We also present an organization of phenotypic data for mammals in the arctic biome, an ancestral reconstruction of the evolution of the phenotypic traits under study, and demonstrate a methodology to apply the tool packages to this cohort when sufficient genomic data is available. Biology Accompanied by two compressed .zip files: 1) Titled Charts 2) Appendices Thesis Arctic TUScholarShare (Temple University) Arctic |
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Open Polar |
collection |
TUScholarShare (Temple University) |
op_collection_id |
fttempleuniv |
language |
English |
topic |
Biology Bioinformatics |
spellingShingle |
Biology Bioinformatics Northover, David orcid:0000-0003-2889-1098 COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES |
topic_facet |
Biology Bioinformatics |
description |
As knowledge of evolutionary processes has expanded over the years, we havedeepened our understanding about how they drive organismal, cellular, and molecular biology and the factors beyond natural selection that are involved. Nevertheless, selection maintains a role in fixing and maintaining successful adaptations to new niches, whether from environmental change or organismal migration. Adaptation should not be considered solely on the level of individual genes and point substitutions as selection occurs on multiple levels. Examination on these multiple levels can further aid in understanding the constraints on evolution and how organisms can attain a phenotype. Here we present two packages of tools for the examination of selection on the levels of protein structure and genetic pathways as well as on the individual gene and sequence levels., followed by examples of potential applications. First, we present a package of Application Programming Interface (API) tools that simplifies use of The Adaptive Evolutionary Database. Second, we present a package of tools implemented in the Rust programming language for fast and reliable analysis of phylogenetic data. Then we describe the phenotypic data and methodology for use of these tools to analyze evolution on multiple levels, where genomic data is available. A broad scale analysis of the protein structural properties of evolutionary genetic changes in proteins is developed and described. We also present an organization of phenotypic data for mammals in the arctic biome, an ancestral reconstruction of the evolution of the phenotypic traits under study, and demonstrate a methodology to apply the tool packages to this cohort when sufficient genomic data is available. Biology Accompanied by two compressed .zip files: 1) Titled Charts 2) Appendices |
author2 |
Liberles, David A. |
format |
Thesis |
author |
Northover, David orcid:0000-0003-2889-1098 |
author_facet |
Northover, David orcid:0000-0003-2889-1098 |
author_sort |
Northover, David |
title |
COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES |
title_short |
COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES |
title_full |
COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES |
title_fullStr |
COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES |
title_full_unstemmed |
COMPARATIVE BIOINFORMATIC AND MOLECULAR EVOLUTIONARY ANALYSIS OF CHORDATE GENES AND GENOMES |
title_sort |
comparative bioinformatic and molecular evolutionary analysis of chordate genes and genomes |
publisher |
Temple University. Libraries |
publishDate |
2020 |
url |
https://hdl.handle.net/20.500.12613/4753 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
http://dx.doi.org/10.34944/dspace/4735 Theses and Dissertations 14312 http://hdl.handle.net/20.500.12613/4753 |
op_rights |
IN COPYRIGHT- This Rights Statement can be used for an Item that is in copyright. Using this statement implies that the organization making this Item available has determined that the Item is in copyright and either is the rights-holder, has obtained permission from the rights-holder(s) to make their Work(s) available, or makes the Item available under an exception or limitation to copyright (including Fair Use) that entitles it to make the Item available. http://rightsstatements.org/vocab/InC/1.0/ |
op_doi |
https://doi.org/20.500.12613/4753 https://doi.org/10.34944/dspace/4735 |
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1766343785010167808 |