BigData 2018: Difference between revisions
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==What is evolutionary genomics?== | ==What is evolutionary genomics?== | ||
Genomes differ among individuals and | Genomes differ among individuals and species. Evolutionary genomics studies genome variability and genome changes using evolutionary principles. Typical applications include identification of human genome variations associated with diseases and identification of pathogen virulence genes. | ||
Genome changes are studied at two levels: (1) within-species/within-population variations (e.g., human genetic variation), and (2) between-species divergence (e.g., human-mouse comparisons). | Genome changes are studied at two distinct levels: (1) within-species/within-population variations (e.g., human genetic variation), and (2) between-species divergence (e.g., human-mouse comparisons). | ||
The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or disease-free. | The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or disease-free. | ||
The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree) not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life. | The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree), not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life. | ||
==Three applications from Qiu Lab== | ==Three applications from Qiu Lab== | ||
Revision as of 14:21, 20 June 2018
What is evolutionary genomics?
Genomes differ among individuals and species. Evolutionary genomics studies genome variability and genome changes using evolutionary principles. Typical applications include identification of human genome variations associated with diseases and identification of pathogen virulence genes.
Genome changes are studied at two distinct levels: (1) within-species/within-population variations (e.g., human genetic variation), and (2) between-species divergence (e.g., human-mouse comparisons).
The key for analyzing genome variations within species is "population-thinking", the idea that there is no one individual genome that is standard, normal, or disease-free.
The key for comparing genomes across species is "tree-thinking", the idea that evolution happens by diversification (like a branching tree), not by climbing a ladder. There is no such thing as "advanced" or "primitive" species. All living species have the exact same evolutionary distances/time of divergence since the origin of life.
Three applications from Qiu Lab
- Comparative genomics of worldwide Lyme disease pathogens
- Evolution of multi-drug antibiotic-resistance Pseudomonas in cancer patients
- Genomic epidemiology of Group B Streptococcus
Reference
- Graur, 2016, Molecular and Genome Evolution, First Edition, Sinauer Associates, Inc. ISBN: 978-1-60535-469-9. Publisher's Website
- Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.
Learning Goals
- Be able to describe evolutionary relationships using phylogenetic trees
- Be able to use command-line tools for batch-processing of genome files
Quizzes & Assignments
- "Tree Thinking Quizzes"
- FASTA manipulations with
bioseq