Course Description
Survey of the wealth of information arising from genomic research conducted on diverse species across the tree of life. Students will explore the evolutionary diversification of genomes in phylogenetically remote organisms and refine critical thinking and technical writing skills through analysis of publications drawn from the recent literature.
Additional Requirements for Graduate Students:
Graduate students will be required to write a review article, in
the format of a reputable journal, on a subject that is closely
associated, but not extensively overlapping, with subject matter
covered in the course.
Athena Title
Genome Evolution
Prerequisite
GENE(BIOL) 3200
Semester Course Offered
Offered fall
Grading System
A - F (Traditional)
Course Objectives
Strategies for exploring the fundamental processing governing life are no longer based merely on a trait-by-trait or a gene-by-gene research paradigm, but are now conducted on global, whole-organism and genome-wide scales. The terminology, experimental logic, and modes of analysis integral to genomic research have become essential tools for any student who wishes to be competitive for a career in 21st century, biology-related fields. However, as always, fundamental talents, such as analytical reasoning, critical thinking, effective writing, and oral presentation skills remain essential qualities for both undergraduate and graduate students. This course aims to familiarize students with the latest developments, research strategies, and modes of analysis used in comparative genomic research. Additionally, it provides considerable practice in critical thinking, analytic, and communication skills through reading, interpretation, and inquiry-based discussion of scientific papers drawn from the recent literature. Students enrolled at both the undergraduate and graduate levels will have opportunity to express their ideas more formally through strategic writing assignments and to revise their work in light of critical feedback from course instructors. Students enrolled at the graduate level will prepare a comprehensive, original review article, in proper journal format, on a topic closely related to the subject matter covered in the course.
Topical Outline
The course syllabus is a general plan for the course; deviations announced to the class by the instructor may be necessary. The Tree of Life How are phylogenies reconstructed? How much confidence can we place in them? How can we use them to design experiments or interpret comparative data? Genome Diversity When and how did genomes evolve? The variety of genomes in the tree of life Viral, eubacterial, archael, mitochondrial, protist (free-living and parasitic), chloroplast, algal, fungal, plant, and animal genomes. Contemporary Genomic Technology How is DNA sequenced? How are entire genomes sequenced? What is a transcriptome and how is it studied? What is a proteome and how is it studied? Survey of articles drawn from the recent literature exploring: Protogenomes and the ‘RNA World’ Hypothesis Viral genomes Eubacterial genomes archael genomes mitochondrial genomes protist genomes (free-living and parasitic) chloroplast genomes algal genomes fungal genomes plant genomes animal genomes Reconstructing the natural history of genomes Embracing technology: What research strategies and modes of analysis are genome biologists using and how do they work? Capturing essential properties in technological language: In light of what we’ve learned, how should we define or redefine terms like: genome chromosome synteny polyploid What phenomena or processes still lack a suitable descriptor? Cataloging the mechanisms of genome evolution: What are the range and frequency of mechanisms we discovered that shape and diversify genomes? Dissecting, quantifying and reporting genomic diversity: What strategies should we employ to organize, categorize, summarize and interpret all this comparative data? For reporting it? Can these answers influence how the raw data is obtained? Back to the Tree of Life; Resolving the time-scale and possible causes of major transitions in genome diversification What are the underlying selective forces governing genome diversification? Expanding the frontier: Where is comparative genomic biology heading? What are the next likely breakthroughs? What are the logical targets for future genomic projects? Are we making full and sufficient use of existing technology? What technological tools do we still lack? What role will you play in the future of genomic biology?
Syllabus