PLB/ZOL 849 Evolutionary Biology Spring 2015
Genome Evolution – April 28th and April 30th
Instructor: Jason Gallant
Recent advances in technology have made it possible to collect genome sequence data from a wide variety of organisms at very little cost. Comparative genomics is an emerging new field that leverages this rapidly proliferating genomics data to address questions regarding the evolution of genomes and gene function.
Meeting 1- April 28th Reading Assignments:
During the first lecture, we will survey the tools and methodological approaches to comparative genomics:
- “Chapter 15: How Genomes Evolve” in Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.
- van Dijk, Erwin L. et al. Ten years of next-generation sequencing technology. Trends in Genetics , Volume 30 , Issue 9 , 418 – 426
- Hawkins, R. David, Gary C. Hon, and Bing Ren. “Next-generation genomics: an integrative approach.” Nature Reviews Genetics 11.7 (2010): 476-486.
Meeting 2- April 30th Reading Assignments:
During our second meeting, we will consider a few “case studies” in comparative genomics. Read ALL of the following and consider the questions during your readings. Write a one page essay on ONE of the assigned papers (determined by your name), addressing each of the questions. Send your essay to firstname.lastname@example.org by April 29th at 5:00PM.
If your last name falls between A and Li, you are assigned:
- Gallant, Jason R., et al. “Genomic basis for the convergent evolution of electric organs.” Science 344.6191 (2014): 1522-1525.
1) What is the central thesis of this paper?
2) Was the genome of the electric eel necessary for this study?
3) How were homologues between fishes identified?
4) More than 20,000 genes were examined in this study, yet only 30 are discussed. Are you convinced of the importance of these genes and the central thesis of this paper?
If your last name falls between Lo and O you are assigned:
- Arnegard, Matthew E., et al. “Old gene duplication facilitates origin and diversification of an innovative communication system—twice.” Proceedings of the National Academy of Sciences 107.51 (2010): 22172-22177.
1) What are the predictions that Scn4aa directly contributes to the parallel evolution of myogenic electric organs? Would you add any additional predictions?
2) What are the functional consequences of positive selection on Scn4aa in electric fish?
3) Do the authors make a compelling case that Scn4aa directly contributed to the parallel evolution of myogenic electric organs?
4) Do you think it is merely coincidence that electric fish have used Scn4aa repeatedly? Can you design a comparative genomics experiment that might address this question?
If your last name name falls between P-Z you are assigned Gallant et al. “Ancient Homology…”
- Gallant, Jason R., et al. “Ancient homology underlies adaptive mimetic diversity across butterflies.” Nature communications 5 (2014).
1) What is the hypothesized “cause” of mimetic wing patterning in Limenitis butterflies? What about in Heliconius butterflies? Why is this considered an example of “ancient homology”?
2) RNA-seq is used in a different way than in study on convergent electric organ evolution. What did the authors find and how does it relate to the findings of the hypothesized “cause” of mimetic wing patterning?
3) The quotation referenced in the beginning of this article is below:
The animal world is full of convergences …If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved. The saying “many roads lead to rome” is as true in evolution as it is in daily affairs.-Ernst Mayr Animal Species and Evolution
The authors of this article seem to demonstrate that fewer roads lead to rome than previously thought, at least for butterflies. What factors might contribute to the same vs. different biochemical pathways underlying the convergent evolution of phenotypic traits?
Below follows a list of readings on topics discussed here for students that may be considering genomics as part of their thesis work, or are eager to go more in depth on some of these topics then the assigned readings go:
- Nagarajan, Niranjan, and Mihai Pop. “Sequence assembly demystified.” Nature Reviews Genetics 14.3 (2013): 157-167.
- Wheeler, David, and Medha Bhagwat. “BLAST QuickStart.” (2007). http://www.ncbi.nlm.nih.gov/books/NBK1734/
- Compeau, Phillip EC, Pavel A. Pevzner, and Glenn Tesler. “How to apply de Bruijn graphs to genome assembly.” Nature biotechnology 29.11 (2011): 987-991.
- Martin, Jeffrey A., and Zhong Wang. “Next-generation transcriptome assembly.” Nature Reviews Genetics 12.10 (2011): 671-682.
- Roux, Julien, Marta Rosikiewicz, and Marc Robinson-Rechavi. “What to compare and how: comparative transcriptomics for Evo-Devo.” bioRxiv (2014): 011213.
- Hardison RC (2003) Comparative Genomics. PLoS Biol 1(2): e58. doi:10.1371/journal.pbio.0000058
- Miller, Webb, et al. “Comparative genomics.” Annu. Rev. Genomics Hum. Genet. 5 (2004): 15-56.
Methodological Approaches to Comparative Genomics:
- Allen, Eric E., and Jillian F. Banfield. “Community genomics in microbial ecology and evolution.” Nature Reviews Microbiology 3.6 (2005): 489-498.
- Luikart, Gordon, et al. “The power and promise of population genomics: from genotyping to genome typing.” Nature Reviews Genetics 4.12 (2003): 981-994.