BIOL 470: Schedule for week of March 23-27
Summary
This will be our first week of class completely online. Please be patient and flexible; I will do likewise. Please let me know if you are having issues learning remotely so we can address problems right away. This schedule is tentative and subject to change.
Assignments:
Fill out survey by Monday, March 23 @ 5 PM HST. Link: https://forms.gle/a3gAVGEp8eTSMoex6
Laulima Discussion on blog/paper readings (due Midnight on Tuesday, April 1)
- Go to Laulima, click “Discussion and Private Messages”, then “Class Discussions”. Post under " Phylogenetics and COVID-19 readings"
Readings:
Emlen & Zimmer, Chapter 8
A scientific blog post and paper about using phylogenies to study COVID-19
- Blog post: http://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356
- Paper by Anderson et al.: https://www.nature.com/articles/s41591-020-0820-9
Schedule
Note that on Monday, class will meet synchronously on Google Meet meet.google.com/osn-ieyh-jjx. Class will be recorded and posted online if you are unable to attend. Remaining instruction will be asynchronous, meaning you can work at your own pace and desired time.
In general, I strongly recommend attending synchronous meetings if you can. I also recommend establishing routine times that you work on asynchronous assignments. A routine will help you develop good work habits, keep you engaged in the class, and prevent you from having to cram later.
Monday, March 23
Dr. Sandy Kawano will talk about her reseach on natural selection in Hawaiian gobies.
We will go over questions and concerns about online instruction
After class, I will post your Midterm Exam 2 grades and send out the key.
Wednesday, March 25
We will return to phylogenetics, this time using DNA and other molecular characters to make inferences about evolution.
Study online module on the gene trees and coalescent simulations:
Watch videos
- Video 1 (15 minutes): Using phylogenies to track COVID-19 (aka SarsCov2)
- Video 2 (12 minutes): Where did COVID19 come from? Where’s it going?
- Read chapter 8 from textbook, plus a paper and blog post on using phylogenies to understand the origins of COVID-19. See links in the “Readings” section.
Note that these readings are highly technical and I don’t expect you to understand much of the detail. Focus on the questions that motivated the study, the evolutionary approaches the authors used, the main conclusions, and remaining uncertainty.
- Discuss video and readings for 1 participation point. Go to Laulima, click “Discussion and Private Messages”, then “Class Discussions”. Post under “Phylogenetics and COVID-19 readings”
Friday, March 27
Finish reading Chapter 8 and additional readings
Study online module on the multispecies coalescent (link TBA, might be weekend or next week)
Continue discussion on video and readings from Wednesday
Activity: simulate multispecies coalescent using genomic data and compile results with class (will be up later today, so work on over the weekend or early next week)