AP Computer Labs: 1- AP Investigation 2: We will do one of two adapted versions. Regardless of which one, watch this video on youtube before lab begins. The program for both versions can be found on the student drive (I think it's the K drive) of the desktops in my room. Just find the folder with your student # and open it. If you're working on this from home, you can download Allele A1 from the Evolutionary Analysis website: faculty.washington.edu/herronjc/SoftwareFolder/AlleleA1.html . Versions are provided that run under MacOS and Windows. If needed, here is the AlleleA1 manual. Before you begin the lab, It's also recommended to watch the Bozeman video on 'Population Modeling'. Although he's using a different program, the concepts and results still apply. ADAPTED VERSIONS OF AP LAB #8:
If there are problems with www.phylogeny.fr site, try the mirror site. If that still doesn't work, make your cladogram with www.uniprot.org.
Also, if the last website doesn't work (T-coffee), there is another site we can try: https://www.ebi.ac.uk/Tools/msa/clustalo/ If that doesn't work, just take a 'snip' and paste it into the document (or a word doc). Save this in your student drive and/or email it to yourself and we'll deal with it later.
Reference Materials for this Unit: 1- "Concepts of Evolution" PPt (from Magnet Biology) is in the Power Point section of this blog (scroll up) 2- Hardy Weinberg Worked Sample Problems 3- 'Hardy Weinberg' PPt (with examples): In Power Point section of this blog (scroll up) 4- Go to youtube.com and search for 'Science with Mr.J'. He has video lectures for almost every chapter in AP Bio, using our book. Since our time is becoming very limited, my 'lectures' over the remaining chapters will also be brief. He does a very good job with covering the material. If you find another lecture series that's good, please let me know! 5- Need help with phylogenetic trees? Here are some very good youtube videos for understanding cladograms (including monophyletic, paraphyletic, polyphyletic, parsimony, etc): Here's one from Kahn Academy that shows you how to 'build a tree' and another one that gives a very clear example of parsimony.
Videos: 1- Bozeman- AP Bio 'Natural Selection'. Complete this sheet. 2- Bozeman- Comparing DNA Sequences. (How to Use BLAST data base) 3- Bozeman- Phylogenetic Trees (alternate: this one from Kahn Academy ) 4- Phylogenetic Trees- watch first. Then, Phylo. Trees Practice. *The guy ('SimpleBiology') who made these made an entire series of Evolution videos recently (fall 2017) and they are REALLY GOOD. 5- Parsimony (and here's another one that gives a very clear example of parsimony). 6- Hardy Weinberg- see SimpleBiology series on youtube, above, (#4) or watch Bozeman Hardy-Weinberg on youtube. 7- BLAST tutorial: This one is the most clear cut for what we are doing, but the example shown uses a protein sequence of amino acids, instead of a nucleotide sequence. This one is good, but you may want to fast forward to around the 7:25 minute mark and start it there. 8- 'Science with Mr.J' video series for AP Bio on youtube.com. More info on this is posted under "Reference Materials", directly above. 9- Stickleback Video with Quiz (we will either do this one or the Bozeman one, below). May have to be done in next unit 10- Bozeman AP Bio Stickleback video and worksheet. May have to be done with next unit.
GAMES: Has anyone heard of the video game 'Phylo'? Here's the info. Hope we have time to try it!