Hi all, For this week we’ll review phylogenetic methods, as described in the Holder and Lewis review, learn more generally about experimental evolution methods, as reviewed by me, and then spend the rest of the time focusing on the question: What are the effects of chance and history on adaptation and evolution, in general? I [...]
Entries from September 27th, 2007
Assignments for 10/2 and 10/4
September 27th, 2007 · No Comments · adaptation, Assignments, experimental evolution, phylogeny
9/27 assignment
September 25th, 2007 · No Comments · Assignments
Please blog this week on the following question: How does the Lerat et al. 2005 article alter your view of the microbial species concept? Is HGT a powerful enough force to erode your confidence of the existence of microbial species? How do these findings change the way we might apply Mayr’s BSC to bacteria?
Phylogenetics background reading
September 25th, 2007 · No Comments · phylogeny
Hi guys, go to: http://micropopbio.org/cooper/2007/09/25/phylogenetics-background-reading/ to find the link to the review on phylogenetic methods. Included in this review are descriptions of parsimony, distance, maximum likeklihood, Bayesian analysis, and assessing the quality, or confidence of any given tree model.
Reponse to Whitaker paper
September 24th, 2007 · No Comments · General
the paper says this towards the end, “Our data show that gene flow among Sulfolobus populations is limited. Either the highly specialized growth requirements ofthese hyperthermophilic acidophiles prevent dispersal, or immigrants are unable to persist in established endemic populations, or both.” I am wondering, hypothetically, if species from say for example Lassen are introduced in [...]
Assignments will now be found on the ASSIGNMENTS blog
September 22nd, 2007 · No Comments · Assignments, General
I’ve put readings for Week 3 up in my new Assignments page, which is linked on the left column of the Micropopbio blog. Its direct link is http://micropopbio.org/cooper/. Since this blog requires that you register to see the material, it should solve the copyright issue and allows us to leave Blackboard for good. Let me [...]
Week 2 summary and thoughts: TSQ
September 20th, 2007 · No Comments · Class notes, General
Dear class, Many of you have now taken full control of your blogs, have incorporated beautiful designs, and have posted provocative content. I will highlight some of these below. Before I do so, I’ll make my own contributions to our group discussion of The Species Question. 1) I had promised a picture to illustrate the [...]
Apologies for the delayed update
September 18th, 2007 · No Comments · Assignments
Dear class, My apologies for the delayed posting of our articles and assignments for this week. Just as I was about to post all of the material, our site went down for reasons that I don’t yet understand. But they should have gone up over the weekend, and for this I am sorry. For Tuesday, [...]
Room change!
September 13th, 2007 · No Comments · General
We are leaving the hot and cavernous HS 214 behind for the cozy confines of Rudman 281! See you there on Tuesday at 11:10, and remember that you need a pass-card to go down the 2nd floor of Rudman; 281 is on the fire-station side of the bldg. Cheers!
Lecture notes for 9.13.07
September 13th, 2007 · No Comments · Class notes, molecular typing, phylogeny
Today we covered: The Cho and Tiedje paper, “Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil”, AEM. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11097926 This article relied heavily on two methods: BOX-PCR, a molecular typing method, and UPGMA, a method of estimating similarity and indirectly, phylogenetic distance. Good descriptions for each of these can be found at: BOX-PCR [...]
How did extremophiles disperse in the first place?
September 11th, 2007 · 1 Comment · General
The Whitaker article in Science on Sulfolobus shows us that extremophiles face the reality of dealing with physical barriers that block their dispersal, but how did they disperse in the first place? Was there one location on the earth where thermophilic acidophiles arose and then disperse, or did they all arise independently due to selection [...]
