Microbial Population Biology

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 point you to [...]

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?

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.

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 Yellowstone, then what [...]

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 [...]

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 [...]

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 [...]

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!

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 (in the context [...]

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 [...]