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Art Poon
Evolutionary consequences of mutation

office: UCSD AVRC Annex
mail: 150 West Washington St.
University of California, San Diego

  • Hon BSc Biology (1998). University of Toronto, Canada.
  • MSc Zoology (2000). University of British Columbia, Canada.
  • PhD Biology (2005). University of California at San Diego, USA.
  • currently doing post-doc research at UCSD.
Updated stupendously infrequently; last update January 4, 2007.

RES

PUB

CON

LNK

This is, for all intents and purposes, my Ph.D. website. If I ever have a bunch of time on my hands (likely never), I'd like to throw together something that's a little more up to date. For example, though compensatory mutation is still a primary research interest of mine, my research has also broadened in scope.

Oh, and I also publish a weekly web-comic now: Go to datamonkeys! the web-comic.

research interests

CAVEAT: This was written while I was doing my master's degree and as a result will come across as a little naive. The world was a warm, shinier place back then ;-)

I am interested in mutation as an evolutionary force. The generally held notion is that most mutations have adverse effects on the fitness of an organism -- that is to say, that most mutations are deleterious. Some of the most brilliant and ambitious experiments in the literature (read: Mukai!) have been devoted to quantifying this nature of mutation. Nevertheless, there remains much to be elucidated about the evolutionary consequences of recurrent mutation. My current research program focuses on the problem of genetic load -- i.e. the reduction in mean fitness -- in finite populations.

There is an abundance of molecular evidence that mutations can compensate for each other's effects. For example, the stem-loop structure of tRNA is sensitive to mutation but can be restored by additional mutations at other points on the sequence. Biological complexity at the molecular, biochemical, regulatory and developmental levels virtually guarantees some degree of compensation.

Mutational models in evolutionary biology, however, do not usually regard compensatory mutation as an important factor. I have found that changing the assumptions of the mutational model such that compensatory mutations are frequent qualitatively changes the predictions of the model. This was carried out for a model of the load caused by fixed deleterious mutations in finite populations.

The next step, then, is to determine whether compensatory mutation is a frequent or rare biological phenomenon. My next project is to perform a mutation accumulation experiment that estimates this rate. [Actually, it turns out that constructing genotypes with site-directed mutagenesis is a difficult but better way to get at this question. That's what I ended up doing. ­ A.P. Oct 8, 2004] There is some indication that compensatory mutations arise at an appreciable rate in a recent experiment carried out by Burch and Chao on the RNA virus phi6.

publications

  • Poon A and SP Otto. 2000. Compensating for our load of mutations: Freezing the meltdown of small populations. Evolution 54(5): 1467-1479.

  • Poon A and L Chao. 2004. Drift Increases the Advantage of Sex in Bacteriophage phi6. Genetics 166: 19-24.

  • Poon A, BD Davis and L Chao. 2005. The Coupon Collector and the Suppressor Mutation: Estimating the Number of Compensatory Mutations by Maximum Likelihood. Genetics 170(3): 1323-1332.

  • Poon A and L Chao. 2005. The rate of compensatory mutation in the bacteriophage phiX174. Genetics 170(3): 989-999.

  • Poon AFY and L Chao. 2006. Functional limits on the fitness effect size of compensatory mutations in the bacteriophage phiX174. Evolution 60(10): 2032-2043.

  • Poon AFY, FI Lewis, SL Kosakovsky Pond, and SDW Frost. 2007. Detection of N-linked glycan interactions by phylogenetic and Bayesian network analysis of HIV-1 envelope sequences. PLoS Computational Biology 3(1): e11.

  • Poon AFY, SL Kosakovsky Pond, P Bennett, DD Richman, AJ Leigh Brown, and SDW Frost. 2007. Adaptation to human populations is revealed by within-host sequence polymorphisms in HIV-1 and hepatitis C virus. In review.

  • Poon AFY, KC Brouwer, SA Strathdee, M Firestone Cruz, RM Lozada, DD Heckathorn, SDW Frost. 2007. Modeling respondent-driven sampling using stochastic context-free grammars. Submitted.

contact information

e-mail: apoonatbiomaildotucsddotedu

links

EDG - Evolution Discussion Group @ UBC

A weekly paper discussion group on current evolutionary biology, convening at the Department of Zoology, UBC. I still look this up sometimes just to see what people are reading, and when I need to select an article for our own journal group.
Canadian Society for Ecology and Evolution
"A non-partisan group of practising ecologists and evolutionary biologists throughout Canada."
"Some Modest Advice for Graduate Students"
Academic wisdom from Stephen C. Stearns. There are many like it out there, but not so many with a sympathetic view to the harsh realities of the graduate career.
American Naturalist
A monthly periodical produced "for the American Society of Naturalists by the University of Chicago Press". Lots of accessible theory, good evolutionary biology and some natural history to keep things real.
Journals in Ecology and Evolution
A comprehensive list of links to academic journals in ecology and evolutionary biology maintained by my supervisor at UBC. Some of the links may be broken, but it is useful to have all the titles in one place.
Phylogeny Programs
A nice resource for phylogenetic software on the web, maintained by J. Felsenstein.
Numerical Recipes Online
The most useful programming guide on my shelf, available in web-form as PostScript or PDF files. Available for C, Fortran and Pascal. I actually own a print copy, but sometimes it's just more convenient to look it up here.