May 2009 Archives

June Conferences

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This month I’m going to two conferences: SMBE and Evolution.

At SMBE, I’ll be giving a poster in poster session #2 on Friday, June 5th. Drop by between 8–9pm and take your picture with Prof. Steve Steve.

At Evolution, I’ll be giving my talk on Tuesday, June 16th at 11am, in the “Population Genetic Modeling” section.

In my previous post, I mention that I will email you a reprint of a paper, if you send an email to [Enable javascript to see this email address.]. I actually do nothing. The reprint is handled automatically using my Procmail. In this post I will explain how I got it to work.

The first thing to note is that my email supports sub-addressing. This means that in the above email address, the mail is delivered to “reed” with argument “2009b”. I use this argument to determine that the sender is looking for a PDF reprint of my recent paper.

Next I had to modify my .procmailrc to copy 2009b requests to a specific folder and reply to them with the paper. Here is my solution, which is based somewhat on the solution for vacation notice emails with Procmail.

PLUS=$1 #copy the sub-address into variable PLUS

[snip]

:0c:
* PLUS ?? ^2009b$
* !^FROM_DAEMON
* !^X-Loop: reed+2009b@[snip]
* !^X-Spam-Status: Yes
"Requests"

   :0 A
   | (formail -r -A"From: reed@[snip]" -A"X-Loop: reed+2009b@[snip]" \
        -I"MIME-Version: 1.0" \
        -I"Content-Type: multipart/mixed; boundary=\"------------070504020300020208040609\""; \
      cat $HOME/papers/2009b.msg ) | $SENDMAIL -oi -t

This solution will copy and auto-reply to the incoming email if it matches the +2009b argument, is not from an email list, has not already been auto-replied to, and is not spam.

To send the reply, I use the formail tool that comes with Procmail to construct the reply. This involves using flags to specifying some email header variables, followed by catting a prespecified email body that contains the encoded attachment. I generated the body by sending myself the email and attachments that I wanted to send out to people, and then copying the body of the message to a text file, 2009b.msg. I just had to copy the boundary header used by my email program to the formail recipe above.

This rule can be expanded to autorespond to multiple requests and to handle formail or sendmail errors.

The final chapter of my dissertation has finally been published in Molecular Ecology. This is the project that got me involved with the software SPAGeDi. Although, none of that work remains in the final version of the paper, I have successfully collaborated with the authors of SPAGeDi to make it portable to Linux and OS X. The portable version will soon be made public.

Anyway, the citation of my paper is

Cartwright RA (2009) Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. Molecular Ecology 18:2327-2336. [doi:10.1111/j.1365-294X.2009.04180.x]

Unfortunately, there is not a free version available yet online. The research was partially funded by NIH, so a copy should show up in pubmed in several months. Until then, you can email me at [Enable javascript to see this email address.] (NB this is not my usual address), and I’ll send you a reprint.

Abstract: Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighborhood sizes, and identity-by-descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic SI on unlinked loci. More importantly both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side effect.

Updates

I haven’t blogged here in a while, but I do have some recent posts on Panda’s Thumb.

I’ve been busy recently. I’ve flown to Oxford and Montreal for postdoc interviews. I’m also preparing a poster for SMBE in Iowa and a talk for Evolution in Idaho.

I’m currently on vacation. We went snorkeling in Florida: Wakulla Springs, Ginnie Springs, Santa Fe River, Ichetucknee River, and Rainbow Springs.

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This page is an archive of entries from May 2009 listed from newest to oldest.

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