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        <title>EEB 5348 -- Population Genetics</title>
        <link>http://darwin.eeb.uconn.edu/eeb348/</link>
        <description>Announcements for EEB 5348, Population Genetics, at the University of Connecticut</description>
        <language>en</language>
        <copyright>Copyright 2008</copyright>
        <lastBuildDate>Wed, 19 Nov 2008 09:43:39 -0500</lastBuildDate>
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            <title>Neutralism and selectionism</title>
            <description><![CDATA[The latest issue of <i>Nature Review Genetics</i> has a paper by Andreas Wagner with some interesting perspective on molecular evolution. I don't plan to discuss it in class, but you might find it interesting. Here's the link.<br /><br /><a href="http://www.nature.com/nrg/journal/v9/n12/full/nrg2473.html">http://www.nature.com/nrg/journal/v9/n12/full/nrg2473.html</a><br /><br />There's also a paper in <i>PLoS Genetics</i> that you might find interesting. It's an alternative to QTL mapping in which all of the data are used simultaneously to predict phenotypes, and the particular loci that have an important influence on the trait emerge more naturally from the analysis.<br /><br /><a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000231">http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000231</a><br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/neutralism-and.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/neutralism-and.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Wed, 19 Nov 2008 09:43:39 -0500</pubDate>
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            <title>Project #3 available</title>
            <description><![CDATA[I've just posted Project #3 to the course web site. You'll find a link to the assignment and the associated data set on the detail page for <a href="http://darwin.eeb.uconn.edu/eeb348/lecture.php?rl_id=432">tomorrow's lecture</a>. I'll need to introduce you to one final software package, Arlequin. The current version is only available on Windows, which is the version I'll show. But I <b><i>think</i> </b>that the earlier version that runs on Macs will work for this project too. The interface is very similar. I may not have a chance to try the Mac version before lecture tomorrow, but I'll do my best to try it with these data by late on Monday, and I'll let you know whether you'll be able to run it on a Mac. ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/project-3-avail.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/project-3-avail.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Sun, 16 Nov 2008 21:06:06 -0500</pubDate>
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            <title>WinQTLCart problems</title>
            <description><![CDATA[I've heard from a few more people about problems. If you get this message and have time before lecture this morning, please try this and let me know what happens.<div><br /></div><div><ol><li>Open up WinQTLCart</li><li>Click on "Open", navigate to the directory where you installed it, open the directory called "Examples", and open the file "Maize.mcd".</li><li>Try an interval &amp;/or a composite interval analysis and see if it runs.</li><li>If it does, try downloading the Problem #4 data again. I just tried it again, and it worked for me. I clicked on the link to open the data file in my browser. (I'm using Firefox rather than IE. I wonder if that could cause a difference.) Once the file was open, I used File->Save to save it on disk.</li></ol></div>]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/winqtlcart-prob.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/winqtlcart-prob.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Wed, 05 Nov 2008 08:36:40 -0500</pubDate>
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            <title>Problems with WinQTLCart</title>
            <description><![CDATA[I've had reports from at least two people that WinQTLCart freezes on them when they try to do an analysis, either IM or CIM. I am investigating and trying to diagnose the problem. In the meantime, if you haven't downloaded WinQTLCart and the data yet, please give it a try and let me know whether or not it works for you and what operating system you're running.<br /><br />I <b><i>think </i></b>I know a workaround, but it's one I'd prefer to avoid using unless we have to. I'd rather fix the problem.<br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/problems-with-w.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/problems-with-w.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Wed, 05 Nov 2008 07:00:19 -0500</pubDate>
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            <title>New reading just posted</title>
            <description><![CDATA[James F. Crow, a <b><i>very </i></b>distinguished and <b><i>very</i></b> influential population geneticist at the University of Wisconsin, has an article that's relevant to today's lecture that just appeared in <i>Annual Review of Genetics</i> -- literally, just appeared. I received a notice in my e-mail box this morning. I've added a link to the article under the detail page for <a href="http://darwin.eeb.uconn.edu/eeb348/lecture.php?rl_id=426">Monday's lecture</a>, since that's the day that has the notes I'll be starting with this morning. Here's the <a href="http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.42.110807.091612">direct link</a>, if you don't want to click through to Monday's notes. ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/new-reading-jus.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/new-reading-jus.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Wed, 05 Nov 2008 06:55:55 -0500</pubDate>
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            <title>A seminar in the Statistics Department</title>
            <description><![CDATA[If you haven't had enough quantitative genetics and you want to see a really hairy application of (a) quantitative genetics and (b) Bayesian statistics, there's a seminar in the Department of Statistics this Friday that you won't want to miss.<br /><br /><b>Hierarchical spatial modeling of additive and dominance genetic<br />
variance for large spatial trial datasets</b><br />
<br />DATE:&nbsp;&nbsp; Friday, November 7, 2008<br />TIME:&nbsp;&nbsp;&nbsp; 4:00 p.m.<br />PLACE: CLAS Building - Room 344<br /><br />Professor Sudipto Banerjee<br />Department of Statistics<br />University of Minnesota<br /><br />Click through for the abstract.<br />]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/a-seminar-in-th.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/a-seminar-in-th.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Mon, 03 Nov 2008 08:27:15 -0500</pubDate>
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            <title>Problem #4 posted</title>
            <description><![CDATA[As promised (threatened?), I've posted the QTL problem. I'll need to show you two or three more things about&nbsp; QTL Cartographer before you can do the whole analysis, but if you'd like to download the data and make sure you can read it into QTL Cartographer, everything is available from the <a href="http://darwin.eeb.uconn.edu/eeb348/lecture.php?rl_id=426">detail page for tomorrow's lecture</a>.<br /><br />Oh, one word of warning. Each analysis for composite interval mapping is going to take a long time. I started an analysis of the %N at 25°C data this morning around 10:00am, and it's still running. I mention this as a warning. You're going to want to start your analyses fairly soon, and you'll probably want to set them to run overnight. If CIL takes inordinately long, which I'll know by lecture tomorrow, we'll settle for an interval mapping analysis instead.<br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/problem-4-poste.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/problem-4-poste.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Sun, 02 Nov 2008 13:16:27 -0500</pubDate>
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            <title>Updated notes on QTL Cartographer</title>
            <description><![CDATA[I've added some additional information on using QTL Cartographer to the online notes. You can find the new version of the notes from the <a href="http://darwin.eeb.uconn.edu/eeb348/lecture.php?rl_id=424">detail page</a> for 29 October. The new part is the section on <a href="http://darwin.eeb.uconn.edu/eeb348/lecture-notes/qtl-cartographer/node4.html">interpreting output files</a>. If you've already printed the notes, you only need to print the pages in this new section if you want a copy. ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/updated-notes-o.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/updated-notes-o.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Sun, 02 Nov 2008 10:56:27 -0500</pubDate>
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            <title>Problem #4 and QTL analysis</title>
            <description><![CDATA[I found a good QTL data set (from maize), so I'll be handing out Problem #4 on Monday. That's the bad news. The good news is that I've decided to make it due on the 14th rather than on the 10th. You'll only have one weekend available, but you'll still have a week and a half to get the analyses done.<br /><br />I'll hand out the final project on the 17th rather than on the 14th as originally planned.<br /><br />On a related note, we'll probably spend about half the lecture on Monday going over some more features of QTL Cartographer, and I will try to type up some supplementary notes that you're likely to find useful in doing your QTL project.<br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/problem-4-and-q.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/11/problem-4-and-q.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Sat, 01 Nov 2008 13:44:37 -0500</pubDate>
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            <title>MHC variation and mating in humans</title>
            <description><![CDATA[Remember the t-shirt article I told you about early in the course? Well, another paper about MHC variation and mate choice in humans just appeared in <a href="http://journals.royalsociety.org/content/f542428772r96x64/fulltext.html"><i>Proceedings of the Royal Society</i></a>. Here's the abstract:<br /><br /><blockquote><span><font size="2"><p>Previous studies in animals and humans show
that genes in the major histocompatibility complex (MHC) influence
individual odours and that females often prefer odour of MHC-dissimilar
males, perhaps to increase offspring heterozygosity or reduce
inbreeding. Women using oral hormonal contraceptives have been reported
to have the opposite preference, raising the possibility that oral
contraceptives alter female preference towards MHC similarity, with
possible fertility costs. Here we test directly whether contraceptive
pill use alters odour preferences using a longitudinal design in which
women were tested before and after initiating pill use; a control group
of non-users were tested with a comparable interval between test
sessions. In contrast to some previous studies, there was no
significant difference in ratings between odours of MHC-dissimilar and
MHC-similar men among women during the follicular cycle phase. However,
single women preferred odours of MHC-similar men, while women in
relationships preferred odours of MHC-dissimilar men, a result
consistent with studies in other species, suggesting that paired
females may seek to improve offspring quality through extra-pair
partnerships. Across tests, we found a significant preference shift
towards MHC similarity associated with pill use, which was not evident
in the control group. <b><i>If odour plays a role in human mate choice, our
results suggest that contraceptive pill use could disrupt
disassortative mate preferences.</i> </b>(emphasis added)<br /></p></font></span></blockquote>
      <p class="vsmall"><strong><br /></strong></p><br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/mhc-variation-a.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/mhc-variation-a.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Fri, 31 Oct 2008 18:08:28 -0500</pubDate>
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            <title>A note about QTL Cartographer</title>
            <description><![CDATA[You'll want to download a copy of <a href="http://statgen.ncsu.edu/qtlcart/index.php">QTL Cartographer</a> for the next problem. More specifically, you'll want to download a copy of <a href="http://statgen.ncsu.edu/qtlcart/WQTLCart.htm">WinQTLCart</a>.<sup>1</sup> Although there's a version available for Linux and Mac OS X, it requires you to use a command line interface that's a lot less convenient. If you'd really like to try the analyses with that interface, I'll do what I can to help, but I have to confess to not being very familiar with it. You may be on your own.<div><br /></div><div>Oh, there's also a nice PDF manual for <a href="http://statgen.ncsu.edu/qtlcart/WQTLCart-3.htm">WinQTLCart</a> available.</div>]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/a-note-about-qt.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/a-note-about-qt.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Annoucements</category>
            
            
            <pubDate>Wed, 29 Oct 2008 10:26:21 -0500</pubDate>
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            <title>What to hand in for Project 2</title>
            <description><![CDATA[For project 2 I'd like you to write out a couple of sentences/paragraphs answering each question.&nbsp; After that, I'd like you to attach the output from WinBUGS and then your WinBUGS code WITHOUT the data.&nbsp; This can be emailed to me to save paper.<br />]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/what-to-hand-in.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/what-to-hand-in.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Tue, 28 Oct 2008 13:17:47 -0500</pubDate>
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            <title>Project 2: how to start</title>
            <description><![CDATA[This is the suggestion I've been giving out, which seems to work well.<br />1)&nbsp; Start with the basic code Kent gave and modify it to fit the <i>Mimulus</i> dataset.<br />2)&nbsp; Starting with question 1, figure out which variables you need to solve for and then find the equations using terms you (well, technically Kent in this case) have already solved for, then write out the equations in WinBUGS format.<br />3)&nbsp; Repeat Step 2 for each problem SEQUENTIALLY.<br />4)&nbsp; Send me your code before you run it.&nbsp; Depending on how you wrote it, there are a couple of different methods to loading the data.<br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/problem-3-how-t.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/problem-3-how-t.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Tue, 28 Oct 2008 13:13:26 -0500</pubDate>
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            <title>Project 2 TA help extended</title>
            <description><![CDATA[I will be available on Wednesday between 8:30 and 5 (with the exception of 12-12:30 for lunch).&nbsp; Please stop by my office in Pharm/Bio if you need help. ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/problem-3-ta-he-1.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/problem-3-ta-he-1.html</guid>
            
                <category domain="http://www.sixapart.com/ns/types#category">Problems and projects</category>
            
            
            <pubDate>Tue, 28 Oct 2008 13:11:51 -0500</pubDate>
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            <title>Project 2 Hint error</title>
            <description><![CDATA[I've discovered an error in the WinBUGS code for the regression.&nbsp; Please use this code:<br /><pre> for (i in 1:n.obs) {<br />    y[i] ~ dnorm(mu[i], 0.001)<br />    mu[i] &lt;- beta0 + beta1*x[i]<br />  }<br />  beta0 ~ dnorm(0, 0.001)<br />  beta1 ~ dnorm(0, 0.001)<br /></pre><br /> ]]></description>
            <link>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/problem-3-hint.html</link>
            <guid>http://darwin.eeb.uconn.edu/eeb348/archives/2008/10/problem-3-hint.html</guid>
            
            
            <pubDate>Tue, 28 Oct 2008 13:08:53 -0500</pubDate>
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