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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Arhua,
<br>
<br>
read.structure is only meant for diploid data - will add a warning on this point in the doc for 1.3-1.
<br>
<br>
So your analysis based on read.structure here is wrong. The other analyses are surely OK. Otherwise use read.table/read.csv to read your structure data into R as a data.frame, and then df2genind with the proper arguments to convert the data into a genind object.<br>
<br>
Best<br>
<br>
Thibaut<br>
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<div class="PlainText">-- <br>
######################################<br>
Dr Thibaut JOMBART<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - Faculty of Medicine<br>
St Mary’s Campus<br>
Norfolk Place<br>
London W2 1PG<br>
United Kingdom<br>
Tel. : 0044 (0)20 7594 3658<br>
t.jombart@imperial.ac.uk<br>
http://sites.google.com/site/thibautjombart/<br>
http://adegenet.r-forge.r-project.org/<br>
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<div style="direction: ltr;" id="divRpF735054"><font color="#000000" face="Tahoma" size="2"><b>From:</b> adegenet-forum-bounces@r-forge.wu-wien.ac.at [adegenet-forum-bounces@r-forge.wu-wien.ac.at] on behalf of Cheng-Hua Huang [arhua@ufl.edu]<br>
<b>Sent:</b> 01 July 2011 17:10<br>
<b>To:</b> adegenet-forum@r-forge.wu-wien.ac.at<br>
<b>Cc:</b> arhuahuang@gmail.com<br>
<b>Subject:</b> [adegenet-forum] Structure-like membership plot<br>
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<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%;">Dear adegent users and Thibaut,</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%;">I would like to ask questions about using DAPC.
</span><span style="font-size: 12pt; line-height: 115%;">I have </span><span style="font-size: 12pt; line-height: 115%;">used
</span>import2genind<span style="font-size: 12pt; line-height: 115%;"> and </span>
<span style="font-size: 10pt; line-height: 115%; font-family: "Tahoma","sans-serif"; color: black;">df2genind</span><span style="font-size: 12pt; line-height: 115%;"> for importing Structure, Genepop, and Fstat files of the same data set to find clusters and
to plot Struture-like membership information. Since I was working on a haploid, asexual fungus collected from three regions, I coded data sets as a pseudo-diploid for Genepop and Fstat files but used the original haploid data set for the Structure format.
Even though I got K=3 for biological interpretation based on BIC, the membership plot derived from the Structure input file was different from those obtained from the other two file formats. The result using the Structure input format showed many admixture
individuals, but the other two input files did not exhibit any admixture individuals (all with membership probability = 1). The latter makes sense to me because the fungus is asexual and genotype flow plays a main role in shaping population structure. Moreover,
recombination is not possible for this fungus. Thus, admixture individuals may not occur. What caused this difference between these input files? How do I interpret these results? Thank you for your help.</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%;">Regards,</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%;">Arhua</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height: 115%;"> </span></p>
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