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<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>Dear Mr Jombart and DAPC users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><o:p><FONT size=3 face=Calibri> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>I used DAPC to analyze genetic structure in a small region with 20 microsatellite markers. I analyzed 330 individuals (14 sampling sites) and found little genetic differences (FST, D Jost), but a significant isolation by distance pattern. A cluster analysis in STRUCTURE resulted in four clusters (STRUCTURE Harvester) but all individuals had more or less equal posterior probability in all of the four inferred clusters. Therefore I assume a panmictic population structure. Since STRUCTURE is known for some problems analyzing datasets under IBD I analyzed the data with DAPC. DAPC resulted in 3 or 4 clusters (and tested up until K=7 to be sure), but in both cases these were randomly distributed among all individuals without a geographic context. Only 94 individuals were not assigned to one cluster with more than 90% and therefore would be counted as “admixed” (example in DAPC tutorial). For me the results of STRUCTURE and DAPC are in conflict to each other, but I don’t know how a panmictic population would look like in DAPC. Distances between sites are small and it is very likely that gene flow occurs among my sampling points, which might cause problems in genetic cluster analyses. I don’t know if I made any mistake in my thinking, that’s why I want to explain my procedure briefly:<o:p></o:p></FONT></FONT></SPAN></P>
<P style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpFirst><SPAN style="mso-ansi-language: EN-US; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin" lang=EN-US><SPAN style="mso-list: Ignore"><FONT size=3 face=Calibri>1.</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>I used dapc and chose 1/3 of the sample size as PC (as suggested) and counted DAs in the plot (100% of the variability was included, 110 PC, 13 DA)<o:p></o:p></FONT></FONT></SPAN></P>
<P style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN style="mso-ansi-language: EN-US; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin" lang=EN-US><SPAN style="mso-list: Ignore"><FONT size=3 face=Calibri>2.</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>To reduce variability I used optim.a.score (smart FALSE). The best a-score was around 0.2 (PC 61)<o:p></o:p></FONT></FONT></SPAN></P>
<P style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN style="mso-ansi-language: EN-US; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin" lang=EN-US><SPAN style="mso-list: Ignore"><FONT size=3 face=Calibri>3.</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>After that I wanted to estimate the number of clusters by find.clusters and used the a-score as number of PCs and repeated the dapc (conserved variance was still 98%, 61 PCs, 2 DA) <o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt 36pt" class=MsoListParagraphCxSpLast><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>I chose k in the BIC values after which the decrease was less compared to the previous, but not the lowest k.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>If I have some mistakes in my procedure I would appreciate some advice. But also if the procedure is okay I cannot explain the contrariness of these two analyses. <o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>Thanks a lot in advance for some help.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>Jutta Geismar <o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>PhD student</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN style="mso-ansi-language: EN-US" lang=EN-US><FONT size=3><FONT face=Calibri>Germany<o:p></o:p></FONT></FONT></SPAN></P></BODY></HTML>