[adegenet-forum] Question about genetic structure in admixed populations

Jutta Geismar Jutta.Geismar at senckenberg.de
Wed Sep 4 15:03:35 CEST 2013

Dear Mr Jombart and DAPC users,
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:
1.       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)
2.       To reduce variability I used optim.a.score (smart FALSE). The
best a-score was around 0.2 (PC 61)
3.       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) 
I chose k in the BIC values after which the decrease was less compared
to the previous, but not the lowest k.
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. 
Thanks a lot in advance for some help.
Jutta Geismar 
PhD student
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