[adegenet-forum] Problems with find.cluster

Siobhan Dennison siobhan.dennison at mq.edu.au
Tue Sep 9 08:31:35 CEST 2014

I am working on genetic structure of a threatened species, and as such have
rather small sample sizes. Two of my four populations are out of HWE, and
so I am using DAPC to look at population clustering because it does not
assume HWE.

The DAPC yielded 4 clusters as I expected, using the location information,
and retaining a very conservative 11 PCs (following a.score). However, when
I wanted to look at clustering with no location priors on the data, things
got a bit weird. I used the find.clusters option in adegenet, and I keep
getting very different results to my other analyses - the lowest BIC falls
at K=1, but the BIC values are extremely low (~420), steadily increasing
from there (I attached the graph FYI).

My Fst values based on microsatellites suggest high differentiation between
the 4 sites. I standardised my Fst values following Miermans 2006, which
gave rather high Fst values (0.2-0.4). My mitochondrial Fst values are also
high (>0.5).

Using Structure with LOCprior (accounting for low sample sizes), I get K=4
as the most likely number of clusters, and PCA also shows delineation
between the four sample sites.

Given that all of my other analyses tell the same story (that there a four
rather differentiated sites), I'm wondering if anyone can tell me where I
might be going wrong here?

Any pointers would be greatly appreciated!!

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