[adegenet-forum] DaPC vs. BAPS results question

Thibaut Jombart thibautjombart at gmail.com
Mon Dec 5 16:10:14 CET 2016

Dear Felipe,

this is always a hard question, as different methods essentially do..
different things. The K-means in find.clusters optimizes the variance
between groups, while BAPS maximizes a likelihood function under a
given population genetics model. So it may be the case that you have
~17 demes roughly at HWE, but that only 4-5 groups are optimum in
terms of clearly delineated groups. And this is assuming both methods
are 'right'. They may be prone to all sorts of biases. Namely, largely
different group variances for the K-means, and deviations from the
original model in BAPS.

Feel free to post the image (or a link to it) of the BIC for
find.clusters if you want a 2-cents advice on the number of K to look


Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College London
Head of RECON: repidemicsconsortium.org
Twitter: @TeebzR

On 5 December 2016 at 14:29, Felipe Hernández <fhernandeu at uc.cl> wrote:
> Good morning,
> I wonder if you may guide me with this question (that may be pretty basic
> surely). After a run DaPC analysis using adegenet, I'm usually getting K
> between 4 and 5 for my dataset (480 hogs, 59 microsats, 39 sampling sites).
> Maximum number of clusters tried are 40. Afterwards, I tried to estimate
> number of clusters (spatial clustering by individuals) using another
> software (BAPS 6.0), but I got an even higher number of estimated cluster
> (K=17), after testing different maximum number of K's (i.e., K=5 through
> K=20). Any clue about what's the reason of this? Maybe related to the
> maximum number of cluster tested? Or, linkage disequilibrium between some
> loci? Sorry if the question is really basic, but I would appreciate any
> advice.
> Regards,
> Felipe
> --
> Felipe Hernández
> Médico Veterinario (DVM), MSc.
> PhD. Candidate
> Interdisciplinary Ecology Program
> School of Natural Resources and Environment
> Wildlife Ecology and Conservation Department
> University of Florida
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