[adegenet-forum] 3D sPCA and the use of temporal data

Sibelle Vilaça sibelletorres at gmail.com
Wed Feb 13 15:37:34 CET 2013

Hi all,
I'm working with a domestic species and I have been trying to integrate
spatio-temporal data with haplotype frequencies. I've been working with
some ancient DNA data, associated with spatial location. I have a small
fragment of the mitochondrial DNA for several hundreds of individuals, each
associated with a geographical coordinate (x,y) and to a 14C dating. I can
see that there is a strong geographical correlation (geographically close
samples show related DNA haplotypes in similar frequencies), but I can also
see that this distribution is also strongly correlated with sampling time.
Because I'm working with a domestic species, this strong influence of time
has to do with Neolithic migrations, the change of haplotypes frequencies
is directly correlated with human migrations and their time of arrival in
different European locations.

Following the list, a saw it was possible to perform a 3D sPCA using depth
data. So, I was wondering if instead of depth data as a Z coordinate, it
would be possible to integrate temporal data on a sPCA, using something
like (x, y, time)? I have a radiocarbon dating for each sample, but I was
thinking of using time frames (or categories) related to the different
human cultures (Neolithic, Mesolithic, etc) since the change in haplotype
frequencies is directly related to the changes in human culture....

Is it possible?

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