[adegenet-forum] Choosing a Connection Network for SPCA

[Alex Krohn]

Hi there,

Bumping this question again to see if anyone has any advice on choosing a
connection network method, or particularly, choosing a biologically
appropriate value for d2 in type 5.

Thanks,

Alex

On Tue, Apr 12, 2022 at 3:00 PM Alex Krohn <alex at tbconservation.org> wrote:

> Hi there,
>
> I'm analyzing a RADseq dataset of snakes across the Eastern and
> Southeastern US. Of course, at that scale, IBD plays a role in the data.
> Thus, I would like to use sPCA to plot patterns of spatial genetic
> variation. I've tried looking at other papers and through the tutorial
> about advice on the connection networks, but haven't found anything. The
> networks have a large influence in the results, so I suppose the values are
> quite important.
>
> Some individuals have the same lat/long, so I'm stuck with types 5-7 in
> sPCA. Type 5 (geographic distance) makes the most sense to me, but I wonder
> what a good value for d2 would be. Would this be the maximum distance that
> an individual might likely travel in its lifetime? A homerange? A guess at
> the spatial extent of a population (e.g. the distance that genes regularly
> flow more often than not)?
>
> I appreciate your advice on this.
>
> Thanks,
>
> Alex
>
> --
> *Alex Krohn, Ph.D.*
> Director of Conservation Genomics
> Tangled Bank Conservation
>
>
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