[adegenet-forum] Any suggestions about conducting a 3-D sPCA?

[Kelvin Gorospe]

Hi everyone,

For my PhD dissertation, I have sampled and mapped (x,y coordinate) every
individual coral (n=2352) of one species within a single, circular coral
reef. They are all genotyped at 6 micro satellite loci. I also have depth
information for each individual coral.

I did some analyses previously and found spatial autocorrelation in the
genetic data. Furthermore, I found that in addition to this x,y spatial
autocorrelation, there is also spatial autocorrelation with regards to
depth (using just a single z coordinate) in the genetic data.

Originally, I was conducting sPCA in R to do some exploratory analysis on
the genetic data vs the x,y coordinates, in hopes of visualizing how
genetic diversity was spatially structured and then comparing this to my
maps of depth for the reef. However, I am wondering if I am approaching
this the wrong way. Instead of treating depth as an environmental variable,
is it better to conduct an sPCA using depth as a single spatial coordinate?
And then look to see if there is a genetic cline along this
single-coordinate system?

Or is it better (or even possible) to do a 3-dimensional sPCA using all
three coordinates together (x,y, depth)? Has anyone ever attempted this?
The reef is essentially shaped like an underwater hill or mound, such that
the shallow sites are in the middle of the reef, and deeper sites are on
the outer slopes or edges. Thus, some corals with similar depths are found
on opposite sides of the reef, while others are found next to each other on
the same side of the reef. If I am interested in exploring a genetic cline
that is partitioned by both space (x,y) and depth (z), then corals on
opposite sides of the reef are "connected" in terms of their depth, while
those on the same side of the reef are "connected" by both space and depth.
Given that, does anyone have any suggestions regarding what connection
network would be best?

Any thoughts you might have would be greatly appreciated!

Thanks for your time and I look forward to hearing from you soon.

-Kelvin
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