Suggested Answer Via Email:  "Have you looked at the ArcGIS tool by Amy Vandergast? I think the diversity tool might work for you as you can input the raw frequency data for each population. I think it is at least a better option than GENELAND as the contour map will be based on the values you input and not on population assignment."  ANY OTHER SUGGESTIONS?  

Dear Kevin. I also remember a method called Allele In Space (AIS) (Miller, 2005, first link) for which you can find a direct application in a paper from Alda et al., 2013 (second link). At this time, I found it nice but I never had the opportunity to test it up to now.

Otherwise, you may also find interesting informations on the TESS program’s webpage (click the third link below), but the method is more appropriated to display admixture proportion in space rather than allele frequencies.

Hope it will help.

Cheers.

http://jhered.oxfordjournals.org/content/96/6/722.full

http://jhered.oxfordjournals.org/content/104/1/36.full

http://membres-timc.imag.fr/Olivier.Francois/admix_display.html

Dear Kevin,

I'm not sure but maybe you could find some useful stuff in the ADEgenet package for R : http://adegenet.r-forge.r-project.org/

There is a lot of interesting stuff to deal with spatialized genetic data.

I'm not a specialist in GIS systems, but you may also find some useful features in QuantumGIS.

Dear Kevin,

Try the on line tool Phylogeoviz., and remember to use Firefox as explorer.

phylogeoviz.org

Do you have any experience with R? You can use it to mark contour maps on a google map...

You'll have to modify the code below a bunch, but it will allow you to map stuff fairly quickly in R once your data is properly formatted. Send me a message if you need some help with your code.

yourmap

I agree that TESS, depending on the type of data you are using, is a useful tool.  Our group has also developed an add-on to TESS, called TESS Ad-Mixer, that is an additional option for displaying spatial interpolations of the Q matrix across space.

I've attached the publication, and here is a link to download the software: http://www.albany.edu/faculty/gonder/Lab/

Article TESS Ad-Mixer: a novel program for visualizing TESS Q matrices

I do this quite often just to look at my data. I bring the raw data into Arc and do an interpolation on it. Pretty straightforward and gives you lots of options for how you want to view it, including the ability to draw contour lines.

If you like to work with the R environment the Gstudio package has some nice features for data exploration and one of those is the fact that you can plot allele frequencies onto a map. I use it quite a lot for data exploration with nuclear microsatellites. Here you have the link to Rodney's tutorial. You can download the package from his github or I think it is already update and ready to be installed from the CRAN.

http://dyerlab.github.io/gstudio/ 

If your comfortable in R I guess the most straightforward way would be the basic heat map function provided in the graphics package: image. It produces very basic heat maps, but with options to add contour lines, sample locations etc. If your data is irregular spaced your will need to interpolate data values on a grid, with for instance the package akima or the function mars in mda. An example of producing a heat map with data interpolation can be found in the R book (p 843 in the old blue version).

Hi i think these papers will help you:

http://www.escholarship.org/uc/item/8kh4r83c

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0CDAQFjAC&url=http%3A%2F%2Fgenome.cshlp.org%2Fcontent%2F8%2F2%2F111.full.pdf&ei=a6EQVMu_EKiQ7Aa4sIDwDQ&usg=AFQjCNGNP5xWQ6gckDthxCOGccpFUyAfVg&sig2=MjxA6cofhBl6uLd0ykwXLA

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=4&cad=rja&uact=8&ved=0CDYQFjAD&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1377074%2Fpdf%2F9545387.pdf&ei=a6EQVMu_EKiQ7Aa4sIDwDQ&usg=AFQjCNFo6JuZP8Al_wT5uuPBUiozE3RX-A&sig2=P6U1fI5gp-kYxacE-k3C1g

http://www.transgenomic.com.cn/subpage/cheap,%20accurate%20and%20rapid%20allele%20frequency%20estimation%20of%20single%20nucleotide%20polymorphisms%20by%20primer%20extension%20and%20dhplc%20in%20dna%20pools.pdf