I am working with three aquatic plant species occuring in island-like habitat (small water bodies) scattered in an intensive agricultural landscape. My main question is to see if there are genetic differences in their populations and how much this is explained by space and by environment. I intend to use RDA analysis (tipical for metacomunnities) but instead of a sp based matrix, use my microsatellites dataset. However I am not quite sure how exaclty I can do this. Please I would appreciate some help, comments or further ideas. Thank you!
Dear Malcolm, thank you very much for your answer :) My microsatellite data consist of 10 Markers (Loci) each marker with two alleles (diploid species) and I have the sizes of the alleles (in base pairs) which would correspond to abundance of species. The problem here is that the markers have two sets of data (two alleles) which give us information about Heterozygosity. When an organism is heterozygous for a certain marker the two alleles sizes are the same, on the contrary if it is heterozygous two different sizes appear. I was thinking to use a genetic distance measurement like Nei...
Dear Sissi
I think you can use your SSR data in FSTAT-format (e.g. PGD-spider easily converts to FSTAT-format) and read it in R using for example the read.fstat function implemented in the R-package “adegenet”. This way you convert your data to a genind object.
https://www.rdocumentation.org/packages/adegenet/versions/2.0.1
Afterwards you can use the R-package “vegan” to perform the RDA using your genetic and ecological data.
https://cran.ism.ac.jp/web/packages/vegan/
Both R-packages are very well documented.
Good luck!
Katharina
Here is also a link to a very useful tutorial for RDA analyses in landscape genomics written by Paul Gugger.
https://github.com/pgugger/LandscapeGenomicsWorkshop_Morelia/blob/master/Exercise4.mdown
Best,
Katharina
visit the link https://mb3is.megx.net/gustame/constrained-analyses/rda
Hi,
We also used a RDA analysis to assess how isolation-by-distance and population structure explained genetic data within our dataset; for this you should use three matrices. One with GPS data, one with population assignments, and one with msat data for which you need to calculate within-individual allele frequencies. See our paper https://academic.oup.com/jhered/article-abstract/109/4/426/4870022?redirectedFrom=fulltext
Good luck!
Best, Thijs
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