Hello,
I was wondering if you could help me. After successfully running lffm_ridge() and lfmm_test() on my dataset I receive two SNPs that are extremly high outliers for multiple environmental varaibles.
I took a look at these SNPs in the vcf and found that both are fixed 0/0 in the all but two populations where all individuals are 1/1. I then thought that perhaps these sites had similar environmental variables (where they are outliers) however they are, in fact, contrasting.
I do not know the ins-and-outs of the method, but I can't understand how these SNPs would look like outliers if the environmnetal variables in the two popualtions are so contrasting?
SNMF population coancestry suggests a K=6, which was then used in the lffm_ridge()
| Cross-entropy |
Ancestry barplot |
 |
 |
The two sites I refer to above (that are fixed at 1/1 at the two outliers) are 30-CCP and 33-TAY, that cluster neatly as different populations. The rest of the sites are 0/0. Below is a screen shot of some of the env variables that these two SNPs show as large outliers.
The env variables (non-sclaed) for these popualtions are below and the range of the variable in the whole dataset...
| Site |
MinTemp |
GDD5 |
CMI |
hedge density |
Broadleaf |
Conif |
| 30-CPP |
1.8 |
20640.0 |
0.53 |
4.481674e-01 |
55 |
3 |
| 33-TAY |
3.6 |
25015.5 |
0.68 |
1.610853e-13 |
60 |
0 |
| overall range of var |
-1.2 - 3.6 |
11817.0 - 26203.5 |
0.25 - 0.72 |
0.0 - 1.197232 |
0 - 60 |
0-100 |
Please can you help me understand this behaviour? To me it would make sense for these SNPs to be outliers if the env variables were similar/ the same but they are not? It makes me concerned about the other outliers identified... or are these just not behaving properly for some reason?
Thank you in advance
Hello,
I was wondering if you could help me. After successfully running
lffm_ridge()andlfmm_test()on my dataset I receive two SNPs that are extremly high outliers for multiple environmental varaibles.I took a look at these SNPs in the vcf and found that both are fixed 0/0 in the all but two populations where all individuals are 1/1. I then thought that perhaps these sites had similar environmental variables (where they are outliers) however they are, in fact, contrasting.
I do not know the ins-and-outs of the method, but I can't understand how these SNPs would look like outliers if the environmnetal variables in the two popualtions are so contrasting?
SNMF population coancestry suggests a K=6, which was then used in the
lffm_ridge()The two sites I refer to above (that are fixed at 1/1 at the two outliers) are 30-CCP and 33-TAY, that cluster neatly as different populations. The rest of the sites are 0/0. Below is a screen shot of some of the env variables that these two SNPs show as large outliers.
The env variables (non-sclaed) for these popualtions are below and the range of the variable in the whole dataset...
Please can you help me understand this behaviour? To me it would make sense for these SNPs to be outliers if the env variables were similar/ the same but they are not? It makes me concerned about the other outliers identified... or are these just not behaving properly for some reason?
Thank you in advance