Input file for "null alleles" (recessive alleles) with microsatellite data
Mslynn
I've used structure before with microsatellite data, but not with the
recessive allele option.
I don't understand how to change the input file. It seems that I have
to add a row after the names of the markers with which will be the
"recessive" allele for that locus. In the case of microsats, how do
you choose such allele since several alleles per locus could be null?
Just picking the one which repeats more as "homozygote"?
Thank you very much!
M.
Thirsa-K
As far as I know, the recessive allele option is mainly meant for loci
where you can unequivocally determine which allele is the recessive
one. Aka: loci with only two alleles (SNPs, RFLP data etc) and not
microsatellites.
So....I would advise you not to use it on your microsat data.
Cheers,
Thirsa
Abby Moore
I have used the recessive alleles option for microsatellite data from
tetraploids, because I know which alleles are present but I don't
know how many copies of each allele they have. In that case, the
value for the recessive allele that you write at the top of the
column for each locus is the same value you use for missing data. My
impression is that if you have null alleles, but not ambiguity in
copy number, then the value for the recessive allele is different
from any of the alleles at the locus and different from the missing
data value. But I have not tried this.
Best,
Abby
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Thirsa-K
recessive alleles are two completely different things and as far as I
know the "recessive allele" option in Structure can not be used as a
way to test for null alleles......
>
> - Tekst uit oorspronkelijk bericht weergeven -
Marina
I've used structure with a data set with 9 loci. First of all, I used
Microchecker to test for the presence of null alleles in the data set.
This program identified the presence of null alleles in locus Cmu2.
This locus had a few individuals that did'nt amplify (after several
trials), but yielded good amplifications in the other loci.
Then, the input file had the following format (with columns for
individual ID and predefined populations)
Cmu1 Cmu2 Cmu3 Cmu4 Cmu11 Cmu13 Cmu14 Cmu15 Cmu17 ---> ROW
OF MARKER NAMES
-9 101 -9 -9 -9 -9 -9 -9
-9
---> ROW OF RECESIVE ALLELES
33596 1 138 146 101 101 142 152 126 138 135 139 118 118 175 179 165
171 162 202
33594 1 140 150 187 187 148 158 134 138 139 139 118 118 179 185 175
179 164 178
33775 1 142 146 187 187 146 154 138 142 131 135 114 118 179 185 165
181 174 188
33776 1 142 142 187 187 154 164 114 126 131 135 114 118 175 185 175
179 188 188
In the row of recesive alleles, you have to give the null allele a
value that doesn't appear in any other allele of the locus, in my case
"101" and put a "-9" for all other loci without null alleles. Then in
the data section, individual 33596 had no amplification in locus Cmu2,
so I assumed that it was in fact a null homozygote (101/101). Don't
forget to check the "row of recesive alleles" option when you start
the project.
I hope this will of help to you
Marina