I have some questions about the IBD-value and IBD-fraction for two of the condensed identity states, $S_1$ and $S_7$.

My questions:

1) Is the IBD-value for the individuals i and j two (2) in $S_1$ and 2 in $S_7$ as well? (We can form the pairs aa aa in $S_1$ and the pairs aa and AA in $S_7$. The number of alleles in $S_1$ (and similarly for $S_7$) for individual i that are IBD with alleles of individual j is therefore 2)

2) Is the IBD-fraction ( or coefficient of relationship) 1 in $S_1$ and 1 in $S_7$ ? (We have the fraction 2/2 in each case since both alleles of each individual are IBD with the alleles of the other individual as described in 1) )

enter image description here

Picture source: http://openi.nlm.nih.gov/imgs/512/114/3579841/3579841_pone.0057003.g001.png

Edit: Comments about the figure: The dots represent alleles for one particular locus. When two alleles are IBD they are connected with a line. We look at two individuals i and j and consider the SAME locus in both individuals. There are only two persons in each of the states. In state $S_5$ individual j is homosygous and it's alleles are also IBD. One of the alleles of i is also IBD with the alleles of individual j. We therefore get the three lines between the alleles.

Definitions used:

IBD-value: "An Identical-By-Descent (IBD) value is the number of alleles which are the same because of descent from a common ancestor. Since each (diploid) individual has two alleles for a given (autosomal) gene, the number of them that are IBD with another individual can only be 0, 1, or 2."

Source: IBD-value in pedigree with inbreeding

Coefficient of relationship: "..is the fraction of genes in two individuals that are identical by descent,..."

Source: https://books.google.no/books?id=Q9ofvKZAmpEC&pg=PA35&lpg=PA35&dq=identicAL+BY+DESCENT+FRACTION&source=bl&ots=oOc4-PBzZg&sig=jJgJarUg36b4DbyT7sphDD6j_7c&hl=en&sa=X&redir_esc=y#v=onepage&q=identicAL%20BY%20DESCENT%20FRACTION&f=false

  • $\begingroup$ Can you please tell a little bit more about the figure, I don't understand it. The dots represent allele I think. Is each dot a different allele? Is each trait is an individual (there are 3 individuals in $S_5$ for example)? $\endgroup$ – Remi.b Sep 19 '15 at 3:56
  • $\begingroup$ Of course @Remi.b. I have added some comments. I hope the comments make the figure more understandable $\endgroup$ – FredikLAa Sep 19 '15 at 9:17

If I've understood the graphs correctly, then I think you are right on both questions. The difference between 1 and 7 is just that the alleles are in LD in 1 but not in 7


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