WOMBAT – A program for Mixed Model Analyses by Restricted Maximum Likelihood

Dealing with `clones'

In some instances we have clones, i.e. subjects which are genetically identical. For instance, monozygotic twins are naturally occuring clones. If these individuals have different identity codes and the same parents, WOMBAT will simply treat them as ordinary full-sibs. Alternatively, if all members of the clone are given the same identity, records on all members of the clone are treated as if they were repeated observations for the same individual. That is not correct either - hence special action needs to be taken.

To model clones correctly, we need to fit the same genetic effects for all members of the clone, but allow for different environmental effects for different individuals. WOMBAT has no in-built option to do this automatically, but can easily be tricked to do so:

  • Give all members of the clone the same genetic identity.
  • For data with repeated records per trait, assign a different code for permanent environmental effects to each clone member.
  • WOMBAT requires the data file to be sorted according to traits within individual. However, it does not require identities to be in ascending or descending order – the program simply checks for a change in identity to determine where the records for a new individual start.
    Hence, the `trick' is to arrange the data file so that members of the same clone do not occur successively (while still keeping records taken on the same individual together and, for multivariate analyses, sorted in ascending trait number). This will cause WOMBAT to assign different residual effects to different individuals and thus model the genetic and environmental covariance structure correctly.
    Example: Individuals "1","2" and "3" belong to a clone given
             the identity "100", "4", "5" and "6" do not belong
             to a clone
    
      Trait Genetic_Code  Record  Individual
        1     100          10          1
        2     100          99          1
        1       4          12          4
        2       4          88          4
        1     100           9          2
        2     100          94          2
        1       5          13          5
        2       5          87          5
        1     100          11          3
        2     100          77          3
        1       6           7          6

WOMBAT is likely to refuse running your analysis on grounds that there are too few “repeated” records per individual or that the data file is not sorted correctly. To override these `safety catches', you need to add the special option “clones”, i.e. your parameter file should have a block

   SPECIAL
       CLONES
   END SPECIAL

Alternatively, if animals are almost – but not 100% – identical, the inverse of the numerator relationship matrix can be constructed as described by Oikawa & Yasuda (2009) and fed into WOMBAT as a *.gin file.

[1989, article]
Kennedy, B. W., & Schaeffer, L. R. (1989). Genetic evaluation under an animal model when identical genotypes are represented in a population. J. Anim. Sci., 67, 1946-1955.
[2009, article | www]
Oikawa, T., & Yasuda, K. (2009). Inclusion of genetically identical animals to a numerator relationship matrix and modification of its inverse. Genetics Selection Evolution, 41(1), 25.

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