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Purpose

SECATEURS is a simple program to `prune' a list of pedigrees, elimating any individuals which are uninformative. It is meant as preliminary step for analyses estimating variance components. In addition, SECATEURS carries out some consistency checks on the pedigree, provides the options to compute inbreeding coefficients and set up the inverse of the numerator relationship (NRM) matrix for pruned pedigree, and provides summary information on the pedigree structure.

What is `pruning' ?

When fitting additive genetic effecs, we include animals which do not have records themselves but are parents of animals represented in the data. If further pedigree information is available, we generally also include effects for parents of parents, parents of grand-parents, etc. in the model of analysis.

Any individual without records connected to only one other animal in the pedigree does not add any information, for example, a parent with a single offspring only and unknown parents him/herself. For the purpose of analysis, this parent can be treated as unknown, and thus eliminated from the analysis. This is equivalent to `absorbing' the equation for this animal, and referred to as `pruning', as the procedure is similar to the removal of `dead wood' in plants. For pedigrees spanning several generations backwards, this should be done repeatedly, as pruning of a parent may make an animal a candidate for pruning because its known parent has become `unknown' in the process. For direct genetic effects, pruning is done downwards, i.e. scanning the pedigree from oldest to youngest animals.

Frequently, we fit parental genetic effects, most commonly maternal effects. If these are assumed uncorrelated to the direct genetic effects, the parental pedigree can be pruned separately. For maternal (or paternal) effects, only animals which have offspring in the data have a `record'. Hence animals in the data which do not have progeny are candidates for pruning, i.e. pruning needs to be carried out upwards as well as downwards the pedigree. This can lead to substantial numbers of parental animal effects which can be disregarded. If the software used for the mixed model analysis allows separate pedigrees or inverses of the numerator relationship matrix to be used for different genetic efffects, pedigrees for maternal of paternal effects should thus be pruned separately.

Why use SECATEURS ?

• `Pruning' reduces the number of levels to be fitted for genetic effects, thus reducing the computational requirements of subsequent analyses.
• Looking at the structure of `pruned' pedigrees gives a better indication of the amount of relationship information available.
• SECATEURS incorporates a fast procedure to calculate inbreeding coefficients (code written by Bruce Tier). Hence, setting up the inverse of the numerator relationship matrix for large pedigrees may be considerably faster than doing so using proprietary variance component estimation software.
• SECATEURS provides some, albeit limited, consistency checks of the pedigree information, and gives some summary information on the structure after `pruning'. Hence, running SECATEURS may be a quick and easy way to have a more detailed look at the pedigree file.