Overview

The Committed Matings feature in MateSel lets you include matings that have already been decided or carried out. These matings may not yet be visible in the main data file (for example, the offspring might not be born yet), but they still affect how future matings should be planned.

Why Use Committed Matings?

The key technical reason for using this feature is to account for breeding contributions that have already been made, but are not represented in the main data file.

Example: Imagine a male has already been used for many matings recently, but his offspring haven’t been born or entered into the main data file yet. If MateSel doesn’t know this, it might allocate even more matings to him (or to his relatives), which can cause long-term inbreeding issues. To avoid this, you can tell MateSel about his Committed Matings so it can reduce (or “penalise”) his use in the current mating session.

The following video explains this feature further. It uses the older “MateSel Legacy” interface, but the feature works the same in newer versions.

How did people do this before?

Before the Committed Matings feature existed, people used a workaround:

• They added “embryos” representing these prior matings to the main data file as candidates.
• They were grouped separately from the active candidates in the current mating session.
• This approach was also used for:
  • Juveniles (not yet sexually mature),
  • Unavailable individuals (e.g. pregnant or lactating females),
  • Or any animal not currently usable, but expected to contribute in the future.

This method worked, but it wasn’t ideal.

How does Committed Matings work?

With the Committed Matings feature:

• All past or pre-decided matings are listed in a separate data file called CommittedMatings.txt.
• MateSel reads this file and includes those matings in its calculations.
• As a result, individuals are represented in the analysis by their parents, even if the offspring don’t yet exist in the main data file.

Why does this work?

• Because coancestry is additive: The coancestry of an offspring to the population is the average of the coancestries of its two parents.

So MateSel can correctly estimate how much each parent (and their relatives) is contributing to the population — including matings that happened in earlier sessions. Benefits over the old “embryo” approach:

• It gives a more accurate picture of breeding contributions across multiple sessions.
• It avoids guesswork about how many embryos to add or how many matings each should represent.
• It keeps the analysis cleaner and easier to manage.

Managing MaxUse

The total number of matings to be derived for any one mating session includes those of previous sessions. When using Committed Matings, the MaxUse setting (maximum matings per candidate) must include both:

• Matings that have already been committed, and
• Any new matings MateSel will assign in the current run.

MaxUse can be set either:

• Manually by the user, or
• Automatically managed by MateSel.

Only the new matings will be carried out in the current session, but MateSel will consider both past and future matings in its optimisation.

Managing Juveniles

For species that have juvenile individuals available at mating time, there are two ways of handling this:

1. Include juveniles as candidates:

• Juvenile males and females are added to the main data file as candidates.
• They can be “grouped” together (e.g., juvenile × juvenile), but won’t actually be mated because they are not mature.
• This allows MateSel to consider them for selection purposes.
• In this case, Committed Matings for adults only need to include matings where the resulting juveniles are not yet in the data file.

2. Do not include juveniles as candidates:

• Juveniles are not added to the candidate list in main data file.
• In this case, Committed Matings must include all past matings whose offspring:
  • Are not yet adult candidates,
  • Or have been removed (culled) from the breeding program.
• This approach does not allow MateSel to select among juveniles at the same time as adult mating decisions.
• This does not give the benefit of selection among juveniles in a manner that accommodates adult selections and matings made simultaneously.

Sometimes a hybrid approach is used — for example, selecting only some juveniles (like “Group 3” juveniles in the prawn breeding illustration below).

Illustrations

The following illustrations give some concept of how Committed Matings can be used. See Kinghorn (2018) for more detail.

An illustrative example in pigs:

An illustrative example in cattle:

An illustrative example in prawns: