I've done a sperm competition experiment in salmonids. All offspring have a known Atlantic salmon mother. Each group of siblings can have an Atlantic salmon (1 individual possible) or brown trout (1 individual possible) father.

The experiment was repeated across several groups of fish.

I thought it would be simple to run paternity to identify species of the father. I want to send this out to pay for someone to run it for me (980 embryo target). However, there seem to be issues with running this type of analyses and it is not clear how to actually do this.

Does anyone have ideas on how we might proceed with this?

thanks