COLONY - Sibship reconstruction (noninvasive samples, co-dominant microsatellite markers), which inputs to choose and how to filter the outputs?

08 February 2022 0 1K Report

Hi Everyone,

I am using the software COLONY to make sibship reconstruction with noninvasive samples (recovered on the field => hairs, feces; using co-dominant microsatellite markers) of Sus scrofa (wild boar) and would like to know how to choose the best inputs and how to use the outputs.

Inputs

I decided to test 3 inputs

1. OFS = all individuals, CMS = all individuals, excluding males , CFS = all individuals, excluding females

2. OFS = all individuals; CMS = CFS = ø

3. OFS = all individuals, CMS = females ; CFS = males

The best log likelihood was for the 2nd model (if there are comparable).

Outputs

I am mainly interested in the Clusters and Family Full-sib outputs. Could it be a good approach to filter the outputs using the probability treshold that is given (e.g. 75%) before conducting further analyses?

Thank you in advance

Best regards,

Fanny

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