M. A. R. de Cara, Blanca Villanueva Santamarina, M. A. Toro Muñoz, J. Fernández
We study here the consequences in fitness and diversity of managing a population in a conservation programme. While using molecular coancestry to calculate optimal contributions can maintain more diversity than using genealogical coancestry, it does not distinguish on whether that diversity is neutral or deleterious, and can thus lead to a decrease in fitness if the initial population had a large inbreeding load. Here we also study the performance of using molecular coancestry measured only on markers at high frequency, or using a measure of coancestry based on runs of homozygosity. Our results show how managing a population with more polymorphic markers can maintain more fitness, but due to having fewer markers, less diversity is maintained. A balance between maintaining diversity and fitness using molecular data is achieved by managing the population using runs of homozygosity.
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