Using genomic tools to maintain diversity and fitness in conservation programmes

Authors

  • María Ángeles Rodríguez de Cara,

    Corresponding author
    1. Departamento de Mejora Genética Animal, INIA, Madrid, Spain
    • Correspondence: María Ángeles Rodríguez de Cara, Laboratoire d'Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS/MNHN/Universite Paris 7, Museum National d'Histoire Naturelle, CP 139, 57 rue Cuvier, F-75231 Paris, France, Fax: +33 1 40 79 32 31; E-mail: adecara@mnhn.fr

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  • Beatriz Villanueva,

    1. Departamento de Mejora Genética Animal, INIA, Madrid, Spain
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  • Miguel Ángel Toro,

    1. Departamento de Producción Animal, E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
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  • Jesús Fernández

    1. Departamento de Mejora Genética Animal, INIA, Madrid, Spain
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Abstract

Conservation programmes aim at maximizing the survival probability of populations, by minimizing the loss of genetic diversity, which allows populations to adapt to changes, and controlling inbreeding increases. The best known strategy to achieve these goals is optimizing the contributions of the parents to minimize global coancestry in their offspring. Results on neutral scenarios showed that management based on molecular coancestry could maintain more diversity than management based on genealogical coancestry when a large number of markers were available. However, if the population has deleterious mutations, managing using optimal contributions can lead to a decrease in fitness, especially using molecular coancestry, because both beneficial and harmful alleles are maintained, compromising the long-term viability of the population. We introduce here two strategies to avoid this problem: The first one uses molecular coancestry calculated removing markers with low minor allele frequencies, as they could be linked to selected loci. The second one uses a coancestry based on segments of identity by descent, which measures the proportion of genome segments shared by two individuals because of a common ancestor. We compare these strategies under two contrasting mutational models of fitness effects, one assuming many mutations of small effect and another with few mutations of large effect. Using markers at intermediate frequencies maintains a larger fitness than using all markers, but leads to maintaining less diversity. Using the segment-based coancestry provides a compromise solution between maintaining diversity and fitness, especially when the population has some inbreeding load.

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