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Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations

Garcia-Dorado, A; Wang, J; Lopez-Cortegano, E; (2016) Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations. G 3: Genes|Genomes|Genetics , 6 (11) pp. 3593-3601. 10.1534/g3.116.032425. Green open access

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Abstract

The inbreeding depression of fitness traits can be a major threat to the survival of populations experiencing inbreeding. However, its accurate prediction requires taking into account the genetic purging induced by inbreeding, which can be achieved using a “purged inbreeding coefficient”. We have developed a method to compute purged inbreeding at the individual level in pedigreed populations with overlapping generations. Furthermore, we derive the inbreeding depression slope for individual logarithmic fitness, which is larger than that for the logarithm of the population fitness average. In addition, we provide a new software, PURGd, based on these theoretical results that allows analyzing pedigree data to detect purging, and to estimate the purging coefficient, which is the parameter necessary to predict the joint consequences of inbreeding and purging. The software also calculates the purged inbreeding coefficient for each individual, as well as standard and ancestral inbreeding. Analysis of simulation data show that this software produces reasonably accurate estimates for the inbreeding depression rate and for the purging coefficient that are useful for predictive purposes.

Type: Article
Title: Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations
Open access status: An open access version is available from UCL Discovery
DOI: 10.1534/g3.116.032425
Publisher version: https://doi.org/10.1534/g3.116.032425
Language: English
Additional information: Copyright © 2016 GARCIA-DORADO et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: INBREEDING DEPRESSION, PURGING COEFFICIENT, RATE OF INBREEDING, DEPRESSION, INBREEDING LOAD, LOGARITHMIC FITNESS
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: http://discovery.ucl.ac.uk/id/eprint/1538936
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