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Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

Grégoire Leroy12*, Tristan Mary-Huard3, Etienne Verrier12, Sophie Danvy4, Eleonore Charvolin2 and Coralie Danchin-Burge5

Author Affiliations

1 AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, 16 rue Claude Bernard, F-75321, Paris 05, France

2 INRA, UMR1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352, Jouy-en-Josas, France

3 AgroParisTech, UMR518 Mathématiques et Informatique Appliquées, 16 rue Claude Bernard, F-75321, Paris 05, France

4 IFCE, F-61310, Le Pin au Haras, France

5 Institut de l’Elevage, 149 rue de Bercy, F-75595, Paris 12, France

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Genetics Selection Evolution 2013, 45:1  doi:10.1186/1297-9686-45-1

Published: 2 January 2013

Abstract

Background

Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate.

Results

Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species.

Conclusions

When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied.