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BackgroundEffective 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.ResultsDepending 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.ConclusionsWhen 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.

Summary Pedigree data of nine French dog breeds, namely Barbet (BAR), Basset fauve de Bretagne (BAF), Beauceron (BEN), Berger des Pyrénées (BRP), Bouledogue Français (BUF), Braque Saint‐Germain (BQG), Dogue de Bordeaux (DOB), Epagneul Breton (EPB) and Montagne des Pyrénées (MOP), were analysed. The effective numbers of ancestors of dogs born from 1997 to 2001 were equal to 6.7 (BAR), 40.2 (BAF), 36.5 (BEN), 16.0 (BRP), 37.0 (BUF), 13.1 (BQG), 28.9 (DOB), 33.3 (EPB) and 34.0 (MOP). The expected contributions of the major ancestors were found to be highly unbalanced in the EPB and BRP. The average coefficient of inbreeding of dogs born from 1997 to 2001 with both parents known was equal to 12.4% (BAR), 3.9% (BAF), 5.4% (BEN), 7.2% (BRP), 3.3% (BUF), 6.0% (BQG), 4.1% (DOB), 4.5% (EPB) and 4.0% (MOP). These values were found to be significantly higher than the average coefficient of kinship between the male and the female parents of these animals, except in the BAR and BQG, revealing an usual practice of mating between related animals. The results are discussed in relation with the demographic situation and the use of each breed. The method used to class an endangered breed and the ways to preserve the genetic variability, when necessary, are evoked.

The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.