Abstract
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.
Highlights
Effective population sizes of 140 populations were computed using pedigree information and six different computation methods
Identity By Descent (IBD) = identity by descent; nb = number; T = average generation length in years; EqG = number of equivalent generations; FIS = fixation index; NeCi = method based on individual coancestry rate; NeCt = method based on coancestry rate between two successive generations; NeFi = method based on individual inbreeding rate; NeFt = method based on inbreeding rate between two successive generations ; Nes = Ne method based on sex ratio; Nev = method based on variance of progeny size; in brackets, minimal and maximal values
IBD = identity by descent; NeCi = method based on individual coancestry rate; NeCt = method based on coancestry rate between two successive generations; NeFi = method based on individual inbreeding rate; NeFt = method based on inbreeding rate between two successive generations; Nes = Ne method based on sex ratio; Nev = method based on variance of progeny size
Summary
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. Variance of progeny size [6], an indicator of both change in allele frequency and inbreeding (at least for unselected populations), is frequently used to compute Ne. A large number of methods focus on the increase in homozygosity over generations by measuring Identity By Descent (IBD) probability. Inbreeding F and coancestry C ( called kinship) coefficients are two classical genealogical estimators of IBD probability [7] that differ according to whether the considered alleles are from a single individual, or two individuals, respectively. The relation between IBD and Ne is based on the classical formula
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