Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach
Fig 5
Influence of phasing and sequencing errors on ABC estimation.
Estimation of population size history in the Holstein cattle breed using ABC, based on whole genome NGS data from n = 25 animals. Summary statistics considered in the ABC analysis were (i) the AFS and (ii) the average LD for several distance bins. LD statistics were computed either from haplotypes or from genotypes, using SNPs with a MAF above 20%. AFS statistics were computed using either all SNPs or SNPs with a MAF above 10 or 20%. The posterior distribution of each parameter was obtained by neural network regression [32], with a tolerance rate of 0.005. Population size point estimates were obtained from the median of the posterior distribution. Generation time was assumed to be five years.