Fig 1.
Estimates of effective population size from linkage disequilibrium (NeLD, sample size of n = 100 individuals), Relate (NeRelate, n = 100), MSMC (NeMSMC, n = 4), and from nucleotide diversity (π), this latter calculated as Neπ = π/(4μ), where μ is the nucleotide mutation rate, for scenarios with different recombination rates (RR in cM/Mb) uniform across the genome.
Simulations assume a fixed population size of N = 1,000 individuals under neutrality (random mating or partial self-fertilization with a frequency of 50% selfed progeny), background selection and selective sweeps (both for random mating populations), with constant mutation rate μ = 10−8 per base per generation. Estimates were obtained including windows of recombination rate between pairs of SNPs ranging from c = 0.0025 to 0.0250 for NeLD and averaging historical estimates of Ne between generations 150 to 350 for NeRelate and NeMSMC. Error bars represent one standard error above and below the mean of the simulation replicates. NeLD estimates were obtained pooling all replicates to speed up computation. All simulations were run for up to 100 replicates.
Fig 2.
Estimates of historical effective population size from linkage disequilibrium (NeLD, sample size n = 100 individuals), Relate (NeRelate, n = 100) and MSMC (NeMSMC, n = 4) from the present generation (generation 0) back to 400 or 1,000 generations in the past.
100 replicates were run of simulations with constant population size (N) under random mating and neutrality (grey), background selection (BS, red) or selective sweeps (SS, green), with constant (1 cM/Mb) or variable recombination rates (RR), and constant mutation rate μ = 10−8 or 10−9 mutations per base per generation for N = 1,000 or N = 10,000, respectively. The true simulated effective size from variance of family size (NeVk = N) is shown in black.
Fig 3.
Estimates of historical effective population size from linkage disequilibrium (NeLD, sample size n = 100 individuals), Relate (NeRelate, n = 100) and MSMC (NeMSMC, n = 4) from the present generation (generation 0) back to 300 generations in the past.
100 replicates were run of simulations with constant population size (N) under random mating and neutrality (grey), background selection (BS, red) or selective sweeps (SS, green), with constant (1 cM/Mb) or variable recombination rate (RR), and constant mutation rate μ = 10−8 or 10−9 mutations per base per generation for N = 1,000 or N = 10,000, respectively. The true simulated effective size from variance of family size (NeVk = N) is shown in black.
Fig 4.
Estimates of historical effective population size from linkage disequilibrium (NeLD, sample size n = 100 individuals), Relate (NeRelate, n = 100) and MSMC (NeMSMC, n = 4) from the present generation (generation 0) back to 600 generations in the past.
100 replicates were run of simulations with constant population size (N) under random mating and neutrality (grey), background selection (BS, red) or selective sweeps (SS, green), with constant (1 cM/Mb) or variable recombination rate (RR), and constant mutation rate μ = 10−8 or 10−9 mutations per base per generation for N = 1,000 or N = 10,000, respectively. The true simulated effective size from variance of family size (NeVk) is shown in black.
Fig 5.
Spearman’s correlation coefficient (r) between nucleotide diversity (π; panel a) or estimates of linkage disequilibrium effective population size (NeLD; panel b) and different diversity variables, estimated within genomic regions.
RR: recombination rate; B: B statistic; P: proportion of polymorphic nucleotides; MAF: Minor Allele Frequency; LoF: number of Loss of Function variants; missense: number of missense variants; gene dens: gene density. Estimates are based on samples of n = 99 for Finnish and n = 16 for Koryaks populations. P-values: * < 0.05, *** <0.001.