Fig. 3: Results in simulated aDNA data.
From: Haplotype-based inference of recent effective population size in modern and ancient DNA samples
a HapNe-LD inference results for simulated aDNA-like data under the “Bottleneck" demographic scenario (dashed lines) where the number s of simulated samples and fraction m of missing SNPs, or equivalently the coverage C, are varied (see Methods). b RMSLE over the first 50 generations for different coverage levels. c Comparison of the accuracy of HapNe-LD based on two sequencing strategies. The orange line reports RMSLE for high coverage data (m = 0, C = 30) with varying sample size s. The blue line reports RMSLE for fixed s = 256 and varying coverage. d HapNe-LD and GONE inference results for a simulation where individuals from a population of constant size of Ne = 20,000 are uniformly sampled over an interval ΔT = 10 generations (gray shaded area). In panels a and d, the light and dark-shaded areas correspond to 95% and 50% confidence intervals estimated using bootstrap quantiles. In (b, c), we report the mean value across ten independent simulations as well as error bars representing 1.96 × s.e.m.
