Estimating the Rate of Gene Conversion on Human Chromosome 21 Badri Padhukasahasram, Paul Marjoram, Magnus Nordborg  The American Journal of Human Genetics  Volume 75, Issue 3, Pages 386-397 (September 2004) DOI: 10.1086/423451 Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 1 A likelihood surface of chromosome 21 data that is based on the fraction of short-range (0–5 kb) incompatible SNP pairs alone. ρ denotes the crossing-over rate, γ denotes the gene-conversion rate, and L(ρ,γ) is the product of the likelihood and an arbitrary constant. Note that estimates of gene conversion decrease rapidly with increasing crossing-over rates and eventually reach zero. A single pairwise summary cannot distinguish between the effects of gene conversion and those of crossing over. The American Journal of Human Genetics 2004 75, 386-397DOI: (10.1086/423451) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 2 Expected values of p(a) and p(b), from simulations under models with uniform crossing over alone (γ=0) and uniform gene conversion alone (ρ=0) at differing rates. Expectations were calculated from 1,000 simulations of 200-kb sequences, with θ=140. For models with gene conversion alone, the mean conversion-tract length was fixed at L=500 bp. The American Journal of Human Genetics 2004 75, 386-397DOI: (10.1086/423451) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 3 The distribution of MLEs of gene conversion ( γˆ) for 1,000 data sets, each simulated at uniform crossing-over rate ρ=40 and uniform gene conversion rate γ=40 (A) and at nonuniform crossing over ρ=40 and uniform gene conversion rate γ=40 (B). The American Journal of Human Genetics 2004 75, 386-397DOI: (10.1086/423451) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 4 The likelihood surface of chromosome 21 data based on p(a) and p(b), for a mean tract length L=500 bp. Likelihoods were calculated from 8,000 simulations of 200-kb sequences for different rates of crossing over (ρ=0–160) and gene conversion (γ=0–300). L(ρ,γ) roduct of the likelihood and an arbitrary constant. The peak is seen at ρ=80 and γ=125. The American Journal of Human Genetics 2004 75, 386-397DOI: (10.1086/423451) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 5 The likelihood surface of chromosome 21 data based on p(a) and p(b), for a mean tract length L=50 bp. Likelihoods were calculated from 2,500 simulations of 200-kb sequences for different rates of crossing over (ρ=0–160) and gene conversion (γ=0–1,500). L(ρ,γ) denotes the product of the likelihood and an arbitrary constant (1,500). The peak is seen at ρ=80 and γ=750. The American Journal of Human Genetics 2004 75, 386-397DOI: (10.1086/423451) Copyright © 2004 The American Society of Human Genetics Terms and Conditions

Figure 6 The MLEs of gene conversion ( γˆ) and crossing over ( ρˆ) for overlapping 2-Mb windows along chromosome 21. The X-axis denotes the location corresponding to the center of the 2-Mb windows, and the error bars indicate ∼95% credible intervals. The horizontal line denotes the chromosomal average of the parameters. The American Journal of Human Genetics 2004 75, 386-397DOI: (10.1086/423451) Copyright © 2004 The American Society of Human Genetics Terms and Conditions