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. 2013 Oct;195(2):563–572. doi: 10.1534/genetics.113.154161

Table 1. Parameter settings that yield a good fit, for a range of realistic effective population sizes and mutation rates.

t t0 N0 N1 N2 ν0 ν1 ν2 b0 b1 b2 x DHC DCH
A.
540 270 15 6 15 0.00012 0.00006 0.00002 0.55 0.55 0.55 12 5.17 1.30
550 280 10 9 10 0.00012 0.00006 0.00002 0.55 0.55 0.55 12 5.06 1.10
570 300 15 3 20 0.00030 0.00022 0.00016 0.55 0.55 0.55 12 5.35 1.29
560 290 20 5 20 0.00030 0.00016 0.00010 0.55 0.55 0.55 12 5.27 1.14
460 250 25 10 12 0.00030 0.00055 0.00045 0.55 0.55 0.55 12 5.42 1.24
B.
580 260 10 7 25 0.00075 0.00020 0.00005 0.51 0.51 0.51 18 5.18 1.26
720 250 15 8 23 0.00015 0.00010 0.00005 0.55 0.55 0.55 18 5.17 1.22
620 250 10 10 17 0.00010 0.00010 0.00005 0.55 0.55 0.55 12 5.30 1.44
660 250 10 12 25 0.00055 0.00025 0.00010 0.51 0.51 0.51 18 5.45 1.76
740 260 10 12 25 0.00035 0.00020 0.00010 0.51 0.51 0.51 15 5.02 2.11
C.
720 260 10 11 13 0.00025 0.00010 0.00010 0.51 0.55 0.51 13 5.08 1.20
740 250 10 7 11 0.00020 0.00010 0.00010 0.52 0.55 0.51 14 5.08 1.33
740 260 10 12 18 0.00020 0.00010 0.00010 0.51 0.55 0.51 12 5.17 1.22
740 260 10 10 15 0.00020 0.00010 0.00010 0.51 0.55 0.51 12 5.22 1.30
680 250 10 9 16 0.00025 0.00010 0.00010 0.51 0.55 0.51 15 5.44 1.59

Information of the plausible range of each input parameter was retrieved from the literature (details in Discussion and Conclusions). Times t and t0 are expressed in thousands of generations (assuming 20 years per generation). Population sizes N0, N1, and N2 are expressed in thousands of individuals. DHC is the calculated average allele length difference on human loci that are typed in chimpanzee and DHC is the reciprocal difference. Top (A): best fits from an explorary parameter search given a broad range of mutation rates (from 10−5 to 10−3), with parameters b0, b1, b2, and x set as default values (b0 = b1 = b2 = 0.55, x = 12). The mutation rates in the two best fits are below the generally accepted range. Although the other three fits yield acceptable mutation rate estimates, the parameter combinations result in very high probabilities of finding polymorphic loci, P(L ≥ x) > 0.25 Middle (B): P(L ≥ x) ≤ 0.25 is assumed to ensure that the probability of choosing polymorphic loci is relatively small. Parameters b0, b1, b2 are set equal and range from 0.51 to 0.55. x ranges from 12 to 18. The best fits are obtained when ν2 is equal to the minimum possible value (5 × 10−5), while fits become slightly worse if ν2 is increased (10−4). Bottom (C): when P(L ≥ x) ≤ 0.25 is still required while b0, b1 and b2 are allowed to vary independently, the parameter search tends to favor b1 > b2 and small x (< 15) to yield best fits. In B and C with t, t0, N, b, and x assuming ranges of possible values when P(L ≥ x) ≤ 0.25, ν0 is always greater than ν1 and ν2; ν1 is greater than or equal to ν2; ν1b1 is always greater than ν2b2.