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Table 3 Family evolution under the cubic BDIM (d = 3).

From: Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models

  N P(d)(1,N) e (d) N E (d) N f (d) N M (d) N M(d) N /E(d) N c(d) du = r du T (d) N
Sc e 130 0.105 12315.7 0.944 12306 4.60 4.84 92.46 21.3
Dme 335 0.222 60759.4 1.390 60755 2.45 1.76 549.65 67.3
Cel 662 0.283 208472 1.804 208469 2.10 1.17 2020.37 212.1
Ath 1535 0.255 1.29*106 1.390 1.29*106 1.93 1.39 3754.83 362.3
Hsa 1151 0.254 756242 1.291 756238 1.65 1.27 2938.07 242.4
Tma 97 0.019 9442.5 0.781 9390 24.5 31.4 18.84 23.1
Mth 43 0.061 1530.2 0.848 1514 7.85 9.24 18.26 7.2
Sso 81 0.073 4799.6 0.960 4786 7.21 7.51 36.71 13.2
Bsu 124 0.088 10265.3 1.059 10254 6.40 6.04 63.38 20.3
Eco 140 0.071 14459.9 0.957 14446 7.34 7.67 65.06 23.9
  1. For the cubic BDIM (d = 3) and for the largest family of size N in each genome, the table shows the probability of formation P(d)(1,N), mean number of events before extinction of the largest family e(d) N ; mean number of events before formation of the largest family from a singleton, f(d) N ; mean times of formation M(d) N and extinction E(d) N (in 1/λ units); the value of coefficient c(d) du = r du ; mean times of formation T(d) N in Ga (109 yrs) under r du = 2 × 10-8. The model parameters were the same as for the linear model according to (2.4). Species abbreviations: Sce, Saccharomyces cerevisiae, Dme, Drosophila melanogaster, Cel, Caenorhabditis elegans, Ath, Arabidopsis thaliana, Hsa, Homo sapiens, Tma, Thermotoga maritima, Mth, Methanothermobacter thermoautotrophicum, Sso, Sulfolobus solfataricus, Bsu, Bacillus subtilis, Eco, Escherichia coli.