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Table 2 Family evolution under the linear BDIM (d = 1)

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

  N P(d)(1,N) *102 e (d) N E (d) N f (d) N M (d) N M(d) N /E(d) N c (d) du T (d) N
Sce 130 0.230 33206.9 2.82 32772 249.80 88.58 7.56 94.4
Dme 335 0.404 127814. 4.72 127567 206.26 43.71 11.67 120.4
Cel 662 0.498 394794. 6.61 394593 215.36 32.58 15.80 170.2
Ath 1535 0.131 2.768*106 5.98 2.77*106 638.27 106.73 22.50 718.1
Hsa 1151 0.166 1.555*106 5.37 1.68*106 468.84 87.31 24.48 573.9
Tma 97 0.039 38872.6 2.25 36306 1231.3 547.26 3.27 201.3
Mth 43 0.315 4539.9 2.03 4234 166.47 77.09 3.33 27.7
Sso 81 0.233 13281.1 2.61 12852 252.47 97.11 4.33 54.7
Bsu 124 0.212 26441.0 3.10 25969 304.97 98.38 5.09 77.6
Eco 140 0.135 34970.6 2.90 40270 431.85 148.91 5.74 123.9
  1. For the quadratic BDIM (d = 2) 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.