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Table 1 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) *10 2 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 0.284 295267 47.46 260080 20381.6 429.5 1.903 1939.3
Dme 335 0.227 778830 153.74 734725 37409.9 243.3 1.784 3337.0
Cel 662 0.160 1.866*106 347.76 1.803*106 68709.6 197.6 1.523 5232.2
Ath 1535 0.016 2.150*107 702.65 2.087*107 529639. 753.8 2.382 63080.0
Hsa 1151 0.026 1.329*107 505.26 1.29*107 300665. 595.1 2.721 40905.5
Tma 97 0.060 681356 31.47 513450 80677.3 2563.6 1.109 4473.6
Mth 43 1.125 37131.5 14.91 28570 4707.04 315.9 1.091 256.8
Sso 81 0.461 129115 30.14 98440 12853.5 426.5 1.253 805.3
Bsu 124 0.284 237343 48.89 202150 22921.0 468.8 1.320 1512.8
Eco 140 0.155 440665 51.67 375943 37959.8 734.7 1.544 2930.5
  1. For the linear BDIM (d = 1) 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 /λ; mean times of formation T(d) N in Ga (109 yrs) under r du = 2 × 10-8. The model parameters were genome-specific as determined previously [12]. and were the same for all model degrees 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.