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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 vλ; 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.