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Table 4 Selection patterns in recombination genes in maize detected using the likelihood ratio test

From: Evolution of meiotic recombination genes in maize and teosinte

Gene

Selection modelsa

% of codons

M0 vs. M3

(2Δl) b

M1 vs. M2

(2Δl) c

M7 vs. M8

(2Δl) d

Under purifying selection

Under positive selection

Evolving neutrally

Dmc1

15.32**

4.12

6.14

100

-

-

Mlh1

50.48**

19.46**

20.54**

93.3

6.7

-

Mre11A

1.06

0.46

0.12

100.0

-

-

Mre11B

24.64**

26.46**

14.23**

96.5

3.5

-

Msh4

0.00

0.00

0.00

100.0

-

-

Mus81-1

22.64**

15.62**

15.74**

97.3

2.7

-

Rad51A1

0.00

0.00

0.00

100.0

-

-

Rad51A2

43.76**

18.94**

20.62**

98.7

1.3

-

Recq4

0.00

0.00

0.00

100.0

-

-

Spo11-1

0.00

0.00

0.00

100.0

-

-

Spo11-2

80.52**

33.78**

35.18**

98.2

1.8

-

  1. a Likelihood ratio tests of selection models. Ratios statistically significant at P = 0.01 are denoted with **
  2. b Model M0 (one ratio) assumes a single dN/dS ratio across all sites in the gene’s coding region. Model M3 (discrete) assumes discrete classes of sites with different ω values. df = 4
  3. c Model M1 (neutral model) assumes all sites are either under purifying selection (ω < 0) or evolving neutrally (ω = 1). Model M2 adds a third category of sites under positive selection (ω > 1). df = 2
  4. d Model M7 (beta model) assumes that ω ranges from 0 (strong negative selection) to 1 (neutral evolution) and varies among sites in the gene’s coding region according to the beta distribution. Model M8 (beta& ω) similarly to M7 assumes that ω varies among sites but allows that, in addition to ranging from 0 to 1, ω may take values > 1 (positive selection). df = 2
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BMC Genomics

ISSN: 1471-2164

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