Table 3

Sites under PDS in the A. thaliana/P. trichocarpa ARF gene family: „Site-specific analysis".

Site-specific analyses

n

dN/dS (ω) under M0

2Δℓ M2 vs. M1 (df 2)

2Δℓ M8 vs. M7 (df 2)

Parameter estimates under M8

Positively selected sites under M2 (BEB)

Positively selected sites under M8 (BEB)

ARF

Node ARF2

5

0.183

0.00

0.56

ρ₀ = 0.957 (ρ₁ = 0.043) (ρ = 0.431)

q = 1.635 ω = 1.09

None

478 540 563 631 758

Node ARF6

7

0.122

0.00

1.04

ρ₀ = 0.997 (ρ₁ = 0.003) (ρ = 0.355)

q = 1.994 ω = 4.49

None

372464476 479 482 485 539

Node ARF7

6

0.154

0.00

13.78**

ρ₀ = 0.973 (ρ₁ = 0.027) (ρ = 0.409)

q = 1.814 ω = 3.086

None

460 526 532534 539 542544 546 550 556 557 558 559 561 562 566568 569 570 574599 608 677 785

Node ARF10

8

0.137

0.00

0.64

ρ₀ = 0.998 (ρ₁ = 0.016) (ρ = 0.413) q = 1.988 ω = 2.69

None

96 449 486570

Node ARF11

5

0.151

0.00

1.74

ρ₀ = 0.932 (ρ₁ = 0.068) (ρ = 0.528)

q = 2.885 ω = 1.00

None

6 334 370 372 376 383 399 412 413 478 529

Node ARF12

6

0.566

19.42**

19.4**

ρ₀ = 0.982 (ρ₁ = 0.018) (ρ = 0.056)

q = 0.054 ω = 10.50

175335389 433 444447 527 567 569 570 572

175335 351 359 389 433 444 447 527 567 569 570 572

Each comparison has n sequences, dN/dS is average ratio over sites under a codon model with one ω. Bold underline, PP ≥ 0.99 of being under positive selection; bold, 0.99>PP ≥ 0.95; italic, 0.95>PP ≥ 0.90; underline, 0.90>PP ≥ 0.70; normal, 0.70>PP > 0.50

Paponov et al. BMC Evolutionary Biology 2009 9:126   doi:10.1186/1471-2148-9-126