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Table 1 Results of selection tests according to six different methods (only sites with suggestion of selection by two or more methods are shown); x—positive selection as indicated by a significant selection test signal

From: Positive selection on two mitochondrial coding genes and adaptation signals in hares (genus Lepus) from China

 

Site

Ancestral

Aminoacid change

PAML

DATAMONKEY

TreeSAAP (Proprety)

Provean

Domain

DYNAMUT

SLAC

FEL

MEME

FUBAR

ΔΔG (kcal/mol)

action

ND4

29

V

A

x

–

–

–

–

x (pK’)

− 0.001

Trans

− 0.127

Destabilizing

101

S

A

–

–

 

x

–

x (Pα)

− 0.547

Trans

1.098

Stabilizing

185

H

S

–

x

x

x

x

–

0.498

Inter

0.461

Stabilizing

187

L

P

–

x

x

  

x (Pα)

− 0.085

Inter

− 0.076

Destabilizing

246

I

V

–

–

x

–

–

x (pK’)

− 0.627

Trans

− 0.643

Destabilizing

305

T

S

–

 

x

x

x

–

− 3.444

Trans

0.052

Stabilizing

425

N

V

–

 

x

x

–

–

− 3.685

Matrix

0.01

Stabilizing

CytB

23

T

A

–

x

x

–

–

x (Pα)

− 1.406

Matrix

0.518

Stabilizing

194

M

L

–

–

–

x

–

x (pK’)

− 0.045

Trans

0.274

Stabilizing

356

I

V

–

–

x

–

–

x (pK’)

0.002

Trans

− 0.083

Destabilizing

  1. Replacements inferred to be function-altering by PROVEAN and DYNAMUT are indicated in bold
  2. Equil. Const. – ioniza., COOH (pK’); α − helical tendencies (Pα)