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Table 2 Characteristics of the 10 non-repetitive and non-coding segments and for concatenated dataset.

From: Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation

    

Mean base frequencies (%)

 

Locus

# aligned sites

(# analyzed) 1

# variable Sites

# PI sites 2

A

C

G

T

Model 3

A1

806 (778)

271

96

32.1

23.5

19.5

25.0

GTR+G

A2

508 (508)

75

27

22.1

23.9

30.4

23.5

HKY+G

A3

485 (473)

151

63

31.4

15.6

14.9

38.2

GTR+G

A4

806 (673)

234

70

28.1

21.0

21.9

28.9

GTR

A5

619 (569)

205

83

32.9

18.0

16.3

32.8

GTR

A6

631 (569)

234

92

34.3

14.9

17.9

32.9

GTR+I

X1

508 (487)

145

63

28.5

18.0

18.6

34.9

GTR+G

X2

586 (565)

154

67

30.3

18.7

20.6

30.5

GTR+G

X3

466 (449)

125

43

33.5

17.0

17.1

32.4

GTR+G

X4

528 (522)

178

79

32.8

19.9

15.2

32.1

GTR+I

Concatenated

6535 (5592)

1791

684

30.6

19.3

19.4

30.7

GTR+G

  1. 1 The number of analyzed sites are after removing poorly aligned sites using the Gblocks program [46].
  2. 2 PI sites = parsimony informative sites
  3. 3 Best fitting substitution models determined using the AIC (see text). (GTR = General time reversible model; HKY = Hasegawa-Kishono-Yano model; G = The shape parameter of a gamma distribution; I = The proportion of invariable sites in the alignment)
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BMC Genomics

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