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Table 2 Characteristics of loci

From: Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)

   

mean base frequencies1

 

heterogeneity of base frequencies2

locus

# aligned sites (# analyzed)

# PI sites1

A

C

G

T

%AT

Chi square

df

P value

ADH-I intron 5 (including partial flanking exons)

 

851 (703)

306

0.27

0.24

0.24

0.25

52

81.80

129

1.00 (NS)

ADH-I partial exons 5,6 (69 codons:1st position 17 variable, 2nd position 4 variable, 3rd position 44 variable)

 

207 (207)

57

0.25

0.24

0.28

0.23

48

52.18

129

1.00 (NS)

ADH-I intron 5

 

644 (499)

249

0.31

0.22

0.24

0.23

54

66.21

129

1.00 (NS)

GAPD-H exons 4–5 and introns 3–5

 

911 (684)

316

0.23

0.20

0.33

0.24

47

104.64

129

0.94 (NS)

GAPD-H exons 4–5 (65 codons: 1st position 5 variable, 2nd position 5 variable2, 3rd position 35 variable)

 

196 (196)

23

0.25

0.22

0.27

0.26

51

35.46

129

1.003 (NS)

GAPD-H introns 3–5

 

713 (486)

292

0.20

0.22

0.33

0.32

44

96.41

129

0.99 (NS)

FGB intron 7

 

1475 (926)

487

0.30

0.18

0.19

0.33

63

36.35

138

1.00 (NS)

combined mtDNA (12S rDNA, Valine-tDNA, 16S rDNA)

 

2903 (2229)

659

0.33

0.25

0.21

0.21

54

135.95

135

0.46 (NS)

12S rDNA

 

1074 (851)

271

0.31

0.26

0.22

0.21

52

79.23

141

1.00 (NS)

16S rDNA

 

1753 (1318)

375

0.34

0.24

0.20

0.22

56

94.30

135

1.00 (NS)

valine tDNA

 

76 (60)

15

0.36

0.21

0.19

0.24

60

59.05

135

1.00 (NS)

  1. 1 number remaining after ambiguously aligned sites removed
  2. 2 base composition heterogeneity based on variable sites only
  3. 3 2nd position P = 0.94 (NS)