Table 2

Summary of the cpDNA loci and the nDNA locus ITS used in this study

Average Pairwise Difference (range)²

Locus

N

Aligned Length (bp)

Characters Constant (percent)

Parsimony Informative Characters (percent)

Autapo-morphies

Nucleotide Substitution Model¹

Within Species

Among Species

Primer Source

n/a

3.12%

see (Neel and Cummings 2004)

(88.40%)

(3.68%)

(0 – 6.20%)

ndhF

6

2131

2002

66

63

TVM

n/a

2.97%

see (Neel and Cummings 2004)

(93.95%)

(3.10%)

(0.42 – 5.00%)

rbcL

37

1331

1205

53

73

GTR+I

0.17%

1.07%

see (Neel and Cummings 2004)

(90.53%)

(4.00%)

(0–0.39%)

(0 – 3.07%)

rpoB

78

375

306

52

17

GTR+Γ

0.31%

2.15%

http://www.kew.org/barcoding/update.html webcite

(81.60%)

(13.87%)

(0–3.19%)

(0 – 5.40%)

rps2

77

665

520

135

10

TVM+Γ+I

0.11%

4.37%

de Pamphilis et al. 1997

(78.20%)

(20.30%)

(0–2.84%)

(0 – 8.59%)

trnT-trnF

79

1868

1479

320

69

TVM+Γ+I

0.29%

3.24%

Taberlet et al. 1991

(79.68%)

(17.13%)

(0–3.29%)

(0 – 6.04%)

psbA-trnH

79

884

669

189

26

TVM+Γ

0.20%

7.75%

Sang et al. 1997; Tate and Simpson 2003

(75.68%)

(21.38%)

(0–2.94%)

(0 – 20.50%)

All cpDNA Loci

79

11076

9592

950

545

TVM+Γ+I

0.31%

3.82%

(86.51%)

(8.57%)

(0–2.0%)

(0 – 7.40%)

ITS

68

733

504

175

54

GTR+Γ+I

0.75%

6.51%

White et al. 1990

(68.76%)

(23.87%)

(0–3.93%)

(0.14 – 21.26%)

All Loci

79

11809

10096

1125

599

GTR+Γ+I

0.36%

4.05%

(85.41%)

(9.52%)

(0.02–1.94%)

(0.04–7.99%)

N = the number of Agalinis species for each locus. Pairwise distances were calculated using Agalinis species only and do not include outgroup taxa.

¹ Nucleotide substitution model as selected using MODELTEST.

² Pairwise differences are based on the maximum likelihood distances calculated using the nucleotide substitution parameters associated with the best fitting model identified using MODELTEST

Pettengill and Neel BMC Evolutionary Biology 2008 8:264   doi:10.1186/1471-2148-8-264