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Table 2 Summary of the cpDNA loci and the nDNA locus ITS used in this study

From: Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae)

        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
    (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%)  
  1. N = the number of Agalinis species for each locus. Pairwise distances were calculated using Agalinis species only and do not include outgroup taxa.
  2. 1 Nucleotide substitution model as selected using MODELTEST.
  3. 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