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

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
			(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

ISSN: 2730-7182