A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

Table 1 Sequence and alignment length, variation and substitution model chosen for each region sequenced

Region	Length range (bp)	Alignment length (bp)	Base changes (variable/parsimony-informative/parsimony-informative excluding outgroup)	Indels (parsimony-informative/parsimony-informative excluding outgroup)	% GC content	Nucleotide diversity, Π (total)	Tajima's D (overall/coding region)	Nucleotide substitution model
rpl32-trnL	426-448	470	46/19/11	8/2	26			TrN+I+G I = 0.69 G = 0.65
rpoB-trnC	419-430	449	37/27/3	8/5	30			F81+I I = 0.95
trnH-psbA	454-458	460	29/20/9	1/0	36			F81+G G = 0.01
CDO504 A	406-409	434	49/38/3	7/2	48	0.0050	-2.81*/-2.25	F81
CDO504 B	389-432	467	86/56/17	12/8	48	0.010	-2.67**/-1.97	TIM+G G = 0.59
DMC1 A	454-458	470	52/29/9	10/4	40	0.0024	-2.67***/(-1.76)	F81+G G = 0.67
DMC1 B	428-451	461	52/34/9	7/4	39	0.0032	-2.27**/(-0.56)	HKY+G G = 0.60 Ti/Tv = 0.87

For length range, only the Australian species are reported. For alignment length, the outgroup Poa annua is also included. Asterisks indicate P-values: * 0.01 <P < 0.05; ** 0.01 <P < 0.001; *** P < 0.001. Brackets indicate P > 0.05

ISSN: 1741-7007