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Table 2 Summary of variable and parsimony informative sites in data partitions.

From: Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Treatment Aligned length Pines only
Variable positions
(% of total)
PI positions
(% of total)
Pines and outgroups
Variable positions
(% of total)
PI positions
(% of total)
All Nucleotides 132085 11179 (8.5) 7761 (5.9) 22834 (17.3) 11534 (8.7)
All Nucleotides without ycf1, ycf2 118935 8755 (7.4) 5852 (4.9) 18978 (16.0) 9038 (7.6)
Exon Nucleotides 62298 4716 (7.6) 3475 (5.6) 8346 (13.4) 4867 (7.8)
Exon Nucleotides without ycf1, ycf2 49044 2291 (4.7) 1566 (3.2) 4489 (9.2) 2381 (4.9)
ycf1 6355 1514 (23.8) 1227 (19.3) 2165 (34.1) 1507 (23.7)
ycf2 6794 910 (13.4) 682 (10.0) 1686 (24.8) 987 (14.5)
ycf1+ycf2 13149 2424 (18.4) 1909 (14.5) 3851 (29.3) 2494 (19.0)
Wang et al. [22] 3513 196 (5.6) 127 (3.6) 482 (13.5) 243 (6.8)
Gernandt et al. [21] 2817 197 (7.0) 128 (4.5) 345 (12.2) 167 (5.9)
Eckert and Hall [20] 3288 217 (6.6) 123 (3.7) 411 (12.5) 206 (6.3)
  1. Data from Gernandt et al. [21] and Eckert and Hall [20] pruned to include only ingroup species and outgroup genera common to our study. (PI = parsimony informative.)