Table 3. Comparisons of Sequence Divergence and Phylogenetic Infromation from Variable Sites among Two Intergenic Spacers and matK Coding Region.
|
cpDNA regions |
% sequence divergence a |
No. of variable sites |
No. of informative sites b |
% informative sites c |
No. of homoplasious sites d |
No. of synapomorpic sites ´d |
% synapomorphic sites f |
|
psbA-trnH |
1.29 |
24 |
13 |
54.2 |
1 |
12 |
92.3 |
|
trnL-trnF |
0.39 |
10 |
6 |
60.0 |
2 |
4 |
66.7 |
|
matK |
0.58 |
53 |
30 |
56.6 |
3 |
27 |
90.0 |
a Average of percent species pairwise sequence divergences estimated using the Jukes-Vantor model. The same species were sequenced for these three regions.
b At a phylogenetically informative site, a nucleotide substitution is shared by two or more species.
c Percentage of phylogenetically informative sites among the total number of variable sites.
d Homoplasious sites of a region are those where nucleotide substitutions phylogenetically conflict with other substitutions in this region, and also the ones that conflict with phylogenies obtained from other DNA regions (e.g., matK and ITS) , i.e, site 44 of trnL-trnF intergenic spacer.
e Difference between number of informative sites and number of homoplasious sites.
f Percentage of synapomorphic sites among informative sites.