Table 3 |
||||||||
|
Nucleotide diversity (by region) in the Chlamydomonas reinhardtii plastid genome. |
||||||||
|
# of sitesa |
S |
# of Indelsb (length nt) |
πc × 10-3 (SD × 10-3) |
π+d × 10-3 (SD × 10-3) |
πsyn × 10-3 |
πnsyn × 10-3 |
Tajima's D-Test (P value) |
|
|
|
||||||||
|
PROTEIN-CODING (by gene) |
||||||||
|
atpA |
501 |
18 |
0 |
17.30 (2.67) |
--- |
71.08 |
0 |
0.06 (>0.1) |
|
atpF |
213 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
atpI |
366 |
3 |
0 |
3.51 (1.43) |
--- |
13.85 |
0 |
-1.01 (>0.1) |
|
cemA |
462 |
2 |
0 |
2.27 (4.40) |
--- |
5.34 |
1.34 |
1.17 (>0.1) |
|
orf1995 |
1896 |
8 |
0 |
1.41 (0.56) |
--- |
2.57 |
1.09 |
-0.96 (>0.1) |
|
petA |
954 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
petG |
45 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
psaJ |
126 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
psbA |
435 |
8 |
0 |
9.61 (1.46) |
--- |
36.5 |
1.7 |
1.48 (>0.1) |
|
psbK |
72 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
rpoC2 |
252 |
6 |
0 |
13.61 (2.85) |
--- |
10.85 |
14.33 |
2.03 (<0.05) |
|
rpl2 |
321 |
2 |
0 |
3.56 (0.74) |
--- |
7.28 |
2.36 |
1.64 (>0.1) |
|
rps2 |
87 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
rps3 |
126 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
rps9 |
462 |
4 |
1 (21) |
3.50 (1.01) |
--- |
9.78 |
1.61 |
-0.04 (>0.1) |
|
rps11 |
105 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
rps12 |
321 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
rps19 |
183 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
tufA |
213 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
ycf3 |
315 |
2 |
0 |
1.81 (1.25) |
--- |
3.84 |
1.19 |
-1.28 (>0.1) |
|
ycf4 |
399 |
0 |
0 |
0 |
--- |
0 |
0 |
--- |
|
INTERGENIC (by region) |
||||||||
|
atpA/psbI |
343 |
1 |
0 |
1.75 (0.51) |
1.75 (0.51) |
--- |
--- |
1.22 (>0.1) |
|
atpF/rps11 |
1556 |
86 |
16 (368) |
25.61 (9.77) |
30.10 (11.15) |
--- |
--- |
-1.08 (>0.1) |
|
atpI/psaJ |
328 |
9 |
0 |
12.49 (2.42) |
12.49 (2.42) |
--- |
--- |
0.61 (>0.1) |
|
petG/rps3 |
805 |
5 |
3 (3) |
2.97 (0.44) |
4.50 (0.76) |
--- |
--- |
0.57 (>0.1) |
|
psaJ/rps12 |
310 |
2 |
0 |
3.38 (0.65) |
3.38 (0.65) |
--- |
--- |
1.17 (>0.1) |
|
psbK/tufA |
828 |
4 |
2 (117) |
1.18 (0.37) |
3.47 (0.53) |
--- |
--- |
0.06 (>0.1) |
|
psbI/cemA |
271 |
3 |
2 (2) |
5.20 (1.18) |
8.86 (2.00) |
--- |
--- |
0.00 (>0.1) |
|
rpl2/rps19 |
808 |
36 |
9 (164) |
27.36 (5.14) |
33.69 (5.70) |
--- |
--- |
0.99 (>0.1) |
|
rps3/rpoC2 |
1474 |
88 |
32 (462) |
41.60 (6.65) |
53.19 (9.01) |
--- |
--- |
0.71 (>0.1) |
|
rps9/ycf4 |
344 |
1 |
1 (21) |
1.65 (0.53) |
3.29 (0.69) |
--- |
--- |
1.03 (>0.1) |
|
rps18/rps2-1 |
1115 |
45 |
19 (418) |
30.47 (9.57) |
42.17 (11.33) |
--- |
--- |
0.90 (>0.1) |
|
ycf3/ycf4 |
179 |
0 |
0 |
0 |
0 |
--- |
--- |
--- |
|
23S-1/23S-2 |
909 |
6 |
2 (46) |
3.97 (0.67) |
5.28 (0.89) |
--- |
--- |
2.10 (<0.05) |
|
23S-2/5S |
89 |
0 |
0 |
0 |
0 |
--- |
--- |
--- |
|
|
||||||||
|
Note: S, number of segregating (i.e., polymorphic) sites; Indels, insertion-deletion events; π, nucleotide diversity; π+, nucleotide diversity including both polymorphic sites and insertion-deletion events; πsyn, nucleotide diversity at synonymous sites; πnsyn, nucleotide diversity at nonsynonymous sites; SD, standard deviation. a Comprises all sites in the nucleotide alignment, including those with indels. b Indels involving more than 1 nucleotide are counted as a single event. Indel length includes the sum of all indels and includes consecutive indel events. c Only includes sites without indels. d Considers all sites, including those with indels. Consecutive indels are counted as a single polymorphic event. Indel states were measured using a multiallelic approach. |
||||||||
|
Smith and Lee BMC Evolutionary Biology 2009 9:120 doi:10.1186/1471-2148-9-120 |
||||||||
