Table 2.
Nucleotide Polymorphisms and Summary Statistics for MEA Promoter, Genic Region, and a Gene Flanking the 5′-end of the Promotera
| Taxon | n | Ltotal | La | Lsilent | L4 | Lsyn | Lintr | Stotal | S4 | πtotalb | πab | πsilb | π4b | πsynb | πintrb | DTajcd | FFLc | Fsc | Hc |
| 5’ Gene | |||||||||||||||||||
| Arabidopsis lyrata | 22 | 378 | 291.1 | 86.9 | 46 | 86.9 | 0 | 19 | 4 | 0.010 | 0.010 | 0.011 | 0.008 | 0.011 | — | −1.878* (−0.922) | −2.262* (−1.701) | −3.817** (−0.566) | −1.558 (−3.983) |
| Arabidopsis lyrata lyrata | 10 | 378 | 290.9 | 87.1 | 46 | 87.1 | 0 | 9 | 3 | 0.005 | 0.003 | 0.011 | 0.013 | 0.011 | — | −1.562 (−1.687+) | −1.355 (−0.461) | −1.964+ (−0.653) | −1.244 (−7.20*) |
| Arabidopsis lyrata petraea | 12 | 378 | 291.3 | 86.7 | 46 | 86.7 | 0 | 12 | 1 | 0.005 | 0.004 | 0.010 | 0.004 | 0.010 | — | −1.141 (−2.087*) | −1.567 (−2.53*) | −0.476 (0.924) | 0.152 (−3.636) |
| Arabidopsis thaliana | 18 | 393 | 307.5 | 85.5 | 46 | 85.5 | 0 | 2 | 1 | 0.001 | 0.000 | 0.007 | 0.005 | 0.007 | — | −0.529 (−0.026) | 0.398 (0.74) | −0.011 (−0.027) | 0.183 (0.444) |
| MEA promoter | |||||||||||||||||||
| A. lyrata | 23 | 804 | — | — | — | — | — | 64 | — | 0.022 | — | 0.022 | — | — | — | −0.248 | −1.166 | 1.135 | −1.941 |
| A. l. lyrata | 10 | 814 | — | — | — | — | — | 39 | — | 0.011 | — | 0.011 | — | — | — | −1.795* | −1.865 | 0.606 | −11.556+ |
| A. l. petraea | 13 | 811 | — | — | — | — | — | 50 | — | 0.017 | — | 0.017 | — | — | — | −0.916 | −0.618 | 3.209 | −14.308+ |
| A. thaliana | 18 | 797 | — | — | — | — | — | 16 | — | 0.005 | — | 0.005 | — | — | — | −0.878 | −0.746 | −2.475 | −2.327 |
| MEA gene | |||||||||||||||||||
| A. lyrata | 28 | 3,844 | 1,545.0 | 2,283.0 | 2,075 | 429.0 | 1,854 | 151 | 114 | 0.010 | 0.004 | 0.013 | 0.014 | 0.008 | 0.015 | −0.195 (−0.273) | −0.676 (−0.677) | −1.19 (−0.242) | −0.735 (−1.836) |
| A. l. lyrata | 13 | 4,058 | 1,572.6 | 2,483.4 | 2,271 | 434.4 | 2,049 | 86 | 72 | 0.006 | 0.002 | 0.008 | 0.009 | 0.005 | 0.009 | −0.579 (−0.537) | −0.544 (−0.656) | −0.203 (0.226) | −16.974 (−15.41) |
| A. l. petraea | 15 | 3,927 | 1,544.7 | 2,366.3 | 2,158 | 429.3 | 1,937 | 124 | 94 | 0.008 | 0.004 | 0.012 | 0.012 | 0.008 | 0.012 | −0.596 (−0.659) | −0.461 (−0.443) | 1.637 (2.411) | −8.771 (−12.267) |
| A. thaliana | 13 | 4,202 | 1,611.8 | 2,588.2 | 2,369 | 446.2 | 2,142 | 50 | 37 | 0.005 | 0.001 | 0.007 | 0.007 | 0.005 | 0.007 | 1.381 (0.796) | 1.623+ (0.757) | 3.896 (1.881) | −1.628 (0.462) |
n, number of chromosomes sampled; L, number of sites used in analysis; S, Number of segregating sites; π, average pairwise differences per site; Subscripts for L, S, π: Xtotal, all sites; Xa, nonsynonymous sites; Xsilent, silent sites (= synonymous and noncoding sites); X4, 4-fold degenerate and noncoding sites; Xsyn, synonymous sites; Xintr, intron sites; DTaj, Tajima's D; FFL, Fu and Li's F; Fs, Fu's Fs; H, Fay and Wu's H; Significance levels were determined by 10,000 random coalescent simulations conditioned on the observed number of segregating sites and assuming no recombination, and statistically significant values (P ≤ 0.05) are bold faced: + 0.05 < P ≤ 0.1; * 0.01 < P ≤ 0.05; **P ≤ 0.01.
Jukes–Cantor correction was used.
Four-fold degenerate and noncoding sites were used. Values in parentheses are for all sites.
All significant values of Tajima's D are more extreme than the range of values calculated from multiple other genes in the same taxa (Wright and Gaut 2005, table 2).