TABLE 2

Levels of variability across the Rps2 locus and among RPS2 functional domains

Position in alignmentNo. sitesDivergencebPolymorphismb
TotalSilentaReplacementaSilentReplacementSilentReplacement
Entire region1–446137551651.92097.1142 (0.0904)55 (0.0280)33 (0.0047)20 (0.0023)
    Excluding A. lyratac42162102.92113.138 (0.0042)20 (0.0023)
5′ noncoding1–1137802802062 (0.0783)7 (0.0017)
    Excluding A. lyratac97597508 (0.0015)
Coding1138–38792709610.92098.171 (0.1266)55 (0.0280)20 (0.0092)20 (0.0023)
    Excluding A. lyratac2727613.92113.120 (0.0091)20 (0.0023)
    LRR2654–37601095248.9846.126 (0.1203)26 (0.0333)8 (0.0087)14 (0.0041)
    Other structurald22557.0168.05 (0.0877)1 (0.0064)0 (0.0)1 (0.0009)
    Nonstructurald1389305.01084.040 (0.1390)28 (0.0272)12 (0.011)5 (0.0012)
3′ noncoding3880–446124124109 (0.0392)6 (0.0035)
    Excluding A. lyratac514514010 (0.0036)
  • a Silent sites include noncoding sites as well as synonymous sites in the coding sequence.

  • b Divergence is shown as number of fixed differences (per site average difference); polymorphism is number of segregating sites (per site nucleotide diversity π).

  • c Results are shown for an alignment not including the consensus A. lyrata sequence, allowing polymorphism to be ascertained at a greater number of sites, for 5′ noncoding, coding, and 3′ noncoding regions.

  • d Other structural regions defined in Mindrinos et al. 1994 (and their positions in alignment) include leucine zipper (1228–1293), nucleotide-binding site (1684–1710, 1912–1926, 2128–2208), transmembrane domain (2158–2208), and hydrophobic N terminus (1156–1203). Nonstructural regions are made up of the coding sequence excluding the leucine-rich repeat region and other structural regions.