Table 1.
Summary of allelic diversity and tests of neutrality of LysM-RLKs in wild tomatoes
| No. Seqs | No. Sites | Haplotypes | π all sites (non,syn,silent) | πa/πs | S | MK p-value (uncorrected) | |
|---|---|---|---|---|---|---|---|
| LYK1 | 1881 | ||||||
| chil v ochr | 17 v 1 | 13 | 0.0027 (0.0016, 0.0059, 0.0059) | 0.28 | 19 | 0.062 | |
| chil v lyco | 17 v 1 | 0.0027 (0.0016, 0.0059, 0.0059) | 0.28 | 0.026 | |||
| peru v ochr | 17 v 1 | 15 | 0.0049 (0.0026, 0.0118, 0.0117) | 0.22 | 43 | 0.185 | |
| peru v lyco | 17 v 1 | 0.0049 (0.0026, 0.0118, 0.0117) | 0.22 | 0.146 | |||
| LYK3 | 1992 | ||||||
| chil v ochr | 17 v 1 | 16 | 0.0046 (0.0011, 0.0160, 0.0159) | 0.07 | 37 | 0.036 | |
| chil v lyco | 17 v 1 | 0.0046 (0.0011, 0.0152, 0.0151) | 0.07 | 0.718 | |||
| peru v ochr | 16 v 1 | 15 | 0.0056 (0.0008, 0.0211, 0.0209) | 0.04 | 51 | 0.005 | |
| peru v lyco | 16 v 1 | 0.0056 (0.0008, 0.0215, 0.0214) | 0.04 | 0.822 | |||
| LYK4 | 1938 | ||||||
| chil v ochr | 15 v 1 | 15 | 0.0080 (0.0061, 0.0138, 0.0137) | 0.44 | 51 | 0.510 | |
| chil v lyco | 15 v 1 | 0.0080 (0.0061, 0.0138, 0.0137) | 0.44 | 0.760 | |||
| peru v ochr | 16 v 1 | 16 | 0.0089 (0.0054, 0.0202, 0.0201) | 0.26 | 80 | 0.275 | |
| peru v lyco | 16 v 1 | 0.0089 (0.0054, 0.0202, 0.0201) | 0.26 | 0.336 | |||
| LYK6 | 1599 | ||||||
| chil v ochr | 15 v 1 | 13 | 0.0151 (0.0119, 0.0246, 0.0246) | 0.48 | 108 | 0.108 | |
| chil v lyco | 15 v 1 | 0.0151 (0.0119, 0.0245, 0.0245) | 0.48 | 0.069 | |||
| peru v ochr | 8 v 1 | 8 | 0.0161 (0.0135, 0.0244, 0.0244) | 0.55 | 87 | 0.118 | |
| peru v lyco | 8 v 1 | 0.0161 (0.0135, 0.0244, 0.0244) | 0.55 | 0.064 | |||
| LYK8 | 1149 | ||||||
| chil v ochr | 13 v 1 | 12 | 0.0048 (0.0044, 0.0064, 0.0064) | 0.69 | 34 | 0.025 | |
| peru v ochr | 17 v 1 | 16 | 0.0052 (0.0042, 0.0087, 0.0087) | 0.47 | 55 | 0.026 | |
| LYK9 | 1890 | ||||||
| chil v ochr | 17 v 1 | 17 | 0.0073 (0.0042, 0.0174, 0.0176) | 0.24 | 74 | 0.818 | |
| chil v lyco | 17 v 1 | 0.0073 (0.0042, 0.0174, 0.0176) | 0.24 | 73 | 0.604 | ||
| peru v ochr | 17 v 1 | 17 | 0.0068 (0.0045, 0.0135, 0.0146) | 0.33 | 79 | 0.813 | |
| peru v lyco | 17 v 1 | 0.0068 (0.0045, 0.0174, 0.0146) | 0.33 | 77 | 0.649 |
Population samples were available for Solanum chilense (chil) and Solanum peruvianum (peru). Single allelic sequences from Solanum ochranthum (ochr) and Solanum lycopersicoides (lyco) were used for outgroup comparisons in the tests of neutrality. Haplotypes, the number of unique alleles in each population sample, apply to the first species listed in column 1, as do values for S, the number of segregating sites. The ratio of non-synonymous to synonymous average pairwise differences (πa/πs) was calculated for S. chilense and S. peruvianum. The McDonald-Kreitman test was applied to each pair of species listed in column 1. Uncorrected p-values for the McDonald-Kreitman analyses are reported, but following correction for multiple testing, none of the corrected p-values were below 5%