Table 1.
Genetic diversity indices for Ceratonia siliqua sampled at four sites based on sequencing 18 SSR loci and comparing three different genotyping procedures: AS (amplicon size scoring), MN (MicNeSs scoring), and IM (independent marker scoring).a
| Populationb | N | AS | MN | IM | IM (only SSR)c | IM (only SNPs and indels)c | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | Priv. | H o | H e | F IS | A | Priv. | H o | H e | F IS | A | Priv. | H o | H e | F IS | A | Priv. | H o | H e | F IS | A | Priv. | H o | H e | F IS | ||
| ESGRA | 19 | 3.667 (0.229) | 0.389 (0.143) | 0.597 (0.048) | 0.515 (0.033) | −0.196 (0.062) | 3.556 (0.294) | 0.333 (0.114) | 0.638 (0.069) | 0.518 (0.044) | −0.250 (0.078) | 3.000 (0.188) | 0.114 (0.055) | 0.421 (0.041) | 0.383 (0.035) | −0.129 (0.036) | 3.350 (0.244) | 0.100 (0.069) | 0.477 (0.051) | 0.430 (0.042) | −0.139 (0.047) | 2.533 (0.256) | 0.133 (0.091) | 0.348 (0.065) | 0.321 (0.058) | −0.115 (0.056) |
| GRLOU | 19 | 3.111 (0.322) | 0.000 (0.000) | 0.447 (0.071) | 0.439 (0.059) | −0.042 (0.070) | 3.167 (0.305) | 0.000 (0.000) | 0.535 (0.067) | 0.479 (0.055) | −0.141 (0.067) | 2.600 (0.197) | 0.000 (0.000) | 0.373 (0.042) | 0.384 (0.042) | −0.027 (0.040) | 2.850 (0.254) | 0.000 (0.000) | 0.413 (0.056) | 0.439 (0.056) | 0.004 (0.056) | 2.267 (0.300) | 0.000 (0.000) | 0.319 (0.062) | 0.310 (0.059) | −0.078 (0.053) |
| LIENF | 20 | 3.333 (0.302) | 0.722 (0.311) | 0.526 (0.048) | 0.527 (0.045) | −0.039 (0.048) | 3.222 (0.329) | 0.111 (0.076) | 0.556 (0.058) | 0.512 (0.047) | −0.111 (0.070) | 2.629 (0.201) | 0.029 (0.029) | 0.386 (0.039) | 0.417 (0.041) | 0.027 (0.034) | 2.800 (0.277) | 0.050 (0.050) | 0.406 (0.048) | 0.446 (0.053) | 0.033 (0.038) | 2.400 (0.289) | 0.000 (0.000) | 0.359 (0.067) | 0.378 (0.064) | 0.019 (0.065) |
| MAIMO | 19 | 4.056 (0.366) | 0.722 (0.311) | 0.553 (0.049) | 0.562 (0.033) | −0.015 (0.061) | 3.722 (0.321) | 0.444 (0.166) | 0.614 (0.073) | 0.524 (0.051) | −0.173 (0.076) | 3.457 (0.189) | 0.457 (0.125) | 0.440 (0.041) | 0.469 (0.034) | 0.051 (0.059) | 3.650 (0.244) | 0.400 (0.184) | 0.505 (0.049) | 0.534 (0.036) | 0.038 (0.072) | 3.200 (0.296) | 0.533 (0.165) | 0.353 (0.066) | 0.383 (0.057) | 0.068 (0.100) |
| Total | 77 | 3.542 (0.157) | 0.530 (0.028) | 0.510 (0.022) | −0.074 (0.031) | 3.417 (0.155) | 0.586 (0.033) | 0.508 (0.024) | −0.166 (0.027) | 2.886 (0.073) | 0.411 (0.015) | 0.417 (0.014) | −0.018 (0.015) | 3.157 (0.098) | 0.457 (0.019) | 0.466 (0.017) | −0.020 (0.020) | 2.524 (0.100) | 0.349 (0.023) | 0.353 (0.022) | −0.016 (0.025) | |||||
A = number of alleles; F IS = inbreeding coefficient; H e = unbiased expected heterozygosity; H o = observed heterozygosity; N = population size; Priv. = number of private alleles.
a
Values presented are mean (SE).
b
Population codes correspond to the information provided in the Materials and Methods.
c
For IM scoring, SSRs and SNPs were split in independent matrices and genetic diversity indices were also calculated.