3.1 | Statistical Analysis and Genetic Diversity
A total library was obtained with 226,279,541 readings with good average quality (Q-score ≥ 30), showing an optimal value (Q ≥ 30) throughout all the sequences (101 bp). Quality only decreases in the last bp, around 75 bp. being selected for this study. 1,038 were selected for this study according with our previously established parameters. Distribution of SNPs minor allele frequencies (MAFs) are shown in Table 2. More than 96.92% of the SNPs for all sampled populations presented MAF values ≤ 0.1, varying from 0.994 in Culimo to 0.969 in Viña del Mar/Valparaíso, with MAF scores ranging up to MAF ≤ 0.4.
Expected heterozygosity values ​​(HE ) were higher than the observed values (HO ) for all populations. The mean HO varied from 0.036 in Culimo to 0.108 in Petorca, and the mean HEvaried from 0.086 in Culimo to 0.145 in Petorca, with an overallHO of 0.014 and an overallHE of 0.024, suggesting both a deficit of heterozygotes. Inbreeding coefficient values (FIS ) for all populations wereFIS >0 (overall value of 0.424), varying from 0.177 in Viña del Mar/ Valparaíso to 0.586 in Culimo, which also indicates a heterozygous deficit and high levels of inbreeding with little or no random mating (Table 3). All FSTcomparisons between populations showed values ​​above 0.049 and below 0.119, with a moderate difference, indicating a tendency of genetic similarity between populations (Table 4). Nei’s genetic distance values were ​​lower than 0.003 in all populations, also indicating that the populations may be genetically similar (Table 4).
Table 2. Frequency of SNPs by minor allele frequencies (MAF) within the six population groups of Jubaea chilensis . (CUL) Culimo, (PET) Petorca, (OCO) Ocoa, (VAV) Viña del Mar/Valparaíso, (COC) Cocalán, (CAN) Candelaria.