Table 1.
Genetic diversity measured by dataset.
| Algerian Sheep Datasets | French Sheep Datasets | French Cattle Datasets | |
|---|---|---|---|
| no. of breeds | 5 | 17 | 7 |
| Microsatellite datasets: | |||
| nb. of individuals | 113 | 425 | 175 |
| nb. of microsatellites | 29 | 21 | 30 |
| nb. of alleles | 343 | 292 | 283 |
| mean A (s.d.) | 11.83 (13.29) | 13.90 (21.59) | 9.43 (11.97) |
| mean HO (s.d.) | 0.77 (0.008) | 0.73 (0.018) | 0.71 (0.015) |
| mean PIC (s.d.) | 0.74 (0.010) | 0.70 (0.018) | 0.67 (0.018) |
| mean Ae (s.d.) | 5.06 (4.67) | 4.46 (3.89) | 3.98 (3.02) |
| SNP datasets: | |||
| nb. of individuals * | 36 | 346 | 152 |
| nb. of SNP | 52,412 | 40,454 | 52,324 |
| nb. of SNP after filtration | 36,493 | 39,800 | 47,286 |
| nb. of SNP after Pruning ** | 15,560 | 31,184 | 24,841 |
| Mean FST from microsatellites datasets (s.d.) | 0.048 (<0.001) | 0.104 (0.004) | 0.076 (<0.001) |
| Mean FST from SNP datasets (s.d.) | 0.048 (<0.001) | 0.105 (0.004) | 0.078 (<0.001) |
| r Pearson *** (p-value) | 0.87 (0.001) | 0.95 (<0.001) | 0.77 (<0.001) |
no.: number; s.d.: standard deviation; A: number of alleles; HO: observed heterozygosity; PIC: polymorphic information content; Ae: effective number of alleles; *: after filtration (see Material and Methods); **: see Material and Methods; ***: Pearson correlation coefficient between pairwise FST values obtained with the microsatellite dataset and the SNP dataset.