Table 2.
Estimates of genetic diversity per population for four analyses (with or without clones, genome aligned or unaligned reads).
| Nova Scotia (NS) |
Massachusetts (MA) |
Maryland (MD) | South Carolina (SC) |
|
|---|---|---|---|---|
| Potential Clones Included | ||||
| Number of samples | 9 | 9 | 6 | 6 |
| Genome-aligned | ||||
| RAD markers with biallelic SNPs (neutral) | 209 | |||
| Proportion of polymorphic SNP | 0.517 | 0.612 | 0.239 | 0.445 |
| Mean observed heterozygosity | 0.213 | 0.290 | 0.112 | 0.161 |
| Mean expected heterozygosity | 0.169 | 0.205 | 0.082 | 0.143 |
| Mean number of alleles per SNP | 1.517 | 1.612 | 1.239 | 1.445 |
| Number of private alleles | 23 | 22 | 4 | 53 |
| Unaligned | ||||
| RAD markers with biallelic SNPs (neutral) | 172 | |||
| Proportion of polymorphic SNP | 0.500 | 0.703 | 0.320 | 0.407 |
| Mean observed heterozygosity | 0.201 | 0.378 | 0.153 | 0.162 |
| Mean expected heterozygosity | 0.163 | 0.258 | 0.110 | 0.148 |
| Mean number of alleles per SNP | 1.500 | 1.703 | 1.320 | 1.407 |
| Number of private alleles | 14 | 12 | 8 | 25 |
| Potential Clones Exclued | ||||
| Number of samples | 4 | 7 | 5 | 6 |
| Genome-aligned | ||||
| RAD markers with biallelic SNPs (neutral) | 212 | |||
| Proportion of polymorphic SNP | 0.505 | 0.632 | 0.250 | 0.434 |
| Mean observed heterozygosity | 0.217 | 0.321 | 0.121 | 0.176 |
| Mean expected heterozygosity | 0.183 | 0.230 | 0.092 | 0.154 |
| Mean number of alleles per SNP | 1.505 | 1.632 | 1.250 | 1.434 |
| Number of private alleles | 22 | 28 | 4 | 40 |
| Unaligned | ||||
| RAD markers with biallelic SNPs (neutral) | 200 | |||
| Proportion of polymorphic SNP | 0.535 | 0.705 | 0.345 | 0.420 |
| Mean observed heterozygosity | 0.261 | 0.402 | 0.176 | 0.178 |
| Mean expected heterozygosity | 0.206 | 0.276 | 0.128 | 0.158 |
| Mean number of alleles per SNP | 1.535 | 1.705 | 1.345 | 1.420 |
| Number of private alleles | 11 | 16 | 8 | 29 |