Table 1.
RAD marker statistics per analyses with or without clones, and using genome aligned or unaligned reads.
| Potential clones included (n=30) | Potential clones removed (n=22) | |||||||
|---|---|---|---|---|---|---|---|---|
| Genome Aligned | No Genome Aligned | Genome Aligned | No Genome Aligned | |||||
| Mean number of RAD markers per individual | 2 305 | (95% CI ± 71; SD = 193) | 2 759 | (95% CI ± 89; SD = 243) | 2 330 | (95% CI ± 75; SD = 206) | 2 737 | (95% CI ± 90; SD = 246) |
| Mean depth of coverage per RAD marker per individual | 48X | (95% CI ± 8; SD = 22) | 49X | (95% CI ± 9; SD = 23) | 51X | (95% CI ± 8; SD = 23) | 54X | (95% CI ± 9; SD = 24) |
| Mean number of polymorphic RAD markers per individual | 139 | (95% CI ± 18; SD = 50) | 261 | (95% CI ± 24; SD = 65) | 142 | (95% CI ± 21; SD = 57) | 252 | (95% CI ± 26; SD = 72) |
| Mean number of SNPs per individual | 174 | (95% CI ± 24; SD = 66) | 360 | (95% CI ± 24; SD = 66) | 179 | (95% CI ± 27; SD = 75) | 356 | (95% CI ± 33; SD = 90) |
| Total Number of RAD markers in the catalog | 2 | 987 | 4 | 065 | 2 | 978 | 3 | 925 |
| Total Number of RAD markers present in all individuals | 1 | 297 | 1 | 251 | 1 | 351 | 1426 | |
| Total number of polymorphic markers present in all individuals | 287 | 248 | 304 | 310 | ||||
| Number of polymorphic RAD markers with 1 SNP | 220 | 204 | 232 | 250 | ||||
| RAD markers candidate neutral | 164 | 145 | 167 | 169 | ||||
| RAD markers candidate balancing selection | 56 | 59 | 65 | 79 | ||||
| RAD markers candidate positive selection | 0 | 0 | 0 | 2 | ||||
| Number of polymorphic RAD markers with >1 SNP | 67 | 44 | 72 | 60 | ||||
| RAD markers candidate neutral* | 47 | 27 | 46 | 31 | ||||
| RAD markers candidate balancing selection* | 6 | 7 | 8 | 13 | ||||
| RAD markers candidate positive selection* | 0 | 0 | 0 | 1 | ||||
| Number of markers candidate neutral | 211 | 172 | 213 | 200 | ||||
| Number of markers candidate balancing selection | 62 | 66 | 73 | 92 | ||||
| Number of markers candidate positive selection | 0 | 0 | 0 | 3 | ||||
| Total number of SNPs present in all individuals | 365 | 298 | 388 | 374 | ||||
| SNPs candidate neutral | 266 | 199 | 269 | 231 | ||||
| SNPs candidate balancing selection* | 68 | 74 | 81 | 107 | ||||
| SNPs candidate positive selection* | 0 | 0 | 0 | 4 | ||||
| Biallelic SNPs candidate neutral + | 209 | 172 | 212 | 200 | ||||
*
Markers containing SNPs with conflicting classifications (e.g. one SNP candidate neutral and another candidate balancing, in the same locus) were excluded from the analyses
+
To avoid violations of the assumption of independence, only one SNP per RAD marker was used for the demographic analyses