Table 1.
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