Table 2 Number of RAD locus clusters and interspecific variants identified for each analysis
From: Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis
Species | Parameters | Analysis pipeline | Minimum taxon coverage | Number of orthologous RAD loci | Number (%) of orthologous RAD loci in genes | Number of variants for relationship estimation | Range of missing interspecific variants in included species | Percentage of missing data in RAxML matrix |
|---|---|---|---|---|---|---|---|---|
Salmonids | Strict | BLASTN | 5 | 3,050 | 375 (12.3) | 6,959 | NA | 0 |
Salmonids | Strict | BLASTN | ≥3 | 22,632 | 1,407 (6.2) | 39,890 | 3,135–21,480 | 25.09 |
All ten species | Relaxed | BLASTN | 10 | 1 | 1 (100.0) | NA | NA | NA |
All ten species | Relaxed | BLASTN | ≥7 | 137 | 106 (77.4) | 1,440 | 37–745 | 25.50 |
All ten species | Relaxed | BLASTN | ≥5 | 452 | 321 (71.0) | 4,094 | 371–2,881 | 36.75 |