TABLE 1.
Count of remaining loci and individuals after each step of two filtering regimes (‘Standard’ and ‘Removing sex‐linked loci’) applied to the genetic datasets of eastern yellow robin (EYR), yellow‐tufted honeyeater (YTH), and Leadbeater's possum (LBP). Minor Allele Count filter was used as an extra filtering step before performing PCA and parentage analyses.
| Filter | EYR | YTH | LBP | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Standard | Removing sex‐linked loci | Standard | Removing sex‐linked loci | Standard | Removing sex‐linked loci | ||||
| # ind | # loci | # loci | # ind | # loci | # loci | # ind | # loci | # loci | |
| No filtering | 782 | 53,324 | 53,324 | 641 | 118,732 | 118,732 | 376 | 9508 | 9508 |
| Secondaries | 782 | 35,663 | 35,663 | 641 | 74,470 | 74,470 | 376 | 8436 | 8436 |
| Sex‐linked | 31,939 | 71,176 | 8365 | ||||||
| Excessively heterozygous | 31,915 | 71,158 | 8309 | ||||||
| Read depth | 782 | 21,577 | 19,584 | 641 | 53,179 | 50,939 | 376 | 6095 | 5998 |
| Locus missing data | 782 | 13,972 | 12,940 | 641 | 16,481 | 15,914 | 376 | 4290 | 4215 |
| Individual missing data | 753 | 13,925 | 12,894 | 628 | 16,421 | 15,872 | 376 | 4290 | 4215 |
| Minor Allele Count | 753 | 13,693 | 12,667 | 628 | 14,908 | 14,340 | 376 | 4062 | 3987 |