Table 2.
Summary of inferred maps under the 3 simulation scenarios. (The proportion of markers that were assigned to the correct or an incorrect chromosome are reported in the first two rows. These values do not always sum to 1.0, as some markers remained unassigned. Among unlinked marker pairs the proportion of pairwise combinations that gave spurious evidence of linkage with LOD > 2.0 or 3.0 are reported. Mean (s.e.) estimates of map length should be compared to simulated lengths of 100 cM (scenarios 1 and 3) or 20 cM (scenario 2). The proportion of replicates where the most parsimonious marker order was the simulated order is reported. Discrepancies between the inferred marker order and the actual marker order were classified into the listed categories and their frequencies are reported.)
| great reed warblers | collared flycatchers | Soay sheep | red deer | |
|---|---|---|---|---|
| scenario 1—microsatellites | ||||
| proportion correctly assigned | 1.00 | 0.99 | 0.99 | 0.95 |
| prop wrongly assigned | 0 | 0 | 0 | 0 |
| prop spurious twopoint LOD>2 | 1.0×10−3 | 2.2×10−4 | 2.2×10−3 | 2.0×10−3 |
| prop spurious twopoint LOD>3 | 0 | 0 | 1.1×10−4 | 3.3×10−4 |
| mean (s.e.) length (cM) | 99.8 (0.6) | 101.5 (1.6) | 99.2 (0.8) | 95.9 (1.4) |
| real order most parsimonious | 0.97 | 0.92 | 0.80 | 0.67 |
| inversions (2 markers) | 0.03 | 0.03 | 0.13 | 0.20 |
| inversions (3 markers) | 0 | 0.02 | 0.02 | 0.02 |
| inversions (>3 markers) | 0 | 0.03 | 0 | 0.02 |
| rearrangement | 0 | 0 | 0.05 | 0.10 |
| scenario 2—SNPs | ||||
| proportion correctly assigned | 1.00 | 1.00 | 1.00 | 0.95 |
| prop wrongly assigned | 0 | 0 | 0 | 0 |
| prop spurious twopoint LOD>2 | 1.1×10−3 | 1.6×10−3 | 8.9×10−4 | 3.4×10−3 |
| prop spurious twopoint LOD>3 | 2.2×10−4 | 1.1×10−4 | 0 | 1.2×10−3 |
| mean (s.e.) length (cM) | 20.2 (0.3) | 19.8 (0.4) | 19.9 (0.4) | 20.7 (0.7) |
| real order most parsimonious | 0.97 | 0.75 | 0.52 | 0.28 |
| inversions (2 markers) | 0.03 | 0.20 | 0.22 | 0.28 |
| inversions (3 markers) | 0 | 0 | 0.02 | 0.02 |
| inversions (>3 markers) | 0 | 0 | 0 | 0 |
| rearrangement | 0 | 0.050 | 0.25 | 0.42 |
| scenario 3—microsatellites with 5% error | ||||
| proportion correctly assigned | 1.00 | 0.97 | 0.94 | 0.84 |
| prop wrongly assigned | 0 | 0 | 0.002 | 0.002 |
| prop spurious twopoint LOD>2 | 1.1×10−3 | 7.8×10−4 | 2.0×10−3 | 2.6×10−3 |
| prop spurious twopoint LOD>3 | 0 | 4.4×10−4 | 3.3×10−4 | 5.6×10−4 |
| mean (s.e.) length (cM) | 162.7 (2.0) | 128.3 (1.4) | 150.6 (2.7) | 154.0 (3.6) |
| real order most parsimonious | 0.45 | 0.48 | 0.27 | 0.13 |
| inversions (2 markers) | 0.40 | 0.20 | 0.28 | 0.13 |
| inversions (3 markers) | 0.07 | 0 | 0.05 | 0.08 |
| inversions (>3 markers) | 0 | 0.02 | 0 | 0.03 |
| rearrangement | 0.07 | 0.02 | 0.23 | 0.38 |
| fission | 0 | 0.30 | 0.17 | 0.23 |