Table 1.
Direct Estimates of svcMRs Based on Short-Read WGS Data from Mutation Accumulation Lines (n = 66) Initiated from nine Genotypes of Daphnia magna Collected Originally from Finland, Germany, and Israel (rates are in bold, length-adjusted rates are in italics)
| Rates (95% CI) (×10–10) per bp per generation | |||||
|---|---|---|---|---|---|
| n | Mean Length (range) | Difference Among Populations? | |||
| Mutation Type | bp | Length-adjusted (× 10−8) | |||
| Short indels | |||||
| (<50 bp) | Insertions | 23 | 3.6 (1–24) | 2.72 (1.4, 4.2) | |
| 0.08 (0.03, 0.1) | |||||
| Deletions | 39 | 3.8 (1–24) | 10.68 (3.6, 21.5) | ||
| 0.3 (0.1, 0.6) | |||||
| Insertion + Deletions | 62 | 3.7 (1–24) | 13.40 (6.1, 24.1) | Yes | |
| χ 2 = 34.9, df = 2, P < 0.0001 | |||||
| Binomial generalized linear mixed model | |||||
| Long deletions and duplications | |||||
| (≥50 bp) | Tandem duplications | 1 | 1,697 (NA) | 0.06 (0, 0.2) | |
| 1.06 (0, 3.2) | |||||
| Deletions | 6 | 1,888 (417–5,508) | 0.98 (0.2, 1.9) | ||
| 11.81 (3.0, 23.3) | |||||
| Tandem duplications + Deletions | 7 | 1,861 (417–5,508) | 1.04 (0.3, 2.0) | No | |
| χ 2 = 1.72, df = 2, P = 0.42 | |||||
| Kruskal–Wallis | |||||
| CNV sites | |||||
| Duplications | 42 | 2,738 (2,000–10,000) | 3.48 (0.3, 8.6) | ||
| 95.35 (5.2, 238.0) | |||||
| Deletions | 10 | 2,400 (2,000–4,000) | 3.05 (0.6, 6.5) | ||
| 76.21 (12.6, 162.0) | |||||
| Duplications + Deletions | 52 | 2,673 (2,000–10,000) | 6.53 (1.6, 12.9) | Yes | |
| χ 2 = 13.44, df = 2, P = 0.0012 | |||||
| Kruskal–Wallis | |||||
The number of observed events (n), the mean length (bp), the mean rates (with 95% CIs) for six categories of mutation, and the net rates for each category include a test for population effects.