Table 1 The effect of sample number under different evolutionary scenarios. Result in this table are based on typical parameter values from the ancient DNA literature and a bouquet sampling scheme (see text). Fixed parameter values are: fragment length = 500 nucleotides, substitution rate per nucleotide site = 1·10-7, number of extant samples = 30. Given these values any combination of the population size parameter (N e ) and the maximal number of generations spanning the sampling interval (g max ) can be translated to a value of the population parameter (θ) and the maximum length of the sampling interval (τ max ) which are measured in units of generations (see text for definition). For various such parameter combinations we here list the associated values of θ, τ max , and the calculated number of ancient samples needed to have a greater than 95% chance of seeing at least one segregating site where the mutation is unique to the ancient individuals (n u ) and the number of ancient samples needed to have a greater than 95% chance of seeing at least one segregating site where the mutation is shared between ancient and extant individuals (n s ).
From: Tree measures and the number of segregating sites in time-structured population samples
N e | θ | g max | τ max | n u | n s |
|---|---|---|---|---|---|
5000 | 0.5 | 1000 | 0.2 | > 50 | > 50 |
- | - | 5000 | 1.0 | > 50 | > 50 |
- | - | 10000 | 2.0 | > 50 | > 50 |
- | - | 30000 | 6.0 | > 50 | > 50 |
- | - | 50000 | 10.0 | > 50 | > 50 |
10000 | 1.0 | 1000 | 0.1 | > 50 | > 50 |
- | - | 5000 | 0.5 | > 50 | > 50 |
- | - | 10000 | 1.0 | > 50 | > 50 |
- | - | 30000 | 3.0 | 42 | > 50 |
- | - | 50000 | 5.0 | 39 | > 50 |
30000 | 3.0 | 1000 | 0.03 | 44 | 3 |
- | - | 5000 | 0.17 | 23 | 5 |
- | - | 10000 | 0.33 | 15 | 7 |
- | - | 30000 | 1.0 | 9 | > 50 |
- | - | 50000 | 1.67 | 7 | > 50 |
50000 | 5.0 | 1000 | 0.02 | 26 | 2 |
- | - | 5000 | 0.1 | 16 | 2 |
- | - | 10000 | 0.2 | 11 | 3 |
- | - | 30000 | 0.6 | 7 | 6 |
- | - | 50000 | 1.0 | 5 | 9 |