Table 1.
Simulation Models.
| Model No. | 1 | 2a | 3a | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11b | 12b | 13b |
| No. of sampled populationsc | 3 | 2 | 2 | 3 | 3 | 4 | 3 | 3 | 3 | 3 | 3 | 3 | 3 |
| θd | 10 | 10 | 10 | 10 | 10 | 10 | 1 | 1 | 10 | 10 | 10 | 10 | 10 |
| t1e | 2 | 2 | 5 | 2 | 2 | 2 | 0.2 | 0.2 | 2 | 2 | 2 | 2 | 2 |
| t2e | 5 | — | — | 5 | 5 | 4 | 0.5 | 0.5 | 5 | 5 | 5 | 5 | 5 |
| t3e | — | — | — | — | — | 5 | — | — | — | — | — | — | — |
| mf | — | — | — | — | — | — | — | — | m1>2 = 0.02 m3>(1,2) = 0.02 | m1>2 = 0.02 m3>(1,2) = 0.02 | m1>2 = 0.2 m3>(1,2) = 0.2 | m1>2 = 0.2 m3>(1,2) = 0.2 | m1>2 = 0.2 m3>(1,2) = 0.2 |
| No. of loci | 10 | 10 | 10 | 50 | 10 | 50 | 50 | 50 | 10 | 50 | 50 | 50 | 50 |
| No. of gene copies per locus | 5 | 5 | 5 | 5 | 20 | 5 | 5 | 15 | 5 | 5 | 5 | 5 | 5 |
| m prior termg | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.5 | 5.0 | 0.05h |
| False positivesi | 0.050 | 0.0 | 0.0 | 0.0 | 0.0 | 0.019 | 0.012 | 0.056 | 0.025 | 0.042 | 0.075 | 0.200 | 0.0130 |
| Mean run duration (h)j | 3 | 1 | 1 | 12 | 48 | 96 | 6 | 20 | 3 | 12 | 48 | 96 | 96 |
| Figure no. | 4 | 4 | 4 | 5 | 5 | 6 | 7 | 7 | 8 | 8 | 9 | 9 | 9 |
Data for models 2 and 3 were taken from data sets simulated for model 1.
Models 11, 12, and 13 all used the same data sets.
Population trees for two-population models, (1,2):3; for three-population models, ((1,2):4,3):5; and for four-population models, ((1,2):5,(3,4):6):7.
The true value for all population size parameters in the model.
Population splitting time values.
Migration rate parameters with nonzero values, rates for all parameters not shown were set to zero.
The upper bound on the uniform prior distribution for migration parameters.
The mean of the exponential prior distribution for migration parameters.
The proportion of those migration parameters that have true values of zero and that are estimated to be significantly different from zero.
The average time required for an analysis on a single PC processor. Run duration depends on the size of the data set, the burn-in duration, the rate of sampling genealogies, and the number of Metropolis-coupled chains specified by the investigator (Hey and Nielsen 2004).