Table 1.
Summary of Simulations Performed.
| Model Violation | # Simulations (39 Total) | Parameter, Simulated Values | Further Details |
| IM model (baseline – no violations), IS evolution | 1 | NA | IS simulation using MS; IS model specified in IMA |
| IM model, HKY evolution | 1 | NA | HKY simulation using SEQ-GEN based on trees simulated in MS; HKY model specified in IMA |
| IM model, IS evolution, HKY substitution model | 1 | NA | Same data sets, priors, and starting seeds as baseline IS runs, but with HKY model specified in IMA |
| IM model, HKY evolution, IS substitution model | 1 | NA | HKY simulation using SEQ-GEN based on trees simulated in MS; analyzed largest sequence blocks with no four-gamete test violations; IS model specified in IMA |
| IM model, GTR evolution, HKY substitution model | 1 | NA | GTR simulation using SEQ-GEN based on trees simulated in MS; HKY model specified in IMA |
| Intralocus recombination, full data set | 6 | ρ per bp = 0.005, 0.01, 0.02, 0.03, 0.04, 0.05 | HKY simulation using SEQ-GEN based on trees simulated in MS; HKY model specified in IMA |
| Intralocus recombination, nonrecombining blocks | 7 | ρ per bp = 0, 0.005, 0.01, 0.02, 0.03, 0.04, 0.05 | Four-gamete criterion used to identify recombination; HKY simulation using SEQ-GEN based on trees simulated in MS; HKY model specified in IMA |
| Introgression from third, unsampled species | 5 | Nefm between first focal species and third species = 0.1, 0.2, 0.3, 0.5, 1.0 | 5-Ma divergence time between third species and common ancestor of focal species; gene flow only with first focal species |
| Population structure | 5 | Nefm among populations within each species = 0.1, 0.2, 0.5, 1.0, 2.0 | Four populations of equal size within each species |
| Linkage among loci | 5 | r among loci = 0.005, 0.01, 0.02, 0.05, 0.1 | |
| Divergent-selective sweep | 4 | Timing: 1 Ma, 10 kYA | Bottlenecks last 100 years; Nef changes are instantaneous; presweep, neutral Nefm = 0.25 |
| Bottleneck size: 1,000, 100 | |||
| Postsweep Nefm: 0.05, 0.01 | |||
| IM model, IS evolution, more complex demography | 2 | NA | Population-size change simulated as instantaneous change or exponential growth |