Figure 1.
The structure effect in a 40-deme constant-size island model.
For each scenario, 100 replicate data sets were generated and analysed with EBSPs. Light blue lines represent the median inferred female effective population size through time from each replicate. Time is measured in kya or thousands of years ago and is based on a molecular clock for buffalo D-loop sequences. Bold black lines represent the simulated size of the structured population (500 females * 40 demes = 20,000 females). Insert into each panel is a histogram of PSC values (on x-axis; see main text) across replicates. Dashed lines show the prior distribution for PSC. The y-axis in the insert histograms marks the frequency of occurrence in each PSC bin out of 100 replicates.
Table 1.
Comparison of EBSP and simulated population sizes under different structural scenarios.
Figure 2.
The structure effect in a 40-deme island model with demographic change.
As Fig. 1, but the bold black line shows the simulated demographic change scenarios (see main text) with one or two changes in population size. Only the intermediary level of gene flow (Nfm = 1.25) is shown.
Figure 3.
Two demographic scenarios under a real data informed island model.
As Figs. 1 and 2, but the island model was modified to conform to the migration matrix estimated for a real biological system, the African buffalo. Only pooled and scattered sampling is shown. Bold lines mark the appropriate simulated population size. Replication was slightly different from Fig. 1 and 2 because it now matters which demes were included in the sample, see main text. Note also that the number of demes was 34, so the sum of the deme size differs from Fig. 1 and 2 (17,000 as opposed to 20,000 females).
Figure 4.
Three different sampling strategies for real data from the buffalo.
Local, pooled and scattered sampling of real D-loop data from 34 African buffalo populations. The replication of each sampling strategy involved random drawing of the appropriate number of samples from demes as explained in the main text.