Subpopulation topology of Model Split and Model Tree for ranging from three to five.

<p>In Model Split, subpopulations are split from one ancestral population simultaneously, forming a star-shaped topology. In Model Tree, populations separate at different time points, forming a tree-shaped topology. The time interval between two consecutive dashed lines is 0.5 scaled in units of generations, where is the effective population size.</p

Accuracy of multiple estimators under Models Split and Tree.

<p>Performance assessment of methods including DIC, STRUCTURE, , Eigenanalysis, Structurama and BAPS. “” is the population differentiation statistic estimated by SmartPCA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021014#pone.0021014-Patterson1" target="_blank">[11]</a> averaged across 50 data sets. STRUCTURE's performance is evaluated based upon both the original model and the correlated alleles or “F” model. Similarly tested is the statistic that relies on STRUCTURE. Eigenanalysis is tested at three significance levels (). Structurama is assessed using both a noninformative prior on and the true value as the starting point. BAPS is evaluated using the individual clustering mode. Blank values in the table indicate that a program did not generate a result.</p

Accuracy of multiple estimators under Models and .

<p>Evaluation of these methods are performed in the same manner as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021014#pone-0021014-t001" target="_blank">Table 1</a>.</p

Performance of DIC on one data set simulated under Model Split for each true value, 1,2,3 and 5.

<p>Performance of DIC on one data set simulated under Model Split for each true value, 1,2,3 and 5.</p

Accuracy of multiple estimators with shorter splitting time among subpopulations.

<p>Evaluation of these methods are performed in the same manner as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021014#pone-0021014-t001" target="_blank">Table 1</a>. Data are simulated under Model Split with the splitting time reduced from to .</p

Accuracy of multiple estimators under Models and Inbred.

<p>Evaluation of these methods are performed in the same manner as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021014#pone-0021014-t001" target="_blank">Table 1</a>.</p

Analysis result of data from the Human Genome Diversity Panel.

<p>A. Estimated DIC for different values of . B. Distruct classification bar plot of individuals from the above data set assuming . Each vertical bar represents one individual and each color represents a different cluster.</p

False positive rate.

<p>False positive rate in a data set of 1000 genes simulated using the coalescent method.</p

Realized coverage of 95% CI for and γ when , varies, and there is linkage among sites.

<p>Results for coalescent model simulations with a distribution on , and no selection . .</p

Example joint distribution of the estimated selection effect and the constraint effect for a particular gene.

<p>Data simulated using PRFREQ. The blue asterisk denotes the true location of parameters.</p