Phylogenetic analysis of migration, differentiation, and class switching in B cells
Fig 4
Controlling false positive rates using down-sampling.
Y axis shows the proportion of 50 simulation replicates in which the SP test from A to B was significant. Simulations were performed on large ladder phylogenies (Methods) at varying rates, biases, and trees per repetition (representing lineages within a simulated repertoire). In each case, simulated lineages were down-sampled to the specified maximum tip-to-state change ratio. (a) Unbiased simulations, significant SP test values indicate false positives. These show that the SP test has a high rate of false positives when the rate of state change is low (i.e. 1 change/mutation/site) and the maximum tip-to-state change ratio is high (> 20). Down-sampling lineages to a maximum tip-to-state change ratio of 10–20, however, controls this false positive rate. (b) Simulations with rates biased from A to B, in which significant SP test values indicate true positives. These results show that down-sampling does not simply reduce power. However, power is lowered when the switching rate is high (>100) or the number of trees/repertoire is low (< 20).
doi: https://doi.org/10.1371/journal.pcbi.1009885.g004