Extended Data Fig. 1: Transfer index expectation and TBE support with random trees.
From: Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
a–d, For each number of taxa (16, 128, 1024 and 8,191 in a, b, c and d, respectively) and random tree model, we compare the transfer index average over 100 runs with the upper-bound p − 1 (top graphs in each panel). We also compare the average transfer bootstrap support (TBE) to 0, and provide the maximum value observed among 100 runs (dashed lines), thus approximating the 1% quantile of the distribution (bottom graphs). In these experiments, the number of random ‘bootstrap’ trees is equal to 1,000. With l ≥ 1,024 (c), the average transfer index with random trees is very close in relative value to the upper-bound p − 1 and the approximation is already satisfying with l = 128 (b). Furthermore, the results are nearly the same for the four random tree models, suggesting that the asymptotic behaviour holds in a number of settings. As expected, the approximation of the transfer index over random bootstrap trees by p − 1 is better with small values of p. These results explain why moderate TBE supports—for example, 70% as used in this article—are sufficient to reject poor branches, as a TBE branch support of 70% cannot be observed by chance, even with a small number of taxa (for example, 16, as in a).
