Applying the Bootstrap in Phylogeny Reconstruction

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A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, background): “Specifically, columns (or sites) in the aligned sequences are resampled with replacement for each gene sampled (with replacement) from the multilocus dataset [48,49].”
How Many Bootstrap Replicates Are Necessary? (2009, unknown): “75% are usually considered to be monophyletic (Soltis and Soltis, 2003).”
Renewing Felsenstein’s Phylogenetic Bootstrap in the Era of Big Data (2018, background): “A difference of just one taxon (highly likely with large datasets) is sufficient for the replicated branch to be counted absent while it is nearly identical to the reference branch 13,20 .”