The future of phylogeny reconstruction

A new approach to phylogenetic analysis, parsimony jackknifing, uses simple parsimony calculations combined with resampling of characters to arrive at a tree comprising well‐supported groups. This is usually much the same as the consensus of most‐parsimonious trees found from extensive multiple‐tree calculations, but the new method is thousands of times faster, allowing analysis of much larger data matrices, and also provides information on the strength of support for different groups. Jackknife frequencies provide a more reliable assessment of support than do alternative methods, notably “confidence probability” (CP) and T‐PTP testing.