Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

Table 3 Summary of the support for relationships among the 170 taxa with sequences from 5 genes and the 119 taxa with sequences from 3 genes.

	Clades With Bootstrap Support
	100%	≥95%	≥90%	≥70%	≥50%	Ave. Quartet Similarity
5-Gene 170-taxa	89	103	109	128	146	0.946
3-Gene 170-taxa	70	93	99	119	137	0.902
Change	19***	10	10	9	9	0.044***
5-Gene 119-taxa	39	51	56	82	94	0.952
3-Gene 119-taxa	49	54	61	77	87	0.942
Change	-10***	-3*	-5**	5	7	0.010***

The support values were obtained from reduced consensus trees, which were made by pruning all but either the selected 170 or 119 taxa from the bootstrap trees and making a consensus from the pruned trees. The first 5 columns show the number of clades in the reduced consensus trees that have the specified level of bootstrap support. The last column shows the average percent of quartets (4-taxon unrooted trees) that are identical between the pruned bootstrap trees. We tested if the observed changes in the bootstrap support or average quartet similarity are greater in the 170 taxa with 5-genes than they would be from a random sample of 170 taxa. Similarly, we tested if the changes in support are less in the 119 taxa with 3 genes than they would be from a random sample of 119 taxa. Significant results are noted with "*" symbols (* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.005).

ISSN: 2730-7182