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

Table 4 Summary of average taxon quartet similarity scores across bootstrap trees.

	Mean Ave. Taxon Quartet Similarity
	3-Gene ML	5-Gene ML	Ave. Change
All taxa	0.937	0.958	0.021
170-taxa	0.928	0.954	0.026***
119-taxa	0.941	0.957	0.016***

The average taxon quartet similarity is the average proportion of quartets (4-taxon unrooted trees) that include a particular taxon that have the same topology among bootstrap trees. The "170 taxa" are the taxa with sequences from all 5 genes, while the "119 taxa" are those with sequences from only the original three genes (18S rDNA, atpB, rbcL). "Ave. Change" shows the difference in the mean of the average taxon quartet similarity between the 3-gene and 5-gene ML bootstrap analyses. We tested if the average change among the 170 taxa is significantly greater than would be expected by randomly selecting without replacement 1000 sets of 170 taxa. Similarly, we tested if the average change among the 119 taxa with 3 genes is significantly less than would be expected by randomly selecting without replacement 1000 sets of 119 taxa. Both tests were highly significant (*** = p ≤ 0.001).

ISSN: 2730-7182