Table 2.

The seven datasets, designed to address seven phylogenetic questions

Dataset	Addressed phylogenetic question	Covered subgroups/FcLM clusters (4 clusters per analysis)	No. of species	No. of OGs	Alignment length (aa)	Coverage [%] all species	Coverage [%] addressed groups
Dataset 1 (complete dataset)	Position of Hymenoptera?	1) Hymenoptera	88	1,343	662,107	61.1	100
		2) outgroup taxa
		3) Mecopterida
		4) Neuropteroidea
Dataset 2	Are Neuropteroidea monophyletic?	1) Neuropterida	71	1,303	643,051	65.0	100
		2) Mecopterida
		3) Coleopterida
		4) Hymenoptera
Dataset 3	Are Megaloptera monophyletic?	1) Raphidioptera	4	358	174,065	100	100
		2) Corydalidae
		3) Sialidae
		4) Neuroptera
Dataset 4	Are Neuroptera and Megaloptera sister groups?	1) Raphidioptera	71	540	242,820	72.9	100
		2) Megaloptera
		3) Neuroptera
		4) remaining holometabolans
Dataset 5	Are Coleopterida monophyletic?	1) Neuropterida	71	972	505,528	66.2	100
		2) Strepsiptera
		3) Coleoptera
		4) remaining holometabolans
Dataset 6a	a) Are Mecopterida monophyletic? or	a) 1) Antliophora	71	1,343	662,107	64.3	100
Dataset 6b	b) Are Antliophora + Coleopterida monophyletic?	2) Amphiesmenoptera
		3) Neuropteroidea
		4) remaining holometabolans
		b) 1) Antliophora
		2) Amphiesmenoptera
		3) Coleopterida
		4) remaining holometabolans
Dataset 7	Relationships within Antliophora?	1) Diptera	71	1,101	557,276	66.5	100
		2) Siphonaptera
		3) Mecoptera
		4) remaining holometabolans

For each dataset, we selected four taxonomic groups (clusters), assigned species to one of the groups, and extracted only those ortholog groups (OGs) that contained a sequence of at least one representative of each group. All species that were not assigned to either of the groups were excluded. Coverage [%] all species: Coverage of the dataset in terms of presence of OGs considering all species. Coverage [%] addressed groups: Coverage of the dataset in terms of presence of OGs considering the four groups defined for each dataset, which is, by definition, 100%.