Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

Table 1 Characterization of matrices assembled for phylogenetic inference

Matrix name	Number of loci	Length (amino acids)	Missing data (%)	Criteria of locus selection
Total1080	1080	385,669	24.15	All loci that after trimming and filtering of paralogs
TaxaMin30	609	199,667	20.44	Loci with at least 30 taxa present
TaxaMin33	162	44,749	20	Loci with at least 33 taxa present
TaxaMin35	88	31,989	13.89	Loci with at least 35 taxa present
60Boot	55	37,682	25.92	Average locus tree bootstrap 60 or more
MareMatrix	143	35,030	20.02	MARE (Misof et al. 2013) algorithm filtering with alpha at 3.15
Slow108	108	33,580	18.91	10 % of the most slowly evolving loci
LowLB	171	60,397	22	Low LB scores in the outgroups, sponge, and ctenophore
Saturation108	108	36,954	19.78	10 % of the least saturated loci
Best108	108	41,808	15.55	10 % of loci scoring best in taxon occupancy, saturation, rate of evolution, average bootstrap, and LB scores
NoOutgr	143	35,022	18.49	As MareMatrix but realigned without Monosiga and Salpingoeca outgroups
NoAmphi	143	35,032	19.75	As MareMatrix but realigned without the sponge Amphimedon
NoOutgrAmphi	143	35,009	18.13	As MareMatrix but realigned without the sponge and the outgroups

ISSN: 1471-2164