Skip to main content

Advertisement

Table 1 Characterization of matrices assembled for phylogenetic inference

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

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