Table 1.

Proportion of contig groups with distances > 2% in each transcriptome comparison

	All	Single-Copy Eukaryotic	Matches to Single-Copy Genome Clusters
Cochliopodium spp.
aC. pentatrifurcatum	7.99%	4.87%	4.17%
aC. minus CCAP 1537/1A	5.89%	3.60%	2.91%
C. pentatrifurcatum vs. C. minus CCAP 1537/1A	9.31%	4.31%	3.95%
C. pentatrifurcatum vs. C. minutoidum CCAP 1537/7	99.96%	99.92%	100%
Endostelium zonatum
PRA-191 YT10 vs. PRA-191 Kang	6.81%	4.77%	4.02%
PRA-191 YT10 vs. LINKS	99.84%	99.77%	99.82%
PRA-191 Kang vs. LINKS	99.83%	100%	100%
Thecamoebida isolates
UK-YT1 vs. Thecamoebida RHP1–1	10.58%	5.56%	4.19%

^aintraspecific comparison of transcriptome data from same species collected using different methods