Table 2.

Homoplasy and hemiplasy in amino acid alignments of genes

Gene confidence set	90% set	80% set
Concordant gene trees
Variable sites	11,641	17,349
Informative sites	1,091	1,549
Homoplastic sites*	154 (27.8%)†	234 (31.0%)†
Discordant gene trees
Variable sites	6,810	11,572
Informative sites	703	1,102
Homoplastic sites–not hemiplastic‡	79 (14.2%)†	46 (6.1%)†
Homoplastic sites–hemiplastic§	320 (57.9%)†	474 (62.9%)†
Total homoplastic sites on species tree	553	754

^*See Fig. 1, Upper Right.

^†% = percent of all homoplastic sites.

^‡Fig. 1, Lower Right.

^§Fig. 1, Lower Left.