Table 2. The numbers of additional steps (S) required to force molecules into monophyly based on amino acid chronology constraints during MP analyses of combined tRNA structure and sequence data.

Chronology	Constraints	S
Miller [16]	((Gly, Ala, Asp, Val, Pro, Ser, Glu, Thr, Leu, Ile), …)	339
	((Gly, Ala, Asp, Val, Pro, Ser, Glu, Thr, Leu, Ile), (…))	357
Brooks et al. [19]	((Cys, Trp, Tyr, Gln, Phe, Leu, Lys, Glu), (Ala, Val, Gly, Ile, Thr, Asp, Ser, Asn, His), …)	516
	((Cys, Trp, Tyr, Gln, Phe, Leu, Lys, Glu), (Ala, Val, Gly, Ile, Thr, Asp, Ser, Asn, His), (…))	530
Trifonov [3]	((His, Lys, Cys, Phe, Tyr, Met, Ini, Trp, Sec), …)	332
	((His, Lys, Cys, Phe, Tyr, Met, Ini, Trp, Sec), (…))	348
Jordan et al. [18]	((Cys, Met, Ini, His, Ser, Phe, Asn, Thr, Ile, Val), (Pro, Ala, Glu, Gly, Lys), …)	550
	((Cys, Met, Ini, His, Ser, Phe, Asn, Thr, Ile, Val), (Pro, Ala, Glu, Gly, Lys), (…))	566
Fournier and Gogarten [21]	((Cys, Glu, Phe, Ile, Lys, Val, Trp, Tyr, Ser), (Asn, Gln, Gly, Leu, Pro, Asp), …)	524
	((Cys, Glu, Phe, Ile, Lys, Val, Trp, Tyr, Ser), (Asn, Gln, Gly, Leu, Pro, Asp), (…))	546
Present study (Type I and II are combined)	((Ser, Sec, Leu, Tyr), …)	139
	((Ser, Sec, Leu, Tyr), (…))	253
Present study (Type I and II are separated)	((Ser, Sec, Leu, Tyr), …)	135
	((Ser, Sec, Leu, Tyr), (…))	232

The length of the most parsimonious trees derived from the combined data set was 10,083 steps. Each constrained group is given in parentheses and groups of tRNA isoacceptors were labeled with IUPAC 3-letter amino acid nomenclature.