TABLE 1.

Gene regions sequenced

A. 21 gene segments adopted from arthropod study of (Regier, Shultz, et al.(2008))
PCR amplicon name	Gene name/function	Fragment length(bp)	Average number of substitutions per nt2 sitea
36fin1_3	Syntaxin	471	0.39
44fin2_3	Glucosamine phosphate isomerase	528	0.85
3007fin1_2	Glucose phosphosphate dehydrogenase	621	1.22
8091fin1_2	Glucose phosphate isomerase	666	1.22
3006fin1_2	Dynamin	222	1.24
113fin1_2	Glycogen synthase	975	1.27
acc2_4	Acetyl-coA carboxylase	501	1.31
69fin2_3	Clathrin coat assembly protein	627	1.36
109fin1_2	Gelsolin	594	1.40
3070fin4_5	Alanyl-tRNA synthetase	705	1.43
262fin1_2	Proteasome subunit	501	1.48
268fin1_2	AMP deaminase	768	1.68
270fin2_3	(Hypothetical protein)	447	1.70
3017fin1_2	Tetrahydrofolate synthase	594	1.74
40fin2_3	Phosphogluconate dehydrogenase	750	1.77
8028fin1_2	Nucleolar cysteine-rich protein	324	1.81
42fin1_2	Putative GTP-binding protein	840	1.95
3059fin1_3	Arginine methyltransferase	732	2.23
197fin1_2	Triosephosphate isomerase	444	2.30
192fin1_2	Glutamyl- & prolyl-tRNA synthetase	402	2.78
265fin2_3	Histidyl-tRNA synthetase	447	3.86
B. Gene segments from (Regier et al.(2009)), with estimated substitution rates
nt3b/noLR1 + nt2c	Gene name	Fragment length	“nt2 est.”d
85.0	CAD	2928	1.60
18.4	DDC	1281	1.62
22.4	Enolase	1134	1.17
10.8	Period	888	6.00
42.4	Wingless	402	0.34

Notes: Provided are PCR amplicon names, gene names/functions and fragment lengths (excluding nucleotide characters of uncertain alignment) of the 21 additional gene regions sequenced for 41 taxa, ordered by evolutionary rate at nt2 on a phylogeny for 13 arthropod exemplars (Regier2008c).

^aAverage number of nucleotide changes per second codon position site, estimated by ML on a constrained tree of 13 divergent arthropod species, from table 2 of (Regier, Shultz, et al.(2008)).

^bAverage number of nucleotide changes per third codon position site, estimated by ML on a constrained tree of 32 species of Bombycoidea (Lepidoptera), from table 4 of (Regier, Cook, et al.(2008)).

^cAverage number of nucleotide changes per site in a character set consisting of nt2 plus all nt1 sites at which no leucine or arginine occurs in any taxon, estimated by ML on a constrained tree of 32 species of Bombycoidea (Lepidoptera), from table 4 of (Regier, Cook, et al.(2008)). This is an estimate of the rate of nonsynonymous change. The ratio of rates at nt3 to rates in this character set is an estimate of the relative rate of synonymous to nonsynonymous substitution.

^dApproximation of nonsynonymous substitution rate, for comparison to the 21 additional gene fragments above. Gene 19 in table 2 of (Regier, Shultz, et al.(2008)), not included in the 21 additional genes of this study, is a 600 base pair piece of CAD. Estimates of nonsynonymous rates (noLR1 + nt2, above) for the five genes genes used by (Regier et al.(2009)) were first converted to proportions of the rate for CAD, then rescaled to reflect the ranking of CAD among the nt2 rates for the 21 additional gene fragments. The result is an approximate scale of comparison for rates of nonsynonymous substitution across all 26 genes, assuming that rates of substitution at nt2 and at nt1 sites undergoing only nonsynonymous substitutions are comparable.