TABLE 3.

Lineage-specific silent changes for low-MCU regions of X chromosome near-telomeric and nontelomeric loci in the D. melanogaster subgroup

	Near telomeric (t)			TRIMCU (tr)			Nontelomeric (nt)			t vs. nt:	tr vs. nt:
	up	pu	dup,pu	up	pu	dup,pu	up	pu	dup,pu	G	G
mel	43.0	119.7	−0.47	19.5	91.5	−0.65	3.0
sim	41.3	81.6	−0.33	31.5	30.8	0.01	4.9*
tei	65.2	50.9	0.12	40.1	22.8	0.28	1.0
yak	98.5	64.0	0.20	93.9	38.1	0.42	36.1	69.9	−0.30	18.2***	33.1***
teiyak	164.1	62.8	0.40	141.3	26.2	0.69	51.8	30.4	0.30	2.4	13.6***
ere	52.7	81.2	−0.21	58.4	35.6	0.24	11.5**
ore	173.7	56.5	0.51	133.8	7.9	0.89	28.2	59.5	−0.36	50.1***	105.6***
ereore	61.9	87.6	−0.17	20.0	4.7	0.62	22.5	55.3	−0.42	3.5	21.0***

Total counts of preferred (up) and unpreferred (pu) silent changes from near-telomeric (5943 codons), near-telomeric region of increasing MCU (TRIMCU), and nontelomeric (2897 codons) regions for low codon bias regions. Codons located within windows of 100 codons with MCU > 0.75 were eliminated from the analysis (see text for details). Total numbers of codons included in the TRIMCU regions are 4900, 3995, 2325, and 1351 for yak, teiyak, ore, and ereore, respectively. d_up,pu, (up − pu)/(up + pu), indicates degrees of deviation from equal numbers of up and pu changes. G-values from 2 × 2 tests of independence for up and pu changes for near-telomeric vs. nontelomeric loci and for TRIMCU vs. nontelomeric loci are given. *P < 0.05, **P < 0.005, ***P < 0.0005. Definitions of TRIMCU regions and abbreviations for lineages are given in Table 2.