Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

Li, Shuwei; Shih, Ching-Hua; Kohn, Michael H

doi:10.1186/1471-2164-11-322

Table 2 Evolutionary correlates of gene constellations^a.

From: Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

			African population			American population
Group	CAI	Ka/Ks	θ_W	θ_π	Tajima's D	θ_W	θ_π	Tajima's D	F_ST	Expr-Div^c	Q_ST
Genes on the autosomes
SG	0.233** (± 0.039)	0.092 (± 0.109)	0.008 (± 0.002)	0.006 (± 0.001)	-1.023 (± 0.363)	0.003 (± 0.001)	0.004 (± 0.001)	0.199 (± 0.689)	0.125 (± 0.097)	2.7%	0.427 (± 0.296)
5PP	0.252** (± 0.039)	0.073* (± 0.079)	0.007 (± 0.003)	0.005 (± 0.002)	-1.058 (± 0.488)	0.003 (± 0.001)	0.003 (± 0.002)	0.514 (± 0.807)	0.153 (± 0.103)	3.5%	0.362 (± 0.272)
EE	0.250* (± 0.037)	0.075* (± 0.100)	0.007 (± 0.002)	0.006 (± 0.002)	-0.928 (± 0.358)	0.003 (± 0.002)	0.003 (± 0.002)	0.380 (± 0.519)	0.142 (± 0.151)	2.5%	0.386 (± 0.275)
5PI-EI	0.236** (± 0.040)	0.097 (± 0.108)	0.007 (± 0.002)	0.005 (± 0.002)	-1.010 (± 0.664)	0.003 (± 0.001)	0.003 (± 0.001)	0.529 (± 0.663)	0.121 (± 0.099)	6.8%*	0.401 (± 0.271)
COS	0.241* (± 0.043)	0.098** (± 0.103)	0.008 (± 0.003)	0.006 (± 0.002)	-0.991 (± 0.528)	0.003 (± 0.002)	0.004 (± 0.002)	0.557 (± 0.828)	0.125 (± 0.109)	4.7%	0.373 (± 0.283)
CSS	0.236** (± 0.041)	0.107** (± 0.117)	0.009 (± 0.003)	0.007 (± 0.003)	-1.038 (± 0.555)	0.004 (± 0.003)	0.004 (± 0.003)	0.098 (± 0.670)	0.111 (± 0.160)	4.2%	0.411 (± 0.294)
Genomic average ^b	0.245 (± 0.041)	0.085 (± 0.095)	0.008 (± 0.003)	0.006 (± 0.002)	-1.020 (± 0.510)	0.003 (± 0.002)	0.003 (± 0.002)	0.469 (± 0.781)	0.134 (± 0.110)	4.0%	0.377 (± 0.279)
Genes on the X chromosome
SG	0.239* (± 0.051)	0.103 (± 0.120)	0.009 (± 0.003)	0.007 (± 0.002)	-0.980 (± 0.455)	0.002 (± 0.001)	0.002 (± 0.001)	0.105 (± 1.083)	0.226 (± 0.125)	0.6%	0.412 (± 0.318)
5PP	0.263** (± 0.040)	0.074* (± 0.074)	0.007 (± 0.003)	0.006 (± 0.002)	-0.891 (± 0.486)	0.002 (± 0.001)	0.003 (± 0.001)	0.433 (± 0.857)	0.233 (± 0.123)	1.9%	0.379 (± 0.295)
EE	0.255 (± 0.037)	0.080 (± 0.056)	0.008 (± 0.001)	0.007 (± 0.001)	-0.886 (± 0.279)	0.003 (± 0.001)	0.004 (± 0.001)	0.625 (± 0.639)	0.219 (± 0.061)	1.1%	0.416 (± 0.309)
5PI-EI	0.247 (± 0.038)	0.090 (± 0.081)	0.009 (± 0.002)	0.007 (± 0.002)	-0.996 (± 0.363)	0.003* (± 0.001)	0.004 (± 0.000)	0.509 (± 0.839)	0.209 (± 0.086)	1.0%	0.364 (± 0.276)
COS	0.254 (± 0.045)	0.096 (± 0.098)	0.008 (± 0.003)	0.007 (± 0.003)	0.814 (± 0.547)	0.002 (± 0.002)	0.003 (± 0.002)	0.453 (± 0.851)	0.215 (± 0.185)	2.6%	0.375 (± 0.268)
CSS	0.242* (± 0.037)	0.096 (± 0.112)	0.008 (± 0.003)	0.006 (± 0.003)	-0.868 (± 0.453)	0.003 (± 0.001)	0.003 (± 0.001)	0.339 (± 0.698)	0.189 (± 0.107)	2.8%	0.344 (± 0.285)
Genomic average ^b	0.255 (0.043)	0.085 (± 0.088)	0.008 (± 0.003)	0.006 (± 0.002)	-0.877 (± 0.489)	0.002 (± 0.001)	0.003 (± 0.002)	0.400 (± 0.857)	0.220 (± 0.141)	2.0%	0.378 (± 0.286)

^ac.f. Additional File 1 for data and Additional file 4 for a summary of sample sizes.
^bAverage values except for the measure for expression divergence (Expr-Div), where the value provided should be considered the genome wide proportion of differentially expressed genes.
^cExpression Divergence: the percentage of differentially expressed genes between D. melanogaster and D. yakuba.
* and ** indicate significant deviation from the genomic average at P-value ≤ 0.05 and P-value ≤ 0.001, respectively (Chi-square test or two-sided Mann-Whitney test, not corrected for multiple testing).

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