Table 2 Open in new tab Estimates of the...

Lineage	NonSyna	Introns	5′ UTRs	3′ UTRs
Divergence
sim–melb	123	187	161	138
simc	57	53	67	51
mel–simd	132	227	138	151
mele	62	74	65	81
αf
sim–melb	0.63 (0.39–0.77)	0.51 (0.25–0.67)	0.66 (0.49–0.79)	0.49 (0.18–0.67)
simc	0.66 (0.41–0.81)	0.22 (−0.27 to 0.53)	0.63 (0.38–0.79)	0.64 (0.35–0.80)
mel–simd	0.68 (0.54–0.81)	0.04 (−0.23 to 0.24)	0.43 (0.22–0.60)	0.75 (0.64–0.85)
mele	0.71 (0.56–0.82)	−0.29 (−0.76 to 0.06)	0.41 (0.14–0.60)	0.79 (0.67–0.88)

Lineage	NonSyna	Introns	5′ UTRs	3′ UTRs
Divergence
sim–melb	123	187	161	138
simc	57	53	67	51
mel–simd	132	227	138	151
mele	62	74	65	81
αf
sim–melb	0.63 (0.39–0.77)	0.51 (0.25–0.67)	0.66 (0.49–0.79)	0.49 (0.18–0.67)
simc	0.66 (0.41–0.81)	0.22 (−0.27 to 0.53)	0.63 (0.38–0.79)	0.64 (0.35–0.80)
mel–simd	0.68 (0.54–0.81)	0.04 (−0.23 to 0.24)	0.43 (0.22–0.60)	0.75 (0.64–0.85)
mele	0.71 (0.56–0.82)	−0.29 (−0.76 to 0.06)	0.41 (0.14–0.60)	0.79 (0.67–0.88)

Table 2

Estimates of the Number of Divergent Sites and the Fraction of Divergence Driven to Fixation by Positive Selection, α (with 90% CIs) for Coding and Noncoding DNA in Drosophila simulans and Drosophila melanogaster, Using Loci Overlapping between This Study and Andolfatto (2005)

Lineage	NonSyna	Introns	5′ UTRs	3′ UTRs
Divergence
sim–melb	123	187	161	138
simc	57	53	67	51
mel–simd	132	227	138	151
mele	62	74	65	81
αf
sim–melb	0.63 (0.39–0.77)	0.51 (0.25–0.67)	0.66 (0.49–0.79)	0.49 (0.18–0.67)
simc	0.66 (0.41–0.81)	0.22 (−0.27 to 0.53)	0.63 (0.38–0.79)	0.64 (0.35–0.80)
mel–simd	0.68 (0.54–0.81)	0.04 (−0.23 to 0.24)	0.43 (0.22–0.60)	0.75 (0.64–0.85)
mele	0.71 (0.56–0.82)	−0.29 (−0.76 to 0.06)	0.41 (0.14–0.60)	0.79 (0.67–0.88)

Lineage	NonSyna	Introns	5′ UTRs	3′ UTRs
Divergence
sim–melb	123	187	161	138
simc	57	53	67	51
mel–simd	132	227	138	151
mele	62	74	65	81
αf
sim–melb	0.63 (0.39–0.77)	0.51 (0.25–0.67)	0.66 (0.49–0.79)	0.49 (0.18–0.67)
simc	0.66 (0.41–0.81)	0.22 (−0.27 to 0.53)	0.63 (0.38–0.79)	0.64 (0.35–0.80)
mel–simd	0.68 (0.54–0.81)	0.04 (−0.23 to 0.24)	0.43 (0.22–0.60)	0.75 (0.64–0.85)
mele	0.71 (0.56–0.82)	−0.29 (−0.76 to 0.06)	0.41 (0.14–0.60)	0.79 (0.67–0.88)

Nonsynonymous sites.

Estimates using D. simulans polymorphism and divergence to D. melanogaster.

Drosophila simulans lineage-specific estimates.

Estimates using D. melanogaster polymorphism and divergence to D. simulans.

Drosophila melanogaster lineage-specific estimates.

Estimates of α were calculated using only P → P/U → U synonymous sites in D. simulans but using all synonymous sites in D. melanogaster. Polymorphisms at a frequency of up to 10% were excluded in all cases.

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