TABLE 4.

QTL affecting variation in pigmentation between D. yakuba and D. santomea

Backcross population	Sex	QTL	Peak LRa	LRa	Effect (SE)b	Effect/σpc	R2d
F1 females × D. yakuba males	F	1A5–13E1	1A5	26.71	0.68 (0.18)	0.31	0.0169
15F4–20E	8E10	87.08	1.44 (0.56)	0.66	0.0584
34B4–57E6	34B4	441.74	1.81 (0.76)	0.83	0.4382
69A1–83C4	80B2	130.57	1.69 (0.69)	0.78	0.1135
M	1A5–13E1	3B1-2	65.13	2.60 (0.65)	0.62	0.0327
15F4–20E	17D6	525.94	6.75 (2.24)	1.62	0.3186
34B4–57E6	34B4	193.19	3.29 (0.70)	0.79	0.1060
69A1–83C4	80B2	216.23	3.51 (0.91)	0.84	0.1227
F1 females × D. santomea males	F	15F4–20E	19C1	53.485	−1.39 (0.68)	−1.27	0.4280
M	1A5–13E1	1A5	67.88	−2.16 (0.45)	−0.61	0.0409
15F4–20E	17D6	450.81	−5.03 (1.84)	−1.42	0.3964
34B4–57E6	34B4	199.18	−1.73 (0.61)	−0.49	0.1397
		69A1–83C4	80B2	133.46	−2.72 (0.76)	−0.77	0.0966

^aQTL regions are estimated from 2 LOD support intervals (P ≤ 0.05). The peak is the cytological location with the highest likelihood ratio (LR). Cytological locations are given on the basis of D. melanogaster cytology (Lemeunier and Ashburner 1976).

^bEffects were estimated from the least-squares means of the two marker locus classes as: , where the subscript is 1 if the marker has a homozygous genotype and 2 if the marker has a heterozygous or hemizygous genotype. The standard error (SE) is listed in parentheses.

^cEffect divided by the phenotypic standard deviation. See footnote ^a for the calculation of the effect.

^dThe proportion of variance explained by the QTL and estimated by , where s² is the variance of the trait, is the sample variance of the residuals, and is the variance of the residuals (Basten et al. 1999).