Supplementary figures (SF) and supplementary tables (ST) Genetic architecture of divergent circadian phenotypes in morning and evening emerging fruit flies Drosophila melanogaster Koustubh M Vaze, KL Nikhil and Vijay Kumar Sharma* Chronobiology Laboratory, Evolutionary and Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, PO Box. 6436, Bangalore , Karnataka, India Running Title: Genetic analyses of early and late flies. *Correspondence to: Vijay Kumar SharmaPhone: (office)/ 2844/45 (lab); Fax: ; Url: Vaze et al. Supp. Figure 1 morning evening % of flies emerged circadian period (hr) (A)(B) early control late SF1. Circadian phenotypes of early, control and late stocks assayed at generation 165. (A) Morning and evening adult emergence, (B) Circadian period of activity/rest rhythm, (C) Adult emergence profiles of early, control and late stocks under LD12:12, and (D) Representative actograms showing differences in circadian period of early, control and late flies. White bar- early, black bar- control and gray bar- late. Error bars are 95% confidence intervals and therefore non-overlapping error bars indicate that means are significantly different from each other. % flies Zeitgeber Time (hr) (C) (D) 24 hr early control late Day1 Day2 Day3.... Day7 early control late SF 2. Variance estimates of 16 progeny generations plotted against coefficients for additive model used in the analysis of generation variances. The coefficients for parental and F1 generations are 0.00, and for backcross generations 0.5, and 1 for F2 generation. (A) morning emergence, (B) evening emergence, and (C) of activity/rest rhythm Coefficients from additive model Blk1 variance variance Blk1 (A) variance Blk2 Blk4 Blk3 Blk2 Blk3 Blk4 Vaze et al. Supp. Figure 2 Coefficients from additive model variance variance (B) variance Blk1 Blk1 Blk2 Blk3 Blk4 Blk2 Blk3 Blk4 Vaze et al. Supp. Figure 2 variance variance variance (C) Coefficients from additive model variance Blk1 Blk1 Blk2 Blk2 Blk3 Blk3 Blk4 Blk4 Vaze et al. Supp. Figure 2 dfMSdfMS Effect Error Fp - level dfMSdfMS Effect Error Fp - level Vaze et al. Supp. Table 1 Selection (S) Window (W) Block (B) S W S B W B S W B Selection (S) Block (B) S B ST 1 (A). ANOVA on the percentage of adult emergence during morning and evening hours in early, control and late stocks. ST 1 (B). ANOVA on circadian period of activity/rest rhythms in early, control and late stocks. 1(1)EEEEEEEE 2(3)ELF1 ELEE 3(4)LEF1 LELL 4(2)LLLLLLLL 5(5)E(E L)BEBE EELEE 6(6)E(L E)BEBE F1EEEE 7(9)(E L)EBEBE BEBE E/LEEF1 8(10)(L E)EBEBE BEBE E/LELF1 9(7)L(E L)BLBL F1LLLL 10(8)L(L E)BLBL LLELL 11(11)(E L)LBLBL BLBL E/LLEF1 12(12)(L E)LBLBL BLBL E/LLLF1 13(13)(E L) F2 E/LLEF1 14(14)(E L)(L E)F2 E/LEEF1 15(15)(L E)(E L)F2 E/LLLF1 16(16)(L E) F2 E/LELF1 Cross No. Autosome Female XX Male X Y Permanent Cytoplasmic factors Transient Maternal factors Cross number in brackets indicate equivalent cross number in de Belle and Sokolowski, ST 2 (A). Scheme of crosses between early (E) and late (L) stocks and inheritance of four hereditary factors in the progeny flies. Notations used for different forms of a hereditary factor arising from crosses between parental stocks F1 = F1 hybrid BE = Back-cross to early parent BL = Back-cross to late parent F2 = F2 hybrid Table modified from de Belle and Sokolowski, 1987 Vaze et al. Supp. Table 2A Test 1Difference between parents (P)1 vs 4 2Dominance (D)1 + 4 vs X chromosome (X) + maternal effects (M)2 vs 3 4Matrenal effects (M)2 vs 3 5X chromosome (X)5 + 9 vs X chromosome interactions vs Y chromosome (Y) vs Y chromosome interactions6 + 9 vs Permanent cyctoplasmic factors (PCF) vs Permanent cytoplasmic intearctions vs Transient maternal factors (TMF) vs Transient maternal factor interactions6 + 9 vs Comparison ST2 (B). Comparisons/contrasts used to test contribution of various hereditary factors to the difference between early and late circadian phenotypes. Vaze et al. Supp. Table 2B dfMSdfMS Effect Error Fp-level R