supplementary figures (sf) and supplementary tables (st)

Download Supplementary figures (SF) and supplementary tables (ST)

Post on 03-Jan-2016

34 views

Category:

Documents

1 download

Embed Size (px)

DESCRIPTION

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* - PowerPoint PPT Presentation

TRANSCRIPT

  • 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-56 0064, Karnataka, IndiaRunning Title: Genetic analyses of early and late flies.

    *Correspondence to: Vijay Kumar SharmaE-mail: vsharma@jncasr.ac.in/ vksharmas@gmail.com; Phone: +91-080-22082843 (office)/ 2844/45 (lab); Fax: +91-080-22081766; Url: http://www.jncasr.ac.in/vsharma.

  • Vaze et al. Supp. Figure 1morningevening% of flies emergedcircadian period (hr)(A)(B)earlycontrollateSF1. 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. (C)(D)

  • 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. variancevarianceBlk2 Blk4 Blk3 Blk2 Blk3 Blk4 Vaze et al. Supp. Figure 2

  • Blk1 Blk1 Blk2 Blk3 Blk4 Blk2 Blk3 Blk4 Vaze et al. Supp. Figure 2

  • Blk1 Blk1 Blk2 Blk2 Blk3 Blk3 Blk4 Blk4 Vaze et al. Supp. Figure 2

  • Vaze et al. Supp. Table 1ST 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.

    dfMSdfMSEffectEffectErrorErrorFp - level

    dfMSdfMSEffectEffectErrorErrorFp - level

    Selection (S) 22.5267.130.350.716Window (W) 11287.35324.0853.460.005Block (B) 33.6200.00----S W21718.8663.12550.760.0001S B67.1300.00----W B324.0800.00----S W B63.1200.00----

    Selection (S) 20.5960.0173.650.0001Block (B) 30.0000.00----S B60.0100.00----

  • CrossNo. AutosomeFemaleXXMaleX YPermanent Cytoplasmic factorsTransient Maternal factorsCross number in brackets indicate equivalent cross number in de Belle and Sokolowski, 1987.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 hybridBE = Back-cross to early parentBL = Back-cross to late parent F2 = F2 hybrid

    Table modified from de Belle and Sokolowski, 1987Vaze et al. Supp. Table 2A

    1(1)EEEEEEEE 2 (3)ELF1F1ELEE3(4)LEF1F1LELL4(2)LLLLLLLL5(5)E(E L)BE EELEE6(6)E(L E)BE F1EEEE7(9)(E L)EBE BE E/LEEF18(10)(L E)EBE BE E/LELF19(7)L(E L)BL F1LLLL10(8)L(L E)BL LLELL11(11)(E L)LBL BL E/LLEF112(12)(L E)LBL BL E/LLLF113(13)(E L)(E L)F2F2E/LLEF114(14)(E L)(L E)F2F2E/LEEF115(15)(L E)(E L)F2F2E/LLLF116(16)(L E)(L E)F2F2E/LELF1

  • TestComparisonST2 (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

    1Difference between parents (P) 1 vs 42Dominance (D) 1 + 4 vs 2 + 33X chromosome (X) + maternal effects (M) 2 vs 34Matrenal effects (M) 2 vs 35X chromosome (X) 5 + 9 vs 6 + 106X chromosome interactions 5 + 10 vs 6 + 97Y chromosome (Y) 14 + 16 vs 13 + 158Y chromosome interactions 6 + 9 vs 5 + 109Permanent cyctoplasmic factors (PCF) 13 + 14 vs 15 + 1610Permanent cytoplasmic intearctions7 + 12 vs 8 + 1111Transient maternal factors (TMF) 6 + 12 vs 7 + 912Transient maternal factor interactions 6 + 9 vs 7 + 12

  • (A)(B)(C)ST 3. Replicate wise ANOVA on the circadian phenotypes of early and late parental stocks and in their progeny. (A) morning emergence, (B) evening emergence, and (c) circadian period.Vaze et al. Supp. Table 3

    dfMSdfMSEffectEffectErrorErrorFp-levelR115469.0810115.5930.09

  • CrossesE early parent, L late parent

    m mean, a additive effect, d dominanceam additive maternal effect, dm dominance maternal effectc cytoplasmic factors, a.a additive-additive interaction a.d additive-dominance interaction, d.d dominance-dominance interaction

    Please note: order of crosses is different from the one in Table 1A . ST 4. Coefficients used to estimate the model parameters. Parameter notations are according to Kearsey and Pooni (1996).Vaze et al. Supp. Table 4

    1EE1101011002LL1-10-10-11003EL1011010014LE101-10-10015E(E L)10.50.51010.250.250.256E(L E)10.50.51010.250.250.257L(E L)1-0.50.5-10-10.25-0.250.258L(L E)1-0.50.5-10-10.25-0.250.259(E L)E10.50.50110.250.250.2510(L E)E10.50.501-10.250.250.2511(E L)L1-0.50.50110.25-0.250.2512(L E)L1-0.50.501-10.25-0.250.2513(E L)(E L)100.5011000.2514(E L)(L E)100.5011000.2515(L E)(E L)100.501-1000.2516(L E)(L E)100.501-1000.25

  • Keys for supplementary Tables ST5-ST10

    Upper case alphabet(s) (A, D, M, E) in upper most row of each tables represent type of genetic models tested. Each of those alphabets represent presence of genetic effect(s) in the model being tested.

    A - m, a D - m, d M - m, am, dm, C E - m, a.a, a.d, d.d

    Small letter alphabets in the middle rows of each table show model parameters which were significant and their estimates were used in the calculation of expected generation means .

    m mean, a additive effect, d dominanceam additive maternal effect, dm dominance maternal effectc cytoplasmic factors, a.a additive-additive interaction a.d additive-dominance interaction, d.d dominance-dominance interaction

    K = number of significant parametersdf = degrees of freedom used for testing goodness of fit (df= 16-k)AIC = Akaike information criteria value ( calculated as described in Bieri and Kawecki, 2003).

    Non significant values are shown in bold letters.Smallest AIC values are shown in bold letters.c2

  • ST 5. Results of all the models tested on generation means of males for morning emergence in four replicates.

    ParametersParametersParametersParametersVaze et al. Supp. Table 5

    R1ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaama.daaaama.daaaa

    k212222222122212df141514141414141414151414141514c232.37464.80255.32286.5036.2338.3939.78273.14567.68752.8351.42226.1054.22466.02105.61AIC36.37466.80259.32290.5040.2342.3943.78277.14571.68754.8355.42230.1058.22468.02109.61

    R2ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaama.daaaama.damaaaa.daa.ddda.aa.ad.d

    k212222222325224df141514141414141414131411141412c219.55344.06140.55162.4020.6324.4624.74133.431740.986.1622.9911.5827.82679.96191.43AIC23.55346.06144.55166.4024.6328.4628.74137.431744.992.1626.9921.5831.82683.96199.43

    R3ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaama.daaaama.daaaaa.aa.da.da.da.dd.dd.d

    k212222522123413df141514141414111414151413121513c247.92525.52136.19213.8087.5566.1521.76198.66768.42258.4961.2145.6637.62321.5459.82AIC51.92527.52140.19217.8091.5570.1531.76202.66772.42260.4965.2151.6645.62323.5465.82

    R4ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaaa.daaaama.daaaaam

    k212222222122212df141514141414141414151414141514c236.06311.2879.19110.1736.5666.7943.4975.04359.72298.3660.1483.5882.051093.7738.02AIC40.06313.2883.19114.1740.5670.7947.4979.04363.72300.3664.1487.5886.051095.7742.02

  • ST 6. Results of all the models tested on generation means of females for morning emergence in four replicates.

    ParametersParametersParametersParametersVaze et al. Supp. Table 6

    R1ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmaama.daaaama.daaaadma.admda.ada.da.da.da.dd.dd.dd.dd.d

    k212223521135505df141514141413111415151311111611c2139.211137.91079.81522.6146.0969.2415.25932.6621838.1494.5072.5114.8919.232011.711.17AIC143.211139.91083.81526.6150.0975.2425.25936.6621840.1496.5078.5124.8929.232011.721.17

    R2ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaama.aaaaama.da.daaaa.daa.ddma.adma.ad.dd.d

    k212323422233322df141514131413121414141313131414c242.58924.25408.60314.0344.6628.6516.17456.85395.741100.7329.05710.8949.20424.08935.15AIC46.58926.25412.60320.0348.6634.6524.17460.85399.741104.7335.05716.8955.20428.08939.15

    R3ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaama.daaaama.daaaa

    k212222222122212df141514141414141414151414141514c254.80335.19209.76197.6763.8772.22105.87383.971285.6620.90118.68476.6490.76329.60145.50AIC58.80337.19213.76201.6767.8776.22109.87387.971289.6622.90122.68480.6494.76331.60149.50

    R4ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmmmmmmmmmaa.daaaama.da.daaaa

    k211222222222212df141515141414141414141414141514c224.66306.18350.00126.4725.4525.3830.04259.21140.06166.1225.8876.3049.05426.3537.35AIC28.66308.18352.00130.4729.4529.3834.04263.21144.06170.1229.8880.3053.05428.3541.35

  • ST 7. Results of all the models tested on generation means of males for evening emergence in four replicates.

    ParametersParametersParametersParametersVaze et al. Supp. Table 7

    R1ADMEADAMAEDMDEMEADMADEAMEDMEADMEmmmmmmmma.dmmmmammaama.daaaamamaaaa.daca.d

    k213222221322222df141513141414141415131414141414c256.54925.65380.17371.6956.78110.21137.31917.197904.3235.45135.11197.91182.449009.5478.05AIC60.54927.65386.17

Recommended

View more >