Supplemental online file Supplemental Figure 1. Observed DNA CV for each location (raw data without corrections). 1 Supplemental Figure 2. DNA CV: Estimated correction parameters and standard deviations (σ) from the model. Parameters for which an estimate is different from zero have a significant effect on DNA CV value. The dot represents the median DNA CV, the heavy line represents the 80% credible interval and the thin line represents the 95% credible interval. 2 Supplemental Figure 3. EROD scores: Estimated correction parameters and standard deviations (σ) from the model. Parameters for which an estimate is different from zero have a significant effect on EROD activity value. The dot represents the median coefficient of variation of EROD value, the heavy line represents the 80% credible interval and the thin line represents the 95% credible interval. 3 Supplemental Figure 4. Oxidative stress: Estimated correction parameters and standard deviations (σ) from the model. Parameters for which an estimate is different from zero have a significant effect on oxidative stress value. The dot represents the median coefficient of variation of each oxidative stress value, the heavy line represents the 80% credible interval and the thin line represents the 95% credible interval. All subfigures were arbitrarily scaled to allow comparisons across different measures of oxidative stress. Values and units are listed in Supplemental Table 6. 4 Supplemental Table 1: Estimated DNA CV parameters for study locations. This table includes the number of individuals per location as well as a description of the posterior distribution including the median as well as the upper and lower 80% and 95% credible intervals. Groups Green Mountain Root River Shellhorn Lawrence Lake Island W2 Schnick's Bay Pig's Eye Pool 2 a N Estimate L95% L80% U80% U95% 33 15 15 18 15 15 32 16 2.41 2.46 2.50 2.53 2.61 2.64 2.69 2.84 2.30 2.31 2.36 2.39 2.46 2.49 2.56 2.70 2.34 2.49 2.52 2.36 2.41 2.44 2.51 2.54 2.61 2.75 2.55 2.60 2.61 2.70 2.73 2.77 2.94 2.60 2.65 2.66 2.76 2.78 2.81 2.98 Aa AB AB AB AB ABC BC C Location medians with the same letter are not significantly different from each other (Cumming and French 2005)." 5 Supplemental Table 2: Estimated correction parameters and standard deviations. The parameter’s posterior distribution including the median as well as the upper and lower 80% and 95% credible intervals. The top of the table (above the dashed line) contains the individual level parameters; the bottom of the table contains the location level parameters. Parameter CV Duplicate Batch Year (2011) Nestling Order slope Estimate 0.21 -0.08 0.12 0.20 -0.01 -0.04 -0.01 L95% 0.20 -0.11 0.08 0.17 -0.11 -0.12 -0.01 L80% 0.20 -0.10 0.09 0.18 -0.08 -0.09 -0.01 U80% 0.22 -0.06 0.16 0.23 0.06 0.01 0.00 U95% 0.22 -0.05 0.18 0.24 0.10 0.04 0.00 6 Supplemental Table 3: Estimated EROD activity (pmol product/min/mg protein) for study locations. This table includes the number of individuals per location as well as a description of the posterior distribution including the median as well as the upper and lower 80% and 95% credible intervals. Location Green Mountain Pool 2 Root River Island Pool 8 Lawrence Lake Shellhorn Schnick’s Bay Pig's Eye a N 20 10 10 8 10 10 8 20 Estimate 25.50 27.50 29.40 31.85 34.74 38.53 44.24 71.16 L95 14.41 14.87 14.86 17.38 21.78 25.47 29.24 60.15 U95 36.51 40.35 43.96 45.86 47.84 51.82 59.39 82.01 L80 18.39 19.07 19.94 22.51 26.13 30.09 34.53 63.86 U80 32.53 35.90 38.62 41.17 43.26 47.18 53.66 78.13 Aa A A A A A AB B Medians not sharing the same letter are significantly different based on 95% credible intervals (Cumming and Finch 2005). 7 Supplemental Table 4: Estimated correction parameters (EROD activity) and standard deviations. The parameter’s posterior distribution including the median as well as the upper and lower 80% and 95% credible intervals. Parameter Estimate 2011 38.35 sigma 21.05 L95 24.81 18.28 U95 51.64 24.67 L80 29.67 19.16 U80 46.86 23.25 8 Supplemental Table 5: Estimated oxidative stress parameters for study locations. This table includes the number of individuals per location as well as a description of the posterior distribution including the median as well as the upper and lower 80% and 95% credible intervals. 9 Response Location Green Mountain Island W2 Lawrence Lake Pig's Eye GSSG/GSH Pool 2 Root River Schnick's Bay Shellhorn Green Mountain Island W2 Lawrence Lake Pig's Eye GSSG (µmol/g) Pool 2 Root River Schnick's Bay Shellhorn Green Mountain Island W2 Lawrence Lake Pig's Eye rGSH (µmol/g) Pool 2 Root River Schnick's Bay Shellhorn Green Mountain Island W2 Lawrence Lake Pig's Eye PBSH (µmol/g) Pool 2 Root River Schnick's Bay Shellhorn Green Mountain Island W2 Lawrence Lake TBARS Pig's Eye (nmol/mg Pool 2 Protein) Root River Schnick's Bay Shellhorn Green Mountain Island W2 Lawrence Lake Pig's Eye TSH (µmol/g) Pool 2 Root River Schnick's Bay Shellhorn N Estimate L95 U95 L80 U80 20 8 10 20 10 10 8 10 20 8 10 20 10 10 8 10 20 8 10 20 10 10 8 10 20 8 10 20 10 10 8 10 20 8 10 20 10 10 8 10 20 8 10 20 10 10 8 10 0.74 1.28 0.61 0.75 0.60 0.60 0.87 0.75 2.68 3.08 3.18 2.52 2.43 2.65 3.30 2.99 5.04 4.78 6.07 4.40 4.67 5.33 5.35 6.25 17.73 14.93 15.26 11.18 13.41 9.09 14.99 16.34 0.77 0.60 0.84 1.13 0.79 0.84 0.54 0.85 22.79 19.76 21.30 15.66 18.02 14.49 20.50 22.57 0.42 0.85 0.24 0.43 0.22 0.15 0.43 0.39 2.32 2.61 2.76 2.17 2.02 2.17 2.82 2.58 3.70 3.09 4.53 3.11 3.14 3.72 3.74 4.77 12.83 8.97 10.06 6.36 7.70 2.79 8.37 10.93 0.55 0.30 0.58 0.90 0.53 0.55 0.22 0.59 17.12 12.46 14.72 10.03 11.47 7.39 12.79 16.13 1.07 1.70 0.99 1.07 0.98 1.00 1.31 1.14 3.03 3.51 3.61 2.87 2.86 3.13 3.78 3.41 6.32 6.44 7.62 5.67 6.15 6.91 7.01 7.71 22.40 20.88 20.85 15.93 19.15 15.28 21.43 21.87 1.01 0.91 1.10 1.36 1.05 1.15 0.84 1.12 28.20 27.20 27.82 21.11 24.18 21.61 27.92 29.08 0.54 1.00 0.37 0.55 0.35 0.32 0.58 0.51 2.45 2.77 2.91 2.29 2.16 2.34 2.99 2.72 4.24 3.66 5.08 3.57 3.71 4.28 4.28 5.29 14.67 11.13 11.76 8.06 9.71 4.94 11.03 12.83 0.63 0.40 0.67 0.98 0.62 0.66 0.33 0.69 19.20 14.98 17.00 11.82 13.94 9.67 15.50 18.38 0.95 1.56 0.86 0.95 0.85 0.86 1.15 1.00 2.91 3.37 3.47 2.75 2.72 2.95 3.60 3.26 5.90 5.88 7.09 5.22 5.63 6.39 6.44 7.21 20.85 18.82 18.84 14.40 17.11 13.04 19.14 20.04 0.92 0.80 1.02 1.28 0.97 1.04 0.74 1.03 26.40 24.57 25.55 19.07 22.01 19.20 25.18 26.72 10 Supplemental Table 6: Estimated correction parameters (oxidative stress) and standard deviations. The parameter’s posterior distribution including the median as well as the upper and lower 80% and 95% credible intervals. Response Parameter Estimate GSSG/GSH GSSG rGSH PBSH TBARS TSH L95 U95 L80 U80 2011 -0.22 -0.55 0.13 -0.44 0 sigma 0.61 0.53 0.71 0.55 0.67 2011 1.17 0.81 1.56 0.93 1.42 sigma 0.68 0.59 0.79 0.61 0.75 2011 3.24 1.9 4.62 2.35 4.12 sigma 2.41 2.1 2.81 2.19 2.67 2011 18.58 13.59 23.41 15.32 21.8 sigma 8.94 7.77 10.46 8.14 9.87 2011 0.33 0.1 0.57 0.18 0.49 sigma 0.43 0.37 0.5 0.39 0.47 2011 21.76 15.97 27.42 18.04 25.6 sigma 10.42 9.04 12.18 9.47 11.5 11 Supplemental Table 7: Pearson correlation coefficient matrix among eight biomarkers (n=84). P value / (R) GSSG GSS.GSSG 0.09 (0.19) GSSG PBSH rGSH TBARS TSH EROD PBSH rGSH TBARS TSH EROD DNA CV 0.0496 <0.001 0.96 0.003 0.83 0.96 (-0.21) (-0.69) (0.01) (-0.33) (-0.02) (0.01) <.0001 0.003 0.36 <0.001 0.02 0.17 (0.39) (0.32) (0.10) (0.40) (0.25) (-0.15) <0.001 0.20 <0.001 0.06 0.23 (0.61) (0.14) (0.99) (0.20) (-0.13) 0.92 <0.001 0.14 0.55 (-0.01) (0.73) (0.16) (-0.07) 0.28 0.01 0.29 (0.12) (0.27) (-0.12) 0.06 0.25 (0.21) (-0.13) 0.38 (0.10) 12 Supplemental Table 8: Loadings for first two axes from Redundancy Analysis (RDA).The axis is a linear combination of the value for each parameter. For example, Axis 1 would be 0.49 * the CV score for a site + -0.937 * the EROD value for a site + -0.743* the TBARS value for a site + -0.535* the TSH value for a site + -0.463 * the tGSH value for a site + -0.412 * the rGSH value. Biological parameters DNA CV EROD TBARS TSH tGSH rGSH Axis 1 Axis 2 0.49 -0.937 -0.743 -0.535 -0.463 -0.412 -1.032 -0.735 -0.166 0.184 0.229 0.246 13