"Supplementary Table 4. Results from linear regression for each damage parameter. Linear and exponential models were constructed for each parameter with year and museum as explanatory variables.  No exponential model was run for histone periodicity index due to values of 0. For models with collection museum as a fixed effect, estimates and p-values correspond to the difference in y-intercept between the reference (NHM London) and the named museum. Total endogenous percent = post-filtering for duplicates and mapping quality (30); raw endogenous percent = prior to duplicate or mapping quality filter. Mean Combined length = mean length of reads (collapsed alignment) and inserts (non-collapsed alignment). All estimates and p-values given in scientific notation to 3 d.p., all other statistics given to 2 d.p."																								
Formula	Model Type	Fixed Effects															F-statistic	p-value	R_	Adjusted R_	AIC	Likelihood Ratio Test		
		Year			Intercept										Model ANOVA of Museum							Log Likelihood	_2	p-value
		Estimate	t-value	p-value	Reference (NHM)	p-value	Edinburgh	p-value	Oxford	p-value	Tullie House	p-value	World Museum	p-value	F-value	p-value								
Total Endogenous Percent ~ Year + Museum	Linear	1.100E-01	3.11	2.45E-03	-1.566E+02	1.94E-02	1.895E+00	4.81E-01	1.859E+00	5.01E-01	3.264E+00	4.43E-01	-8.167E+00	2.55E-03	3.33	1.31E-02	"(5,104) 3.32"	8.02E-03	0.14	0.10	812.46	-399.23	576.74	< 2.20E-16
ln(Total Endogenous Percent) ~ Year + Museum	Exponential	3.000E-03	1.20	2.22E-01	-2.080E+00	6.66E-01	-1.765E-01	3.66E-01	1.817E-02	9.28E-01	1.528E-01	6.21E-01	-1.699E-01	3.78E-01	0.48	7.52E-01	"(5,104) 0.55"	7.30E-01	0.03	-0.02	235.71	-110.86		
Raw Endogenous Percent ~ Year + Museum	Linear	1.775E-02	0.32	7.54E-01	5.234E+01	6.30E-01	1.287E+00	8.06E-01	2.918E+00	5.26E-01	5.710E+00	4.36E-01	-8.590E+00	1.44E-01	1.88	1.20E-01	"(5,104) 1.83"	1.13E-01	0.08	0.04	924.37	-455.19	704.61	< 2.20E-16
ln(Raw Endogenous Percent) ~ Year + Museum	Exponential	9.318E-04	0.41	6.85E-01	2.632E+00	5.56E-01	-2.204E-01	2.26E-01	2.130E-02	9.09E-01	1.049E-01	7.15E-01	-1.354E-01	4.50E-01	0.58	6.75E-01	"(5, 104) 0.47"	8.00E-01	0.02	-0.03	219.76	-102.88		
Mean Combined Length ~ Year + Museum	Linear	1.867E-01	8.43	2.29E-10	-3.026E+02	2.05E-13	3.100E+00	7.91E-02	1.601E+00	3.76E-01	-1.025E+00	7.12E-01	-6.307E+00	4.04E-04	5.61	3.95E-04	"(5,104) 16.83"	3.69E-12	0.45	0.42	718.73	-352.37	911.46	< 2.20E-16
ln(Mean Combined Length) ~ Year + Museum	Exponential	2.923E-03	8.32	3.71E-13	-1.588E+00	2.22E-02	5.194E-02	6.41E-02	2.021E-02	4.81E-01	-2.713E-02	5.38E-01	-1.043E-01	2.38E-04	6.15	1.75E-04	"(5,104) 16.82"	3.74E-12	0.45	0.42	-192.73	103.36		
Estimated Mean Fragment Length ~ Mean Combined Length	Linear	7.203E-01	24.71	< 2.20E-16	-2.613E+01	< 2.20E-16	-	-	-	-	-	-	-	-	-	-	"(1,108) 610.7"	< 2.20E-16	0.85	0.85	513.20	-253.60	637.61	< 2.20E-16
ln(Estimated Mean Fragment Length) ~ Mean Combined Length	Exponential	3.608E-02	22.46	< 2.20E-16	6.190E-01	5.05E-09	-	-	-	-	-	-	-	-	-	-	"(1,108) 504.3"	< 2.20E-16	0.82	0.82	-124.41	65.21		
_ ~ Year + Museum	Linear	-4.600E-04	-11.08	< 2.20E-16	9.600E-01	< 2.20E-16	-1.436E-02	2.75E-05	-3.435E-03	3.10E-01	-9.405E-03	7.22E-02	4.002E-03	2.18E-01	6.62	8.68E-05	"(5,104) 34.86"	< 2.20E-16	0.63	0.61	-663.07	338.54	636.32	< 2.20E-16
ln(_) ~ Year + Museum	Exponential	-8.100E-03	-10.89	< 2.20E-16	1.308E+01	1.16E-14	-2.144E-01	4.38E-04	-8.492E-02	1.65E-01	-1.477E-01	1.17E-01	9.016E-02	1.25E-01	5.18	7.65E-04	"(5,104) 31.40"	< 2.20E-16	0.60	0.58	-26.76	20.38		
5' First Base C-T Deamination Proportion ~ Year + Museum	Linear	-4.971E-06	-1.35	1.80E-01	1.400E-02	5.02E-02	-5.634E-04	5.54E-02	-7.308E-04	1.63E-02	7.974E-04	8.61E-02	5.592E-04	5.40E-02	5.41	5.35E-04	"(5,104) 4.39"	1.16E-03	0.17	0.13	-1195.63	604.81	1159.40	< 2.20E-16
ln(5' First Base C-T Deamination Proportion) ~ Year + Museum	Exponential	-1.200E-03	-1.71	9.03E-02	-3.030E+00	3.18E-02	-1.245E-01	2.98E-02	-1.784E-01	2.77E-03	1.648E-01	6.83E-02	9.727E-02	8.42E-02	6.59	9.05E-05	"(5,104) 5.28"	2.30E-04	0.20	0.16	-36.20	25.10		
Histone Periodicity Index ~ Year + Museum	Linear	-2.100E-05	-1.86	6.61E-02	4.700E-02	3.24E-02	-2.587E-03	4.14E-03	-1.853E-03	4.39E-02	-2.906E-03	3.99E-02	-2.933E-03	1.06E-03	4.57	1.95E-03	"(5,104) 5.63"	1.24E-04	0.21	0.18	-	-	-	-
Preseq-Estimated Maxium Unique Reads ~ Year + Museum	Linear	6.197E+05	2.80	6.84E-03	-1.125E+09	1.14E-02	1.455E+07	3.19E-01	-	-	3.029E+07	1.20E-01	-2.258E+07	1.09E-01	1.82	1.53E-01	"(4,64) 2.04"	9.94E-02	0.11	0.06	2617.70	-1302.80	2500.90	< 2.20E-16
ln(Preseq-Estimated Maxium Unique Reads) ~ Year + Museum	Exponential	8.734E-03	2.92	4.78E-03	1.034E+00	8.60E-01	3.070E-01	1.21E-01	-	-	5.152E-01	5.07E-02	-2.811E-01	1.38E-01	2.46	7.04E-02	"(4,64) 2.45"	5.50E-02	0.13	0.08	116.80	-52.40