Max Planck Institute for Evolutionary Anthropology 1 Reconciling X-ray microtomography of recent fossils and paleogenetics: simple technical solutions and good practices P. Tafforeau, A. Le Cabec, A. Immel, M. Bonazzi, V. Schuenemann, A. Herbig, H. Temming, B. Viola, J.-J. Hublin and J. Krause 12/09/2015ESHE 2015 London

Strong impact on aDNA in case of very high dose Normalized quantity of aDNA depending on X-ray dose accumulation using high flux irradiation setup (93.74 Gy/s) at the ESRF 12/09/20152ESHE 2015 London

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12/09/2015ESHE 2015 London4 ESRF, ID19 dose vs. resolution in the period

Using propagation phase contrast for low dose high quality imaging Phase contrast imaging is one of the most important aspects of synchrotron imaging. Phase contrast can typically be 1000 times more sensitive than X-ray absorption contrast. For similar data quality, synchrotron can then use less X- ray dose than conventional scanners, or reach far better quality with similar X-ray dose. 12/09/20155ESHE 2015 London

absorption 12/09/20156ESHE 2015 London

1m propagation phase contrast, edge detection 12/09/20157ESHE 2015 London

Reconstruction after single distance phase retrieval 12/09/20158ESHE 2015 London

absorption Paganin phase retrieval Phase contrast edge detection 12/09/20159ESHE 2015 London

12/09/2015ESHE 2015 London10 ESRF, ID19 dose vs. resolution in the period

12/09/2015ESHE 2015 London average dose reduction by 30 times -98.4% -95.3% -88.0%

12/09/2015ESHE 2015 London total average dose reduction by 90 times compared to 2010 ! -99.4% -98.1% -98.3%

12/09/2015ESHE 2015 London13 Since 2014, only the sub-micron resolution scans can significantly degrade aDNA. All the other configurations are in the safe range, and will be even safer in 2016

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What about conventional microCT ? As it represents the vast majority of scans performed on fossils ? 12/09/2015ESHE 2015 London15

Dosimetry experiment on two conventional microCTs at the MPI-EVA Same dosimeter system than for the synchrotron experiment. Measures as water equivalent surface dose. Many measurements to test effects of current, intensity, distance, filters on the BIR scanner and the skyscan 1173 Plotting of the results on the risk scale derived from the synchrotron experiments. Ongoing development of a calculation tool to have reasonable dose estimation for conventional microCTs (using tungsten source). 12/09/2015ESHE 2015 London16

12/09/2015ESHE 2015 London17 BIR scanner, 100 kV, 10 W no filter, 2 hours BIR scanner, 100 kV, 10 W no filter, 2 hours Skyscan 1173, 100 kV, 8 W no filter, 2 hours Skyscan 1173, 100 kV, 8 W no filter, 2 hours With conventional uCT, dose increases with the square power of the resolution, then do not use resolution higher than necessary.

Just 0.1mm brass is sufficient to go in the safe zone. 1mm aluminium filter would be less efficient. 0.5mm of aluminium would have nearly no effect. 12/09/2015ESHE 2015 London18 BIR scanner, no filter 0.1mm brass 0.25mm brass

12/09/2015ESHE 2015 London19 Skyscan 1173, no filter 2 hours scan Skyscan 1173, no filter 2 hours scan

12/09/2015ESHE 2015 London20 Skyscan 1173, no filter 2 hours scan Skyscan 1173, no filter 2 hours scan Skyscan 1173, no filter 10 x 2 hours scans Skyscan 1173, no filter 10 x 2 hours scans Dose is cumulative ! Multiple scans, even at medium resolution and over decades or centuries can finally lead to aDNA degradation !

12/09/2015ESHE 2015 London21 BIR scanner, 0.1mm brass 2 hours scan BIR scanner, 0.1mm brass 2 hours scan BIR scanner, 0.1mm brass 10 x 2 hours scans BIR scanner, 0.1mm brass 10 x 2 hours scans With the use of a minimum amount of brass or Cu filter, the risk in case of several scans still exists, but is lower.

12/09/2015ESHE 2015 London22 BIR scanner, 0.1mm brass 2 hours scan BIR scanner, 0.1mm brass 2 hours scan ESRF, ID Synchrotrons, thanks to phase contrast, can produce far better data than conventional uCT with similar X-ray dose. We can all continue to scan recent fossils without endangering paleogenetics just by following simple rules. Synchrotrons, thanks to phase contrast, can produce far better data than conventional uCT with similar X-ray dose. We can all continue to scan recent fossils without endangering paleogenetics just by following simple rules.

Good practices to reconcile microCT and paleogenetics 23 With conventional sources, use metallic filters (at least 0.1mm of brass or copper, not only aluminium) to remove the lowest energies in the spectrum. Do not use resolution higher than necessary. Avoid multiple scans. Do not rescan a sample when access to previous data would be possible and sufficient. Data sharing with open access for scans after publication is part of the solution. Keep precise track of the scan history of the specimens (with all the parameters) and locations, especially for high resolution scans. Curators should have track records of scans, as well as play active role in data sharing policies. 12/09/2015ESHE 2015 London

All these results on conventional sources are based on the original synchrotron experiments performed with very high photon flux. We strongly encourage other teams to make similar tests on aDNA degradation based on irradiations with conventional scanners, as the far lower flux could lead to potentially different results. We would be happy to provide our dose estimator to any team that would like to perform similar experiments on conventional sources (but real dosimetry is evidently better) We can all continue to scan recent fossils, we just have to be careful and responsible. With X-rays, better safe than sorry Wrap it up (with thin brass filter) Wrap it up (with thin brass filter) Thank you for your attention 12/09/201524ESHE 2015 London