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Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants

Chris Mays, Joseph J. Bevitt, and Jeffrey Stilwell

Plain Language Abstract

A high-resolution, three-dimensional model of a fossil seed cone from the Chatham Islands revealed the presence of internal fossil resin (amber). Its distribution of resin bodies supports the affinity with the modern conifer genus Sequoia (Family Cupressaceae). The model was constructed employing neutron tomography (a technique analogous to X-ray computed tomography [CT], but with neutrons instead of X-rays), and the high neutron attenuation contrasts between the resin, the enclosing organically preserved (coalified) plant remains, and sediment matrix allowed for a clear-cut segmentation of these different components. The results demonstrate the feasibility of detecting different organic compounds within a given fossil specimen using neutrons. With emerging advances in this technology, a wider variety of organic compounds and anatomical features within a given specimen should be discernible; this will have far-reaching implications for the forms and functions of fossils, as well as their post-burial histories and conservation.

Resumen en Español

in progress

Traducción: Enrique Peñalver (Sociedad Española de Paleontología) or Diana Elizabeth Fernández

Résumé en Français

in progress

Translator: Antoine Souron

Deutsche Zusammenfassung

Ausloten der Grenzen von Neutronen-Tomographie in der Paläontologie: dreidimensionales Modellieren von in situ Harzen innerhalb fossiler Pflanzen

Computer-Tomographie ist eine zunehmend beliebte Technik um Fossilien zerstörungsfrei zu untersuchen. Während sich die Röntgen-Computer-Tomographie (CT) seit der ersten Anwendung bei Fossilien in den frühen 1980er Jahren stark weiterentwickelt hat, bleiben Anwendung und Grenzen von Neutronen-Tomopgraphie (NT) relativ unerforscht in der Paläontologie. Die höchstauflösenden neutronentomographischen Scans in der Paläontologie bislang wurden von Austrosequoia novae-zeelandiae (Ettingshausen) Mays and Cantrill gemacht, ein Stück, das aus den mittelkretazischen Schichten (Cenoman; ~100–94 Ma) der Stratham Inseln (östliches Zealandia) stammt. Bislang wurde die Art mit in situ Harz (Bernstein) identifiziert. Die neue neutronentomographische Analyse wies ein ungewöhnlich hohes Neutronendämpfungssignal für fossiles Harz auf. Die resultierenden Daten lieferten einen starken Kontrast und deutliche dreidimensionale Repräsentanzen: 1) des fossilen Harzes; 2) es inkohlten Pflanzenmaterials und 3) der Sedimentmatrix. Diese Daten vereinfachten das anatomische Modell eines endogenen Harzkörpers innerhalb der Zapfen-Achse und des Deckblattkomplexes. Form und Verteilung der Harzkörper unterstützen eine nahe Verbindung mit Sequoia Endlicher (Cupressaceae), einer Gruppe von Koniferen, deren heutige Mitglieder nur in der nördlichen Hemisphäre gefunden werden. Diese Untersuchung demonstriert die Umsetzbarkeit von NT als Möglichkeit chemisch verschiedene organische Verbindungen innerhalb von Fossilien zu unterscheiden. Wir machen hier konkrete Empfehlungen in Bezug auf: 1) die Eignung von fossilen Erhaltungsarten für NT; 2) die Erhaltung von organischen Stücken mit wasserstoffhaltigen Konsolidierungsmitteln und Klebemitteln; und 3) die Anwendung von Zukunftsmethoden (Neutronenphasenkontrast) für weitere Verbesserungen bei der Abbildung von fein-detaillierten anatomischen Strukturen. Diese Funde zeigen, dass wir die konzeptionellen Grenzen von NT als ein Mittel zum virtuellen Extrahieren von Fossilien oder zum Abbilden ihrer internen Anatomie selbst wenn sie in Matrix eingeschossen sind, noch lange nicht erreicht haben.

Schlüsselwörter: Neutronen-Tomographie; Harz; Zapfen; Cupressaceae; Kreide; Erhaltung

Translator: Eva Gebauer

Arabic

Translator: Ashraf M.T. Elewa

 

 

maysChris Mays. Department of Palaeobiology, Naturhistoriska riksmuseet, Box 50007, S-104 05 Stockholm, Sweden; School of Earth, Atmosphere and Environment, Monash University, 9 Rainforest Walk, Clayton, Victoria 3800, Australia. This email address is being protected from spambots. You need JavaScript enabled to view it.

Chris Mays’ research interests have focused on the palaeoenvironments and floral ecosystems of the south polar and sub-polar regions during past greenhouse intervals. From 2012–2017, Chris was undergraduate lecturer and postdoctoral researcher at Monash University’s School of Earth, Atmosphere & Environment. During this time, his research involved the sedimentary successions and both palynological and macrofloral fossils of New Zealand (the Chatham Islands, South Island), Australia (Victoria, Tasmania), and the Antarctic Peninsula. In order to document the fossils from a series of previously unknown localities, he employed a range of emerging imaging and ‘virtual palaeontology’ techniques, such as neutron tomography and synchrotron X-ray tomography. In 2016, he was awarded the inaugural Mary Wade Award by the Australian Association of Palaeontologists (AAP) for the publication of his monograph on the mid-Cretaceous palynology of the Chatham Islands. Most recently, he has undertaken a postdoctoral fellowship at the Naturhistoriska riksmuseet (the Swedish Museum of Natural History), Stockholm, Sweden. This project focuses on the extinction and recovery trends of the terrestrial flora during the end-Permian mass extinction. He is also Associate Editor for Alcheringa: An Australasian Journal of Palaeontology. His work has been supported by the Australian Research Council, the National Science Foundation, the Australian Nuclear Science and Technology Organisation, AAP, Monash University, National Geographic and the Paleontological Society.

Chris received his B.Sc. (Hons) in 2008 from the University of Melbourne, Australia, and his Ph.D. in 2012 from Monash University, Australia.

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bevittJoseph J. Bevitt. Australian Nuclear Science and Technology Organisation, Research Office, B3, New Illawarra Road, Lucas Heights, NSW 2234, Australia. This email address is being protected from spambots. You need JavaScript enabled to view it.

Joseph is a neutron-scattering scientist at the Australian Centre for Neutron Scattering (ACNS) and manager of the Research Office of the Australian Nuclear Science and Technology Organisation. This incorporates the User Office, Grants Office and Knowledge Centre (Australia's nuclear library) functions. These functions support the user programs of the landmark facilities for Australian science; the OPAL research reactor, Centre for Accelerator Science, ACNS, cyclotron facility and the Australian Synchrotron.

Joseph is an instrument scientist on the DINGO radiography/tomography/imaging station at the OPAL Research Reactor, Deputy President of the International Society for Neutron Radiology and a guest research fellow of the Dinosaur Evolution Research Centre at Jilin University, China. He collaborates with museums and universities to pioneer the use of neutron microCT (3-D imaging of objects using neutrons with micrometre resolution) in the areas of palaeontology, archaeology and cultural heritage. Specific applications are to: 1) digitally excavate and reconstruct fossilised remains; 2) investigate disease and medical practice in ancient time; and 3) determine methods of manufacturing ancient cultural artefacts.

Joseph received his B.Sc. and Ph.D. from the University of Sydney, Australia.

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stilwellJeffrey D. Stilwell. School of Earth, Atmosphere and Environment, Monash University, 9 Rainforest Walk, Clayton, Victoria 3800, Australia and Australian Museum, 1 William Street, Sydney NSW 2010, Australia. This email address is being protected from spambots. You need JavaScript enabled to view it.

Jeffrey Stilwell’s current research embraces the integration of palaeontological data in 'big picture science', especially the potential to employ applied palaeontology methods in deciphering ancient greenhouse earth systems. He is renowned for his long-term research on ancient polar greenhouse Earth environments and ecosystems, especially in southern latitudes in Antarctica, New Zealand-Chatham Islands and Australia. Professor Stilwell has published >70 peer reviewed articles and five books/monographs in the fields of geology and palaeontology. His research portfolio includes many Australian government grants since 1996 (Australian Research Council [ARC] grants, including APD, ARF, DP, LP, and LIEF schemes; National Geographic Society Committee for Research and Exploration grants (x3); ANSTO awards; Australian Synchrotron award; and many industry grants). Stilwell discovered the first in situ Mesozoic Australian amber in May 2011, as part of a study on Cretaceous-aged sediments in the Otway Basin. This major discovery led to a 2014–17 ARC-DP project on the abundant amber, which in turn, has resulted in comparable deposits with diverse inclusions of animals, plants and microorganisms—many groups of which have no prior fossil record in Australia, and in some instances, the entire Southern Hemisphere. He is currently working with many colleagues from Australia and Europe to learn more about southern Australia’s evolutionary heritage during critical intervals in Earth history from ~230 to 40 million years ago.

Jeff received his B.Sc. and M.Sc. from Purdue University, Indiana, and Ph.D. from the University of Otago, New Zealand.

 

 

FIGURE 1. 1) Map of eastern Zealandia including New Zealand and the Chatham Islands, grey areas = emergent, grey outline = 2000 m isobath, boxed area is displayed in Figure 1.2. 2) Map of the Chatham Islands, grey areas = emergent, boxed area is displayed in Figure 1.3. 3) Geological map of the Waihere Bay area, northwest Pitt Island, fossil locality recorded in this study is indicated, age estimates from the following sources: Tupuangi Formation (Mildenhall, 1994; Mays and Stilwell, 2013), Kahuitara Tuff (Mildenhall, 1994; Stilwell, 1998), other estimates (Campbell et al., 1993; Panter et al., 2006). Modified from figures 1 and 3 of Mays et al. (2015b) with permission.

 figure1a

FIGURE 2. Austrosequoia novae-zeelandiae (Ettingshausen, 1887) Mays et al., 2017, PL1227. 1) Transverse section of a partially exposed, desiccated ovulate cone. 2) Neutron tomographic reconstruction largely encapsulated in sedimentary matrix, white indicates high neutron attenuation, oblique-transverse view. 3) Volume rendering of neutron tomographic reconstruction, RNA = Relative Neutron Attenuation, grid texture on RNA spectrum indicates relative transparency, regions of highest neutron attenuation represent in situ resin within cone axis and minor enclaves of resin near the distal ends of the bract-scale complexes, desiccation exhibited by large gaps in coalified organic remains (blue/green), oblique-transverse view. 4) Greyscale histogram from neutron tomographic reconstruction of PL1227 (16-bit) these values represent the neutron attenuation of the reconstructed volume, colours and transparency textures as per Figure 2.3, threshold values presented in Table 2, the spectrum has been cropped at the extremes for this graphical representation.

See Appendix for an animation of the virtually extracted specimen illustrated in Figure 2.3.

 figure2a

FIGURE 3. Artist’s reconstruction of ovuliferous cone and fertile shoot of Austrosequoia novae-zeelandiae (Ettingshausen, 1887) Mays et al., 2017, artist: Mali Moir.

figure3a

 

 

APPENDIX

Austrosequoia novae-zeelandiae (Ettingshausen, 1887) Mays et al., 2017, animated volume rendering of neutron tomographic reconstruction, Relative Neutron Attenuation (RNA) spectrum and scale as per Figure 2, PL1227. Click on image to download or run animation.

fig10 

 

TABLE 1. Neutron radiograph data collection parameters for illustrated specimen (PL1227).

Scan parameter Value
Total sample dimensions (mm) 62×58×14
Scintillator composition ZnS/6LiF
Scintillator dimensions (mm) 100x100x0.05
Rotation angle (°) 0.25
Total rotation (°) 180
Projections 720
No. of frames/projection 3
Frame exposure (secs) 60
No. of dark and beam profile images 6 each
Radiograph pixel width (mm) 0.0161

 

TABLE 2. Resin volume estimates and segmentation thresholds, all values are from visualisations performed with Avizo 9.0.1, volumes based on voxel diameter = 16.1 μm, “max.” and “min.” refer to the software maximum and minimum absolute spectrum values (0 and 65535, respectively), total = coalified plant remains + fossil resin, relative resin volume (%) = (fossil resin / total) × 100.

  Neutron attenuation segmentation thresholds  Volume
(no. of voxels)
 Volume
(μm3)
 
Medium Lower Upper
Air Min. 30700 - -
Matrix 30700 38500 1.60×10 6.67×1012
Bract-scale complex 1        
Coalified plant remains 38500 52250 1.59×10 6.65×10
Fossil resin 52250 Max. 2.61×10 1.09×10
Total 38500 Max. 1.62×10 6.76×10
Relative resin volume (%)       1.61
Bract-scale complex 2        
Coalified plant remains 38500 52250 7.05×10 2.94×10
Fossil resin 52250 Max. 6.65×10 2.78×10
Total 38500 Max. 7.12×10 2.97×10
Relative resin volume (%)       0.94
Bract-scale complex 3        
Coalified plant remains 38500 52250 1.14×10 4.74×10
Fossil resin 52250 Max. 9.98×10 4.16×10
Total 38500 Max. 1.15×10 4.78×10
Relative resin volume (%)       0.87
Bract-scale complex 4        
Coalified cone scale 38500 52250 8.49×10 3.54×10
Fossil resin 52250 Max. 1.13×10 4.73×10
Total 38500 Max. 8.60×10 3.59×10
Relative resin volume (%)       1.32