The Geochemistry of Fossil Pigment Preservation
Lead Research Organisation:
University of Manchester
Department Name: Earth Atmospheric and Env Sciences
Abstract
The Geochemistry of Fossil Pigment Preservation
Principal Investigator: R.A. Wogelius
Co-Investigators: P.L. Manning, W.I.Sellers, B.E. van Dongen
Summary
The University of Manchester Palaeontology and Geochemistry Groups, in collaboration with the Stanford Synchrotron Radiation Lightsource and other international partners, has recently shown that newly developed analytical techniques can resolve previously undetected chemical information about fossilized tissues. Several publications from this group (Wogelius et al., 2011; Edwards et al., 2011; Barden et al., 2011; Bergmann et al., 2010) have combined state-of-the-art synchrotron rapid scanning x-ray fluorescence imaging (SRS-XRF) with other sensitive techniques in order to show the chemical details of exceptionally preserved bones, feathers, skin, and a range of other soft tissues. Most importantly, this work has shown that patterns of copper distribution in the soft tissues of a number of fossils may successfully be used as biomarkers for the original distribution of eumelanin pigment. This finding was used to restore the eumelanin patterns within the oldest documented bird with a fully derived avian beak, the 120 million year old Confuciusornis sanctus. However, besides eumelanin, there are a number of other pigments that are important for life. In particular, chemical detection of phaeomelanin would provide critical information about the evolution of avian and mammalian species. Building on our successes with identifying and mapping the chemical residues of eumelanin and beta keratin, herein we propose an analytical and experimental plan to enhance our ability to detect and image key components of soft tissue. First of all we will perform a series of experiments with extant soft tissue so that we can monitor and determine the breakdown reactions of organic compounds as a function of host lithology, moisture content, and trace metal inventory. Secondly, we will complete an analytical programme, including SRS-XRF imaging, which will include these experimental run products as well as a series of time-stepped fossil samples of varying ages and host lithology so that we may build up a database which allows us to refine our general understanding of reaction paths during fossil degradation. Because the techniques we have developed are non-destructive we now have opened up the possibility for detailed analysis of extremely rare specimens which hold important information but cannot be destructively sampled. Finally, these experimental and analytical results from fossils and comparable extant species will be combined in order to answer several critically important questions in palaeontology, biology, and geochemistry, such as:
1) What are the key factors that control the breakdown kinetics of eumelanin, and thus what conditions favour exceptional preservation?
2) How does the presence of melanin affect the fossilisation process?
3) Can we reliably detect phaeomelanin as opposed to eumelanin, since the presence of this alternative form will improve our ability to resolve further aspects of fossil colour?
4) Because phaeomelanin is only found in birds and mammals, can it be used as a biomarker for endothermy and/or homeothermy?
5) Finally, can we reliably resolve the residues of other chemical pigments?
Project partners:
University of Nancy, CNRS, Prof. R. Michels
Feather degradation experiments
SLAC Linear Accelerator Center, Linac Coherent Light Source, Dr. U. Bergmann
SRS-XRF scans of large objects and x-ray spectroscopy
SLAC Linear Accelerator Center, Stanford Synchrotron Radiation Lightsource, Prof. C. Kao
SRS-XRF scans of large objects
DIAMOND Lightsource, Prof. Fred Mosselmans
XAS spectroscopy
Principal Investigator: R.A. Wogelius
Co-Investigators: P.L. Manning, W.I.Sellers, B.E. van Dongen
Summary
The University of Manchester Palaeontology and Geochemistry Groups, in collaboration with the Stanford Synchrotron Radiation Lightsource and other international partners, has recently shown that newly developed analytical techniques can resolve previously undetected chemical information about fossilized tissues. Several publications from this group (Wogelius et al., 2011; Edwards et al., 2011; Barden et al., 2011; Bergmann et al., 2010) have combined state-of-the-art synchrotron rapid scanning x-ray fluorescence imaging (SRS-XRF) with other sensitive techniques in order to show the chemical details of exceptionally preserved bones, feathers, skin, and a range of other soft tissues. Most importantly, this work has shown that patterns of copper distribution in the soft tissues of a number of fossils may successfully be used as biomarkers for the original distribution of eumelanin pigment. This finding was used to restore the eumelanin patterns within the oldest documented bird with a fully derived avian beak, the 120 million year old Confuciusornis sanctus. However, besides eumelanin, there are a number of other pigments that are important for life. In particular, chemical detection of phaeomelanin would provide critical information about the evolution of avian and mammalian species. Building on our successes with identifying and mapping the chemical residues of eumelanin and beta keratin, herein we propose an analytical and experimental plan to enhance our ability to detect and image key components of soft tissue. First of all we will perform a series of experiments with extant soft tissue so that we can monitor and determine the breakdown reactions of organic compounds as a function of host lithology, moisture content, and trace metal inventory. Secondly, we will complete an analytical programme, including SRS-XRF imaging, which will include these experimental run products as well as a series of time-stepped fossil samples of varying ages and host lithology so that we may build up a database which allows us to refine our general understanding of reaction paths during fossil degradation. Because the techniques we have developed are non-destructive we now have opened up the possibility for detailed analysis of extremely rare specimens which hold important information but cannot be destructively sampled. Finally, these experimental and analytical results from fossils and comparable extant species will be combined in order to answer several critically important questions in palaeontology, biology, and geochemistry, such as:
1) What are the key factors that control the breakdown kinetics of eumelanin, and thus what conditions favour exceptional preservation?
2) How does the presence of melanin affect the fossilisation process?
3) Can we reliably detect phaeomelanin as opposed to eumelanin, since the presence of this alternative form will improve our ability to resolve further aspects of fossil colour?
4) Because phaeomelanin is only found in birds and mammals, can it be used as a biomarker for endothermy and/or homeothermy?
5) Finally, can we reliably resolve the residues of other chemical pigments?
Project partners:
University of Nancy, CNRS, Prof. R. Michels
Feather degradation experiments
SLAC Linear Accelerator Center, Linac Coherent Light Source, Dr. U. Bergmann
SRS-XRF scans of large objects and x-ray spectroscopy
SLAC Linear Accelerator Center, Stanford Synchrotron Radiation Lightsource, Prof. C. Kao
SRS-XRF scans of large objects
DIAMOND Lightsource, Prof. Fred Mosselmans
XAS spectroscopy
Planned Impact
1) Academia. This proposed research will benefit a wide circle of academia including not only Palaeontology and Geochemistry but also Biology, Physics, Analytical Chemistry, and Environmental Science. This is already discussed in the "Academic Beneficiaries" document, but essentially our work will have technological, conceptual, and theoretical impacts across a broad cross-section of academia.
2) Public sector. Our work has already prompted the USDOE investment in SRS-XRF technology at the SLAC National Accelerator Laboratory and our continued success at SSRL will inspire other facilities to do the same. What we learn has already had an impact on Museum curation methodologies and will continue to drive the development of new ways to handle precious specimens. Since what we are developing is non-destructive, we also envision that our work will increase Museum resource allocation for chemical analysis of rare specimens that are off limits for destructive analysis.
3) Business/Industry. What we have done so far has already impacted on the technological development of commercial FTIR systems and positively affected sales of FTIR instruments. We expect that industry will have increased demand for synchrotron access and that there will be parallel needs for technological development coming out of our work, in, for example, detectors and sample chambers. NERC has already selected our work for a REF Impact of Science Case study because what we learn about trace metal complexation informs us directly about the development of enhanced sequestration methods in land-based disposal of hazardous and radioactive wastes. Fossil specimens are the only cases of sequestration that have run for periods longer than the million years required for radwaste safety cases and as such we need to learn from these natural analogues. An improved understanding of melanin may have potential impacts on understanding melanogenesis and melanoma.
4) General public- cultural impact will be that of answering fundamental scientific questions that humans have pondered ever since Darwin, such as "What were the colors of past life?", and "How did birds become so colorful?" Our research has already had significant cultural impact.
For instance see the attached letter from Poppy Leeder at NERC detailing our contributions to Planet Earth Online (Roy Wogelius PE letter_NERC.pdf).
5) Direct impacts of staff development. PDRA and technician will be trained in state-of-the-art analytical methods which can be applied to any chemical problem that might arise in a range of business applications, from analyzing environmental toxins to screening manufactured components of Formula 1 cars.
2) Public sector. Our work has already prompted the USDOE investment in SRS-XRF technology at the SLAC National Accelerator Laboratory and our continued success at SSRL will inspire other facilities to do the same. What we learn has already had an impact on Museum curation methodologies and will continue to drive the development of new ways to handle precious specimens. Since what we are developing is non-destructive, we also envision that our work will increase Museum resource allocation for chemical analysis of rare specimens that are off limits for destructive analysis.
3) Business/Industry. What we have done so far has already impacted on the technological development of commercial FTIR systems and positively affected sales of FTIR instruments. We expect that industry will have increased demand for synchrotron access and that there will be parallel needs for technological development coming out of our work, in, for example, detectors and sample chambers. NERC has already selected our work for a REF Impact of Science Case study because what we learn about trace metal complexation informs us directly about the development of enhanced sequestration methods in land-based disposal of hazardous and radioactive wastes. Fossil specimens are the only cases of sequestration that have run for periods longer than the million years required for radwaste safety cases and as such we need to learn from these natural analogues. An improved understanding of melanin may have potential impacts on understanding melanogenesis and melanoma.
4) General public- cultural impact will be that of answering fundamental scientific questions that humans have pondered ever since Darwin, such as "What were the colors of past life?", and "How did birds become so colorful?" Our research has already had significant cultural impact.
For instance see the attached letter from Poppy Leeder at NERC detailing our contributions to Planet Earth Online (Roy Wogelius PE letter_NERC.pdf).
5) Direct impacts of staff development. PDRA and technician will be trained in state-of-the-art analytical methods which can be applied to any chemical problem that might arise in a range of business applications, from analyzing environmental toxins to screening manufactured components of Formula 1 cars.
Organisations
- University of Manchester (Lead Research Organisation)
- Stanford University (Collaboration)
- DIAMOND LIGHT SOURCE (Collaboration)
- SLAC National Accelerator Laboratory (Project Partner)
- Diamond Light Source (Project Partner)
- Stanford University (Project Partner)
- French National Centre for Scientific Research (Project Partner)
Publications

1. Manning, P.L.
(2014)
Trace-metal jacket: The role of melanin pigment in the preservation of Archaeopteryx feathers.
in Meeting Program and Abstracts


Anne J.
(2014)
Bone physiology through particle physics.


Anné J
(2018)
Morphological and chemical evidence for cyclic bone growth in a fossil hyaena
in Journal of Analytical Atomic Spectrometry

Anné J
(2017)
Visualisation of developmental ossification using trace element mapping
in Journal of Analytical Atomic Spectrometry

Anné J
(2014)
Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates.
in Journal of the Royal Society, Interface

Anné J
(2016)
Chemistry of bone remodelling preserved in extant and fossil Sirenia.
in Metallomics : integrated biometal science

Barden H
(2014)
Bacteria or melanosomes? A geochemical analysis of micro-bodies on a tadpole from the Oligocene Enspel Formation of Germany
in Palaeobiodiversity and Palaeoenvironments
Description | We have discovered several things. 1) That there are organic-metal complexes that serve as biomarkers for melanin pigments 2) These complexes can be mapped using synchrotron technology in extant as well as extinct organisms 3) Patterning of the chemistry can indicate pigment patterns in fossils, revealing a new method to restore pigmentation to long extinct organisms 4) The organic-metal residues can also indicate other types of biochemical residue, and reveal information about diet, healing, and growth. 5) We have provided the first ever chemical identification of pheomelanin residue in the fossil remains of an extinct animal species. |
Exploitation Route | Three research groups are already following on from our work and the use of chemical imaging is growing rapidly in palaeontology. |
Sectors | Chemicals Education Environment Culture Heritage Museums and Collections |
URL | https://www.research.manchester.ac.uk/portal/en/researchers/roy-wogelius(21f0c497-d219-46d5-80ca-2cfcdd453d4d)/publications.html |
Description | Our findings have been used in high school physics textbooks to teach how synchrotron radiation can be applied to difficult problems in analytical chemistry. Our methodology has also branched into the work that I do via other funding into radioactive waste disposal. We are examining ancient bone material using the methods pioneered for fossils to detect and characterize actinide incorporation. Finally, what we have learned about avian biochemistry over the past 150 million years will likely have an impact on pet food formulations in the not too distant future. |
First Year Of Impact | 2018 |
Sector | Chemicals,Education,Environment |
Impact Types | Cultural |
Description | Jurassic Foundation |
Amount | $2,000 (USD) |
Organisation | Jurassic Foundation |
Sector | Charity/Non Profit |
Country | United States |
Start | 05/2014 |
End | 06/2015 |
Description | Marie Curie Fellowship to Dr. Fabian Knoll |
Amount | £276,000 (GBP) |
Organisation | European Research Council (ERC) |
Sector | Public |
Country | Belgium |
Start | 08/2014 |
End | 10/2016 |
Description | Outreach support |
Amount | £5,000 (GBP) |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 05/2014 |
End | 06/2014 |
Description | President's Scholarship |
Amount | £70,000 (GBP) |
Organisation | University of Manchester |
Sector | Academic/University |
Country | United Kingdom |
Start | 08/2012 |
End | 08/2015 |
Description | STFC Science in Society Fellowship |
Amount | £202,261 (GBP) |
Funding ID | ST/M001814/1 |
Organisation | Science and Technologies Facilities Council (STFC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2013 |
End | 12/2016 |
Description | University of Manchester Research Centre Grant- Interdisciplinary Centre for Ancient Life |
Amount | £30,000 (GBP) |
Organisation | University of Manchester |
Sector | Academic/University |
Country | United Kingdom |
Start | 03/2014 |
End | 04/2016 |
Title | In situ helium chamber |
Description | We developed a rapid loading flexible chamber mount with a He purged chamber for completing X-ray rapid scanning at high and low Z for irrelgular samples. This device has already been used by other research groups and we lead the field in developing these types of sample chambers. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2013 |
Provided To Others? | Yes |
Impact | Enables much more rapid sample turnaround and low Z scanning. |
URL | http://www.ical.manchester.ac.uk/ |
Title | Data from: Fossilization of melanosomes via sulfurization |
Description | |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
Title | Fossil Chemical Database |
Description | It is a fossil chemical database including XRF, XRD, and FTIR data |
Type Of Material | Database/Collection of data |
Provided To Others? | No |
Impact | This has not gone public yet, but we plan to make it accessible before the completion of our grant. It will contain hundreds of scans and images of fossil material. |
URL | http://www.ical.manchester.ac.uk/ |
Description | Microfocus synchrotron analysis |
Organisation | Diamond Light Source |
Country | United Kingdom |
Sector | Private |
PI Contribution | We have developed microfocus sample chambers, stages, and quantitative protocols. |
Collaborator Contribution | High resolution, stable microfocus X-ray beams. |
Impact | See publications |
Start Year | 2012 |
Description | Synchrotron Rapid Scanning X-ray fluorescence |
Organisation | Stanford University |
Department | SLAC National Accelerator Laboratory |
Country | United States |
Sector | Public |
PI Contribution | Sample chambers, mounting methods, data analysis |
Collaborator Contribution | Unique rapid scanning setup for large objects |
Impact | See publications |
Start Year | 2007 |
Description | Royal Society Summer Exhibition "Palimpsests, Palaeontology, and Particle Physics" |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | WE reached and inspired thousands of people, from 5 year-olds to Royal Society Fellows. We appeared on the BBC, several newspapers, and the NERC website. |
Year(s) Of Engagement Activity | 2012 |
URL | http://sse.royalsociety.org/2012/exhibits/chemical-ghosts/ |
Description | Royal Society Summer Exhibition X-Appeal |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | This form really isn't appropriate for this activity. This was a major event which highlighted X-ray science applied to palaeontology to the entire country. We are planning an international conference on this topic hosted by the RS. We are also planning an international workshop for curators based on our work, |
Year(s) Of Engagement Activity | 2014 |
URL | http://sse.royalsociety.org/2014/x-appeal/ |