The Geochemistry of Fossil Pigment Preservation

Lead Research Organisation: University of Manchester
Department Name: Earth Atmospheric and Env Sciences


The Geochemistry of Fossil Pigment Preservation
Principal Investigator: R.A. Wogelius
Co-Investigators: P.L. Manning, W.I.Sellers, B.E. van Dongen

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.


10 25 50
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) In research now in press 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

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 2013
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 06/2014 
End 06/2015
Description Marie Curie Fellowship to Dr. Fabian Knoll
Amount £276,000 (GBP)
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 09/2014 
End 10/2016
Description Outreach support
Amount £5,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 06/2014 
End 06/2014
Description President's Scholarship
Amount £70,000 (GBP)
Organisation University of Manchester 
Sector Academic/University
Country United Kingdom
Start 09/2012 
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 Academic/University
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 04/2014 
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. 
Title Data from: Fossilization of melanosomes via sulfurization 
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. 
Description Microfocus synchrotron analysis 
Organisation Diamond Light Source
Country United Kingdom 
Sector Academic/University 
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 Private 
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
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