Using light to describe the ancient world

Archive for the ‘X-ray’ Category

#Elemental mapping of tissues in flat fossils

X-ray fluorescence chemical map of an ancient teleost fish. From Gueriau et al. PLoS One 2014: doi:10.1371/journal.pone.0086946.g001

X-ray fluorescence chemical map of an ancient teleost fish. From Gueriau et al. PLoS One 2014: doi:10.1371/journal.pone.0086946.g001

We often think of fossils as being solid and three-dimensional body parts, like dinosaur bones or ancient sea shells, and we can imagine these fossils being part of an organism that lived in ancient times. Eventually that organism would have died and become buried under sediment. Sometimes sediment does an excellent job of preserving fossils through deep time. But not always – sometimes the weight of the sediment crushes the fossil almost completely, flattening out the three-dimensional features. Working with flat fossils can be tricky if you are interested in the fine details of these ancient body parts. Pierre Gueriau and colleagues recognised this problem, and described a chemical imaging technique that can better help with visualising these flattened remains.

Gueriau and colleagues used x-ray fluorescence to study crushed fossils. X-ray fluorescence is useful for describing the elemental composition of a fossil. When this elemental information is collected from many thousands of points, there is enough information to build an elemental map. Researchers can visualise the distribution of elements in a fossil by assigning different colours to different elements. So how does this help to visualise the structure of a crushed fossil?

…Here, we discriminate tissues in exceptionally well-preserved fossils on the basis of their content in chemical elements from majors to traces, in particular trace rare earths and transition metals, and alkaline earths. We exploit the distinct affinities of mineralized tissues and authigenic phases for fixing elements as a source of contrast between hard and soft fossil parts. Our results are based on the identification of spatial distributions of more than twenty elements in entire fossils through synchrotron X-ray spectral raster-scanning…”  – Gueriau et al. PLoS One 2014

So, different parts of the fossils actually contain slightly different elemental compositions. Using false colour maps, where different colours correspond to different elements, the authors were able to produce images like this:

 

Figure 1. Synchrotron X-ray fluorescence mapping of major-to-trace elements in fossils from the OT1 Lagerstätte. (A–C) Optical photographs of the specimen of the shrimp Cretapenaeus berberus MHNM-KK-OT 01a (A), the usual teleost fish MHNM-KK-OT 02 (B) and the newly identified teleost fish MHNM-KK-OT 03a (C). (D–F) False color overlays of elemental distributions reconstructed from a full spectral decomposition of the synchrotron raster-scanning data. (D) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the shrimp (scan step: 100×100 µm2, 26,751 pixels). (E) False color overlay of neodymium (red), strontium (green) and iron (blue) distributions from the characteristic teleost fish (scan step: 125×123 µm2, 21,120 pixels). (F) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the newly identified teleost fish (scan step: 100×100 µm2, 50,851 pixels). Images demonstrate the strong elemental contrast between fossil skeletal and soft tissues. The yellow and red squares in C indicate the two areas that were mapped at higher spatial resolution in Fig. 2. The scale bar is 5 mm and applies to all panels. doi:10.1371/journal.pone.0086946.g001

Figure 1. Synchrotron X-ray fluorescence mapping of major-to-trace elements in fossils from the OT1 Lagerstätte. (A–C) Optical photographs of the specimen of the shrimp Cretapenaeus berberus MHNM-KK-OT 01a (A), the usual teleost fish MHNM-KK-OT 02 (B) and the newly identified teleost fish MHNM-KKOT 03a (C). (D–F) False color overlays of elemental distributions reconstructed from a full spectral decomposition of the synchrotron raster-scanning data. (D) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the shrimp (scan step: 100×100 µm2, 26,751 pixels). (E) False color overlay of neodymium (red), strontium (green) and iron (blue) distributions from the characteristic teleost fish (scan step: 125×123 µm2, 21,120 pixels). (F) False color overlay of neodymium (red), yttrium (green) and iron (blue) distributions from the newly identified teleost fish (scan step: 100×100 µm2, 50,851 pixels). Images demonstrate the strong elemental contrast between fossil skeletal and soft tissues. The yellow and red squares in C indicate the two areas that were mapped at higher spatial resolution in Fig. 2. The scale bar is 5 mm and applies to all panels. doi:10.1371/journal.pone.0086946.g001

The authors were able to produce incredibly detailed maps of fossils because they were using a synchrotron as the source of their x-rays. The high-energy, tightly focused x-ray beam from the synchrotron meant that a great deal of data could be quickly gathered from one tiny spot on each fossil. Repeat several thousand times to produce a map!

#PLOSONE: Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils http://dx.plos.org/10.1371/journal.pone.0086946

Gueriau P, Mocuta C, Dutheil DB, Cohen SX, Thiaudière D, et al. (2014) Trace Elemental Imaging of Rare Earth Elements Discriminates Tissues at Microscale in Flat Fossils. PLoS ONE 9(1): e86946. doi:10.1371/journal.pone.0086946

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#African fossil penguins, behind the scenes

A diverse group of penguins lived in Africa 10-12 million years ago. Dr. Dan Ksepka and I recently co-wrote an article describing these ancient penguins, and Dan has a great summary on his blog. I thought I would take this opportunity to show some of the ‘behind the scenes’ work that helped with the article but was not included in the final cut.

One of the first things we wanted to know was the age of the fossil penguin bones. Eventually we would solve this problem with stratigraphy – one of our first moves, though, was to see if the burial environment of the fossils we had just found was similar to the burial environment of fossil penguins that had previously been described. The burial environment for these already-described penguins is around five million years old.

The chemistry of fossil bones can be useful for describing different burial environments. Water that flows between grains of sediment can have very different chemical compositions in different burial environments, and water can alter the chemistry of a fossil bone in a distinct way. If two fossils have very similar elemental compositions, then you can start thinking about how they might have come from the similar burial environments. Likewise, if fossil bones have distinct chemical compositions, then it might be telling you that the bones also have different ages. Of course, fossils with the same age can be buried in different burial environments, so checking for similarities in burial environment is just a preliminary step.

Analysing the chemistry of a fossil bone is easy to do when you have access to a handheld x-ray fluorescence spectrometer. Two of the penguin bones that I analysed are shown below – most of a humerus from a ~5 million year old Inguza predemersus, and the head of a humerus from one of the newly found penguins (Sphenisciformes B). I collected XRF data from these specimens and found the same proportion of calcium and phosphorus in each fossil. This isn’t surprising – these are the two major ingredients of bone.

Fossil bones from the Western Cape of South Africa.

Fossil bones from the Western Cape of South Africa.

Both of these fossil bones are orange-brown-ish, and both have roughly the same proportion of iron. Iron oxides (rust) can produce orange-brown colours in fossils. So, no great differences in calcium, phosphorus or iron. Strontium, however, was a large component of the newly discovered bone, and represented a smaller proportion of the Inguza bone. Strontium can be fairly mobile, however, and bones from the same locality can have different amounts of strontium.

Energy dispersive x-ray fluorescence spectra from fossil penguin bones.

Energy dispersive x-ray fluorescence spectra from fossil penguin bones.

The most surprising and interesting results were at the higher end of the energy scale. A peak that might represent uranium was very clear in the spectrum from the newly discovered fossil penguin, and comparatively weak in the spectrum from Inguza. Likewise, a peak that might represent yttrium is distinct in the spectrum from Inguza, and weak in Sphenisciformes B. These trace elemental differences, combined with the variation in strontium concentration, are telling us that the two fossil bones have been altered by groundwater in different environments. We took this to mean that the bones were from different burial environments….

….and sure enough, the Inguza fossil was buried around 5 million years ago in a sandy river channel, and Sphenisciformes B was buried between 10 and 12 million years ago in a gravelly estuary. Of course, this conclusion was brought to us by sedimentology and stratigraphy, but it is very nicely supported by spectroscopy.

Thomas DB and Ksepka, DT. 2013. A history of shifting fortunes for African penguins. Zoological Journal of the Linnean Society. DOI: 10.1111/zoj.12024

Portable and non-destructive chemical measurements

Handheld XRF instrument analysing a fossil Eland (Taurotragus oryx) horn core from Elandsfontein, a Middle Pleistocene locality in the Western Cape of South Africa

The mining and quarrying industries can summon deep emotions when mentioned in polite conversation. Polar views might be offered by your friends and family, with words like “destructive” and “irreparable” countered with “employment” and “vital”. While mining issues carve deep ravines into the political landscape in my home town, some of the most productive fossil sites that I have visited were discovered by agricultural quarrying. Indeed, many fossil sites around the world have been discovered serendipitously by digger, tractor or shovel.

The mining industry has also contributed to analytical advances in fossil studies. X-ray fluorescence spectroscopy (XRF) is an analytical technique that uses x-rays to probe the chemical composition of a sample. This is traditionally performed in a dedicated lab, where samples are ground to flour, mixed with another powder, fused into glass, and analysed in a room-sized instrument. In stark contrast, a range of portable instruments are produced that can perform x-ray fluorescence spectroscopy in the field. These instruments have been optimised for the mining industry, providing a rapid way of targeting mineral-rich areas. The chemical mapping that is applied in the hunt for platinum and gold is conceptually identical to describing the heterogeneous burial environments of different fossils: elements, minerals and rocks vary from place to place. Following this logic, we used a handheld XRF instrument to describe the burial environments of fossil bones in the Western Cape of South Africa.

We studied fossil antelope bones and teeth from two Pleistocene localities, one that has always been located inland, and one that presently crops out along the coast (Thomas and Chinsamy, 2011). Bones from the inland site are iron rich, whereas bones from the coastal site feature an abundance of calcium (more than what you expect for just bone). Although this is a simple conclusion, we discovered that the chemical information provided by handheld XRF needs some careful interpretation. Several factors can influence handheld XRF data: the distance between the sample and the instrument, the density of the sample, the calibration of the in-built software. The most informative approach is to analyse the raw x-ray fluorescence spectra, not the elemental concentrations. Principal components analysis score values provide meaningful groups, and the corresponding loadings help to understand those groups. Our key finding from studying fossils with an instrument originally designed for mining exploration was that multivariate statistics are essential (unavoidable, indispensible, vital and crucial) for interpreting the dataset. Only once the chemometics are sorted will the chemical and paleontological story spring to life.

 

Thomas, D. B., Chinsamy, A. 2011. Chemometric analysis of EDXRF measurements from fossil bone. X-ray Spectrometry 40: 441–445

#News: Fossil feather colouration

Roy Wogelius and colleagues describe feather pigmentation using synchrotron sourced x-ray fluorescence.

Two papers were published early last year that described colour in fossil feathers. One in Nature, and one in Science. These studies were based on a brilliant deduction by Jacob Vinther, who realised that colour structures seen in modern feathers may be preserved in fossils. This work was later applied to a newly described fossil penguin, with curious results. The colour structures identified by Vinther are associated with trace elements, which can also be used to reconstruct colour patterning in fossil feathers. Roy Wogelius and colleagues recently mapped the surface of a Late Cretaceous bird fossil, using x-ray fluorescence, allowing them to reconstruct provide even more insight into fossil colour patterns. The Royal Society of Chemistry have provided an excellent summary of the article.

Wogelius RA, Manning PL, Barden HE, Edwards NP, Webb SM, Sellers WI, Taylor KG, Larson PL, Dodson P, You H, Da-qing L and Bergmann U. 2011. Trace Metals as Biomarkers for Eumelanin Pigment in the Fossil Record. Science DOI: 10.1126/science.1205748

Image from Wikimedia Commons

News: Most ancient algal hard tissues

The earliest origin of hard tissues in the Eukaryotic Domain can now be traced back to the mid-Neoproterozoic thanks to Phoebe Cohen, her coauthors, and spectroscopy.

Carbon. Calcium. Phosphorus. These three ingredients are used to build the bones of every living animal. And every extinct animal. Indeed, the first bones were also built using carbon, calcium and phosphorus, but the bones of animals are not the only hard tissues made using these key ingredients. Some living algae also build phosphatic skeletons. And so did some extinct algae, including three mid-Neoproterozoic (717–812 Ma) species from Canada.

Phoebe Cohen and colleagues (including J. William Schopf) recently presented the “…earliest compelling evidence of biologically controlled eukaryotic biomineralization known in the fossil record…” Eukaryotes are organisms whose cells contain complex structures enclosed within membranes, like you, me and trees, and unlike bacteria (which are prokaryotes). The evidence for biomineralization of the algal scales includes traces of carbon, calcium and phosphorus detected using energy-dispersive x-ray fluorescence spectroscopy. These three elements are remnants of ancient phosphatic tissues. The chemistry of phosphatic tissues can be mimicked by minerals that form during burial, however, but Cohen and colleagues state that “…none of the scales… are deformed or show any evidence of either phosphate replacement or secondary apatite overgrowths…” Another possibility for the mineralised structures is replacement of calcium carbonate with calcium phosphate over time, but “…the possibility that these fossils were originally composed of calcium carbonate can be discounted due to the absence of (1) carbonate pseudomorphs, (2) any carbonate signal in the Raman spectra, and (3) cast and mold structures characteristic of phosphate replacement…” So,  the earliest origin of hard tissues in the eukaryotic Domain can now be traced back to the mid-Neoproterozoic thanks to spectroscopy.

Cohen PA, Schopf, JW, Butterfield NJ, Kudryavtsev AB, Macdonald FA, 2011. Phosphate biomineralization in mid-Neoproterozoic protists. Geology 39, 539-542.

Image modified from Wikimedia Commons

#Recent news: Chemical images of Archaeopteryx

Chemical mapping has revealed the remnants of feathers preserved in this specimen of Archaeopteryx

Synchrotron rapid scanning X-ray fluorescence has given the world more than just an impressive acronym. In fact, SRS-XRF has been used to describe hidden feather traces and bone chemistry in a specimen of Archaeopteryx. SRS-XRF is a chemical mapping technique that applies the basic approach of XRF (see X-ray fluorescence below) to points spaced 100 μm apart, allowing elemental maps to be made at a staggering rate of one square centimetre every 30 seconds. Uwe Bergmann and colleages reported their SRS-XRF maps of Archaeopteryx last year, where they show a phosphorus distribution that picks out all of the bone, as well as shafts of feathers. Zinc was shown almost exclusively associated with the bone, and may reflect the original diet of Archaeopteryx. This study is a great step forward in visualising otherwise unseen fossil evidence.

Bergmann U, Morton RW, Manning PL, Sellers WI, Farrar S, Huntley KG, Wogelius RA, Larson P. 2010. Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging. Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1001569107

Image from Wikipedia

#News: Eocene reptile skin

Edwards and colleague have described preserved organic material in the skin of a 50 million year old lizard

Nick Edwards and coauthors have just published a description of compounds from the skin of an Eocene reptile from Green River Formation, USA. Using a bevy of techniques, including Fourier-transform infrared spectroscopy, synchrotron x-ray fluorescence spectroscopy and x-ray diffractometry, Edwards and colleagues describe residual “…amide and sulphur compounds…[that] are most probably derived from the original beta keratin in the skin…”, as well as copper concentrations comparable to modern day geckos. You can find the article at here

N.P. Edwards, H.E. Barden, B.E. van Dongen, P.L. Manning, P.L. Larson, U. Bergmann, W.I. Sellers and R.A. Wogelius (2011) Infrared mapping resolves soft-tissue preservation in 50 million year old reptile skin. Proc. R. Soc. B. Published online 23rd March. doi:10.1098/rspb.2011.0135

Image from Wikipedia

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