Using light to describe the ancient world

Archive for October, 2011

#News: Spectroscopic proof for fossil feather pigmentation

Fossil feathers from Gansus yumenensis have recently revealed evidence for the preservation of original pigmentation structures. The above reconstruction of Gansus was created in 2006 (by Mark Klinger/CMNH) before melanosomes had been used to describe fossil feather pigmentation (i.e. prior to the publication of Li et al. 2010). Barden et al. (2011) indicate that that eumelanin is indeed preserved in some Gansus yumenensis feathers, which may have imparted a dark colouration to some feathers.

Microorganisms can be a bit of a problem when interpreting fossil soft tissues (see Schweitzer et al. 2005 and Kaye et al. 2008) and the problem compounds when the soft tissues are bacteria-sized and bacteria-shaped. Consider melanosomes: these sphere to cigar shaped bodies are lipid sacks stuffed full of melanin that give rise to a variety of colours. Bacteria, unfortunately, can mimic the “…size, form, spatial arrangement, organisation and apparent embedding within soft tissue…” shown by melanosomes (Barden et al. 2011).  Melanosomes have been used to describe colouration in ancient birds and dinosaurs (e.g. Clarke et al. 2010; Li et al. 2010; Zhang et al. 2010): these ancient feather artworks obviously assume that the pigment structures are melanosomes, and not bacterial reproductions. Validation may require closer scrutiny. In other words, we should check to see if the palette used to produce these master artworks actually contains paint.

This is exactly what Holly Barden and colleagues have done (Barden et al. 2011). Barden et al. (2011) combined “…morphological (imaging) and organic geochemical techniques to analyse feathers from the early Cretaceous Chinese bird Gansus yumenensis…”. Gansus was an aquatic bird that lived in the ancient Changma basin in what would become the Gansu Province of northwestern China (early Aptian/Aptian, 125 to 112 Ma). Mid-infrared spectroscopy was among the roster of geochemical techniques used to analyse two fossil feathers from Gansus yumenensis, providing the first reported used of vibrational spectroscopy on fossil feathers. Barden et al. (2011) also collected mid-IR spectra from pure melanin as a comparative standard “…The infrared spectra obtained from the fossil feathers were clearly different from those taken within the surrounding matrix…[t]he matrix showed only the presence of an inorganic silica band, whereas the fossil feathers also showed carboxylic acid, ketone, hydroxyl and potential secondary amine peaks..[t]hese peaks all occur in the Sepia officinalis melanin spectra and the responsible functional groups are clearly seen in the chemical structure of eumelanin…” Further, “…FTIR analysis revealed no bands characteristic of modern bacteria including CH bending from fatty acids or P-O-C and P-O-P stretching from phospholipids, ribose and phosphate chain pyrophosphate…” Hence, Barden and colleagues demonstrated that pigment bodies have indeed been preserved in the fossil feathers of Gansus yumenensis.

Barden HW, Wogelius RA, Li D, Manning PL, Edwards NP, van Dongen, BE. 2011. Morphological and geochemical evidence of eumelanin preservation in the feathers of the Early Cretaceous bird, Gansus yumenensis. PLoS ONE 6: e25494. doi:10.1371/journal.pone.0025494

Clarke JA, Ksepka DT, Salas-Gismondi R, Altamirano AJ, Shawkey MD, D’Alba L, Vinther J, DeVries TJ, Baby P. 2010. Fossil evidence for evolution of the shape and color of penguin feathers. Science 330: 954–957.

Kaye TG, Gaugler G, Sawlowicz Z .2008. Dinosaurian soft tissues interpreted as bacterial biofilms. PLoS ONE 3: e2808. doi:10.1371/journal.pone.0002808

Li Q, Gao K-Q, Vinther J, Shawkey MD, Clarke JA, D’Alba L, Meng Q, Briggs DEG, Prum RO. 2010. Plumage color patterns of an extinct dinosaur. Science 327: 1369–1372.

Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK. 2005. Soft-tissue vessels and cellular preservation in Tyrannosaurus rex. Science 307: 1952–1955

Zhang F,KearnsSL, Orr PJ, Benton MJ, Zhou Z, Johnson D, Xu X, Wang X. 2010. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 463: 1075–1078.

Image credit: Mark A Klingler/CMNH 


Near infrared scanning for ancient DNA

Near infrared spectroscopy could be useful for detecting ancient DNA in fossil bone.

Deoxyribonucleic acid (DNA) is very rarely preserved in fossil bone. The fossil record for soft tissues is incredibly sparse, and the recovery of ancient DNA (aDNA) generally requires highly specific preservation conditions. Like most rare treasures though, the benefits of finding aDNA are immense: relationships between living and extinct groups can be established (e.g. Baker et al. 2005) and reconstructions of once living organisms can be entertained (e.g. Jurassic Park). The importance of aDNA is embodied in the Australian Centre for Ancient DNA, an entire research centre at the University of Adelaide dedicated to its study (prospective PhD students should check out this link). Finding aDNA is a difficult task, and one that would benefit from a rapid, non-destructive technique. Like near infrared spectroscopy.

Near-infrared (NIR) spectroscopy is most useful for characterising compounds constructed from light atoms, like soft tissues, which are mostly carbon, hydrogen, oxygen and nitrogen. In contrast, NIR is less adept at detecting bone mineral, which contains abundant calcium and phosphorus. This combination of these positive and negative biases makes NIR a potentially useful technique for finding aDNA. Bone mineral is essentially invisible with NIR spectroscopy, but soft tissues stand out like beacons. Ancient DNA may be found alongside collagen, the organic scaffold on which bone mineral is deposited, which is readily detectable with NIR. Further, entire surfaces of bones can be analysed with NIR using hyperspectral imaging. In essence, NIR hyperspectral imaging could be used to rapidly screen fossil bones for aDNA: surfaces of fossil bones could be mapped, allowing regions with telltale signs of preserved soft tissues to be identified.

For more detail on the prospective uses of NIR hyperspectral imaging in paleontology, check out my recent article in NIR News.


Thomas DB. 2011. Illuminating fossils by NIR. NIR News 22: 6-8.

Baker AJ, Huynen LJ, Haddrath O, Millar CD, Lambert DM. 2005. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas ofNew Zealand. Proceedings of the NationalAcademy of SciencesUSA102: 8257-8262.

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