Molecular Taphonomy Research Articles

Preservation of proteins in the geosphere.

Deep-time protein preservation has attracted increasing interest and rapid research activity within the palaeobiological community in recent years, but there are several different viewpoints without a cohesive framework for the interpretation of these proteins. Therefore, despite this activity, crucial gaps exist in the understanding of how proteins are preserved in the geological record and we believe it is vital to arrive at a synthesis of the various taphonomic pathways in order to proceed forward with their elucidation. Here we take a critical look at the state of knowledge regarding deep-time protein preservation and argue for the necessity of a more nuanced approach to understanding the molecular taphonomy of proteins through the lens of diagenetic pathways. We also propound an initial framework with which to comprehend the chemical changes undergone by proteins via the concept of 'proteagen'.

Assessing the usefulness of Raman spectroscopy and lipid analysis of decomposed human bones in forensic genetics and molecular taphonomy

Bones are among the structures most likely to be recovered after death. However, the low quantity of preserved DNA and complex processing from sample to DNA profile make forensic DNA analysis of bones a challenging task. Raman spectroscopy and gas chromatography-mass spectrometry (GC/MS), have the potential to be useful as screening tools for DNA analysis and in decomposition studies. The objective of this research was to assess the usefulness of such molecular investigations. Femur samples collected from 50 decomposing human bodies were subjected to Raman spectroscopy and GC/MS. Assessment of nuclear DNA quantity and short tandem repeat (STR) genotyping efficiency were also performed. Raman parameters (crystallinity, carbonate-to-phosphate ratio, mineral-to-matrix ratio) and detected lipids were recorded. Background fluorescence proved problematic for Raman analysis of forensic bones. Regardless, it was not associated with less preserved DNA or less detected STR alleles. Fatty acids, hydrocarbons, and five types of fatty acid methyl esters (FAMEs) were detected. The main phosphate peak position in Raman spectra was significantly correlated with preserved DNA (p = 0.03713), while significantly more STR alleles were detected in bones containing methyl hexadecenoate (p = 0.04236). Detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which are not associated with the level of preservation of endogenous DNA. The techniques assessed have shown to be useful in molecular taphonomy studies and forensic genetics.

Molecular Taphonomy of Heme: Chemical Degradation of Hemin under Presumed Fossilization Conditions.

The metalloporphyrin heme acts as the oxygen-complexing prosthetic group of hemoglobin in blood. Heme has been noted to survive for many millions of years in fossils. Here, we investigate its stability and degradation under various conditions expected to occur during fossilization. Oxidative, reductive, aerobic, and anaerobic conditions were studied at neutral and alkaline pH values. Elevated temperatures were applied to accelerate degradation. High-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) identified four main degradation products. The vinyl residues are oxidized to formyl and further to carboxylate groups. In the presence of air or H2O2, cleavage of the tetrapyrrole ring occurs, and hematinic acid is formed. The highest stability of heme was observed under anaerobic reductive conditions (half-life 9.5 days), while the lowest stability was found in the presence of H2O2 (half-life 1 min). We confirmed that the iron cation plays a crucial role in degradation, since protoporphyrin IX, lacking iron, remained significantly more stable. Under anaerobic, reductive conditions, the above-mentioned degradation products were not observed, suggesting a different degradation pathway. To our knowledge, this is the first molecular taphonomy study on heme, which will be useful for understanding its fate during fossilization.

Chemistry and Analysis of Organic Compounds in Dinosaurs.

Simple SummaryFossils of dinosaurs other than birds are at least 66 million years old. Nevertheless, many organic compounds have survived fossilization and can still be found in the fossils. This article describes the discovery of organic molecules in dinosaur fossils. It provides a review of the analytical methods used for their detection and characterization, and presents the wide range of chemical organic compounds, including small molecules and polymers, that have been found in dinosaurs to date. The difficulties in unambiguously confirming the presence of some of the organic molecules in these fossils are also discussed. This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.

Identification of lanostanes, A-ring methylated steranes and secosteranes in late Neoproterozoic crude oils by GC×GC-TOFMS: New insights into molecular taphonomy of steroids

The late Neoproterozoic marine succession (Marwar Supergroup) deposited in the Bikaner-Nagaur Basin in western India is an excellent provenance to study steroid biomarkers. Traditional one-dimensional gas chromatography mass spectrometry (GC–MS) and metastable reaction monitoring (MRM) transitions have been previously employed for routine biomarker analyses of crude oils and sediments. The present study with GC×GC-TOFMS (time-of-flight mass spectrometer) demonstrates an improved distribution of the sterane compounds segregated from the co-eluting n-alkanes, cycloalkanes and triterpanes in terminal Proterozoic crude oils. The steranes identified here offer novel insights into the molecular taphonomic alteration of eukaryotic lipids during the late Neoproterozoic. The presence of lanostane and 3β alkyl steranes is probably indicative of a depositional environment stressed by high salinity. To the best of our knowledge, this is the oldest known record of lanostane steroids found in the geosphere. Secosteranes with an open C-ring form as a result of diagenetic cleaving of carbon–carbon bonds. The concomitant presence of 2α-, 3β - and 4α-methyl steranes (A-ring methylated steranes) reflects specific biological input and a distinct palaeo-depositonal environment. The 3β - and 2α-methyl steranes probably form by migration of methyl substituents within the steroid structure. The recognition of a diverse range of steroid compounds by GC×GC-TOFMS advocates its excellent analytical potential in the study of natural products in geological samples. Hence, this state-of-the-art technology will be worth using for re-evaluating and investigating hydrocarbon biomarkers in order to minimize the gaps that exist in the understanding of biotic evolution over geological time scales.

Molecular preservation in mammoth bone and variation based on burial environment

Biomolecules preserved in fossils are expanding our understanding of the biology and evolution of ancient animals. Molecular taphonomy seeks to understand how these biomolecules are preserved and how they can be interpreted. So far, few studies on molecular preservation have considered burial context to understand its impact on preservation or the potentially complementary information from multiple biomolecular classes. Here, we use mass spectrometry and other analytical techniques to detect the remains of proteins and lipids within intact fossil mammoth bones of different ages and varied depositional setting. By combining these approaches, we demonstrate that endogenous amino acids, amides and lipids can preserve well in fossil bone. Additionally, these techniques enable us to examine variation in preservation based on location within the bone, finding dense cortical bone better preserves biomolecules, both by slowing the rate of degradation and limiting the extent of exogenous contamination. Our dataset demonstrates that biomolecule loss begins early, is impacted by burial environment and temperature, and that both exogenous and endogenous molecular signals can be both present and informative in a single fossil.

Taphonomy: process and bias through time

1. Taphonomy: bias and process through time Peter A. Allison & David J. Bottjer 2. Taphonomic overprints on biodiversity: a database approach to the quantification of Phanerozoic trends Austin Hendy & Carl Brett 3. Taphonomy of shelly taxa through time: were aragonitic infauna selectively dissolved? V.Paul Wright & Lesley Cherns 4. Taphonomy of shelly taxa through time: shell durability in mixed carbonate/clastic sequences Carl E. Brett, Austin Hendy, Peter A. Allison 5. Taphonomy of animal organic skeletons though time Neal Gupta & D.E.G.Briggs 6. Molecular taphonomy of plant organic skeletons Margaret E. Collinson 7. The relationship between continental landscape evolution and the plant-fossil record: Long term hydrologic controls on preservation Robert A. Gastaldo & Timothy M. Demko 8. Hierarchical control of terrestrial vertebrate taphonomy over space and time: Discussion of mechanisms and implications for vertebrate paleobiology Christopher Noto 9. Taphonomy of carbonate microfacies through time James Nebelsick, Michael Rasser, & Davide Bassi 10. Taphonomy of reefs through time Rachel Wood 11. Silicification through time Susan Butts and D.E.G. Briggs 12. Phosphatization through the Phanerozoic Steve Dornbos 13. Three-dimensional morphological (CLSM) and chemical (Raman) imagery of cellularly mineralized fossils J. William Schopf, Abhishek B. Tripathi, & Anatoliy B. Kudryavtsev 14. Taphonomy in temporally unique settings: Precambrian Lagerstatte - out of this world? Nicola McLoughlin, David Wacey, & Martin Brasier 15. Taphonomy in temporally unique settings: the Ediacaran interval Jonathan Antcliffe, Richard Callow, & Martin Brasier 16. Mass extinctions and changing taphonomic processes Margaret L. Fraiser, Matthew Clapham, & David J, Bottjer

Chemometric analysis of functional groups in fossil remains of the Dicroidium flora (Cacheuta, Mendoza, Argentina): Implications for kerogen formation

Abstract Studied samples include eight Gondwanan species of the Dicroidium flora: seed ferns (3), conifer (1), cycad-related (1), unknown affinity gymnosperms (2), and one undetermined axis from two Middle to Upper Triassic localities (Cacheuta, Mendoza, central western Argentina). Based on differing preservation states and sample treatments, four sample forms are established: (1) compressions, (2) cuticles, (3) cuticle-free coalified layers, and (4) associated coal samples. The purpose of the study is firstly to analyze the sample forms using Fourier transform infrared (FTIR) spectrometry, contributing to filling an existing gap of chemical information for Gondwanan pant fossil remains. Secondly, semi-quantitative chemical parameters, calculated by area integration of infrared spectra, are treated using principal component analysis to infer statistical groupings as a function of chemical structures (functional groups). From the initial two-component solution, based on the 8 × 41 data matrix, a subset matrix (4 × 29) could be isolated which also yielded a two-component solution (in each case, cumulative explained variance is at least 89%). Results include the distinction between the coaly forms (1) compressions and (3) cuticle-free coalified layers mainly based on the carbonyl contents and branching and length of the hydrocarbon side chains. The highly aliphatic nature of cuticles, which is indicative of biomacromolecules (cutin), is noted. Similarities in functional groups are recorded with types of kerogen and coal macerals. The result enables us to postulate that the functional groups characterizing the different modes of preservation of our fossil remains are likely related to the propensity to generate oil and gas/condensate from the kerogen. Our data have the potential for future studies with implications for chemotaxonomy, molecular taphonomy, and paleoclimatology.

Macromolecular composition of Palaeozoic scolecodonts: insights into the molecular taphonomy of zoomorphs

Dutta, S., Hartkopf-Fröder, C., Mann, U., Wilkes, H., Brocke, R. & Bertram, N. 2010: Macromolecular composition of Palaeozoic scolecodonts: insights into the molecular taphonomy of zoomorphs. Lethaia, Vol. 43, pp. 334–343. Biogeochemistry and molecular taphonomy of biopolymers of marine zoomorphs are poorly known. In order to obtain insights into this issue we report on the biogeomacromolecular composition of hand-picked, well-preserved scolecodonts of Ordovician, Silurian and Devonian age using micro-Fourier transform infrared (micro-FTIR) spectroscopy, Curie point pyrolysis-gas chromatography-mass spectrometry (Cupy-GC-MS) and tetramethylammonium hydroxide (TMAH)-assisted thermochemolysis-GC-MS. The present study reveals that scolecodonts are composed of both aliphatic and aromatic moieties. The micro-FTIR spectra of scolecodonts are characterized by aliphatic CHx (3000–2800 and 1460–1450/cm) and CH3 (1375/cm) absorptions and aromatic C=C (1560–1610/cm) and CH (3050/cm and 700–900/cm) absorptions. The major pyrolysis products from the scolecodonts include aromatic hydrocarbons such as alkylbenzenes, alkylnaphthalenes and alkylphenols. Aliphatic hydrocarbons are represented by a homologous series of n-alkenes and n-alkanes. The compounds released upon thermochemolysis with TMAH are saturated and unsaturated fatty acids (as their methyl esters), n-alkenes/alkanes and aromatic acids (as their methyl esters). No protein/amino acid-derived compounds have been recognized in the pyrolysates or in the thermochemolysates, and it is concluded that protein/amino acid-related compounds, which are commonly found in the jaws of extant polychaetes, were destroyed due to diagenetic processes. Obviously, excellent morphological preservation and low thermal alteration are not paralleled by a similar degree of chemical preservation. □Biogeomacromolecules, micro-FTIR, pyrolysis-GC-MS, scolecodonts, thermochemolysis-GC-MS.

Molecular taphonomy of macrofossils from the Cretaceous Las Hoyas Formation, Spain

Macromolecular analysis of fossil fish scales from the Cretaceous Las Hoyas Formation (using pyrolysis-gas chromatography-mass spectrometry) revealed a dominant aliphatic composition (C 8 to C 22) whereas modern fish scale is proteinaceous (largely collagenous). Structural analysis of the aliphatic polymer using thermochemolysis revealed the importance of ester linkages; saturated fatty acids C 14 to C 18 (particularly C 16) are the most abundant. These acid components and their unsaturated counterparts are evident in the lipid composition of modern fish scales. Thus, the aliphatic composition of the fossil scales is probably a result of the incorporation of lipids (including a C 19 aromatic hydrocarbon) from the original indicating preservation by in situ polymerization of labile aliphatic components. Fossil arthropods and plants from the same deposit also show a dominant aliphatic macromolecular component, likely derived predominantly by crosslinking of free lipid precursors. Differences in the relative distribution of molecular components indicate likely chemosystematic differences between different fossil groups.

Molecular Taphonomy of Metasequoia

Abstract Chemical analysis of the leaves of modern Metasequoia and other gymnosperms revealed the presence of structural polyesters, guaiacyl lignin units and polysaccharides, but no long chain recalcitrant aliphatic constituent. Analysis of Tertiary fossil Metasequoia showed the presence of polysaccharides, lignin and a long chain aliphatic polymer. Tertiary fossil conifers similarly revealed the preservation of lignin and a long chain aliphatic polymer (up to C33) with limited preservation of polysaccharides. Experimental maturation of modern pine needles generated a composition with a long chain aliphatic polymer and additional phenolic compounds similar to those seen in the fossils. Experimental maturation of the structural polyester cutin and a pure model C16 and C18 fatty acid mixture yielded fatty acids and an aliphatic polymer less than C20 suggesting that polymers greater than C20 may be incorporated into the fossil macromolecule from longer-chain plant waxes. Thermochemolysis of the fossil conif...

Molecular preservation of plant and insect cuticles from the Oligocene Enspel Formation, Germany: Evidence against derivation of aliphatic polymer from sediment

The 25 Ma lacustrine deposit of Enspel, Germany, is important for molecular taphonomy as weevils from this site have yielded the oldest preserved traces of chitin. These weevil cuticles show excellent morphological and ultrastructural preservation. Plant cuticle is also preserved but it is obscured or distorted by diatom impressions. Molecular analysis of dicotyledonous angiosperm leaf from the Enspel deposit revealed the presence of polysaccharide, guaiacyl and syringyl related lignin, and possibly degraded protein moieties in the insoluble macromolecular component. Analysis of fossil conifer leaf showed the same moieties, but syringyl related lignin units were absent. Py-GC/MS revealed C 9–33 n-alkyl components from both types of leaf, with C 13,14,29 homologues being the most abundant n-alkanes. TMAH pyrolysis yielded a fatty acid distribution ranging in carbon number from C 6–30, with the C 16,18,14 components being the most abundant. Analysis of fossil weevil cuticle also revealed the presence of an aliphatic polymer as evidenced by C 9–33 n-alkyl components in the pyrolysate and C 6–26 FAMEs (predominantly even-numbered C 14−18 components) in the TMAH pyrolysate. Pyrolysates of the sediments contain alkanes with distributions similar to those observed in the fossils; however, TMAH pyrolysates of sediments were distinct from those of the fossils with C 20–22 components being the most abundant in the conifer-bearing sediment and the even-numbered C 22–26 components dominating in the weevil-bearing sediment. Thus, the aliphatic polymers in the fossils and sediment are different, apparently comprised of moieties of different chain length. This suggests that the aliphatic polymer in the plant and insect fossils is not derived from migration from the organic-rich host sediment.

Molecular taphonomy of animal and plant cuticles: selective preservation and diagenesis

The nature of organic material and the environment in which it is deposited exert a major influence on the extent to which biomacromolecules are preserved in the fossil record. The role of these factors is explored with a particular focus on the cuticle of arthropods and leaves. Preservation of the original chemistry of arthropod cuticles is favoured by their thickness and degree of sclerotization, and the presence of biominerals. Decay and burial in terrestrial as opposed to marine, and anoxic rather than oxygenated conditions, likewise appear to enhance preservation. The most important factor in the long–term preservation of the chemistry of both animal and plant cuticles, however, is diagenetic alteration to an aliphatic composition. This occurs even in amber, which encapsulates the fossil, eliminating almost all external factors. Some plants contain an original decay–resistant macromolecular aliphatic component but this is not the case in arthropods. It appears that the aliphatic components of many plant as well as animal fossils may be the result of diagenetic polymerization. Selective preservation as a result of decay resistance may explain the initial survival of organic materials in sediments, but in many cases longer–term preservation relies on chemical changes. Selective preservation is only a partial explanation for the origin of kerogen.

Molecular taphonomy of arthropod and plant cuticles from the Carboniferous of North America: implications for the origin of kerogen

Analyses of identifiable organic fossil remains of animals and plants have considerable potential to resolve conflicting models of organic matter diagenesis and kerogen formation (e.g. selective preservation versus random polymerization). Fossil cuticles of arthropods (scorpion, eurypterid) and plants (cordaite, pteridosperm) from Upper Carboniferous strata of Lone Star Lake, Kansas, USA and Joggins, Nova Scotia, Canada were analysed by pyrolysis–gas chromatography/mass spectrometry and examined by electron microscopy. Recent Pandinus (scorpion) and Araucaria (conifer) provided a basis for comparison. Pyrolysis of Recent dewaxed scorpion cuticle yielded products derived from chitin and proteins. These products were absent in the fossil arthropod cuticles, however, which yielded an homologous series of alkanes and alkenes, together with phenolic and other aromatic constituents. Recent dewaxed plant cuticle yielded fatty acids, phenols and carbohydrate-derived compounds indicative of cutin polyester and associated lignocellulose. The pyrolysates of the fossil plant cuticles, on the other hand, were dominated by alkane–alkene doublets, with minor phenolic and other benzenoid components. There is no evidence that the preservation of these cuticles as particulate organic matter in kerogen is simply a result of selective preservation. Nonetheless, the chemistry and morphology remain characteristic of a particular taxon, thereby eliminating the possibility of incorporation of randomly repolymerized materials or the transfer of material between plant and animal residues. The aliphatic moieties in the fossil cuticles are thought to be the result of polymerization of the associated epicuticular, cuticular and/or tissue lipids during diagenesis.

Ancient dna from pleistocene fossils: Preservation, recovery, and utility of ancient genetic information for quaternary research

Until recently, recovery and analysis of genetic information encoded in ancient DNA sequences from Pleistocene fossils were impossible. Recent advances in molecular biology offered technical tools to obtain ancient DNA sequences from well-preserved Quaternary fossils and opened the possibilities to directly study genetic changes in fossil species to address various biological and paleontological questions. Ancient DNA studies involving Pleistocene fossil material and ancient DNA degradation and preservation in Quaternary deposits are reviewed. The molecular technology applied to isolate, amplify, and sequence ancient DNA is also presented. Authentication of ancient DNA sequences and technical problems associated with modern and ancient DNA contamination are discussed. As illustrated in recent studies on ancient DNA from proboscideans, it is apparent that fossil DNA sequence data can shed light on many aspects of Quaternary research such as systematics and phylogeny. conservation biology, evolutionary theory, molecular taphonomy, and forensic sciences. Improvement of molecular techniques and a better understanding of DNA degradation during fossilization are likely to build on current strengths and to overcome existing problems, making fossil DNA data a unique source of information for Quaternary scientists.

Molecular taphonomy of membrane constituents the search for the most primitive membranes

Taphonomy is the study of fossilization processes, and includes "reconstruction" of past animals from their fossils. At the molecular level, the study of the organic constituents of sediments (crude oils and coals, but also clays, shales, etc) has yielded hundreds of structures, essentially in the hands of P.Albrecht and his co-workers in Strasbourg. These are sometimes hardly modified molecular fossils of known natural products. For instance, cholestane "must" come from cholesterol : reductions are frequent molecular taphonomic processes. Diacholestane, also frequently present in sediments, might be derived from "diasteror', an unknown but biosynthetically reasonable rearranged cholesterol ; however, the ease of rearrangement of cholesterol to diasterane derivatives by moderate heating with clays suggests rather that diacholestane derives also from cholesterol ; Wagner-Meerwein rearrangements are reasonable taphonomic processes. To interpret data from organic geochemistry, one must therefore collect trustworthy precise structural data, rely on the extensive catalogs of natural products structures and of biosynthetic process, and know which molecular taphonomic processes are plausible. Known molecular fossils belong to several natural products families, including porphyrins obviously derived from bacterial pigments ; by far most of them are derived from terpenoid precursors, as expected as biodegradation of highly branched structures is notoriously difficult. It was also not unexpected to find, frequently, molecular fossils of some arch~eal lipids : phytane and pristane, which could also have come from chlorophyll or from tocopherols, but also bisphytane, the structure of which became meaningful only once the C40 chains of phospholipid ethers of thermophilic and of methanogenic arch~ea became known. In other cases, while the structures of the precursors could be derived without doubt, they did not tally with any known one. The most spectacular case of these "orphan fossils" has been that of the ubiquitous geohopanoids, triterpene derivatives carrying an additional n-C 5 chain, for which more than 250 structures have been fully demonstrated ; their ubiquity and abundance in sediments make them probably the most abundant natural products on Earth ! Their precursors, the bacterial hopanoids, were discovered initially in two particular bacteria, but later, by M.Rohmer, in many very varied bacteria, with very varied structures (more than 40 established so far, including the fantastic adenosylhopane). Based on the molecular dimensions and amphiphilic character of bacterial hopanoids, we postulated that they reinforce bacterial membranes like

Molecular taphonomy of plant tissue at the Miocene Clarkia site, northern Idaho

The 17–20 million year old Miocene locality at Clarkia, northern Idaho, has become renowned as the first site to yield amplifiable DNA of geological age. This discovery has opened up the possibility of phylogenetic studies on fossil tissue using preserved DNA. However, the conditions required for DNA preservation in the fossil record are not understood. An organic geochemical study of fossil tissue and sediments has been undertaken at the Clarkia site to assess the preservation of other less labile compounds, such as leaf waxes, structural polysaccharides, cutins, lignins and chlorophyll pigments. Previous organic geochemical studies have developed an understanding of the behaviour of these compound classes in different environments. The relative behaviour of the compound classes and the preservation of individual compounds within each class can therefore help in the interpretation of the biogeochemistry of this site which may in turn shed light on the reported preservation of fossil DNA.Leaf waxes are preserved but a selective loss of long chain esters has occurred, and microbial degradation products of triterpenoids have been identified. Structural polysaccharides and cutins have been lost from the leaf tissues. A highly resistant aliphatic polymer is preserved in the mesophyll and epidermal regions of the leaves, with lignin identified in leaf vein tissues. Various degradation products of chlorophyll have also been identified. The organic geochemical results are all consistent with microbial degradation within the leaf tissues and sediment. Excellent morphological preservation is not accompanied by mutual chemical preservation. The survival of DNA in this environment is extremely surprising. However, preservation of plant polyphenols may provide an answer to this anomaly.