Biomacromolecules of Algae and Plants and their Fossil Analogues

A review of our current understanding of resistant biomacromolecules derived from present and past algae and higher plants is presented. Insight in the nature of recent and fossil macromolecules is strongly hampered by the difficulties in obtaining the material in pure and unaltered form. For the extant material, avoiding artificial condensation and structural alteration as a result of chemical isolation and purification of biomacromolecules requires constant attention. To date, several types of sporopollenin seem to occur. One type is characterised by oxygenated aromatic building blocks, in particular p-coumaric acid and ferrulic acid. The other type is thought to consist predominantly of an aliphatic biopolymer. In this review it is concluded that extant sporopollenin consists of the aromatic type, whereas the aliphatic component of fossil sporopollenin is due to early-diagenetic oxidative polymerization of unsaturated lipids. The cuticles of most higher plants contain the aliphatic biopolyester cutin. Additionally, cuticles of drought-adapted, mostly CAM plants, seem to contain the non-hydrolysable aliphatic biopolymer cutan. Only a very few algae are able to biosynthesize resistant, (fossilisable) cell walls: some Chlorophyta, Eustigmatophyta and Prasinophyta produce the aliphatic biopolymer algaenan. Some Dinophyta are also capable of producing algaenan cell walls. Additionally, some taxa produce highly resistant cyst-walls with a high proportion of aromatic moieties. For the morphologically well-preserved fossil material, contamination by organic particles other than the target taxon is hard to eliminate and can contribute to either the aliphatic or aromatic signal. Furthermore, post-mortem migration of aliphatic moieties into, and their condensation onto the macromolecule might occur, e.g. by oxidative polymerization. These phenomena hamper the evaluation of the aliphatic signature of fossil plant material and may for example explain the preservation of initially cutin-based cuticles or non-algaenan containing algae. The extent to which migration and in situ formation of aromatic moieties plays a role in modifying resistant algal macromolecules, notably under elevated temperature and/or pressure conditions, still remains an open question.     

The organic preservation of fossil arthropods: an experimental study

Modern arthropod cuticles consist of chitin fibres in a protein matrix, but those of fossil arthropods with an organic exoskeleton, particularly older than Tertiary, contain a dominant aliphatic component. This apparent contradiction was examined by subjecting modern cockroach, scorpion and shrimp cuticle to artificial maturation (350 degrees C/700 bars/24 h) following various chemical treatments, and analysing the products with pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). Analysis of artificially matured untreated cuticle yielded moieties related to phenols and alkylated substituents, pyridines, pyrroles and possibly indenes (derived from chitin). n-Alkyl amides, C16 and C18 fatty acids and alkane/alk-1-ene homologues ranging from C9 to C19 were also generated, the last indicating the presence of an n-alkyl component, similar in composition to that encountered in fossil arthropods. Similar pyrolysates were obtained from matured pure C16 and C18 fatty acids. Py-GC/MS of cuticles matured after lipid extraction and hydrolysis did not yield any aliphatic polymer. This provides direct experimental evidence that lipids incorporated from the cuticle were the source of aliphatic polymer. This process of in situ polymerization appears to account for most of the fossil record of terrestrial arthropods as well as marine arthropods that lacked a biomineralized exoskeleton.     

Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians

The Ediacaran Doushantuo biota has yielded fossils that include the oldest widely accepted record of the animal evolutionary lineage, as well as specimens with alleged bilaterian affinity. However, these systematic interpretations are contingent on the presence of key biological structures that have been reinterpreted by some workers as artefacts of diagenetic mineralization. On the basis of chemistry and crystallographic fabric, we characterize and discriminate phases of mineralization that reflect: (i) replication of original biological structure, and (ii) void-filling diagenetic mineralization. The results indicate that all fossils from the Doushantuo assemblage preserve a complex mélange of mineral phases, even where subcellular anatomy appears to be preserved. The findings allow these phases to be distinguished in more controversial fossils, facilitating a critical re-evaluation of the Doushantuo fossil assemblage and its implications as an archive of Ediacaran animal diversity. We find that putative subcellular structures exhibit fabrics consistent with preservation of original morphology. Cells in later developmental stages are not in original configuration and are therefore uninformative concerning gastrulation. Key structures used to identify Doushantuo bilaterians can be dismissed as late diagenetic artefacts. Therefore, when diagenetic mineralization is considered, there is no convincing evidence for bilaterians in the Doushantuo assemblage.     

Interpreting ‘shelly’ fossils preserved as organic films: the case of hyolithids

Most studies of Burgess Shale‐type preservation have focussed on soft‐bodied organisms, but ‘shelly’ fossils are also preserved as carbonaceous films. These films are usually interpreted as coherent organic layers – often external sheaths or periostracal layers – that were present in the original mineralized elements. The example of hyolithids shows that the organic films of skeletal parts do not represent original ‘layers’, but a composite resulting from the coalescence, into a single carbonaceous film, of all the preservable organic matter present in the skeletal element. The diagenetic processes that led to Burgess Shale‐type preservation, which involve the polymerization of organic matter and the loss of original internal structure and chemical integrity of the original tissues, are entirely compatible with – and could account for – the characteristics observed in the fossil films of hyolithid skeletal elements. These observations have general implications for the interpretation of other organisms preserved as carbonaceous films, such as the diverse and often problematic Cambrian sponges.     

Preservation of hypericin and related polycyclic quinone pigments in fossil crinoids

The fringelite pigments, a group ofphenanthroperylene quinones discovered in purple coloured specimens of the Upper Jurassic crinoid Liliocrinus, demonstrate exceptional preservation of organic compounds in macrofossils. Here we report the finding of hypericin and related phenanthroperylene quinones in Liliocrinus munsterianus from the original 'Fringeli' locality and in the Middle Triassic crinoid Carnallicrinus carnalli. Our results show that fringelites in fact consist ofhypericin and closely related derivatives and that the stratigraphic range of phenanthroperylene quinones is much wider than previously known. The fossil occurrence of hypericin indicates a polyketide biosynthesis of hypericin-type pigments in Mesozoic crinoids analogous to similar polyketides, which occur in living crinoids. The common presence of a characteristic distribution pattern of the fossil pigments and related polycyclic aromatic hydrocarbons further suggests that this assemblage is the result of a stepwise degradation of hypericin via a general diagenetic pathway.     

Vibrational spectroscopy of fossils

Over the last two decades, there has an been increasing interest in applying vibrational spectroscopy in palaeontological research. For example, this chemical analytical technique has been used to elucidate the chemical composition of a wide variety of fossils, including Archaean putative microfossils, stromatolites, chitinozoans, acritarchs, fossil algae, fossil plant cuticles, putative fossil arthropods, conodonts, scolecodonts and dinosaur bones. The insights provided by these data have been equally far ranging: to taxonomically identify a fossil, to determine biogenicity of a putative fossil, to identify preserved biologically synthesized compounds and to elucidate the preservational mechanisms of fossil material. Vibrational spectroscopy has clearly been a useful tool for investigating various palaeontological problems. However, it is also a tool that has been misapplied and misinterpreted, and thus, this review is dedicated to providing a palaeontologist who is new to vibrational spectroscopy with a basic understanding of these techniques, and the types of chemical information that can be obtained. Two example applications of these techniques are discussed in detail, one looking into fossil palynomorph taxonomy and other into the enigmatic Burgess Shale‐type preservation.     

Chemical preservation of tail feathers from Anchiornis huxleyi,a theropod dinosaur from the Tiaojishan Formation (Upper Jurassic,China)

A panel of geochemical techniques is used here to investigate the taphonomy of fossil feathers preserved in association with the skeleton of the Jurassic theropod Anchiornis huxleyi. Extant feathers were analysed in parallel to test whether the soft tissues morphologically preserved in the fossil also exhibit a high degree of chemical preservation. Scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) indicate that clays and iron oxide pseudomorphs occur in the surrounding sediment and also reveal the preservation of melanosome-like microbodies in the fossil. Carbon gradient along a depth profile and co-occurrence of carbon and sulphur are shown in the fossil by elastic backscattering (EBS) and particle-induced x-ray emission (PIXE), which are promising techniques for the elemental analysis of fossil soft tissues. The molecular composition of modern and fossil soft tissues was assessed from micro-attenuated total reflectance fourier transform infrared spectroscopy (micro-ATR FTIR), solid-state ¹³C nuclear magnetic resonance (CP-MAS ¹³C NMR) and pyrolysis gas chromatography mass spectrometry in the presence of TMAH (TMAH-Py-GC-MS). Results indicate that the proteinaceous material that comprises the modern feathers is not present in the fossil feathers. The fossil feathers and the embedding sediment exhibit a highly aliphatic character. However, substantial differences exist between these samples, revealing that the organic matter of the fossil feathers is, at least partially, derived from original constituents of the feathers. Our results suggest that, despite the morphological preservation of Anchiornis feathers, original proteins, that is keratin, were probably not preserved in the 160-myr-old feathers.     

The taphonomy of colour in fossil insects and feathers

Colouration is an important multifunctional attribute of modern animals, but its evolutionary history is poorly resolved, in part because of our limited ability to recognize and interpret fossil evidence of colour. Recent studies on structural and pigmentary colours in fossil insects and feathers have illuminated important aspects of the anatomy, taphonomy, evolution and function of colour in these fossils. An understanding of the taphonomic factors that control the preservation of colour is key to assessing the fidelity with which original colours are preserved and can constrain interpretations of the visual appearance of fossil insects and theropods. Various analytical approaches can identify anatomical and chemical evidence of colour in fossils; experimental taphonomic studies inform on how colour alters during diagenesis. Preservation of colour is controlled by a suite of factors, the most important of which relate to the diagenetic history of the host sediment, that is, maximum burial temperatures and fluid flow, and subsurface weathering. Future studies focussing on key morphological and chemical aspects of colour preservation relating to cuticular pigments in insects and keratinous structures and nonmelanin pigments in feathers, for example, will resolve outstanding questions regarding the taphonomy of colour and will enhance our ability to infer original colouration and its functions in fossil insects and theropods.     

Exceptional fossil preservation and the cambrian explosion

Exceptionally preserved, non-biomineralizing fossils contributeimportantly to resolving details of the Cambrian explosion,but little to its overall patterns. Six distinct "types" ofexceptional preservation are identified for the terminal Proterozoic-Cambrianinterval, each of which is dependent on particular taphonomiccircumstances, typically restricted both in space and time.Taphonomic pathways yielding exceptional preservation were particularlyvariable through the Proterozoic-Cambrian transition, at leastin part a consequence of contemporaneous evolutionary innovations.Combined with the reasonably continuous record of "Doushantuo-typepreservation," and the fundamentally more robust records ofshelly fossils, phytoplankton cysts and trace fossils, thesetaphonomic perturbations contribute to the documentation ofmajor evolutionary and biogeochemical shifts through the terminalProterozoic and early Cambrian. Appreciation of the relationship between taphonomic pathwayand fossil expression serves as a useful tool for interpretingexceptionally preserved, often problematic, early Cambrian fossils.In shale facies, for example, flattened non-biomineralizingstructures typically represent the remains of degradation-resistantacellular and extracellular "tissues" such as chaetae and cuticles,whereas three-dimensional preservation represents labile cellulartissues with a propensity for attracting and precipitating earlydiagenetic minerals. Such distinction helps to identify theacuticular integument of hyolithids, the chaetae-like natureof Wiwaxia sclerites, the chaetognath-like integument of Amiskwia,the midgut glands of various Burgess Shale arthropods, and themisidentification of deposit-feeding arthropods in the Chengjiangbiota. By the same reasoning, putative lobopods in the SiriusPasset biota and putative deuterostomes in the Chengiang biotaare better interpreted as arthropods.     

Primary and diagenetic microstructures in trilobites

McAllister, John E. & Brand, Uwe 1989 01 15: Primary and diagenetic microstructures in trilobites. Lethaia , Vol. 22, pp. 101–111. Oslo. ISSN 0024–1164.
Ordovician and Devonian trilobites were studied by scanning electron microscopy (SEM) to define primary and diagenetic microstructures. Primary structures such as Osmólska cavities and hexagonal surface openings are present in samples obtained from both shale and limestone lenses in shales. Generally, samples with primary microstructures are also geochemically well preserved. Diagenetic microstructures were found in samples from shales and limestones, but those from limestones are the most geochemically and microstructurally altered. 'Dendritic' patterns and fused matrices were found in the altered cuticles of trilobites of different species and ages and are therefore considered a normal feature of the diagenetic alteration of cuticular calcite. Primary and diagenetic microstructures of trilobite cuticles are independent of size, species and age of the specimens, but are largely controlled by lithology and thus diagenesis. * Trilobita, primary-, diagenetic microstructures, fossil diagenesis .     

Lognormal distribution of water permeability and organic solute mobility in plant cuticles

It is shown that water permeabilities and organic solute mobilities in plant cuticles have a lognormal distribution. Seven-hundred and fifty values for rate constants of desorption (～mobility) of 2,4-D from isolated Citrus aurantium L. cuticles from a population of leaves were pooled and analysed. A histogram of the rate constants of individual cuticles showed a skew distribution with a strong tail to higher values. Cuticular membranes with high values did not differ from others in visual appearance and were not leaky. After log-transformation of original data an almost perfect normal distribution was obtained. Statistical tests showed that a normal distribution of original values is not acceptable. Inspection of older data for water permeability in the same species and experiments using large samples of cuticles from leaves of Pyrus communis L. and Stephanotis floribunda Brongn. and from fruits of Capsicum annuum L. showed a similar distribution, as did inspection of data for experiments with organic solutes. A lognormal distribution was found for cuticles of plants from growth chambers, glasshouses and outdoors as well as for water permeability of intact leaves of Hedera helix L. For small samples the overestimation from using the arithmetic mean of original data can be high, but use of the geometric mean or the median leads to smaller deviations. Removing cuticular waxes from cuticles produced normally distributed samples. A normal distribution was also obtained when organic compounds which increase solute mobility were sorbed into cuticles.     

Chemical taphonomy of biomineralized tissues

Biomineralized tissues are chemically altered after death, and this diagenetic alteration can obscure original biological chemical features or provide new chemical information about the depositional environment. To use the chemistry of fossil biominerals to reconstruct biological, environmental or taphonomic information, a solid appreciation of biomineralization, mineral diagenesis and biomineral–water interaction is needed. Here, I summarize the key recent developments in the fields of biomineralization and post‐mortem trace element exchange that have significant implications for our understanding of the diagenetic behaviour of biominerals and the ways in which biomineral chemistry can be used in palaeontological and taphonomic research.     

Fossilization of melanosomes via sulfurization

Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur‐bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur‐rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py‐GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF‐SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non‐sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur‐rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.     

Chemical evidence of preserved collagen in 54-million-year-old fish vertebrae

Collagens are the most abundant proteins in the animal kingdom. They form the structural framework of connective tissues such as bones, tendons and skin, and play important biomechanical role in supporting tissue functions. The preservation of collagen in deep time is a topic of intense debate. Here we provide indisputable evidence for the presence of collagen in early Eocene fish vertebrae using online pyrolysis comprehensive two dimensional gas chromatography time-of-flight mass spectrometry (py-GC×GC-TOFMS) and immunofluorescence analysis. The presence of cyclic dipeptides such as diketodipyrrole, 2,5-diketopiperazine of proline-proline and 2,5-diketopiperazine of proline-glycine along with other nitrogen-bearing molecules in the pyrolysis products of the studied fossils unequivocally demonstrate that collagen can withstand degradation and diagenetic alteration. Immunofluorescence study also confirms the presence of collagen-I in the fossilized fish vertebrae. Contrary to common opinion, the present findings suggest that the preservation of collagen in fossilized soft tissues is not rare. We propose that one of the essential factors controlling preservation of collagen is the establishment of a suitable microenvironment within the fossil, inhibiting diagenetic alteration including microbial decay.     

Plant/animal interactions during the upper carboniferous

This paper discusses evidence for plant/animal relationships in the Upper Carboniferous. Close interactions are examined from the study of fossil plants and animals preserved in coal swamp and coastal plain environments. Evidence for plant/animal interactions is in the form of: (1) animal morphology, including both vertebrates and invertebrates. The vertebrates are dominated by amphibians; however, a few reptiles are known and are mostly carnivores or insectivores. The invertebrate communities are dominated by arthropods, many of which are herbivores. Millipedes, springtails and mites are present on the forest floor and in peats, with insects dominating above ground environments. The diets of the animals have been studied using evidence from gut contents, coprolites, anatomy and comparisons to modern representatives. (2) Plant morphology, including positive stimulation (i.e., dispersal vectors) or in terms of negative stimulation such as protection against herbivory. These data include plant anatomy and morphology, evidence of herbivory in the form of chewed leaves, bored seeds and megaspores, etc. Evidence is provided that suggests that the medullosan seed fern pollen typeMonoletes may have been dispersed by animal vectors. Information on plant/animal relationships in a single environment is based on a study of coprolites extracted from permineralizations (coal balls). Assemblages of coprolites found in these coal balls suggest that they were formed principally from mites, Collembola and millipedes, and demonstrates that the association of soil arthropods, which is important in modern soil ecosystems, was already dominating similar environments in the late Carboniferous. The abundant fossil evidence for plant/animal interrelationships during the Upper Carboniferous should be evaluated when considering co-evolution.     

Taphonomic experiments resolve controls on the preservation of melanosomes and keratinous tissues in feathers

Fossils are a key source of data on the evolution of feather structure and function through deep time, but their ability to resolve macroevolutionary questions is compromised by an incomplete understanding of their taphonomy. Critically, the relative preservation potential of two key feather components, melanosomes and keratinous tissue, is not fully resolved. Recent studies suggesting that melanosomes are preferentially preserved conflict with observations that melanosomes preserve in fossil feathers as external moulds in an organic matrix. To date, there is no model to explain the latter mode of melanosome preservation. We addressed these issues by degrading feathers in systematic taphonomic experiments incorporating decay, maturation and oxidation in isolation and combination. Our results reveal that the production of mouldic melanosomes requires interactions with an oxidant and is most likely to occur prior to substantial maturation. This constrains the taphonomic conditions under which melanosomes are likely to be fossilized. Critically, our experiments also confirm that keratinous feather structures have a higher preservation potential than melanosomes under a range of diagenetic conditions, supporting hitherto controversial hypotheses that fossil feathers can retain degraded keratinous structures.     

The cuticle of the enigmatic arthropod Phytophilaspis and biomineralization in Cambrian arthropods

Lin, J.‐P., Ivantsov, A.Y. & Briggs, D.E.G. 2011: The cuticle of the enigmatic arthropod Phytophilaspis and biomineralization in Cambrian arthropods. Lethaia, Vol. 44, pp. 344–349. Many non‐trilobite arthropods occur in Cambrian Burgess Shale‐type (BST) biotas, but most of these are preserved in fine‐grained siliciclastics. Only one important occurrence of Cambrian non‐trilobite arthropods, the Sinsk biota (lower Sinsk Formation, Botomian) from the Siberian Platform, has been discovered in carbonates. The chemical compositions of samples of the enigmatic arthropod Phytophilaspis pergamena Ivantsov, 1999 and the co‐occurring trilobite Jakutus primigenius Ivantsov in Ponomarenko, 2005 from this deposit were analysed. The cuticle of P. pergamena is composed of mainly calcium phosphate and differs from the cuticle of J. primigenius, which contains only calcium carbonate. Phosphatized cuticles are rare among large Cambrian arthropods, except for aglaspidids and a few trilobites. Based on recent phylogenetic studies, phosphatization of arthropod cuticle is likely to have evolved several times. □arthropod cuticle, Burgess Shale‐type preservation, fossil‐diagenesis, phosphatization.     

Secular distribution of Burgess-Shale-type preservation

Burgess-Shale-type preservation is defined as a taphonomic pathway involving the exceptional organic preservation of non-mineralizing organisms in fully marine siliciclastic sediments. In the Phanerozoic it occurs widely in Lower and Middle Cambrian sequences but subsequently disappears as a significant taphonomic mode. The hypothesis that this distribution derives solely from a secular increase in the depth of bioturbation is falsified: low bioturbation indices do not prevent the rapid enzymatic degradation of organic structure, nor do they account for the conspicuous absence of comparable preservation during the Vendian. An earlier, Late Riphean (ca. 750–850 Ma), interval of enhanced organic-walled fossil preservation suggests a long-term recurrence in Burgess-Shale-type taphonomy that is independent of metazoan activity. A model based on the potentially powerful anti-enzymatic and/or stabilizing effects of clay minerals on organic molecules is proposed to account for Burgess-Shale-type preservation. Long-term changes in average clay mineralogies and the ocean chemistry that determines their interaction with organic molecules are likely to have induced the pronounced secular distribution of these fossil biotas, while regional variations in tectonism, weathering, etc., explain their non-uniform geographic distribution; the close correlation between exceptional, organic-walled fossil preservation and volcano-genic sedimentation in Tertiary lake deposits provides a compelling analogue. Recognition of a temporal control on Burgess-Shale-type preservation constrains the evolutionary scenarios that can be drawn from such biotas; significantly, neither the initial rate of appearance, nor the ultimate fate of Burgess-Shale-type taxa can be directly assessed. □ Taphonomy, exceptional preservation, organic preservation, fossil Lagerstätten, Burgess Shale, clay mineralogy, clay-organic interactions, secular change, Cambrian, Proterozoic.     

Taphonomie des plantes et interprétations paléoécologiques. Une synthèse

The taphonomy is a powerful and requisite tool for environmental reconstructions of ancient plant communities. Necrobiotic processes, which lead to the production of plant fragments, inform us on fossil plant physiology. Among the processes that can be drawn from necrobiotic studies is the retention of leaf organs on plants, the relative quantity of pollen grains produced by different fossil species or the significance of wildfire dynamics in ancient plant communities. Biostratinomy examination is a fundamental tool for elucidating fossil plant habitats. Numerous experimental data allow paleobotanists for evaluating the role of transport in the origin of fossil assemblages. Autochthonous plant assemblages, which are characterised by the preservation of fossil rooting structures, are relatively rare in the nature. In consequence, the search for palaeoecological information from parautochthonous to allochthonous assemblages has been a priority in taphonomy. As a result, taphonomic models have been elaborated in well-known sedimentological contexts, such as small lacustrine deltas, which allow for the distinction between riparian or perideltaic plant remains. Lithospheric processes modify plant debris after burial. The differences in the degrees of transformations (or alterations) during the diagenesis provide for information about the original morphology and biochemical composition of the plant tissues, which are also paleoecologically useful. Thus, amber diagenesis modifies resin biochemistry into new molecules that are still informative from the chemotaxonomical point of view.