The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic “nematophytes” have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert.

Abstract The ichnogenus Psilonichnus Fürsich, 1981 is recorded for the first time from the Mississippian (Brigantian regional substage) limestones of the Slievenaglasha Formation from the west coast of County Clare, Ireland. This record extends the known range of Psilonichnus which has previously been recorded from rocks of Jurassic or younger age. The trace maker of the burrows described herein has not been preserved and remains unknown; however, the ichnogenus Psilonichnus is generally ascribed to the burrowing activities of decapod crustaceans such as crabs or shrimp. Decapods from the Paleozoic are poorly known and assigning the traces to a maker must be treated with caution. However, this record indicates that burrowing organisms using a similar life strategy to modern decapods were established by Brigantian times. These examples are assigned to the Glossifungites ichnofacies, as they occur on an omission surface in a shallow marine carbonate firmground. The burrows were subsequently infilled with deposits of possible storm origin. Glacioeustatic sea-level fluctuation related to the onset of the Late Paleozoic Ice Age is a common feature of Carboniferous sedimentary successions at this level, and the Irish (Mississippian) Psilonichnus horizon occurs just below a significant regional sequence boundary at the top of the Slievenaglasha Formation.

Rainfall events can stimulate carbon dioxide (CO2) emissions (i.e. the Birch Effect). However, the contribution of wetting-induced CO2 emissions to annual C emissions remains largely unquantified, as does the impact of different rainfall amounts/wetting intensities, particularly at the field scale. In this study, the short-term impact of simulated rainfall amounts (equivalent to 1, 2, 5, 10, 15, 20 and 25 mm h−1) on soil CO2 emissions from a coastal grassland ecosystem were investigated for summer and autumn periods and the results used to assess their impact on annual CO2 emissions. Wetting intensities >2 mm h−1 resulted in greater CO2 emissions (P < 0.05) than smaller wetting intensities (1 and 2 mm h−1). For wetting intensities >2 mm h−1, cumulative CO2 emissions were largely independent of wetting intensity. Significant inverse correlations between cumulative CO2 emissions and soil moisture content prior to water addition (InitSWC) were shown for all wetting intensities. A significant inverse relationship was also shown when all data were combined (r2 = 0.37, P < 0.001), although a better fit (r2 = 0.68, P < 0.001) was obtained when wetting intensities <2 mm h−1 were omitted. This indicates that factors associated with soil drying prior to water addition have the major impact on CO2 emissions, particularly at greater wetting intensities. Using the relationship between CO2 emissions and initial soil water content, together with in situ soil moisture and rainfall measurements, episodic wetting events were estimated to potentially increase the annual C emissions budget by up to 14%, although this will be critically dependent on the extent of soil drying and the frequency of any rainfall events associated with periods of low soil water content.

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.

Pterosaurs were the first vertebrates to achieve true flapping flight, but in the absence of living representatives, many questions concerning their biology and lifestyle remain unresolved. Pycnofibres-the integumentary coverings of pterosaurs-are particularly enigmatic: although many reconstructions depict fur-like coverings composed of pycnofibres, their affinities and function are not fully understood. Here, we report the preservation in two anurognathid pterosaur specimens of morphologically diverse pycnofibres that show diagnostic features of feathers, including non-vaned grouped filaments and bilaterally branched filaments, hitherto considered unique to maniraptoran dinosaurs, and preserved melanosomes with diverse geometries. These findings could imply that feathers had deep evolutionary origins in ancestral archosaurs, or that these structures arose independently in pterosaurs. The presence of feather-like structures suggests that anurognathids, and potentially other pterosaurs, possessed a dense filamentous covering that probably functioned in thermoregulation, tactile sensing, signalling and aerodynamics.

Feathers are remarkable evolutionary innovations that are associated with complex adaptations of the skin in modern birds. Fossilised feathers in non-avian dinosaurs and basal birds provide insights into feather evolution, but how associated integumentary adaptations evolved is unclear. Here we report the discovery of fossil skin, preserved with remarkable nanoscale fidelity, in three non-avian maniraptoran dinosaurs and a basal bird from the Cretaceous Jehol biota (China). The skin comprises patches of desquamating epidermal corneocytes that preserve a cytoskeletal array of helically coiled α-keratin tonofibrils. This structure confirms that basal birds and non-avian dinosaurs shed small epidermal flakes as in modern mammals and birds, but structural differences imply that these Cretaceous taxa had lower body heat production than modern birds. Feathered epidermis acquired many, but not all, anatomically modern attributes close to the base of the Maniraptora by the Middle Jurassic.

The soft tissues of many fossil vertebrates preserve evidence of melanosomes-micron-scale organelles that inform on integumentary coloration and communication strategies. In extant vertebrates, however, melanosomes also occur in internal tissues. Hence, fossil melanosomes may not derive solely from the integument and its appendages. Here, by analyzing extant and fossil frogs, we show that non-integumentary melanosomes have high fossilization potential, vastly outnumber those from the skin, and potentially dominate the melanosome films preserved in some fossil vertebrates. Our decay experiments show that non-integumentary melanosomes usually remain in situ provided that carcasses are undisturbed. Micron-scale study of fossils, however, demonstrates that non-integumentary melanosomes can redistribute through parts of the body if carcasses are disturbed by currents. Collectively, these data indicate that fossil melanosomes do not always relate to integumentary coloration. Integumentary and non-integumentary melanosomes can be discriminated using melanosome geometry and distribution. This is essential to accurate reconstructions of the integumentary colours of fossil vertebrates.

Given their increasing trend in Europe, an understanding of the role that flooding events play in carbon (C) and nitrogen (N) cycling and greenhouse gas (GHG) emissions will be important for improved assessments of local and regional GHG budgets. This study presents the results of an analysis of the CO2 and N2O fluxes from a coastal grassland ecosystem affected by episodic flooding that was of either a relatively short (SFS) or long (LFS) duration. Compared to the SFS, the annual CO2 and N2O emissions were 1.4 and 1.3 times higher at the LFS, respectively. Mean CO2 emissions during the period of standing water were 144 ± 18.18 and 111 ± 9.51 mg CO2–C m−2 h−1, respectively, for the LFS and SFS sites. During the growing season, when there was no standing water, the CO2 emissions were significantly larger from the LFS (244 ± 24.88 mg CO2–C m−2 h−1) than the SFS (183 ± 14.90 mg CO2–C m−2 h−1). Fluxes of N2O ranged from −0.37 to 0.65 mg N2O–N m−2 h−1 at the LFS and from −0.50 to 0.55 mg N2O–N m−2 h−1 at the SFS, with the larger emissions associated with the presence of standing water at the LFS but during the growing season at the SFS. Overall, soil temperature and moisture were identified as the main drivers of the seasonal changes in CO2 fluxes, but neither adequately explained the variations in N2O fluxes. Analysis of total C, N, microbial biomass and Q10 values indicated that the higher CO2 emissions from the LFS were linked to the flooding-associated influx of nutrients and alterations in soil microbial populations. These results demonstrate that annual CO2 and N2O emissions can be higher in longer-term flooded sites that receive significant amounts of nutrients, although this may depend on the restriction of diffusional limitations due to the presence of standing water to periods of the year when the potential for gaseous emissions are low.

Abstract. Given their increasing trend in Europe, an understanding of the role that flooding events play in carbon and nitrogen cycling and greenhouse gas (GHG) emissions will be important for improved assessments of local and regional GHG budgets. This study presents the results of an analysis of the CO2 and N2O fluxes from a coastal grassland ecosystem affected by episodic flooding that was of either a relatively short or long duration (SFS and LFS sites, respectively). Compared to the SFS, the annual CO2 and N2O emissions were 1.4 and 1.3 times higher at the LFS, respectively. Mean CO2 emissions during the period of standing water were 144 ± 18.18 and 111 ± 9.51 mg CO2-C m−2 h−1, respectively, for the LFS and SFS sites. During the growing season, when there was no standing water, the CO2 emissions were significantly larger from the LFS (244 ± 24.88 mg CO2-C m−2 h−1) than the SFS (183 ± 14.90 mg CO2-C m−2 h−1). Fluxes of N2O ranged from −0.37 to 0.65 mg N2O-N m−2 h−1 at the LFS and from −0.50 to 0.55 mg N2O-N m−2 h−1 at the SFS, with the larger emissions associated with the presence of standing water at the LFS and during the growing season at the SFS. Overall, soil temperature and moisture content were identified as the main drivers of the seasonal changes in CO2 fluxes, but neither adequately explained the variations in N2O fluxes. Analysis of total Carbon (C), Nitrogen (N), microbial biomass and Q10 values, indicated that the higher CO2 emissions from the LFS were linked to the flooding-associated influx of nutrients and alterations in soil microbial populations. These results demonstrate that annual CO2 and N2O emissions can be higher in longer-term flooded sites that receive significant amounts of nutrients and where diffusional limitations due to the presence of standing water is limited to periods of the year when the temperatures are lowest.

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

Few fossil vertebrate skeletons are complete and fully articulated. Various taphonomic processes reduce the skeletal fidelity of decaying carcasses, the effects of most of which are reasonably well understood. Some fossil vertebrates, however, exhibit patterns of disarticulation and loss of completeness that are difficult to explain. Such skeletons are one of two variants. They are incomplete, often markedly so, but the preserved parts are highly articulated. Alternatively, they are complete, or nearly so, but articulation varies markedly between parts of the body. A characteristic feature is the absence of skeletal elements that, on the basis of their larger size and/or greater density, would be predicted to be present. Here we erect a model, termed “stick ‘n’ peel”, that explains how these distinctive patterns originate. The model emphasizes the role of decay products, especially fluids released from the carcass while resting on the sediment surface. These fluids permeate the sediment below and around the carcass. As a result, skeletal elements on the downward facing side of the carcass become adhered to the sediment surface, and are less likely to be remobilized as a result of current activity than others. The pattern of articulation and, especially, completeness is thus not what would be predicted on the basis of the size, shape and density of the skeletal elements. The effects of stick ‘n’ peel are difficult to predict a priori. Stick ‘n’ peel has been identified in vertebrate fossils in lacustrine and marine settings and is likely to be a common feature of the taphonomic history of many vertebrate assemblages. Specimens becoming adhered to the substrate may also explain the preservation in situ of the multi-element skeletons of invertebrates such as echinoderms, and integumentary structures such as hair and feathers in exceptionally preserved fossils.

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.

Evidence of original coloration in fossils provides insights into the visual communication strategies used by ancient animals and the functional evolution of coloration over time [1-7]. Hitherto, all reconstructions of the colors of reptile integument and the plumage of fossil birds and feathered dinosaurs have been of melanin-based coloration [1-6]. Extant animals also use other mechanisms for producing color [8], but these have not been identified in fossils. Here we report the first examples of carotenoid-based coloration in the fossil record, and of structural coloration in fossil integument. The fossil skin, from a 10 million-year-old colubrid snake from the Late Miocene Libros Lagerstätte (Teruel, Spain) [9, 10], preserves dermal pigment cells (chromatophores)-xanthophores, iridophores, and melanophores-in calcium phosphate. Comparison with chromatophore abundance and position in extant reptiles [11-15] indicates that the fossil snake was pale-colored in ventral regions; dorsal and lateral regions were green with brown-black and yellow-green transverse blotches. Such coloration most likely functioned in substrate matching and intraspecific signaling. Skin replicated in authigenic minerals is not uncommon in exceptionally preserved fossils [16, 17], and dermal pigment cells generate coloration in numerous reptile, amphibian, and fish taxa today [18]. Our discovery thus represents a new means by which to reconstruct the original coloration of exceptionally preserved fossil vertebrates.

The Lujiatun Unit (Yixian Formation) yields some of the most spectacular vertebrate fossils of the Jehol Group (Lower Cretaceous) of NE China. Specimens are preserved both articulated and three-dimensional, unlike the majority of Jehol fossils, which are near two-dimensional compression fossils. The site has been referred to as the ‘Chinese Pompeii’ because the dinosaurs and other animals were assumed to have been killed and buried by hot, airborne volcanic debris and ash in a single event; this has yet to be confirmed. Field and laboratory evidence for the sedimentological context of the fossils from the Lujiatun Unit is described in detail, and used to assess whether the fossil remains correspond to a single depositional event and whether this event was the direct result of volcanic activity. Fossils of the Lujiatun Unit occur in several horizons of volcaniclastic sediments that represent multiple depositional events. Petrological analysis shows that the fossil-bearing sediments were remobilised and deposited by water. The Lujiatun dinosaurs and other fossils were therefore not killed by a single airborne volcanic ash, but in multiple flood events with a high load of volcaniclastic debris.

The fossil record of nonbiomineralized chordates is surprisingly extensive. As with most exceptionally preserved fossils, key anatomical features in non-biomineralized chordate fossils are often preserved in less than pristine condition, and potentially only a subset of those originally present. How taphonomic processes impacted on the anatomy of fossils can be constrained by experimental decay of extant analogues. We experimentally decayed tadpoles of Xenopus laevis to document the rate at which various nonbiomineralized tissues degrade and identify changes over time in their ultrastructure. Tissues decayed under identical conditions and sampled at the same time often differed in the level of ultrastructural detail. This is termed an inconsistent pattern of decay and introduces unpredictable taphonomic noise to any dataset. We integrated these results with data from anuran tadpole fossils from the Miocene of Spain and confirm that the nerve cord is less decay resistant than the notochord. Only the notochord is likely to be preserved organically. The nerve cord is only likely to be preserved if replicated in authigenic minerals (calcium phosphate). This is more likely than for other extremely decay-prone tissues, a result of the nerve cord's chemistry in vivo. Two tissues of similar recalcitrance do not, therefore, have equal fossilization potential. On the basis of the experimental and fossil data, structures preserved in amphibians from the Permian Saar-Nahe Basin of Germany are interpreted as fossilized nerve cords, not notochords.

Biases in preservation shape the fossil record, and therefore impact on our reconstructions of past environments and biodiversity. Given the intensive recent research in the general fields of taphonomy and exceptional preservation, surprisingly, fundamental questions remain unanswered about species-level variation in skeletal preservation potential at low taxonomic levels (e.g. between genera from the same family, or between taxa from related families) across myriad groups with multi-element skeletons. Polyplacophoran molluscs (chitons sensu lato) are known from the late Cambrian to Recent, and possess a distinctive articulated scleritome consisting of eight overlapping calcareous valves. The apparent uniformity of living chitons presents an ideal model to test the potential for taphonomic biases at the alpha-taxon level. The vast majority of fossil chitons are preserved as single valves; few exhibit body preservation or even an articulated shell series. An experimental taphonomic programme was conducted using the Recent polyplacophorans Lepidochitona cinerea and Tonicella marmorea (suborder Chitonina) and Acanthochitona crinita (Acanthochitonina). Experiments in a rock tumbler on disarticulated valves found differential resistance to abrasion between taxa; in one experiment 53.8–61.5% of Lepidochitona valves were recovered but 92% of those from Tonicella and 100% of elements from Acanthochitona. Chiton valves and even partly decayed carcasses are more resistant to transportation than their limited fossil record implies. Different species of living chitons have distinctly different preservation potential. This, problematically, does not correlate with obvious differences in gross valve morphology; some, but not all, of the differences correlate with phylogeny. Decay alone is sufficient to exacerbate differences in preservation potential of multi-element skeletons; some, but not all, of the variation that results is due to specimen size and the fidelity of the fossil record will thus vary intra-specifically (e.g. between ontogenetic stages) as well as inter-specifically.

Exceptional biotas—those in which the non-biomineralized tissues of organisms are preserved—are an important record of the evolutionary biology of the late Neoproterozoic—early Phanerozoic interval. Most of these biotas exhibit one of four modes of preservation: preservation of either 1) internal and external detail (Doushantuo-type preservation) or, 2) external cuticles (Orsten-type preservation) in calcium phosphate; 3) coating in pyrite films and infills (Beecher's Bed-type preservation); and 4) preservation of organic remains (Burgess Shale-type preservation). The global environmental and temporal distribution of each mode of preservation is reasonably well constrained, but not why these taphonomic windows existed when they did. The late Neoproterozoic – early Phanerozoic interval is characterized by complex, interlinked, physical, geochemical and biological changes to the Earth's biosphere and geosphere. The changing ecology of marine environments (from matground to mixgrounds: the ‘Agronomic Revolution’) occurred via an intermediate phase of stiffened, but not microbially bound sediments that extended the interval over which exceptional preservation occurred. Prolonged eustatic sea-level rise across flat-lying continental platforms ensured environments conducive to exceptional preservation were developed and, critically, sustained over large contiguous areas. During this, regolith on continental surfaces was recycled, providing an integral source of sediment and ions relevant to mineral authigenesis. Superimposed on these broad-scale changes are specific drivers that controlled the duration of individual taphonomic windows; elucidating these requires a better understanding of the environmental context and diagenetic history of fossiliferous successions at the intra-basinal scale.

Nature's most spectacular colours originate in integumentary tissue architectures that scatter light via nanoscale modulations of the refractive index. The most intricate biophotonic nanostructures are three-dimensional crystals with opal, single diamond or single gyroid lattices. Despite intense interest in their optical and structural properties, the evolution of such nanostructures is poorly understood, due in part to a lack of data from the fossil record. Here, we report preservation of single diamond (Fd-3m) three-dimensional photonic crystals in scales of a 735,000 year old specimen of the brown Nearctic weevil Hypera diversipunctata from Gold Run, Canada, and in extant conspecifics. The preserved red to green structural colours exhibit near-field brilliancy yet are inconspicuous from afar; they most likely had cryptic functions in substrate matching. The discovery of pristine fossil examples indicates that the fossil record is likely to yield further data on the evolution of three-dimensional photonic nanostructures and their biological functions.