Experimentally observed soft‐tissue preservation near a marine brine seep

A sea urchin placed on the sea floor near an active brine seep was recovered after 13 years with detailed soft‐tissue preservation. Growth of an amorphous calcium carbonate solid with small amounts of the mineral bassanite occurred on the spines and test. The solid also exhibits striations at both the macro‐ and microscopic scales that preserve the muscle texture of the sea urchin. Such soft‐tissue replacement and mineralization could lead to exquisite fossilization. Soft‐tissue mineralization has been previously replicated in controlled laboratory conditions; however, this is the first report of the lithologic replication of soft tissues in an open marine experiment. Examples of extraordinary fossil preservation, or Lagersätten, give a distinct snapshot of the past and have led to a greater understanding of the history of life. Soft‐tissue lithification occurs in special circumstances in which local chemical conditions (often mediated by decay or bacterial factors) promote early diagenetic mineralization, the first steps of which are observed in this instance. The preservation of articulated skeletons, especially within echinoderms, is normally attributed to rapid burial, but that may not be necessary given that this urchin was at or very near the sediment–water interface for 13 years.     

Decaying in different clays: implications for soft‐tissue preservation

Lagerstätten, places where soft‐bodied organisms became mineralized, provide a substantial bulk of palaeobiological information, but the detailed mechanisms of how soft‐tissue preservation takes place remain debatable. An experimental taphonomy approach, which allows for direct study of decay and mineralization, offers a means to study the preservational potential of different soft‐bodied organisms under controlled conditions. Here we compare the preservational capacity of two types of clay (kaolinite and montmorillonite) through a long‐term (24 month) experiment involving the burial and decay of small crustaceans. Our experimental design is innovative in that it models catastrophic sedimentation in fine‐grained colloidal suspension, which is believed to form Lagerstätten deposits. We demonstrated better preservation of buried organisms in clays compared to water, and in kaolinite compared to montmorillonite. As aluminium cations were present in high concentrations in kaolinite sediment but not in montmorillonite, the better preservation in kaolinite is attributed to the tanning properties of aluminium, which catalyses cross‐linking in proteins, protecting them from bacterial degradation. Anaerobic environments and acidification also slow down decay, but they are less effective than tanning. Kaolinite and montmorillonite replaced the crustacean integuments differently: in the remains buried in kaolinite, Al and Si were detected in equal proportions, while in those buried in montmorillonite, the Si content appeared to be much higher even in comparison with the initial sample of the clay. These variations probably arose from the different dynamics of acidic hydrolysis in the two clays associated with anaerobic decomposition of organic matter. Our results show that the preservation mechanism includes multi‐component interactions between the solution, mineral, sediment and organic remains; taken separately, any single component explains little. The specific conditions that occur within the colloidal clay sediments can facilitate conservation and start fast mineralization according to chemical properties and elemental content.     

Soft‐Bodied Fossils Are Not Simply Rotten Carcasses – Toward a Holistic Understanding of Exceptional Fossil Preservation

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non‐biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay‐prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils.     

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.     

Taphonomic experiments imply a possible link between the evolution of multicellularity and the fossilization potential of soft‐bodied organisms

The reliability of evolutionary reconstructions based on the fossil record critically depends on our knowledge of the factors affecting the fossilization of soft‐bodied organisms. Despite considerable research effort, these factors are still poorly understood. In order to elucidate the main prerequisites for the preservation of soft‐bodied organisms, we conducted long‐term (1–5 years) taphonomic experiments with the model crustacean Artemia salina buried in five different sediments. The subsequent analysis of the carcasses and sediments revealed that, in our experimental settings, better preservation was associated with the fast deposition of aluminum and silicon on organic tissues. Other elements such as calcium, magnesium, and iron, which can also accumulate quickly on the carcasses, appear to be much less efficient in preventing decay. Next, we asked if the carcasses of uni‐ and multicellular organisms differ in their ability to accumulate aluminum ions on their surface. The experiments with the flagellate Euglena gracilis and the sponge Spongilla lacustris showed that aluminum ions are more readily deposited onto a multicellular body. This was further confirmed by the experiments with uni‐ and multicellular stages of the social ameba Dictyostelium discoideum. The results lead us to speculate that the evolution of cell adhesion molecules, which provide efficient cell–cell and cell–substrate binding, probably can explain the rich fossil record of soft‐bodied animals, the comparatively poor fossil record of nonskeletal unicellular eukaryotes, and the explosive emergence of the Cambrian diversity of soft‐bodied fossils.     

Photoperiodic induction of diapause: opening the black box

Abstract.  Over several decades, formal experiments measuring diapause responses to variable light inputs have indicated that photoperiodic time measurement in insects is accomplished either by a nonoscillatory 'hourglass-like' mechanism or by oscillatory components of the circadian system. Although both are possible given the present state of our knowledge, a substantial body of evidence strongly suggests that night-length measurement is a function of the circadian system, and that 'hourglass-like' clocks are manifestations of damping circadian components. The two types of time measurement, 'hourglass' and circadian, are therefore parts of a spectrum of mechanisms differing in their damping coefficients. If this view is correct, it may follow that genes and proteins involved in circadian timing are also involved in photoperiodism, although additional genes, or known 'clock' genes used in novel ways, may also play a part. This review outlines the experimental evidence for the oscillator clock theory of photoperiodism and suggests ways in which further progress may be made.     

Bayesian molecular dating: opening up the black box

Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a ‘molecular clock’. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the ‘black box’ of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales.     

Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization

Exceptionally preserved fossils provide major insights into the evolutionary history of life. Microbial activity is thought to play a pivotal role in both the decay of organisms and the preservation of soft tissue in the fossil record, though this has been the subject of very little experimental investigation. To remedy this, we undertook an experimental study of the decay of the brine shrimp Artemia, examining the roles of autolysis, microbial activity, oxygen diffusion and reducing conditions. Our findings indicate that endogenous gut bacteria are the main factor controlling decay. Following gut wall rupture, but prior to cuticle failure, gut-derived microbes spread into the body cavity, consuming tissues and forming biofilms capable of mediating authigenic mineralization, that pseudomorph tissues and structures such as limbs and the haemocoel. These observations explain patterns observed in exceptionally preserved fossil arthropods. For example, guts are preserved relatively frequently, while preservation of other internal anatomy is rare. They also suggest that gut-derived microbes play a key role in the preservation of internal anatomy and that differential preservation between exceptional deposits might be because of factors that control autolysis and microbial activity. The findings also suggest that the evolution of a through gut and its bacterial microflora increased the potential for exceptional fossil preservation in bilaterians, providing one explanation for the extreme rarity of internal preservation in those animals that lack a through gut.     

Fossilization processes of graptolites: insights from the experimental decay of Rhabdopleura sp. (Pterobranchia)

Laboratory experiments documenting the decomposition pattern of extant organisms are used to reconstruct the anatomy and taphonomy of fossil taxa. The subclass Graptolithina (Hemichordata: Pterobranchia) is a significant fossil taxon of the Palaeozoic era, represented by just one modern genus, Rhabdopleura. The rich graptolite fossil record is characterized by an almost total absence of fossil zooids. Here we investigated the temporal decay pattern of Rhabdopleura sp. tubes, stolons and single zooids removed from the tubarium. Tubes showed decay after four days, when fuselli began to separate from the tube walls. This rapid loss may explain the absence of fuselli from some graptolite fossils. The black stolon did not show decay until day 155. One day after their removal, zooids quickly decomposed in the following temporal sequence: (1) tentacles; (2) ectoderm; (3) arms; (4) gut; (5) cephalic shield, leading to complete disappearance of recognizable body parts in the majority of experimental zooids within 64–104 h. The most resistant zooid features to decay (61 days) were black‐pigmented granules. These results indicate that tubes and the black stolon would persist for weeks across death, transport and burial, whereas a complete decay of zooid features occurs in few days, providing an explanation for the overall poor record of fossil graptolite zooids and suggesting that recorded silhouettes of fossil zooids may be attributed to fossil decay‐resistant pigments.     

Unveiling biases in soft‐tissue phosphatization: extensive preservation of musculature in the Cretaceous (Cenomanian) polychaete Rollinschaeta myoplena (Annelida: Amphinomidae)

The process of soft‐tissue phosphatization (the replication of labile tissues by calcium phosphate) is responsible for many instances of high‐resolution soft tissue preservation, often revealing anatomical insights into the animals that so preserved. However, while much work has gone into exploring key issues such as biases and micro‐controls, phosphatization remains poorly understood as a taphonomic process. Here, using camera lucida, plain‐light microscopy and SEM imagery, we address this issue by describing the taphonomy and fidelity of the musculature of Rollinschaeta myoplena Parry et al., a phosphatized annelid from the Cretaceous Konservat‐Lagerstätten of Hakel and Hjoula, Lebanon, with an unprecedented quantity of three‐dimensional soft‐tissue preservation. Analysis highlights two strong, previously recognized biases affecting the process of phosphatization: (1) a taxonomic bias restricted to R. myoplena that triggers unusually extensive phosphatization; and (2) a tissue bias whereby longitudinal and parapodial musculature show markedly higher fidelity in comparison to the musculature of the intestine and body wall circular muscles. Potential explanations for these biases include internal phosphate‐enrichment by relative muscle density, the relative rate of decay and the physiology of musculature. Incongruence between experimental decay series for polychaetes and the prevalence of labile tissue preservation over recalcitrant tissues in R. myoplena exposes the limits of decay experiments for understanding exceptional preservation.     

Experimental fossilization of the Thermophilic Gram-positive Bacterium Geobacillus SP7A: A Long Duration Preservation Study

Recent experiments to fossilize microorganisms using silica have shown that the fossilization process is far more complex than originally thought; microorganisms not only play an active role in silica precipitation but may also remain alive while silica is precipitating on their cell wall. To better understand the mechanisms that lead to the preservation of fossilized microbes in recent and ancient rocks, we experimentally silicified a Gram-positive bacterium, Geobacillus SP7A, over a period of five years. The microbial response to experimental fossilization was monitored with the use of LIVE/DEAD staining to assess the structural integrity of the cells during fossilization. It documented the crucial role of silicification on the preservation of the cells and of their structural integrity after several years. Electron microscopy observations showed that initial fossilization of Gram-positive bacteria was extremely rapid, thus allowing very good preservation of Geobacillus SP7A cells. A thick layer of silica was deposited on the outer surface of cell walls in the earliest phase of silicification before invading the cytoplasmic space. Eventually, the cell wall was the only recognizable feature. Heavily mineralized cells thus showed morphological similarities with natural microfossils found in the rock record.     

Opening the black box: an open‐source release of Maxent

This software note announces a new open‐source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. The new release (ver. 3.4.0) will be hosted online by the American Museum of Natural History, along with future versions. It contains small functional changes, most notably use of a complementary log‐log (cloglog) transform to produce an estimate of occurrence probability. The cloglog transform derives from the recently‐published interpretation of Maxent as an inhomogeneous Poisson process (IPP), giving it a stronger theoretical justification than the logistic transform which it replaces by default. In addition, the new R package, maxnet, fits Maxent models using the glmnet package for regularized generalized linear models. We discuss the implications of the IPP formulation in terms of model inputs and outputs, treating occurrence records as points rather than grid cells and interpreting the exponential Maxent model (raw output) as as an estimate of relative abundance. With these two open‐source developments, we invite others to freely use and contribute to the software.     

Life history in a model system: opening the black box with Arabidopsis thaliana

A broad research programme in Arabidopsis thaliana has provided estimates of selection on specific alleles in specific contexts, and identified geographic patterns of alleles in genes linked to timing of flowering. A closely related field has successfully captured many key axes of the evolution of timing of flowering in other monocarpic species through statistical and demographic modelling of large empirical databases. There has as yet been no synthesis between these two fields. Here we examine ways in which the two fields inform each other, and how this synergy will shape our knowledge of life-history evolution as a whole.     

Experimental investigation of insect deposition in lentic environments and implications for formation of Konservat Lagerstätten

Terrestrial insects are often remarkably well preserved in lacustrine Konservat Lagerstätten. However, the assumption that carcasses should sink fast through the water column seems contradictory as this scenario is unlikely due to excessive buoyancy and surface tension. The mechanisms that promote rapid and permanent emplacement onto the sediment surface (RPESS) of such terrestrial animal remains are not fully understood. Here we use taphonomic experiments to show that floating in water, growth of microbial biofilms and reception of rapid sediment load promote RPESS of terrestrial insect remains in lentic water bodies. Our results show that the optimum conditions for RPESS occur when terrestrial insects enter a lentic water body in articulation, experience brief decay in association with growth of microbes, then are buried rapidly by airborne volcanic ash. These results provide a model for preservation of articulated terrestrial insects and emphasize the importance of microbial activity and volcanism for insect preservation in lacustrine Konservat Lagerstätten.     

A rare non‐trilobite artiopodan from the Guzhangian (Cambrian Series 3) Weeks Formation Konservat‐Lagerstätte in Utah,USA

We describe a weakly biomineralized non‐trilobite artiopodan arthropod from the Guzhangian Weeks Formation of Utah. Falcatamacaris bellua gen. et sp. nov. is typified by a thin calcitic cuticle, broad cephalon without eyes or dorsal ecdysial sutures, an elongate trunk with distinctively sickle‐shaped pleural spines and a long tailspine with a bifurcate termination. The precise affinities of Falcatamacaris gen. nov. are problematic due to the presence of unique features within Artiopoda, such as the peculiar morphology of the pleural and posterior regions of the trunk. Possible affinities with aglaspidid‐like arthropods and concilitergans are discussed based on the possession of 11 trunk tergites, edge‐to‐edge articulations and overall body spinosity. The new taxon highlights the importance of the Weeks Formation Konservat‐Lagerstätte for further understanding the diversity of extinct arthropod groups in the upper Cambrian.     

Gene expression profiling: opening the black box of plant ecosystem responses to global change

The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Because the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical, and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and nonmodel species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.     

Synchrotron analysis of a ‘mummified’ salamander (Vertebrata: Caudata) from the Eocene of Quercy,France

An incomplete ‘mummy’ from the Phosphorites du Quercy (presumed Eocene) was identified as a salamander during the 19^th century. The specimen has now been computed tomography (CT) scanned, and this revealed the incomplete skeleton (with perfectly preserved bones) and soft tissues (lung). The fossil represents a new, well‐characterized taxon. Despite the absence of the skull, several features allow a phylogenetic analysis. The fossil belongs to pseudosaurian caudates; it is tentatively assigned to the Salamandridae, although affinities with Plethodontidae cannot be definitely ruled out.     

Anoxia can increase the rate of decay for cnidarian tissue: Using Actinia equina to understand the early fossil record

An experimental decay methodology is developed for a cnidarian model organism to serve as a comparison to the many previous such studies on bilaterians. This allows an examination of inherent bias against the fossilisation of cnidarian tissue and their diagnostic characters, under what conditions these occur, and in what way. The decay sequence of Actinia equina was examined under a series of controlled conditions. These experiments show that cnidarian decay begins with an initial rupturing of the epidermis, followed by rapid loss of recognisable internal morphological characters. This suggests that bacteria work quicker on the epidermis than autolysis does on the internal anatomy. The data also show that diploblastic tissue is not universally decayed more slowly under anoxic or reducing conditions than under oxic conditions. Indeed, some cnidarian characters decay more rapidly under anoxic conditions than they do under oxic conditions. This suggests the decay pathways acting may be different to those affecting soft bilaterian tissue such as soft epidermis and internal organs. What is most important in the decay of soft polyp anatomy is the microbial community, which can be dominated by oxic or anoxic bacteria. Different Lagerstätte, even of the same type, will inevitably have subtle difference in their bacterial communities, which among other factors, could be a control on soft polyp preservation leading to either an absence of compelling soft anthozoans (Burgess Shale) or an astonishing abundance (Qingjiang biota).     

SOFT‐MI: A novel microfabrication technique integrating soft‐lithography and molecular imprinting for tissue engineering applications

An innovative approach has been employed for the realization of bioactive scaffolds able to mimic the in vivo cellular microenvironment for tissue engineering applications. This method is based on the combination of molecular imprinting and soft‐lithography technology to enhance cellular adhesion and to guide cell growth and proliferation due to presence of highly specific recognition sites of selected biomolecules on a well‐defined polymeric microstructure. In this article polymethylmethacrylate (PMMA) scaffolds have been realized by using poly(dimethylsiloxane) (PDMS) microstructured molds imprinted with FITC‐albumin and TRITC‐lectin. In addition gelatin, an adhesion protein, was employed for the molecular imprinting of polymeric scaffolds for cellular tests. The most innovative aspect of this research was the molecular imprinting of whole cells for the development of substrates able to enhance the cell adhesion processes. Biotechnol. Bioeng. 2010;106: 804–817. © 2010 Wiley Periodicals, Inc.