Experimental Decay of Soft Tissues !

—The exceptionally preserved fossil record of soft tissues sheds light on a wide range of evolutionary episodes from across geological history. Understanding how soft tissues become hard fossils is not a trivial process. A powerful tool in this context is experimentally derived decay data. By studying decay in a laboratory setting and on a laboratory timescale, an understanding of the processes and patterns underlying soft-tissue preservation can be achieved. The considerations and problems particular to experimental decay are explored here in terms of experimental aims, design, variables, and utility. Aims in this context can relate to either reconstruction of the processes of soft-tissue preservation, or to elucidation of the patterns of morphological transformation and data loss occurring during decay. Experimental design is discussed in terms of hypotheses and relevant variables: i.e., the subject organism being decayed (phylogeny, ontogeny, and history), the environment of decay (biological, chemical, and physical) and the outputs (how to measure decay). Variables and practical considerations are illustrated with reference to previous experiments. The principles behind application of experimentally derived decay data to the fossil record are illustrated with three case studies: the interpretation of fossil color, feasibility of fossil embryos, and phylogenetic bias in chordate preservation. A rich array of possibilities for further decay experiments exists and it is hoped that the methodologies outlined herein will provide guidance and a conceptual framework for future studies. 
 INTRODUCTION ! Fossils are old. At first, it would seem that they are so old that researchers would have no hope of experimentally investigating the patterns and processes of fossilization. After all, research proposals for projects on the scale of millions of years are unlikely to be awarded funding. Fossilization, however, is not a linear process with respect to time. The majority of anatomical change and loss occurs in the early stages in the formation of a fossil, after which little change generally takes place. These early stages can be experimentally investigated on a laboratory timescale ranging from hours to months. This is especially relevant to the exceptionally preserved soft-tissue fossil record. Non-biomineralized tissues such as cuticle, muscles, and nerves are lost to decay relatively quickly following death and as such, the soft anatomy of an organism is locked in a post-mortem race between decay and fossilization (Briggs, 1995). In those rare instances that preservation wins, the spectacular fossils that result shed unique and powerful light on a wide range of evolutionary events ranging from the Cambrian explosion of animal life to the origin of bird flight in dinosaurs (Briggs et al., 1994). Soft tissues, however, are extremely labile. They are never preserved as an accurate facsimile of the original organism’s in-vivo anatomy in the way that skeletons can be; instead, they have been distorted and changed by the processes of decay and loss that are intrinsic to their fossilization. To make sense of exceptionally preserved fossil soft tissues, we need an understanding of the processes that led to their formation and how the data they provide might have been transformed by their formation. In fact, it is difficult to interpret this class of fossils without experimentally derived data. This review will discuss how experimental taphonomy aims to unlock both the processes and patterns of decay, i.e., the processes that make it possible for soft tissues to become part of the fossil record and the patterns of data loss and transformation that can occur during fossilization. The nature of experimental design and the multitudinous variables involved in taphonomic experiments are also addressed. Finally, examples are used to illustrate how the findings of taphonomic experiments can be applied to paleontological data, and in some instances, transform our interpretation of fossils. In: Reading and Writing of the Fossil Record: Preservational Pathways to Exceptional Fossilization. The Paleontological Society Papers, Volume 20, Marc Laflamme, James D. Schiffbauer, and Simon A. F. Darroch (eds.). The Paleontological Society Short Course, October 18, 2014. Copyright © 2014 The Paleontological Society. THE PALEONTOLOGICAL SOCIETY PAPERS, V. 20 AIMS: PATTERN AND PROCESS ! All experiments, taphonomic or otherwise, require a clear understanding of how their design and results will address the aim of the experiment. The aims of experimental taphonomy can be loosely classified as relating to either the processes or the patterns of decay and fossilization, both described below. Questions of process concern the mechanisms by which soft tissues are preserved and become part of the fossil record. Questions of pattern aim to identify the sequences of loss and transformation of tissues and morphology that occur during decay. With respect to processes, two main pathways have been described for the mechanisms of preservation: organic preservation and authigenic microbially mediated preservation (Briggs, 2003). Organic preservation occurs when decay has been sufficiently retarded to allow the original organic b i o m o l e c u l e s o f t h e o r g a n i s m ( e . g . , macromolecules, lipids, proteins) to be preserved (Briggs et al., 2000; Briggs, 2003). This kind of preservation can be enhanced by particular kinds of subsequent diagenesis (Butterfield, 2003; Page et al., 2008). Biomolecules will be transformed during the fossilization process, and this transformation can be investigated experimentally. For example, maturation experiments demonstrate fossil arthropod cuticle is more similar in terms of aliphatic composition to decayed or matured arthropod chitin than to fresh chitin (Gupta et al., 2006; Gupta and Summons, 2011). Because organic preservation essentially requires retardation of decay, it can be experimentally investigated through identification and/or manipulation of the factors that affect rates of tissue decomposition. Anaerobic conditions and rapid burial are often cited as requisites for o r g a n i c p r e s e r v a t i o n a n d h a v e b e e n experimentally tested in this context (Allison, 1988, 2001; Briggs and Kear, 1993a). The second pathway, microbially mediated mineralization, is in some respects diametrically opposed to organic preservation. While organic preservation requires retardation of decay and preservation of the original biomolecules, authigenic mineralization relies on the fast action of microbes actively decaying structures to leave a characteristic c h e m i c a l s i g n a t u r e , b e t h a t t h r o u g h phosphatization, pyritization, or some other mechanism (Briggs, 2003). It has been demonstrated that this kind of mineralization can be induced in a lab setting on laboratory time scale; Briggs and Kear (1993b, 1994a) and Hof and Briggs (1997) were able to create conditions for calcium phosphate to form during the decay of crustaceans—in effect, a step towards creation of artificial fossils in the lab. Similar experiments also demonstrate the feasibility of mineralization of embryos (Raff et al., 2006; Hippler et al., 2012). Not only do experiments such as these enable identification of the conditions necessary for mineralization, but they can also unlock the nature of the specific mechanisms involved. For example, Raff et al. (2008) characterized the bacterial communities that comprise fossil forming biofilms, while Sageman et al. (1999) characterized the chemical microenvironments that are conducive to soft-tissue preservation. Consideration of the factors affecting rates of decay are therefore imperative to understanding both the mechanisms of organic preservation and authigenic mineralization. A complementary aim to unlocking processes of preservation is the reconstruction of patterns of transformation and loss of data during that preservation process. In some ways, these aims are related, but they are considered here as addressing different methodological questions. Reconstructing taphonomic processes generally concerns chemical changes, while reconstructing patterns of morphological changes requires knowledge of anatomical changes. Patterns of morphological transformation during decay can take place on a macro-scale of whole individuals, through the sub-cellular or organelle level. For example, McNamara et al. (2013a) demonstrated that melanosomes (pigment organelles) are transformed during maturation in terms of their geometry, which has ramif icat ions for interpretations of fossil color. At another sizelevel up, transformation of the morphology of giant bacteria and metazoan embryos during decay has been used to frame interpretations of fossils of disputed affinity (Raff et al., 2006; Cunningham et al., 2012a, b). At the level of body structures, Briggs and Kear (1994b) related the series of morphological changes taking place during decay in the muscle arrangement of amphioxus in relation to the muscle arrangement of fossil conodonts, while Sansom et al. (2013) reconstructed sequences of transformation of vertebrate anatomical complexes, such as feeding apparatus, appendages, skull, etc. At the level of whole animals , t ransformat ions in the arrangement of bodies during decay can shed light on fossil interpretations; e.g., decay of modern