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Laboratory I

Fossils and Their Preservation

Objective: The objective of this lab is to understand the processes that preserve organisms in the fossil record, and to appreciate the biological information that can be garnered from fossils. You will also learn the major types of preservation. Since some information is always lost during preservation, you should think particularly about what each type of preservation tells us about the once-living organism.

The fate of most organic material produced by living systems is to be decomposed to carbon dioxide and water, and recycled into the biosphere. The circulation of elements through biogeochemical cycles indicates that decomposition is, indeed, efficient; however the presence of organic material in sedimentary rocks (e.g., coal, petroleum, dispersed organic matter, and fossils) shows that some organic matter-or its traces-escapes these cycles to be preserved in the rock record. Paleontology relies on this preserved material-fossils-as evidence of past life. In the early history of modern paleontology, fossils were thought of mostly as static parts of the rock record. This fostered description and classification as the main activities of scientific paleontologists. However, a shift in emphasis to thinking of fossils as "once-living organisms" gave paleontology a more biological flair and, more importantly, opened a new world of research questions. Today, well-trained paleontologists will have extensive backgrounds in both the geological and biological sciences.

Organisms become fossilized in a variety of ways. Each type of preservation carries different information about the once-living organism. Thus, an appreciation of fossils requires that one understand the processes of fossilization, and how each type of preservation may influence our view of the organism that produced the fossil.

The study of how organisms or their parts become fossils is called taphonomy. Taphonomy is literally everything that happens to an organism-or part of an organism-from the moment that it dies or is shed until it is collected and curated for scientific study. Figure 1.1 illustrates some of the many taphonomic pathways an organism may take from its living community to the museum drawer.

Fossil preservation can take place at a number of levels. Each level contains a different type of information.

Microstructural or Cellular Level Not all organic compounds are equally resistant to chemical degradation and decay. The mineral component of shells and bones easily resists bacterial degradation. (Remember that bone and shell are composite materials made up of both mineral and organic components. Each component may behave differently in a given preservational environment.) Plant cell walls (cellulose and lignin) are far more likely to escape decomposition than are internal membranes and organelles, which are rich in protein, lipids and sugars. Preservation of cytological details has been reported in fossil plants, vertebrate bone and some microorganisms, but occurrences are rare, and most reports of fossilized nuclei and organelles should be read with caution. Secondary compounds, such as those impregnating or covering cells, can also be resistant to decomposition; examples include waxes, cutin (which comprises plant cuticle), chitin in arthropods and fungi, and sporopollenin (which forms the external shell of spores, pollen, and the resting cysts of some marine algae).

Diagram - Taphonomy

Figure 1.1: Some of the many possible fates of organisms and their parts as they enter the fossil record.

Tissue Level Decay-resistant materials are distributed differentially throughout the bodies of organisms. Consequently, some tissues are more amenable to preservation in the fossil record than others. The microscopic shells of pollen and spores are the most common of all fossils. Their abundance is due first to sporopollenin from which they are constructed, and second to the abundance with which plants produce them. The calcite or aragonite shells of invertebrates are the next most commonly preserved fossils. Teeth are the most commonly preserved tissues in vertebrates, with bone coming in a distant second. It is unusual, but not impossible, for soft tissue (muscle, connective tissue, skin etc.) to be preserved. However, when these tissues are preserved, they can lead to quantum leaps in our understanding of ancient organisms.

Organ Level Some organisms tend to break apart, both in life (organ senescence or dispersal in the case of plants) and after death (vertebrate bones are particularly vulnerable to being scattered if not buried immediately; clam valves commonly separate after death); dispersed parts may be transported before settling into the sediment to be buried and become fossils. Assemblages of fossils that are preserved close to where the organism originally lived are called autochthonous ; assemblages that have been transported are referred to as allochthonous . Whether an assemblage is autochthonous or transported has obvious implications for what sorts of ecological interpretations we can make from it.

Organism Level Not all organisms in a given community are equally likely to find their way into the fossil record. Processes of fossilization often favor large parts (the bones of large dinosaurs rather than those of a shrew; limb bones rather than ribs) or parts composed of resistant materials (wood rather than flowers; mineral rather than chitinous shells). Also, organisms that live and die in sites with conditions favorable for preservation are more commonly preserved than are their counterparts growing far from water, anoxic environments, or active sedimentation.

The differential hydrodynamic properties of plant or animal parts can lead to segregation of different parts in the fossil record. For example, waves or currents may winnow small, light shells from a death assemblage, leaving behind only large, clunky shells

Environmental Level Fossil preservation depends on removing the organism from the zone of aerobic decomposition or physical destruction. This is most easily accomplished by burial. Consequently, sediment-rich coastal areas, epicontinental seas, swamps, deltas, lakes, lowland flood plains, and volcanic areas are good spots for fossilization. Arid regions and mountainsides are not likely candidates for fossil preservation (with the exception of exquisitely preserved plant material from Pleistocene packrat middens and mummified animals remains in the southwestern United States). Because some environments are more amenable to fossil preservation, the fossil record gives paleontologists a selective at past environments.

All of these taphonomic factors influence the information that can be recovered from the fossil record. While taphonomic filtering does not preclude biological interpretation of fossils, taphonomy can introduce substantial biases into the record and influence our interpretation of the fossils, and thus our reconstruction of the organisms. It is, therefore, important always to keep in mind the mode of preservation when drawing any interpretations from fossils 1 .

Conditions Required for Plant Fossil Preservation

Three conditions are required for the preservation of plant fossils: 1) Removing the material from oxygen-rich environment of aerobic decay; 2) Introducing the fossil to the sedimentary rock record (a.k.a., burial); and 3) "Fixing" the organic material to retard anaerobic decay, oxidation or other physical or chemical agents of destruction. Consequently, fossils are generally preserved in environments very low in oxygen (e.g., anaerobic sediment) because most decomposers (e.g., fungi, most decomposing bacteria and invertebrates) require oxygen for metabolism. Such sediments are commonly gray, green or black rather than red, a sedimentary signal of oxygen-rich conditions. The "fixing" requirement means that organism must fall into an environment rich in humic acids or clay minerals, which can retard decay by blocking the chemical sites onto which decomposers fasten their degrading enzymes. Plant material or bone can also be "fixed" by removing degradable organic compounds during the process of charring by wildfire. This is a common and spectacular mode of preservation for flowers. For mineral shells of many marine invertebrates, "fixation" may be as simple as the natural inversion of aragonite to calcite. Thus, burial may be the only key to the preservation of mineral shells. Furthermore, acid environments may actually harm both bone and shell because natural acids tend to dissolve the mineral carbonates. This creates the interesting but frustrating observation that fossil plants (which require acid conditions for preservation) and fossil vertebrates (which require basic conditions) are almost never found together.

Fossils can be incorporated into the rock record in areas where sediment is being deposited, which usually, but not always, requires the presence of water. Consequently, streams, flood plains, lakes, swamps, and the ocean are good candidates for fossil-forming systems. Blowing (eolian) sand may bury vertebrates allowing good preservation, but this medium tends not to lock out enough oxygen to preserve organic material well.

As you look at the various modes of preservation in lab, note the characteristics of the rock matrix in which fossil is preserved. Note color, grain size (i.e., sand, silt, clay), mineral composition (quartz, clay, mica, organic-rich, organic-poor), and any other unusual features. If you aren't familiar with the basic features of sedimentary rocks, they may start out all looking the same?don't worry. Take some extra time to make systematic observations of each specimen: What color is it? Can you see the sediment grains with your naked eye? With a hand lens? How would you classify them (round or angular)? Is the rock shiny or dull? Does it have uniform or mixed composition? Do you notice sedimentary layers or other features (ripple marks, animal tracks)? Just be patient; you'll train your eye to recognize rock types in no time.

Types of Fossils - Modes of Preservation

Eight broad categories of fossils are commonly recognized. Although these categories seem well-defined, a given fossil may fall into several categories or may elude them all. Consequently, these categories should be thought of as modes of preservation rather than shoe boxes into which all fossils must fit. When thinking about types of fossils and modes of preservation, it is more important to consider what types of biologically interesting information is or is not present than to fret over strict classifications. With that caveat, the basic types of fossils include:

Fossils that preserve the body of the ancient organism (body fossils ):

1. Unaltered remains - original tissues intact as with drying, freezing or preservation in amber, may be slightly distorted.

2. Compression-impression - two-dimensionally flattened with or without a film of organic material.

3. Mold-cast - three dimensional preservation where the original is not present 2 .

4. Recrystalization - aragonite reverts to calcite or may be altered to dolomite.

5. Permineralization - mineral-bearing fluid impregnates the cells of an organism without the loss of original materials (other than cell contents).

6. Dissolution-replacement - original material dissolved away and replaced by another mineral.

Fossils where the body of the organism is no longer present but some evidence of its existence remains (trace fossils ):

7. Molecular fossils - molecules that survive in the geologic record even when no other traces of the organism persist. Some examples include biochemical breakdown products of chlorophyll, flavinoids, collagen, DNA, lipids, and proteins.

8. Trace fossils - tracks, trails, burrows and other evidence that organisms were present.

Each type of fossil carries different types of anatomical and biological information. Consequently, to piece together the most complete picture of an ancient organism, paleontologists hope for the same organism preserved in several different styles.

Unaltered Remains Unaltered remains are the grail of paleontologists because they preserve the organisms' body intact. Natural mummies, frozen mammoths, pack rat middens that preserve a cross section of plant material in an area, are important windows into these ancient times and places. Unfortunately, the conditions (dry or ice) seldom persist for geologically long periods, and so most unaltered remains tend to be geologically recent. An important exception to this generalization is amber, the polymerized resin of various kinds of trees. Arthropods, plant material and small vertebrates trapped in resin, which is later metamorphosed to amber, can be preserved in spectacular detail. However, they aren't quite "unaltered" as organic compounds in the resin tend to "pickle" the organism, making it unsuitable for some types of biochemical analyses.

Compressions and Impressions Compressions are fossils that have suffered physical deformation such that the three-dimensional organism is compressed to more-or-less two-dimensions. Compressions retain organic matter, usually more or less coalified (reduced to a black film composed mostly of carbon). Compressions of leaves, for example, differ from impressions in that some organic substance, often cuticle, is preserved. Compressions are excellent records of external form, especially for planar structures like leaves.

Impressions are two-dimensional imprints of organisms or their parts found, most commonly, in fine-grained sediment such as silt or clay. Impressions are essentially compressions sans organic material. If the sediment is very fine-grained, impressions may faithfully replicate remarkable details of original external form, regardless of subsequent consolidation of the sediment. Impressions may also occur if, when layers of rock are split apart, the organic material adheres to only one side of the rock. In this case, the side with organic material is the compression, known as the "part", while the corresponding impression is known as the "counterpart".

One particularly interesting type of impression forms in "dirty" sand. In this type of sediment, relatively coarse sand grains are mixed with silt and clay. This type of sediment is common in river and flood plain environments, lakes and in many marine settings. When an organism falls into this type of sediment and begins to decay, the first organic bonds to break leave charged molecular tails hanging off the surface. This charged tail attracts clay particles with opposite charge that linger within the sediment. The clay migrates to the organism's surface, coating it. This has two remarkable consequences: First, further decay is retarded because clay is occupying sites of organic reaction. Second, the minute grain size of clay (<0.0039 mm) allows fine detail to be preserved. Because most of the sediment is relatively coarse (sand grain size 0.5-1.0 mm), the organic material is commonly lost later, but an exquisitely detailed impression is retained in the clay film. This mode of preservation is important in the Dakota Sandstone flora of Cretaceous age. It is also key to the preservation of soft tissue in remarkable animal fossils such as the Jurassic bird Archaeopteryx and the strange Cambrian invertebrates of the Burgess Shale.

Impressions, like compressions, record information about external shape and morphology of plant organs. However, because they lack organic material, cuticle and organic carbon cannot be recovered from them. In cases of impressions in very fine-grained sediment, some cellular detail can be recovered by making a latex of silicone rubber cast of the impression.

Casts and Molds When sediment is deposited into cavities left by the decay of some organic structure, a cast results. A mold is essentially a cavity left in the sediment by the decayed an organic object. Molds are generally unfilled, or may be partially filled with sediment (in this case, the sediment filling the mold would make a cast). Casts and molds commonly lack organic matter.

Molds are formed when soft sediment surrounding the structure lithifies or hardens before the structure decays. When the mold fills in with sediment that subsequently hardens, a cast is formed. Molds of an internal hollow structure like the inside of an empty shell are common. Such molds can be confusing because you are looking at the inside of the fossil-what in life would have been empty space or filled with soft parts. Like compressions and impressions, casts and molds record external (or sometimes internal) features well, but provide no cellular or tissue information. Unlike compressions/impressions, molds and casts often are truer records of the original three-dimensional shape of the structure.

Recrystalization Recrystalization is a narrow type of preservation, but because it is important to so many marine invertebrate fossils, we consider it separately. The mineral shells of most modern invertebrates are composed of the calcium carbonate mineral, aragonite. When aragonite shells are buried, the increase in pressure causes the unstable aragonite to shift crystal form to become calcite. Further metamorphism may cause fusion of small calcite crystals into larger ones. Still further metamorphism may introduce magnesium into the crystal structure of calcite, shifting the shell's composition to the mineral dolomite. Recrystalization commonly cannot be observed except by microscopic observation. Thus, it is impossible to recognize the initial stages of recrystalization without making a thin section of the fossil. Recrystalization is important to note here because any degree of recrystalization indicates that the fossil has been altered by pressure (and/or heat) from its original biological state. Such alteration may also have destroyed DNA and altered protein structure, signaling caution for the paleontologist interested in biochemical studies of fossil invertebrate shells.

Permineralization Permineralization occurs when tissues are infiltrated with mineral-rich fluid. Minerals (commonly silica, carbonate, phosphate, pyrite or rarely other water-soluble minerals) precipitate in cell lumens and intercellular spaces, thus preserving cellular structures of the organism in three dimensions. Because the original mineral and organic material (commonly cell membranes and walls but in some cases finer detail) is preserved, permineralizations can yield detailed information about the internal structure of the once-living organism.

Silica permineralization (silification) commonly occurs in areas where silica-rich volcaniclastic sediments are weathering, for example the famous upright trees in Yellowstone National Park, or the Permian-age invertebrates of the Glass Mountains in Texas. Silification is also an important preservational mode for Precambrian microbial remains deposited in near-shore marine environments.

Permineralization with calcium carbonate (calcite or dolomite) is particularly common in Carboniferous coal seams, where whole regions of peat were permineralized. Called coal balls (because of their sometimes round or ellipsoidal shape) or widow makers (because of their tendency to drop out of mine roofs onto the heads of unsuspecting miners), these fossils commonly preserve a hodge-podge of plants and plant organs and give us a level of understanding of these extinct plants unsurpassed at most times in Earth's past.

Permineralizations in pyrite (an iron-sulfur mineral) are particularly important in Devonian rocks where coal balls and well-preserved plant compactions are rare or unknown. These pyritized fossils often occur in the presence of sea water (a source of sulfur), and are characteristic of plant tissues washed into marine basins. Pyrite permineralizations offer a challenge to the museum curator because iron in pyrite exists in a reduced state and tends to oxidize when exposed to air. Upon oxidization, most of the structures are lost. This is called "pyrite disease" in fossils and is characterized by a mold-like appearance on the cut surface of the coal ball. To prevent destruction, the surface can be coated with a sealant. Coal balls can also be stored in an low-oxygen medium like glycerin or antifreeze.

Permineralization with phosphate is the most common type in marine settings. It most commonly occurs in shallow water were circulation is restricted and seawater may be concentrated by evaporation. Extraordinary preservation of microscopic invertebrate embryos and single-celled organisms are common in this type of preservation.

Dissolution-Replacement Dissolution and replacement occur when minerals actually replace internal structures. In replaced specimens, cellular details are lost with the dissolution of original mineral and organic material. This style of preservation is sometimes called "petrifaction". However, petrifaction has a colloquial meaning that might encompass what we distinguish as "permineralization". Therefore, for the purpose of this course, permineralization refers to those specimens in which original mineral and organic material is preserved, while replacement refers to specimens in which this detail is lost.

Replacement fossils can be frustrating because you expect them to have cellular detail but they do not. Therefore, they commonly only provide the type of three-dimensional preservation of external form characteristic of casts and molds. A good example of dissolution and replacement is the wood of Petrified Forest National Park in Arizona. The beautiful colors that make the wood desirable for collectors is produced by the replacing minerals.

Molecular Fossils As more becomes known about the chemistry of modern plants and animals, paleontologists have begun to examine the fossil record for corresponding chemical data. For example, characteristic breakdown products of chlorophylls and lignins have been found in well-preserved fossil leaves. Lipids and their derivatives have also been recovered from sediments. Some carbohydrate break-down products may also survive in sediment. A special class of these, oleananes, are synthesized by flowering plants, some ferns and lichens. An increase in abundance of these molecules in sediments of mid to Late Cretaceous age has been used to document the increasing abundance of flowering plants during this interval (Moldowan et al. 1994 Science 265:768-771). In another stunning example, genetic material was recovered from Tertiary leaves. As testament to the anoxic requirement for preservation of most molecular fossils, the RNA recovered from these fossil leaves degraded within a few seconds when exposed to air, so special preparation techniques were developed to harvest and transport the material to the lab for amplification and sequencing. Although flashy, this type of preservation has not yet led to big new insights. From this study of Tertiary RNA, the researchers discovered that the Tertiary oaks were related to modern oaks, not a big surprise to anyone.

Fossil DNA and RNA have also been making headlines in the scientific press. In some exceptional cases, genetic material or proteins have been sufficiently well-preserved to permit their use in the reconstruction of evolutionary relationships, in much the same way as one might sequence living organisms. However, much of this work is controversial due to the difficulty of preserving and isolating these fragile molecules. Also, contamination by other materials is a common and difficult to recognize problem.

Molecular fossils are recovered and studied using chromatographic techniques, mass spectrometry, and spectrophotometry. The preservation of these chemical products is highly variable, and depends on oxygen levels during deposition, temperatures experienced by the rocks since preservation, and many other physical and chemical factors. In a similar vein, geochemists have investigated the chemistry of petroleum and its precursors in an attempt to understand its formation.

A more mainstream application of organic chemistry to the study of ancient plants is that of stable carbon isotopes. During photosynthesis, plants reduce carbon from carbon dioxide to form organic molecules. This ratio of carbon-12 to carbon-13 in the resulting compounds gives information on the proportion of these isotopes in the atmosphere (interesting for geological questions relating to global carbon cycling) and about the physiology of the plant itself.

Trace Fossils Trace fossils are any sign or indication that an organism has been present other than its actual body (or part thereof). Trace fossils may be burrows, footprints, casts of roots in soil, the soil itself, trails, bite marks, borings and so on. Trace fossils are particularly interesting because they give paleontologists insight into behavior. For example, the first suggestion that some dinosaurs may have lived in family groups or herds and migrated came from track ways in which many footprints of the same species were traveling in the same direction. Trace fossils suggest who may have preyed upon whom, in what densities some invertebrates lived, and in some extraordinary cases, captured moments in the Earth's past. In one particularly compelling example from the Triassic, a small, bipedal dinosaur approached a larger, lizard-like quadruped from behind on a muddy river bank. The dinosaur circled the quadruped, who apparently paused, swished its tail and bobbed its head (marks of both head and tail are clearly visible on the shale). The dinosaur then trotted off.

While compelling for the stories they tell, trace fossils can also be frustrating, because the identity of the maker is often unclear. For example, a coelom is required for multicellular animals to burrow through sediment. In the latest Precambrian, trace fossil evidence for such burrowing first appears, but we have no idea of the identity of these first coelom-bearing burrowers.

Questions for Further Thought

1. What clues from the rock record or the fossils themselves might tell you whether a fossil assemblage was autochthonous, transported only a little bit, or truly allochthonous?

2. Above we discussed an example where waves or currents winnow small, light shells from a death assemblage, leaving behind only large, clunky shells. What sorts of problems might this create for the paleontologist? What questions could you ask from such an assemblage? What questions could you not ask? When life and death assemblages under these conditions have been compared, how are they similar and different (see discussion in Prothero, Chapter 1)?

3. You want to study the composition of proteins in clam shells from the Miocene, but are worried that they may have been altered. What evidence might you look at to tell whether the shells had been changed by taphonomic processes.

4. You have found a large collection of Triceratops bones in a Cretaceous-age river channel in central Wyoming. You believe that the deposit represents a mass kill of individuals that drowned while attempting to cross a river in flood. You want to use the collection to reconstruct the demography (proportion of individuals of different ages) of the herd. Before you begin, you need to know what sorts of taphonomic processes might influence your interpretation of demography. Describe observations or experiments you might make or do to address these taphonomic questions.

5. Why do impressions in sandstone preserve less detail than do impressions in clay? Why does grain size matter?

1 Once your family and friends learn that you've taken a paleontology class, they may start to bring you fossils to identify. This can be a fun challenge. About half of the time, what they bring you isn't a fossil at all. This is hard news to break; be gentle. However, when they do appear with a fossil, the first question you should ask your friend is "where did this come from?" You want to try to get some information about the geological context from which the fossil came. This may give you clues to the fossil's taphonomic history and may thus help you better interpret the fossil itself. If they don't know where the fossil came from, you have a good opportunity to explain the importance of geologic context.

2 Mold = negative image

Cast = positive image

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