Paleontology and the Fossil Record: _{Reading the clues}

When did people first recognize fossils?

People wondered about fossils for centuries and millennia before paleontology became a scientific discipline. Many myths and legends about colossal beasts likely came from interpretations of fossils by ancient peoples from around the world. Early philosophers in Greece such as Aristotle reflected on the meaning of fossils and how they came to be. In 1086, a Chinese scientist–Shen Kuo –wrote about fossils found in a dry northern habitat. He surmised that they were the remains of bamboo that no longer grew in that region, concluding that it had moved elsewhere due to climate. He may have been looking at fossils of the extinct Calamites plant.

While Kuo correctly recognized fossils as dead organisms, 500 years later, Renaissance Europeans imagined that fossils were the products of Earth trying to reproduce life forms in rock. But Italian artist and scientist Leonardo da Vinci, like Kuo, suspected they were ancient creatures' remains. Noting holes on fossilized mollusk shells (e.g., clams, snails, squid), da Vinci wondered if organisms sometimes left marks behind as holes, burrows, or impressions in the sand (Da Vinci, 1504-1510).

The earliest fossil finders in the Americas were native peoples. For example, the Wyandots, natives of the Great Lakes region of the United States, have a legend to explain the fossilized mastodon bones (a distant cousin of elephants) they found in salt bogs near Lake Huron. As recorded by an ethnologist in the 1800s, the Wyandots believed that these “Witch Buffalo” used to live around the lake but were eventually wiped out, leaving their bones behind (Mayor, 2007).

Enslaved Africans contributed to the emergence of paleontology as a discipline in the United States. In the 1700s, natural history was typically the purview of wealthy men of European descent; however, one of the first fossil identifications was made by enslaved men, as reported by British naturalist Mark Catesby who did not share their names (Catesby, 1771). Thanks to their African roots, the enslaved workers in South Carolina, upon unearthing a fossil tooth on the Stono plantation, recognized its resemblance to an elephant tooth. It was the molar of a Columbian mammoth.

By the turn of the century, French natural scientist George Cuvier, based on the Stono plantation identification as well as other discoveries, formally introduced the concept of extinction to the modern study of biology. Cuvier concluded that some species had wholly died out and were no longer on Earth at all. His public lecture on “Memoir on the Species of Elephants, Both Living and Fossil,” (translated) demonstrated the concept of extinction by describing how a mammoth’s fossilized bones were distinct from any living elephant’s.

In Figure 2, what differences can you detect? (top left - elephant jaw; bottom left - mammoth jaw; top right - mammoth teeth; bottom right - elephant teeth)?

Cuvier noticed that both Indian elephants and the extinct mastodons had ribbon-like teeth adapted for grinding plant materials. However, the elephant (Figure 2, top left and bottom right) had fewer and flatter teeth, resulting in wider ribbons than in the mastodon’s teeth (Figure 2, top right and bottom left). Eventually, Cuvier would assemble a museum of animals no longer found on Earth—fossils—fueling the new science of paleontology.

How do fossils form?

Let’s return to Figure 1B for a moment. The smooth appearance of the rock containing the dragon shark fossils is typical of a “sedimentary” rock called “limestone.” Other kinds of sedimentary rock form when sand, mud, or other particles pile up and get cemented together over a long period. Limestone forms from the remains of marine animals collected on the ocean floor, with shells and skeletons made of calcium carbonate compressed into solid rock (see our module, The Rock Cycle).

Dead animals or plants can sometimes be entombed in sediments. If covered quickly enough, they resist decay in low-oxygen environments such as the ocean floor or the bottom of a lake. Over time, the sediments pile up and gradually get compressed into rock. Meanwhile, the organism trapped inside may eventually become a fossil, depending on the conditions it experiences after it is buried.

Typically, although the organic material that forms the organism's soft body slowly decays, hard parts may remain. Sediments and minerals may seep in, filling the space with mineral deposits and gradually replacing the original material. The formerly living organism slowly becomes one with the rock. Even if all of the original skeleton eventually dissolves and is replaced by sediments and minerals, a detailed cast (a replica) of the carcass may remain. Sometimes an impression or “mold” of the original organism is preserved in the rock after the original remains are long gone. Fossilization processes often require many thousands of years to go from the burial of the organism to the fossil preserved in a rock.

Fossil = remains or imprint of an ancient organism preserved in rock (“ancient” typically defined as more than 10,000 years old)

Most fossils are found in sedimentary rocks with a watery past. But rarely, fossils can form on land. This often occurs when animal or plant remains are quickly buried in a mudslide, sandstorm, or volcanic eruption. Some extinct animal species have been discovered in hardened tree resin (“amber”) and nowhere else. For example, Japanese postdoctoral student Shuhei Yamamoto collaborated with colleagues in Ukraine and Russia to describe a new species of ship-timber beetle encased in Ukrainian amber. (Yamamoto et al., 2022).

Looking at one of his beetle specimens below, how would you imagine it ended up fossilized? (Figure 3)

“Amber fossils” typically form when a sap-like resin oozes from a tree, capturing the organism in sticky goo and carrying it along as it flows. As a result, these fossils tend to be from tiny organisms, such as insects or frogs that live in trees and are lightweight enough to get stuck in sap. You will not find an entire crocodile or tyrannosaur fossilized in amber, although bits and pieces sometimes show up!

Not everything fossilizes equally

A fossil taxon's observed temporal range almost always underestimates its true range due to incomplete fossil preservation and recovery.

“Fossilization” is an irregular process, requiring the right materials at the right time. Complex conditions are needed for fossils to form.

For instance, since soft tissues decay so quickly, they rarely fossilize. Similarly, fungi, plants, protists, and invertebrates that lack hard parts usually fully decompose quickly and are unlikely to fossilize. As a result, the fossil record skews toward organisms with bones, shells, or woody stems, that take longer to decompose and have more time to mineralize into fossils. Vertebrates with hard internal bones and certain invertebrates with hard exoskeletons dominate the fossil record. For this reason, we know far more about some extinct organisms than others. Still, these softer organisms may leave impressions in hardening clay, sand, or mud that become fossilized, leaving behind evidence that the organism once existed even if no remains are preserved in the rock.

Trace fossils

Picture what happens if you press your foot into wet cement or your hand into clay. Once it hardens, the impression you made becomes permanent. Although there are no traces of your actual hand, the impression it left behind provides lots of information about your anatomy. “Trace fossils” happen when the remains of the original organism are not preserved, but evidence of anatomy and behavior are recorded in the rock instead, i.e., traces of the organism’s life.

What sorts of impressions might organisms leave behind? (See Figure 4 for examples).

According to French paleontologists, the textures in Figure 4 were made by animals several hundred million years ago (Moreau and Gand, 2022), but the identity of the animals is tough to diagnose. Indeed, trace fossils (also known as “ichnofossils”) often get separate scientific names because they cannot always be definitively associated with the organism that made them. The cigar-like fossil is classified as Scoyenia gracilis (a scientific name for the tubular burrow of an unknown small animal). The long horizontal lines perpendicular to the burrow get their own classification as Diplopodichnus biformis, roughly translating to “the two-ridged trackway of an unknown animal walking on the sediment.”

Trace fossils include impressions of parts or the whole body of an organism, but also:

• nests burrows and boreholes
• tracks and trails
• bite and scratch marksfeces, called “coprolites”
• stomach contents

Paleobiologist Kay Behrensmeyer is a pioneer in understanding if and when organisms’ remains fossilize. In her landmark paper on “taphonomy” (the study of fossilization), she wrote, “With fossils, natural processes have done the sampling and created the biases.” (Behrensmeyer et al., 2000). Those natural processes include sedimentation and mineralization, which contribute to fossilization.

What might you do if you wanted to study the factors that determine fossilization?

Behrensmeyer conducts experiments in modern environments to figure out what happened in ancient ones. In Amboseli National Park, Kenya, she has watched how bones from dead elephants and other animals get scattered, weathered, and decayed over time, depending on the conditions they encounter. Her work reveals biases, such as the bones of small animals getting buried more readily than large animal bones, thereby increasing the chance of fossilization. If not properly considered, this bias could lead paleontologists to underestimate the population density of large animals in similar environments on land in the fossil record.

Because fossilization is subject to the environment’s interaction with an organism’s remains, any fossils represent just a portion of the organisms that lived in that geographic area.

Stratigraphy as a story of life on earth

The successive series of stratified formations are piled on one another, almost like courses of masonry.

The Danish anatomist Niels Stensen (“Steno”) was one of the first known people to propose the mechanism for fossilization, explaining how fossils end up buried within layers of rock. Through observations of the rock layers in Italian cliffs, Steno hypothesized that rocks had originally been liquid, which flowed and then hardened to create the layers. Some layers contained fossils, suggesting that organisms had been buried and turned to stone. In 1669, in a geological treatise, Steno put forth the principles that became “Steno’s Law of Superposition.” (Steno, 1669).

Indeed, these “stratigraphic layers” (or “strata”) are produced when sediment accumulates and gets compacted over time; each layer represents a period of steady sediment accumulation or an intrusion of molten rock rising up from below and spreading out (See our module History of Earth’s Atmosphere II).

In Figure 5, what makes the layers distinct in this fossil-containing area of Pakistan?

The distinct appearance in the photos and the patterning of layers in the depiction represent their diverse materials. Note that each layer is given its name as a “formation.”

Using your logic, which of the layers in Figure 5 was laid down first?

The yellow layer is the oldest, followed by the light green, the pink, and so on. Like constructing a layer cake, adding a top layer before the bottom one was in place would be impossible. This is the principle of superposition… (Steno’s Law)

Consider Figure 6, a depiction of fossils found in deeper layers of rock (older) and shallower layers of rock (younger). The red line marks 50,000 years when no fossils are found in the rocks.

How do the types of fossils below the red line compare to those above the red line?

You can see that some fossilized organisms below the red line don’t appear above and that the density of fossils above the red line is lower. You’re looking at the evidence for an extinction event in which most species (seven out of nine) did not survive (see our Mass Extinctions module).

So, while an individual fossil is evidence of one animal that died, fossils can collectively tell a larger story of the planet's history. Fossils found by Charles Darwin and his contemporaries contributed to the development of the theory of evolution by natural selection, first published in On the Origin of Species (Darwin, 1859). The realization that life on Earth is constantly evolving dramatically shaped our understanding of its history.

We use the fossil record to understand evolution. But, if only certain organisms fossilize, our understanding of evolutionary relationships and how organisms evolved is more challenging to understand. British biologists Robert Sansom and Matthew Wills evaluated the impact of “fossilization biases” using a database of 78 modern animals (Sansom and Wills, 2013). They plotted family trees from the datasets, removed all soft tissue data, and replotted. Ignoring the soft tissues (like the fossil record, mostly) changed the positions of species in their family trees, showing that bones and other hard parts only give us part of the story.

The distribution of fossils over time

The fossil record, and thus our understanding of extinction and mass extinction, is heavily biased toward certain kinds of organisms, certain habitats and regions, and certain time periods.

Biases that impact how organisms fossilize influence our understanding of life’s whole arc on Earth. Different geologic periods are characterized by different groups of organisms whose characteristics affect the evidence they leave behind.

Several billion years ago, among the earliest life included single-celled cyanobacteria, followed by tiny invertebrate animals. These organisms lacked any hard body parts, leaving only the smallest traces in the fossil record despite their importance in paving the way for later kinds of organisms. During the “Cambrian Period” 500 million years ago, even though vertebrate animals with bones were not yet widespread in our oceans, many other marine animals with hard parts left a record of existence.

Based on Figure 7, what features of the Cambrian animals might have increased their chance of fossilization?

You’ll notice that many of the Cambrian animals had hard body coverings. The Cambrian Period was a time of evolutionary innovation as animals became active hunters and burrowers, evolving harder body support structures that were much more likely to fossilize. For example, trilobites had hard shells and lived in oceans worldwide for nearly 300 million years. Accordingly, millions of trilobite fossils have been recovered, representing more than 20,000 different distinct species.

The first vertebrates also appeared in the Cambrian Period: fish. Early fishes had cartilage skeletons, like sharks do today, which are softer than bone and rarely fossilize. Eel-shaped fish from Cambrian were “jawless” but fortunately for us, their teeth were hard enough to survive the ravages of time and fossilize. In 2022, Bulgarian paleontologist Plamen Andreev and colleagues discovered fossilized teeth from the oldest known jawed fish --Qianodus duplicis -- dating to 439 million years ago (Andreev et al., 2022).

Looking at a reconstruction of the fish Qianodus duplicis(Figure 8), what features might have fossilized? 

We may never have known that this species existed without the fossilized teeth. This emergence of hard teeth in early vertebrates marks a point when paleontologists have more data to track the history of life on Earth.

Geographic bases

We find that a global power imbalance persists in paleontology, with researchers in high- or upper-middle-income countries holding a monopoly over paleontological knowledge production by contributing to 97% of fossil data.

In addition to biases toward hard-body animals and environments that promote sedimentation, like lake beds and the ocean floor close to shorelines, there are also biases in where we can search for fossils today.

Mauritian paleontologist Nussaïbah B Raja and colleagues (Raja, 2022) analyzed how more recent colonial history and economic factors have influenced our understanding of life in the deep past. Using data from the Paleobiology Database (PBDB; www.paleobiodb.org), they observed that wealthier countries, like the US, UK, and Germany, have accumulated the most paleontological data over the last 30 years. However, most of the actual fieldwork has taken place in lower-income countries. Raja points to colonialism as the root of the imbalance and notes a bias toward interest in vertebrate fossils. Her work calls for more geographically balanced investments in paleontology and the development of more robust paleontological science in countries lacking it.

Despite geographic sampling biases, fossils (especially larger ones) continue to be discovered in places where paleontologists are not intentionally searching. In 2017, a Portuguese man working in his backyard found enormous rib bones. After unearthing them, paleontologists confirmed that they were fossilized bones from an 82-foot-long sauropod dinosaur, the largest sauropod found in Europe (University of Lisbon, 2022).

It’s fair to say that we have only scratched the surface of the record of past life on Earth preserved in fossils.

Fossils in perspective

Fossils are excellent tools for discovering species that went extinct and for determining what species lived during different geologic periods. They can also reveal where species lived and in what types of ecosystems. Think back to the dragon shark fossil in Figure 1. What was a shark doing in the New Mexico mountains anyway?

Dracopristis hoffmanorum was a shark adapted for shallow lagoons and estuaries. Its fossilized remains are one of multiple pieces of evidence that North America was once flooded with huge, shallow seas. What are now mountains in Colorado and neighboring states were then extensive reefs teaming with prehistoric life. So, fossils can reveal information about extinct animals and the ancient habitats they inhabited.

In rare instances, fossils directly reveal interactions between species, such as feeding relationships (see our Trophic Ecology module). In a 2023 study (Therrien et al.), paleontologists reported the first instance of a fossil tyrannosaurid dinosaur containing a stomach full of its last meal. About 75 million years ago, the tyrannosaurid had fed on a smaller dinosaur species (Citipes sp.). It must have died soon after that because the legs of the two baby Citipes remained in its stomach, fossilized (Figure 9).

Although fossils can also help us construct family trees, they do not provide a complete picture of the evolutionary relationships of organisms. Many gaps remain, and some transitional species, which do not persist for long, may be lost forever. However, molecular analyses complement the study of fossils and can sometimes help fill in the gaps in our knowledge including providing insight into how habitats have changed through time.

For example, Chinese geoscientists Shucheng Xie and colleagues analyzed the fossilized remains of an organic molecule called C31 n-alkane found in the leaf wax of grasses and herbs. This helped them piece together the ancient vegetation of the Loess Plateau (Xie et al., 2002). Specifically, they found that the Plateau was an open grassland rather than a forested habitat during the last interglacial period. This kind of fossil data helps paleontologists reconstruct past ecosystems and landscapes, piece by piece.

The development of knowledge from paleontology proceeds slowly. As researchers continue to find and interpret fossils and develop new techniques to assess ancient ecosystems, our picture of life’s history on Earth becomes increasingly accurate and detailed.