GEOL 204: The Fossil Record

What Good is a Fossil Record?

That is to say, what benefit does society receive from the existence of fossils of the ancient world? There are many of them that are scientific, or even aesthetic:

• Direct evidence of transitions and origins of modern groups of organisms
• ONLY evidence of extinct branches of the Tree of Life
• ONLY evidence of the reality of mass extinction events: without the fossil record, we would not be aware that situations can arise that wipe out huge majorities of the living individuals and species on the Earth!
• And many fossils are aesthetic pleasing, to the point that most nations have national parks or monuments centered on such fossils, or showcase them in museums, and so on

But are there any pragmatic benefits? YES!

• Fossils are one of the primary indicators of past climate change (which we saw early in the course)
• Fossils are markers of "pristine" (non-human influenced) biodiversity

The Holocene Extinctions

The Holocene Epoch of the Quaternary Period of the Cenozoic Era is our name for "modern" times: that is, the last 11,700 years. This is the time since the end of a 1000-year cool snap (the Younger Dryas) during the deglaciation from the Last Glacial Maximum. During this time humans discovered agriculture, developed cities, started using metals, and created writing (and thus a written history).

Compared to the earlier Pleistocene Epoch, the Holocene has been an epoch of climate stability. It was rare in the Pleistocene to have a 12 kyr warm pulse with only a degree or two of average change; instead, we see fluctuations of up to 7-9 C°:

And all our agricultural, freshwater, coastline, etc., needs were developed in the context of this period of stability.

Agriculture has allowed human populations to soar:

Agriculture allowed humans to capture more and more of the land's biomass. Also, as agricultural lands expanded, wildlife tended to be displaced, bringing their population down. Furthermore, wild species of animals were domesticated into new forms (aurochs into cattle; boars into pigs; mouflon into sheep; wild goats into goats; wild horses into horses; wild asses into donkeys; etc.): the wild species tended to decline from habitat loss and hunting while the domestic forms flourished under human husbandry.

The colonization of the Brave New Worlds (Sahul and the Americas) was not the end of the expansion of Homo sapiens. During the Holocene humans spread to many oceanic islands in the Pacific, Indian Ocean, and elsewhere. In the wake of new arrivals, many species became extinct. For example, the total number of bird species at 1 CE was probably 3000 more than today, largely do to losses of island avian species.

Let's take a look at some of the patterns of extinction.

Historic Cases Recognized at the Time

• The dodo (Raphus cucullatus) of Mauritius was extinguished not so much by direct overhunting but by introduction to its island home of rats and pigs, which ate the eggs and babies of this giant flightless pigeon. The species was extinct by 1662.
• The Great auk (Pinguinus impennis) was a large flightless sea bird of the North Atlantic. It is the actual species for which the name "penguin" was coined (and later transferred to the distantly-related Southern Ocean clade we now call by this name). This was directly over-hunted to extinction. The last definite sighting was on 3 July 1844, when a sailor records wringing the necks of two individuals. (A later sighting in 1852, however, might be valid).
• Stellar's sea cow (Hydrodamalis gigas), the 8-10 m long largest of the manatee-dugong family, lived in the northernmost Pacific. First known to Western science in 1741, it was hunted to extinction in only 27 years by whalers.

But there are many other larger-scale or more dramatic extinctions during the Holocene:

Madagascar: Humans (settlers from Borneo, rather than nearby southeastern Africa) reached the island of Madagascar between 350 and 550 CE. They arrived with an agricultural system based on slash-and-burn. Through a combination of habitat destruction and direct hunting, they wiped out such as:

• The elephant bird (Aepyornis maximus), a giant flightless herbivorous bird, and possible inspiration for the legends of the roc
• Two species of dwarf hippopotamus
• Several species of large-to-giant lemurs, including one which rivaled the gorilla in size

New Zealand: These islands remained uninhabited until 1280 CE, when Polynesians first arrived. By 1400 (possibly before) they had wiped out many taxa, including:

• The nine species of moa (Dinornithiformes), giant flightless birds, some of which reached 3.6 m (12 feet) tall
• Haast's eagle or Fuller's eagle (Hieraaetus moorei), one of the largest birds of prey of all time and apex predator of New Zealand
• The two species of adzebills (Aptornis), flightless predatory ground birds.

In the case of the moa there is direct evidence of hunting and feeding by humans, and this seems likely in the case of the adzebills, too. The Haast's eagles were probably victims of trophic collapse: with the moa gone, there were no targets left (other than men) large enough to serve as prey.

Tasmania: Part of Sahul, it was isolated from mainland Australia as the sea rose in the last deglaciation. Its inhabitants lost a substantial part of earlier technology, such as bone tools, boomerangs, hooks, sewing, and the ability to start fires. In many ways, they had reverted to Homo erectus-grade technologies. In Tasmania some of the larger animals that were wiped out on mainland Australia survived, most famously the thylacine or Tasmanian tiger or Tasmanian wolf (Thylacinus cynocephalus. This animal was a marsupial predator strongly convergent on placental wolves. With the settlement by Europeans in 1803, a systematic campaign of extermination of both the Tasmanian people and Tasmanian tiger began. Sadly, both were successful. The native population of Tasmania was hunted down to the last individual and their language and culture lost for all time: the last full-blooded Tasmanians were the women Truganini who died on 8 May 1876 and Fanny Cochrane Smith who died in 1905. The thylacines actually survived longer, with the last specimen dying in captivity on 7 September 1936. Below is a compilation of all surviving film footage of this species (all of it in zoos, rather than in the wild):

The mainland Old World: But these are all small, isolated lands. Surely extinction hasn't happened in recent times on the continents? Sadly, here to. For example, the quagga (Equus quagga quagga, an extinct southern African subspecies of plains zebra: 12 August 1883), the aurochs of Eurasia (Bos primigenius, although technically a pseudoextinction as the domestic cow Bos taurus is a descendant: 1637), the tarpan of Eurasia (Equus ferus ferus, the ancestor of the domestic horse Equus caballus: 1879 for the last scientifically verifiable non-hybrid), and others. And the extinctions in North America were particularly striking.

Continental North America: Here the extinctions included not only rare forms, but some of the most common species to inhabit the continent:

• The passenger pigeon (Ectopistes migratorius), once the most common bird species in the continent. Their flocks had hundreds of thousands to perhaps millions of individuals. Wiped out in the wild by the end of the 19th Century by a combination of habitat loss (deforestation for farms) and large-scale commercial hunting for feathers and meat; the last individual "Martha" died in the Cincinnati Zoo on 1 September 1914.
• The Carolina parakeet (Conuropsis carolinensis), which lived as far north as New York and Wisconsin. Killed as commercial pests, and for their feathers, and vanished in the wild during the early 20th Century. The last individual "Incas" died on 18 February 1918, in the very same cage that "Martha" had died in.
• The ivory-billed woodpecker (Campephilus principalis), the largest North American woodpecker. Vanished on the mainland by 1944 by over-logging of their habitat in the American southeast. Hopeful signs that it might have survived in the early 2000s have not panned out, and it seems likely these were misreports of the more common (but similar) Dryocopus pileatus.

A very, very close call was Bison bison, the plains bison, largest and by far most common large mammal of North America after the megafaunal extinction. Their huge herds made them essentially hunt-proof to the Folsom points--and later bows and arrows--of Native Americans. But arrival of advanced rifle technology, the expansion westward of American farming and railroads, and a tremendous market for bones for fertilizer and hides for many numerous uses led to commercial hunting on a phenomenal scale, bringing species dangerous close to extinction at the end of the 19th Century. Once hundreds of millions formed vast herds, but by 1890 less than 1000 individuals remained. Political and social action from the grassroots on up to Congress and the White House led to protection of this symbol of the American West, and the species was saved and once again roams the West.

20th Century: Beginning of the Sixth Mass Extinction: But all these pale in comparison to the widespread ecological devastation of the 20th and 21st Century. The huge increase in human population, and the requirements to feed this population and supply us with homes and products, means we impact the biosphere on an ever-increasing scale:

It is no longer direct hunting that is the major issue (although still ongoing on land in the form of the pet trade, trade in exotic animal products like ivory, and slaughtering rare species for "traditional Eastern medicine" ingredients). The primary dangers are:

• Overfishing, resulting in the collapse of many commercial fisheries around the world in order to feed a growing population. Indeed, many large-bodied fish species are no longer commercially viable, so more and more species are being used up. Instead of becoming sustainable, we are fishing down the trophic pyramid, so that all commercial fish species are either fully exploited or over exploited.
• Deforestation and Other Habitat loss for farming, logging, and other development: humans now capture large parts of the net primary productivity of the land surface; consequently, that's less habitat for everything else
• This includes freshwater habitat loss: lakes drained, river channels dammed, etc.
• Eutrophication from fertilizer and soil runoff, converting many places close to shore into "dead zones"
• Ocean acidification, a byproduct of increasing CO₂ in the atmosphere, causing calcifying organisms like corals and mollusks to weaken and/or die.

It has been argued that the net result of this is that Earth is in the sixth major mass extinction, as the impact now includes the marine realm, small organisms, etc. (and not just the megafauna). Like all mass extinctions, this stems from the fact that the environmental changes are happening faster than organisms can evolve to adapt to them. Although extinction rates are no where near the level of the Big Five, we have instigated the same type of causes that happened before (extreme eutrophication, like the Ordovician-Silurian and Devonian-Carboniferous; ocean acidification, at least a partial contributor to the Permo-Triassic and Triassic-Jurassic [and PETM]).

A somewhat unexpected discovery is that the general public greatly underestimates the predicament of the better known and "charismatic" species. That is, some species which are overexposed publicly (such as giraffes and elephants) are assumed to be less threatened, whereas in reality they have had catastrophic population crashes in the last several decades. Below is seen the percent loss of species over time on the left, and the percent who incorrectly answered the question "Is this species endangered?" (correct answer for all is "yes"):

from Courchamp et al. (2018 PLoS Biology 16(4): e2003997

Modern conservation ecologists now refer to defaunation: a combination of global extinction, regional extinction (aka "extirpation"), and population decline.

Other Anthropocene Effects of Biodiversity

Defaunation isn't the only change (or at least not directly). Climate change means that when different temperatures reach different spots in a year during its annual cycle; so the preferred seasonal ranges for animals or growing zones for plants change. This might result in changes in the phenology (seasonal life cycle events) of different species: sometimes this disrupts the evolved patterns of growth and development.

Additionally, there are trophic cascades and other ecosystem cascades by the loss of key species within an ecosystem. In trophic cascades, loss of apex predators removes checks on the large herbivores, which may result in overfeeding by these, reduction of plant diversity, etc. Sometimes the effects can be even more complex. Ecosystem cascades are the more general category. We saw with the loss of the mammoths, the mammoth steppe biome with its high diversity was lost. Similar changes are seen in the modern world as "architect" animals are removed.

And for our own parochial interest: the living world provides ecosystem services: activities which are beneficial (or even required) for human life and economy, but for which we do not pay. Some such benefits are:

• Photosynthesis, and thus both the base of the food chain and the oxygen we breath
• Litter decomposition
• Carrion removal
• Water filtration
• Carbon cycling
• And much more

Paleontology to the Rescue? Conservation Paleobiology

A big part of the crisis, however, is that even though it is incredibly fast by geologic timescales, this is going on slower than society notices. Additionally, by the time that field ecology really got going, especially in the marine realm (the mid-20th Century), the crisis was well underway. So how do we know what is really "natural"?

That is where conservation paleobiology comes in. Largely pioneered by invertebrate paleontologist Jeremy Jackson, conservation paleobiology works by looking at the fossil record of the latest Quaternary and early Holocene to get a description of the biodiversity of the contemporary species prior to any significant influence of humans. Furthermore, more ancient crises (like PETM and mass extinction recoveries) give us evidence of how the biosphere reacts to tremendous rapid changes. This evidence from the fossil record allows conservation biologists to make better plans in dealing with current and near-future changes.

It has been noted that conservation paleobiology gives us a tremendous amount of useful data, such as:

• Identify invasive species (especially if those invasions were before the mid-1800s, when the big naturalist surveys of regions began)
• Measure the historic variability of systems, because multi-decade and century or longer boom & crash cycles and the like haven't been all the way through their fluctuations of the mere century, or half century, or quarter century, of detailed analysis of an ecosystem
• Quantifying past & present biodiversity (lists of species) and biomass (numbers of individuals) of a given spot
• Identify limits of habitat ranges & tolerances (e.g., although jaguars [Panthera onca] may be limited to the tropics today, but ranged as far north as the Canada border as recently as the early Holocene)
• Detecting recent shifts in species geographic ranges
• Assessing changes in genetic diversity & identity (for those specimens we can get genomes from)
• Identify lost nodes within food webs (see more below in re-wilding)
• Disentangling human vs. non-human processes (just as paleoclimatology unraveled the natural vs. anthropogenic components of modern climate change)
• Developing restoration targets
• Evaluating extinction risk
• Informing decisions on rewilding
• Informing strategies for the design and selection of wildlife reserves
• Establishing conservation priorities (because as much as we'd like, we can't save everything)

Filling in the Gaps: Re-Wilding

But is extinction really the end? A few paleontologists and other scientists have suggested methods to recover ancient ecosystems, or even ancient species.

Rewilding: If a species still persists in some region, but has undergone extirpation at another, it is possible to reintroduce it. But what about cases where the extinct taxon is globally extinct? It might be possible rewild it: that is, to introduce to a habitat a closely related species with similar biology and ecology to replace the original one. These efforts are already ongoing at various sites in the world, and generally show promise (so long as unwanted introduced invasives can be eliminated, too.)

Rewilding can benefit an ecosystem by restoring links that were once present, and thus increase the biodiversity and productivity of that region. This way habitats can be reestablished where key taxa are extinct. (In particular, megafauna tend to be major architects of ecosystems.) For instance, a great number of large fruits with huge seeds (like avocados) no longer have natural dispersers. That is because the animals which DID swallow these fruit and distributed the seeds are largely extinct: various proboscideans, giant ground sloths, big marsupials, giant tortoises, etc. (depending on where you are on the planet). These are also the sorts of animals that have preferentially died out in the Pleistocene and Holocene extinctions.

A promising example of rewilding to reestablish an old link in an ecosystem is on Mauritius (a small island in the Indian Ocean, east of Madagascar). Although famous for the dodo, Mauritius had a number of other recent extinctions: in particular, two species of giant tortoise of the genus Cylindraspis. Like other living giant tortoises, these were fruit eaters. They were the major animals to eat the large fruit of the native ebony tree Diospyros egrettarum. This species is down to a mere 10 individuals on Mauritius, and a few hundred on a offshore island. These seeds of the ebony tree do not germinate well on their own. But introducing the giant Aldabra tortoise (Aldabrachelys gigantea) to that offshore island has resulted in a spread of the slow-growing ebony plant. Similar experiments elsewhere show that reintroduction of the Aldabra giant tortoise (in combination with removal of invasive plants and animals) help old ecosystems reestablish their links.

We can see trophic cascades (and their reversal) at play at the reintroduction of wolves after an absence of 7 decades to Yellowstone Park:

In general, we recognize that some species are ecosystem engineers: through their own actions, they environment around them is transformed. We saw an earlier example of this with the mammoth steppe: the feeding (and pooping) habits of Mammuthus resulted in a high-productivity grasslands, supporting a diverse community of animals and plants. (And the loss of the mammoths resulting in the disappearance of this biome.) Modern ecosystem engineers including the living proboscideans (who clear out patches in the forest by breaking down trees) and beavers (whose dams produce small lakes that support diverse wildlife). Various extinct animals presumably had similar roles (e.g., extinct proboscideans and giant ground sloths also as creating patches in the woods.)

Ecological engineers are just one example of a keystone species: a species with a disproportionately large effect on its natural environment. The keystone species need not directly shape its environment: for instance, see the video about wolves in Yellowstone.

So many people interesting in rewilding are not simply interested in reintroductions (putting species back where they once lived.) They are specifically interested in restoring ecosystem structure by the return of lost keystone species.

Pleistocene rewilding takes this to a greater extreme. Many ecosystems once relied on giant mammal species. Although the megafauna of the Pleistocene are gone, there are sometimes close relatives from some part of the world that might be used to "fill in" ecologically in regions like North America or Pleistocene Park (which actually IS an ongoing project) in boreal northeastern Siberia. The idea is to release ecological equivalents (lions or tigers for Panthera atrox; Indian elephants for mammoths, etc.; and so forth), to allow an approximation of the Pleistocene ecosystem to return.

There are some problems with this approach, however:

• Although close relatives, they are NOT the same species, and will have different requirements and habits
• Indeed, they would technically be invasive species, with all the problems that contains (with rare exceptions: horses for North America and Siberia, for instance, where they are returning a lost species directly)
• The global climate change means that the environmental conditions will NOT be those of a Pleistocene interglacial anymore, but something new
• And pragmatically, if Western farmers objected to the reintroduction of wolves to Yellowstone, they are unlikely to accept prides of lions and herds of elephants wandering over their ranches!

But do they actually have to be close relatives? A study from the Spring of 2020 examined key attributes of extant introduced animals and recently extinct mammals of those same regions in terms of feeding types, digestion types, habitat, etc., to find what the closest matches were in terms of ecosystem function. In some cases the closest matches were close relatives (for instance, the living capybara Hydrochoerus hydrochaeris for the Pleistocene southern North American capybara Neochoerus aesopi.) But in other cases the "nearest neighbors" in terms of ecosystem function were very distant relatives: for instance, the introduced sambar deer Rusa unicolor for the Pleistocene giant kangaroo Sthenurus stirlingi in Australia. It led the researchers to speculate that the hippos (Hippopotamus amphibius) introduced by drug lord Pablo Escobar to Columbia might restore the ecological function of the recently extinct toxodonts. Whether this study is supported by observations of wildlife environmental interaction remains to be seen.

Is Extinction Forever? The Possibility of De-Extinction

De-Extinction: But what if we didn't have to make do with partial replacements? What if instead we could REALLY bring back a fossil species? Is it possible to de-extinct (I think the term "re-extant" would be better) fossil species?

Theoretically, there are several approaches, now that fossil genomes have been recovered:

• In vitro fertilization using frozen sperm. The first generation would be a hybrid (for example, a woolly mammoth-Indian elephant cross), but successive backcross hybrids would increase the percentage of original fossil material.
• Cloning from a frozen cell: a nucleus from a fossil is inserted into a de-nucleated ovum of a related species, stimulated to divide, and placed in a surrogate mother.
• Sequencing DNA from fossil specimens, creating artificial chromosomes, and cloned as above.

Two projects are ongoing. The so-called Lazarus Project is working to de-extinct the gastric-brooding frog Rheobatrachus silus, which was wiped out in the wild in the mid-1980s. Another team has attempted to clone the extinct-in-2000 Iberian ibex Capra pyrenaica pyrenaica (the clone died minutes after birth). And (although technically not totally extinct), the northern white rhino (Ceratotherium simum cottoni) has only two living members, both in captivity: the last male died 18 March 2018. These two females are too old to bear young. But sperm and eggs have been collected from various individuals, and since May 2016 attempts have been made to fertilize the eggs, with the intention to implant the embryos into the very closely related southern white rhino (C. s. simum).

In Spring 2025 a biotech firm named Colossal claimed to have produced de-extinct dire wolves (Aenocyon dirus). What has been described reveals that these are actually genetically modified grey wolves (Canis lupus) in which 16 or so genes from the known dire wolf genomes have been inserted. So they might be better described as "dire-ized wolves".

If restored, the restored species could be restored to the wild as in re-wilding, removing the objection to it being the wrong species. But a whole new set of problems arise:

• Limited gene pool: how many different individuals might be cloned?
• Loss of any behavioral information transmitted from parent to offspring (especially in birds and mammals, not all behavioral traits are inherited instincts; much has to be learned from observing the adults)
• Very incomplete ecosystems, if the idea is to recreate Pleistocene faunas (most species won't be available)
• It may be that the reason for the extinction is still in operation (if it were a disease, or pollution, or whatever), so you would just bring back a species to let it die again.
• Finding a habitat in which to reintroduce it
• Potential policy, legal, or social conflicts over reintroduction
• And potential negative side effects.

A whole additional set of problems lie with trying to clone birds and other animals with shelled eggs. Getting the new genetic material into the egg is very difficult since you can't simply deal with the egg after they have left the body (as in fish and amphibians with external fertilization) or reimplant eggs removed for fertilization (as in therian mammals). Indeed, although we have cloned some fish, amphibians, and mammals, as of May 2025 no one has successfully cloned a bird or other sauropsid: not even a chicken! So do not expect clones of dodos, passenger pigeons, moa, (or Mesozoic dinosaurs!) anytime soon.

And, of course, the whole "world has changed--and will change a lot more VERY soon--since the Pleistocene" issue applies. Is it worth billions of dollars to bring back wooly mammoths to a world in which their cold habitat disappears?

Perhaps the most important issue, though, is that conservation money is rather limited. There are many critically endangered habitats and species in the world today; does it make more sense to try and protect these, or try and bring back an extinct form?

But one thing that you, as a student of the fossil record, should NOT argue is that various species were "meant to die". As we have seen, extinction is NOT some preordained fate, even though it does fall on the majority of species. And in particular, Holocene and Pleistocene extinctions are largely (either directly or indirectly) OUR fault.

If you want more information and debates (pro and con) about the de-extinction concept, the TED conference in which the term was introduced is available online. Also, the 2014 Howard Hughes Medical Institute BioInteractive series of talks was about the Sixth Extinction and how we should respond.

Some Relevant Videos

If you are made of stern stuff, you can check out the very well-done documentary Racing Extinction