GEOL 204 Dinosaurs, Early Humans, Ancestors & Evolution:
The Fossil Record of Vanished Worlds of the Prehistoric Past

Spring Semester 2018
Awful Changes: Origins, Extinctions & The Fossil Record

Detail from Henry de la Beche's 1830 cartoon "Awful Changes", featuring Professor Ichthyosaurus

"Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely-graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against the theory." -- Chapter 9 "On the Imperfection of the Geological Record", On the Origin of Species by Means of Natural Selection (1859), Charles Darwin

"Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists -- whether through design or stupidity, I do not know -- as admitting that the fossil record includes no transitional forms. The punctuations occur at the level of species; directional trends (on the staircase model) are rife at the higher level of transitions within major groups." --The Panda's Thumb (1980), Stephen Jay Gould

"All these facts, consistent among themselves, and not opposed by any report, seem to me to prove the existence of a world previous to ours, destroyed by some kind of catastrophe. But what was this primitive earth? What was his nature that was not subject to man's dominion? And what revolution was able to wipe it out to the point of leaving no trace of it except some half-decomposed bones?" "Espèces d'éléphans" (1796), Georges Cuvier

"Amidst the vicissitudes of the earth's surface, species cannot be immortal, but must perish, one after another, like the individuals which compose them. There is no possibility of escaping from this conclusion." -- Principles of Geology, Vol. 2 (1837), Sir Charles Lyell

BIG QUESTION: How do new species form? What are extinctions and mass extinctions?

Speciation: The Pattern of the Origin of Species
As with many things, we run into problem with typological thinking: the idea that there are ideal types of things, and that we judge a specimens membership in a group by how well it conforms from that type. Instead, we find that variation is the reality. So we need to use population-based thinking. (Next lecture we will add tree-based thinking.)

Darwin's species concept is worth revisiting:

An important issue which is commonly forgotten comes out here: descendants are descendants of only a small part of any ancestral group! That is, entire species do not evolve into entire other species. Instead, only some small subset of any given species population is the ancestral group leading to a particular descendant. This points to several different aspects:

Note: this relates to a common anti-evolutionary rant, which goes a long the lines of "if people evolved from monkeys, how come there are still monkeys". Ignoring lots of other problems with this statement (such as the fact humans didn't evolve from any living monkey species; that "monkeys" aren't one thing, but are a vast number of species; etc.), this misses important aspects of how evolution works! Just because some monkeys evolved into apes which evolved into humans does not require that ALL monkeys evolved into apes and ALL apes evolved into humans. Plus, it doesn't mean that monkeys were TRYING to evolve into humans, or DESTINED to do so.

(Here's a way to restate an analogy to this anti-evolution argument: "If [for example] your ancestor came from Ireland (or Norway, or India, or whatever), why are there still Irish/Norwegians/Indians/etc.?")

Speciation is the process of the origin of a species. It doesn't happen immediately or instantaneously: it is indeed a process rather than an instantaneous event. (In fact, except in rare cases, it is unlikely that it you there during it that you would recognize it as such.)

Some aspects of the origin of species to consider:

During the 20th Century (especially during the first half), evolutionary biologists assumed the dominant trends were sympatry and anagenesis. However, as a better understanding of genetics was developed, some (including Mayr) argued that allopatry, peripatry, and parapatry (which all require cladogenesis) were actually more common.

The problem, of course, is that speciation takes time, and field biologists are unlikely to observe it. If only there were some sort of record of changes over time. Say, for example, a fossil record...

Creeps or Jerks: Phyletic Gradualism vs. Punctuated Equilibrium
Prior to the 1970s most paleontologists considered a model which became known as phyletic gradualism:

In 1972 paleontologists Niles Eldredge and Stephen Jay Gould proposed an alternative, which they called punctuated equilibrium.:

The punctuated equilibrium model helped explain some aspects of paleontology. As Darwin noted (see quote at top), we do not see an endless series of slight gradations, each stratum with a slightly different version. Instead, species remain largely unchanged for most of their duration, with new closely-related species appearing suddenly in the fossil record. In fact, if it weren't like this, biostratigraphy would not really work! As the punctuated equilibrium supporters argued, "stasis is data".

During the 1970s and 1980s (and continuing today, but at with much less rancor), the debate over "evolution by creeps" vs. "evolution by jerks" continued. At least in the fossil record, punctuated equilibrium seems

How long are punctuation events? In a rare case, Smithsonian paleontologists Gene Hunt, Michael Bell, and Matthew Travis found that a population of the stickleback species Gasterosteus doryssus got isolated in a lake in Nevada in the Miocene Epoch. In this particular case, there were annual layers, allowing them to measure an excellent sample over time and document its change. They found the period of transition from the ancestral form to the descendent took only about 2000 generations (about 4000 years), after which the population was mostly stable. Events on the 103 year scale are unlikely to show up in the fossil record except in such situations (high sample size, restricted location, annual record), as the fossil record is much better at picking up events at the scale of 104, 105, or greater.

Supporters of the punctuated equilibrium model had to wonder how equilibrium was maintained. Evolutionary stable scenarios seem to be at least part of the reason.

Why the punctuations? A likely cause is that environmental changes are rather quick on the geologic time scale, with stable conditions in between. Rapid shifts in climates will result in shifting population ranges, shifts in habitat availability, etc. This leads to the prediction that we should see evolutionary shifts (speciations, extinctions, etc.) concentrated at moments of environment change: the so-called "Turnover-Pulse Model".

In summary, punctuated equilibrium may well be due to the following combination of aspects:

A historical note: a close read of The Origin shows that Darwin did consider cladogenesis and parapatry/peripatry as critically important in most speciation, and that anagenesis of the main part of the ancestral population was almost never the case.

"Missing Links" As An Outdated Concept
One of the most problematic terms in popular discussion of evolution is "missing link". Coined by Lyell, it was used in the 19th Century for a potential but as-of-then undiscovered link between humans and other primates. Subsequently is has been used as the idea of an as-yet undiscovered intermediate form between two particular species.

The term is problematic for a couple reasons:

So it has a very small chance that given fossils are the ancestors of the species you are interested in. However, it might well be a more general early relative, and that could be useful indeed.

Transitional Forms
Finding a direct ancestor might be hard, but finding an early relative is easier. And since relatives share many of their same traits, finding early relatives can help establish the anatomical (and ecological, and so forth) transitions involved in that part of the tree of life.

Darwin pointed out that there is not the continuous series of transitions that might expected from a gradualistic model of evolution in the fossil record, but noted that the fossil record was great for higher-level transitions. And this record is vastly better now than in the 1850s!

Here are a handful of interesting transitions recorded in the fossil record:

Some important thing to note about these:

"Intermediate forms" is another related term used in the field. Basically, however, every taxon is intermediate between its closest relative and the groups more distantly related.

An important thing to revisit before we move on: the specter of typological thinking. Our minds like to think of discrete types of things. However, when dealing with evolution, there is a continuum of form from one to another. Remember: at no time did a mother of one species give birth to a daughter of another species! It is only from a distance in time do we see the accumulation of changes.

This applies for groups above the species as well. At not moment in the history of life would you witness a population of one major group giving rise to a population belonging to another major group. It would always look just like ordinary speciation. It is only from a distance that we see the Tree of Life.

Macroevolutionary Patterns
Macroevolution is the term for evolution above the level of the species. In a real sense, it is the summed effect of multiple rounds of microevolutionary (below the species level) changes. But some patterns only become apparent on the grander scale.

We have already seen correlated progression (the summed affect of adaptions consistent with a particular mode of life) and divergence (the splitting of one ancestral group into two or more distinct descendant lineages) as examples of macroevolution. Here are a few more:

"Dead as a Dodo": Defining Extinction
What is extinction? It depends on your context, with different definitions (or at least different emphases) according to different types of scientists: (All of these essentially mean the same thing: there are no more of that kind of organism).

Only two types of taxa can go extinct: species and clades. Old-fashioned gradistic paraphyletic groups could "go extinct" even though their descendants (and thus their genome) persisted on.

The extinction of the dodo (Raphus cucullatus) of Mauritius after the 1660s indicated that species could be driven to extinction by human activity. But there was a great debate in the latest 18th/earliest 19th century as to whether natural extinctions might be possible. Some argued that the Creator would not create something merely to destroy it; others argued that the interactions within the natural world were too closely knit to allow any one species to go extinct without the entire ecosystem collapsing. But the weight of the evidence-- backed by the comparative anatomical studies of Cuvier and his colleagues, as well as more complete exploration of the world-- indicated that there were indeed fossil species no longer present in the world. So people accepted the existence of natural extinctions.

A History of Mass Extinction Studies
Even more, Cuvier demonstrated the existence of mass extinctions (or "revolutions" as he called them): the loss of great parts of the diversity of life, to be replaced by other forms. Furthermore, Cuvier assumed that these revolutions were the products of catastrophes of some sort.

Regardless of their cause, geologist John Phillips (in 1841) used the pattern of fossil diversity, and especially the crash of diversity to define the Eras of the Phanerozoic: thus the boundaries between the Paleozoic and Mesozoic Eras and between the Mesozoic and Cenozoic Eras were mass extinctions.

But not everyone was convinced that mass extinctions were real phenomena. 19th Century geologist Charles Lyell and Charles Darwin thought that there were no mass extinctions: rather, what we thought were Cuvier's "revolutions" were no more than extended gaps in the rock record, making the gradual loss and addition of species at the ordinary rate appear to be the sudden loss and appearance. In Darwin's words (from The Origin):

In the early 20th Century at least some paleontologists resurrected Cuvier's ideas of 'revolutions' under the name of global diastrophism ("diastrophism" being an old world for "geological uplift, mountain building"). Leading scientists such as the American Museum's H.F. Osborn thought that periods of mountain building occurred worldwide, resulting in major climate shifts and causing intense droughts, climate changes, etc.

As it turns out, both the Lyell/Darwin and Osborn ideas were testable by the same observation. Both required that the extinction boundaries would occur at unconformities (erosional surfaces): in the former case, because all the missing record was lost; in the latter, because global diastrophism would cause uplift and erosion. But when many extinction sites were sampled, no such unconformities were found. Something else must be going on.

In the mid-20th Century paleontologist Norman Newell finally coined the term "mass extinction" and recognized these as "crises in the history of life". Because of advances in understanding geologic time, it was recognized that Lyell and Darwin's "gap" argument did not work: there simply wasn't enough missing time to turn these boundaries into "simply business as usual, with missing rock". As for causes, Newell (who worked primarily on marine invertebrates) argued they were mostly due to rapid sea level changes and/or changes in atmospheric composition. Around the same time, German paleontologist Otto Schindewolf argued that some mass extinctions might have been caused by cosmic causes (such as comets colliding with Earth.)

In the later 20th Century paleontologist Jack Sepkoski finally gave us a good working definition for mass extinctions:

Or, in other words, mass extinctions:

Agents of Destruction
When talking about "causes" of mass extinction, we have to recognize we are talking about several different things:

When identifying reasonable causal agents for any given mass extinction, we have to evaluate if that agent:

Some paleontologists have described a distinction between pulse and press extinctions. Pulse extinctions are rapid catastrophic events, which do not allow for adaptive changes during the episode itself. These are the "Game of Thrones" events: you either win or you die. In contrast, press extinctions would be series of events spread out for 100s of thousands of years. In principle, it allows for evolution to select variations throughout this extended interval, so a taxon which is doing poorly early in the event might become progressively better at surviving it over time. (That said, no one has made a good case for any pulse aspect to mass extinctions.)

A related set of terms are proximate vs. ultimate causes. Proximate causes are the events that directly brings about the change. Ultimate causes are the phenomena that sparks the proximate causes. For example, the proximate cause for the sinking of the Titanic was the flooding of the decks through the hole ripped in its side by the iceberg; the ultimate causes were (among other things) failure to spot the iceberg sufficiently in advance to turn it. For any given extinction (or mass extinction), we have varying levels of success in identifying the proximate or ultimate cause.

A problem with all mass extinction studies is the issue of stratigraphic resolution: that is, how closely does our observed record match the actual event itself. The same set of observed data of species disappearing one-by-one running up to a stratigraphic boundary might potentially be explained as a gradual extinction OR it might be explained by the fact that we are statistically unlikely to recover the last population of any given species. This is the Signor-Lipps Effect: the observation that the stochastic nature of fossil preservation and recovery will tend to "smear" out an instantaneous extinction to make it look gradual.

In order to counteract the Signor-Lipps effect we need to have very high sample sizes of fossils and of stratigraphic horizons running up to the possible event. But nature doesn't always provide us with this, so we always have to remember that our ability to definitively say when a particular taxon went extinct is limited.

The Big Five
The 1970s and 1980s saw renewed interest in mass extinction studies, in response to research of the K/Pg event 66 Ma (the one that ended the giant dinosaurs): first, the Russell and Tucker supernova hypothesis, and then the Alvarez et al. discovery of the iridium spike (more about these specifics in a few lectures). While this was going on, invertebrate paleontologist Jack Sepkoski was assembling a huge data base of the diversity of marine life through time. This data (like Phillip's in the 1840s, and Newell's in the mid-20th Century) helped reveal the presence of mass extinctions. In this case, however, Sepkoski worked with fellow paleontologist David Raup in 1982 to reveal statistically a difference between "background extinctions" and "mass extinctions".

In this study, Raup and Sepkoski idenfitied what came to be called "The Big Five": mass extinctions which were statistically quite different from the ordinary level of diversity collapses. Raup and Sepkoski identified the Big Five mass extinctions: the Ordovician/Silurian (O/S, 443.8 Ma), the Devonian/Carboniferous (D/C, 358.9 Ma), the Permian/Triassic (P/Tr, 252.17 Ma), the Triassic/Jurassic (Tr/J, 201.3 Ma), and the Cretaceous/Paleogene (K/Pg, 66.0 Ma). We will look at the Era-ending events (P/Tr and K/Pg) in detail in the next lectures, so let's briefly look at the O/S, D/C, and Tr/J.

Various studies may lose some of these mass extinctions as barely larger than background (especially the D/C), and some mass extinctions may represent multiple events (dividing up P/Tr into two; turning the D/C into two; etc.) the count maybe be more than 5. But we'll stick with the Big Five for this course. (This doesn't meant that there aren't minor mass extinctions: some moderate mass extinctions do seem to exist.)

Let's take a look at the characteristics of the three non-Era ending events:

Ordovician/Silurian (443.8 Ma): The Ordovician Period saw a dramatic increase in biodiversity, but crashes at the end. Perhaps 85% of species are lost (although the total number is less than later ones: there were fewer total species known for the Ordovician than for later in the Phanerozoic.) There is devastation within brachiopods, bryozoans, graptolites, trilobites, and conodonts, but more major clades were lost. A fair amount of evidence suggests there were two pulses of extinction, separated by about 1 Myr.

Despite some news items in the 2000s suggesting a "hypernova" or "gamma ray burster" (extremely huge supernova) explosion being the cause, there is zero (zip, nada, no) evidence for this. Instead, this event coincides with a major period of glaciation. It has been suggested that this might have been responsible for the extinction by perhaps reducing the available habitat area in the shallow marine realm (because of a major sea-level drop), and/or a major period of anoxia from global eutrophication, due to the influx of considerable amount of nutrients from material scraped off the continents from glaciers.

Devonian/Carboniferous (358.9 Ma): For a long time (and to some researchers, some still consider it) to be two extinctions: a first strong one between the Frasnian and Famennian Stages of the Late Devonian Epoch, and the final Devonian/Carboniferous event (also called the "Hangenberg Event"). But newer studies tend to support a single major terminal Devonian event, with the Frasnian/Famennian event as a result of the Signor-Lipps event. This is characterized by a collapse of major reef community (the tabulate-stromatoporoid reef community); as today, reefs in the mid-Paleozoic were MAJOR centers of biodiversity, so collapse of the reef community dragged numerous other species with it. Additionally, there are losses of primitive grades and clades of fish ("ostracoderms", "placoderms", and acanthoidians). There are also major extinctions within trilobites (again), eurypterids, echinoderms (with some major clade losses), conodonts (again), bryozoans (again), and ammonoids (for the first but not the last time). Many of these survived with only a few handful of species to repopulate the Carboniferous.

Although Schindewolf proposed an asteroid impact as the cause for this (without any direct evidence), this is currently best explained as a result of the spread of vascular land plants! With the first rain forest and the first seed plants in the continental interior, there was considerable burial of excess carbon (leading to cooler temperatures and reduced continental shelf space). More importantly, increased mechanical and chemical weathering on the continents leads to increased nutrients into the sea leading to marine phytoplankton booms leading to eutrophication and anoxia. (Indeed, modern coral reefs are suffering from these effects locally because of increased runoff due to human activities in these regions.)

Triassic/Jurassic (201.3 Ma): In some ways a repeat of the P/Tr on a smaller scale. The final extinction of the conodonts, a major diversity crash in ammonoids (AGAIN!), loss of once-major groups of brachiopods and bryozoans, collapse of some corals and sponges, and on land loss of primitive seed plant groups, various diapsid reptiles (especially the majority of the pseudosuchians outside of Crocodylomorpha), and of various therapsids (basically everything but mammals and their immediate closest kin).

The causal agent here is the Central Atlantic Magmatic Province (CAMP for short), a major field of volcanics and intrusive igneous rocks associated with the break-up of Pangaea and the formation of the Central Atlantic Ocean basin. It is comparable in scale to the Siberian Traps of the P/Tr in terms of the area covered and volume erupted, but apparently lower levels of carbon released: "only" 2200-2500 Gt C as CO2 and 4300 Gt C as CH4.

Some minor mass extinctions include:

General Patterns
In general it is a truism that mass extinctions would occur when the rate of extinction greatly exceeds the rate of origination of new species. But are extinction and origination events independent in time, space, and cause? And are these happening gradually throughout the history of a lineage? After all, evidence points towards a general pattern being turnover-pulses: both extinctions and originations/divergences driven at the same time by environmental shifts.

Mass extinction is thus a "Game of Thrones": you only survive or you die. It happens when environmental change happens with such severity that organisms cannot adapt to the shifting conditions. The resultant pattern of life history is long periods of relative stability in terms of groups represented, punctuated by mass extinctions and resorting of the players of the game.

There are some recurring patterns after many mass extinctions. These include:

It has also been noted that after a mass extinction event, taxa that live close to the sediment-water interface typically recover well, but extend upwards and downwards from it as time goes by.

A brief video about the Big Five:

and another, longer one:

A video about Lazarus taxa and Zombie taxa, among others:

And why "living fossils" aren't really a thing:

To Lecture Schedule

Last modified: 7 March 2018

Face of the placoderm fish Duknleosteus, member of a group that died out in the Devonian/Carboniferous Mass Extinction