Cetacean Evolution and Diversity

Scientists have known for hundreds of years that whales were mammals (e.g., they give live birth, have sparse hair, produce milk for young). For most of that time, however, where they fit in the mammal family tree was a mystery, and very few fossils had been found that showed their transition from land to water. But an explosion of discovery and research over the past 30-40 years has solidified our understanding of how, when, and where whales evolved from their terrestrial mammal ancestors. In this lab you will:

  1. Watch a video describing the evolution of cetaceans and explore these transitions using 3D models. You will answer a set of questions about these transitions in the Whale Evolution Quiz.
  2. Watch a video overview of extant cetaceans and learn to identify local whales and dolphins from their external features, especially those you can see from above water while on a whale watching tour. You may then be quizzed on your ability to identify these local species.

There are five questions throughout this lab. A .docx file with those questions can be downloaded here:

Cetacean Evolution

Cetaceans can be categorized taxonomically into three major groups: Archaeocetes (ancient whales), Mysticeti (baleen whales), and Odontoceti (toothed whales). Arachaocetes have ancestral morphologies including external hind limbs, semiaquatic lifestyle (e.g., giving birth on land), and heterodont/diphyodont dentition. In contrast, extant whales have more telescoping (elongated) skulls and are completely aquatic (no external hind limbs). You’ll learn more about them in the next section.

In the latter half of the 20th century, increasingly powerful molecular tests confirmed that whales were most closely allied with artiodactyls, the even-toed ungulates like antelope, deer, pigs, and giraffe. By the 1990s, analyses were starting to place cetaceans (Order Cetacea) within Order Artiodactyla as a sister taxon to hippopotamuses. This meant Cetacea was no longer a valid order (you can’t have an order within an order!); Artiodactyla became Order Cetartiodactyla, whales and hippopotamuses were placed into Suborder Whippomorpha, and Order Cetacea was downgraded to Infraorder Cetacea (Mysticeti and Odontoceti are “parvorders”).

Phylogenetic tree showing several lineages of Archaeocetes branching off first, followed by extant Mysticeti and Odontocetic (Crown Cetacea). Hippopotamidae are shown as the sister taxon to all Cetaceans.
Evolutionary tree of Cetacea

1. Looking at the phylogenetic tree in the figure, Arachaocetes is a group that includes all of the stray branches off of the tree before crown cetaceans evolved. What type of taxonomic group is this (hint: it ends in “–phyletic”)? What type of taxonomic groups are Mysticeti and Odontoceti?

In 2001, two publications reported on the morphology of whale astragalus bones (ankle bones), which have pulley-shaped grooves that improve flexion and are adaptations for high speed running; extant Cetaceans lack these bones entirely as they lack hindlimbs. They compared the astragalus bones of several Eocene archaocetes to those of extant terrestrial cetartiodactyls and other mammals. Artiodactyls have a double pulley shaped (grooved) astragalus allowing flexion both above and below the bone; most other mammals have a single pulley above the bone, but the base is flat. Compare the Pakicetus (an archaocete) astragalus to those of other extant mammals:

Four astragalus bones side by side showing a single pulley morphology on Canis, and double pulley morphology on Pakicetus, Sus, and Odocoileus.
Astragalus bones from one carnivore (Canis), one ancestral cetacean that still had hindlimbs (Pakicetus), and two extant terrestrial ungulates (Sus and Odocoileus)

2. What does this discovery tell us about the evolution of cetaceans and what can cetacean fossils tell us that extant cetacean bones cannot?

Watch this video on whale evolution:

The earliest archaeocetes look fairly terrestrial, while the most recent look very similar to extant cetaceans. The earliest archaocete clade is Pakicetidae, which lived in Indo-Pakistan in the early to middle Eocene (47-53 Mya). They probably moved between terrestrial and freshwater environments, feeding on freshwater prey. They retain many features typical of early terrestrial artiodactyls (e.g., long limb bones, no telescoping of the cranium).

Artist rendering of Pakicetus inachus
Pakicetus inachus (Nobu Tamura ( – Own work, CC BY 3.0, )

Intermediate between Pakicetids and later archaocetes, were the Ambulocetidae, which lived in the middle Eocene (46-48 Mya). Ambulocetus was probably an ambush predator with an alligator-like lifestyle, waiting for prey in shallow fresh water.

Articulated museum skeleton of Ambulocetus natans
Ambulocetus natans (Momotarou2012 – Own work, CC BY-SA 3.0, )
Artists rendering of Ambulocetus swimming in water
Ambulocetus swimming (Nobu Tamura email:[email protected] – Own work, CC BY-SA 4.0, )

3. What changes in skull, limb, and body morphology do you see between Pakicetus and Ambulocetus?

Next up, Protocetidae first evolved in Indo-Pakistan but then diverged and spread rapidly through North Africa and North America from 37-48 Mya. They likely lived in marine environments in coastal areas foraging for fish and invertebrates. They still had a pelvis and well-developed hindlimbs, but the sacrum is weaker, suggesting limited ability to walk on land. The vertebrae are beginning to become more uniform, reflecting a more undulatory mode of swimming.

View this 3D model of the protocetid Maiacetus. Load the model and experiment with the controls. Leave this model open in a new browser tab for the next step.

The final archaeocete family we’ll explore is Basilosauridae. This group lived all over the world in the middle to late Eocene and were fully aquatic. They likely ate vertebrate and invertebrate prey and swam with both undulatory and oscillatory movements.

In a new browser tab, view the 3D model of the basilosaurid Dorudon. In these browser windows you can not only manipulate the model, but also take measurements. Move your mouse arrow over the tip of the tail of Maiacetus and press “S”. A dot should appear on the tail tip. Now move your arrow over the tip of the nose and press “E”. A second dot and a line connecting the dots appears and you should see a measurement in the upper left corner of the screen. Write this down. Now measure the length of the humerus bone in the same way. Do this for both Maiacetus and Dorudon.

4. Calculate the ratio of humerus:body length for each species and report them. What does the difference in this ratio suggest about the changing lifestyle of these groups? Describe THREE other pieces of morphological evidence of evolutionary change can you see in the models?

In addition to the shifts in morphology over the course of cetacean evolution, their lifestyles can also be studied using evidence from the fossil record. While most large bodied mammals require a source of freshwater and cannot desalinate large amounts of salt water, modern cetaceans have evolved this ability. Researchers have studied the drinking behaviors of extant and extinct cetaceans using stable oxygen isotopes. 16O and 18O are the two most common isotopes of oxygen and the ratios of the isotopes differ in fresh and salt water. Marine (oceanic) water has higher concentrations of 18O than does freshwater, and we can analyze the oxygen isotopes in the calcium phosphate of mammalian bones to determine what type of water they were drinking and, therefore, living in. Below is a figure showing the oxygen isotope ratios of modern marine and freshwater cetaceans along with those of extinct cetaceans.

Graph showing oxygen isotope ratios of modern and extinct cetacean species.
Stable oxygen isotopes of extant and extinct cetaceans. Modified from Thewissen & Bajpai 2001, Bioscience 51(12). Copyright Oxford Academic.

5. Interpret the figure above, and compare and contrast the types of bodies of water that early cetaceans (e.g., pakicetids, ambulocetids), later proto- and remingtonocetids, and most modern marine cetaceans live in.

Modern Whale Diversity and Identification

The modern extant cetaceans are divided into two groups: the Mysticeti (baleen whales) and Odontoceti (toothed whales). Baleen whales are named for their large plates of baleen (made of strands of keratin) and lack of true teeth, but baleen whales evolved from toothed mysticetes that eventually lost their true teeth and were either toothless or had/have baleen plates. Odontocetes have retained their teeth (although most now have simple homodont dentition) and have the ability to echolocate to detect prey, other whales, and underwater topographic features.

Watch the video below to learn about modern cetacean diversity:

Now that you have a handle on the types of extant cetaceans that live all over the world, it’s time to learn to identify some local whales. Many of you may have taken a whale watching trip at some point, and the waters off of Southern California have a number of baleen and toothed whales that you can spot with regularity. For the remainder of this lab, you will learn to identify the local species of whales using images from the surface of the water so that the next time you go on a whale watching trip, you will be able to identify what you see!

For each of the 10 species below examine the 3D model and associated photographs. You should, on your own, conduct Google Image searches of each species to find more images that show the same features and use these to study from. Learn to identify the distinguishing characteristics of each species. You may be quizzed using actual photographs (not the ones below) to demonstrate your ability to identify these species.

Odontoceti (dolphins and porpoises)

Short-beaked common dolphin (Delphinus delphis):

Most common year round with megapods in Summer. Look for a distinctive cream-colored patch on the side of the thorax with pale white underbelly; stout but distinctive beak, eye surrounded by pale color; 1.5-2m in length.

Teddy Llovet; ; Attribution 2.0 Generic (CC BY 2.0)
Stuart Wilson;; Attribution 2.0 Generic (CC BY 2.0)

Bottlenose dolphin (Tursiops truncates):

Common year round. Uniformly gray with pale white underbelly; distinctive crease between the melon and short stubby beak; 2-4m in length.

Brandon Trentler 2.0 Generic (CC BY 2.0)
Ed Clayton; 2.0 Generic (CC BY 2.0)

Risso’s dolphin (Grampus griseus):

Less common but mainly Summer and Fall. Lacks a beak; body pale gray and usually heavily scarred; 3m in length

© Citron, CC BY-SA 3.0,
Don Owens; 2.0 Generic (CC BY 2.0)
Don Owens; 2.0 Generic (CC BY 2.0)

Harbor porpoise (Phocoena phocoena):

Less common and only north of Pt. Conception. Small body with gray dorsum fading to a white pale underbelly, very small triangular dorsal fin; 1.4-1.6m in length

Erik Christensen; CC BY-SA 3.0,
Ecomare/Salko de Wolf Den Hoorn Texel – Ecomare, CC BY-SA 4.0,

Pacific White Sided Dolphin (Lagenorhynchus obliquidens):

Rare but mainly in Winter and Spring; Distinctive white patches on the side of the thorax and down the dorsal sides of the tail; bicolored dorsal fin that is more hooked than other dolphins; very short beak; 1.7-2.5m in length

NOAA; ; Attribution 2.0 Generic (CC BY 2.0)
Joe McKenna; 2.0 Generic (CC BY 2.0)

Mysticeti (baleen whales):

Humpback whale (Megaptera novaeangliae):

Very common especially in Fall and Winter; Humped back with oddly stumpy dorsal fin; variable color on underside of fluke (black – white blotches – all white); long white pectoral fins; 14-17m in length

Anna Borenstein;; Attribution 2.0 Generic (CC BY 2.0)
Dan; 2.0 Generic (CC BY 2.0)
Laurel’sPhotos;; Attribution 2.0 Generic (CC BY 2.0)

Gray whale (Eschrichtius robustus):

Very common but mainly in Winter and Spring. They make the longest migration of any mammal on earth when they travel from Alaska down the coast towards Mexico in December-February, and then back northward in March-May. No dorsal fin but small hump and many bumps down the posterior dorsum; Gray mottled skin and fluke; More pale top of the head; 12.8-16.8m in length

Sam Beebe; 2.0 Generic (CC BY 2.0)
Sam Beebe; 2.0 Generic (CC BY 2.0)
Sam Beebe; 2.0 Generic (CC BY 2.0)

Minke whale (Balaenoptera acutorostrata):

Common Winter through Summer; Short body; curved sickle-shaped dorsal fin; white band across pectoral fins; varying degrees of white bands on flank; doesn’t usually expose tail fluke; 7.8-8.8m in length

Vaughn Mullen; 2.0 Generic (CC BY 2.0)
Jtweedie1976;; Attribution 2.0 Generic (CC BY 2.0)
RobOo;; Attribution 2.0 Generic (CC BY 2.0)

Blue whale (Balaenoptera musculus):

Less common but mainly seen in Summer; Huge body (largest animal to ever live); mottled gray or blue-gray; very small dorsal fin far back on body; white underside to tail fluke; 23-24m in length

David Slater; 2.0 Generic (CC BY 2.0)
Jerry Kirkhart; 2.0 Generic (CC BY 2.0)
Kenny Ross;; Attribution 2.0 Generic (CC BY 2.0

Fin whale (Balaenoptera physalus):

Less common but mainly seen in Spring; Distinctive boundary between dark gray dorsum pale underbelly at pectoral fins; strongish dorsal fin but not hooked; doesn’t usually expose tail fluke; 18-19m in length

Charlie Jackson; 2.0 Generic (CC BY 2.0)
Pam Gaynor; 2.0 Generic (CC BY 2.0)

Now that you have seen all of the local species, go back and study your images and learn the names of each species. If you are interested in purchasing a field guide to learn more about identifying the marine mammals of California (including pinnipeds), I recommend Allen et al. 2011 (information below).


  • Allen, S.G., Mortenson, J., Webb, S., 2011. Field Guide to Marine Mammals of the Pacific Coast. University of California Press, Berkeley, 569pp.
  • Marx, F.G., Lambert, O., Uhen, M.D., 2016. Cetacean Paleobiology. Wiley Blackwell, West Sussex, 319pp.
  • Thewissen, J.G.M. & Bajpai, S. 2001. Whale Origins as a Poster Child for Macroevolution. Bioscience, 51(12), 1037-1049.


Mammal Origins & Evolution


Mammals have been the dominant terrestrial megafauna on Earth since the extinction of the dinosaurs 65 million years ago. They have left an extensive fossil record, and their earliest ancestors that were distinct from other amniote lineages date back to the early Carboniferous period, 315 million years ago. But true mammals (members of Class Mammalia) wouldn’t appear until the mid-late Triassic, about 70-80 million years later! In this lab, you will explore the evolutionary history of the lineage that produced the mammals through media and 3D models of actual fossils. Then you will take virtual tours of two museums to learn more about mammal evolutionary history.

There are nine questions to answer in this module, and you can download a .docx file with just the questions here:

The early mammal relatives and all of their decendants make up a giant branch of the vertebrate tree called Synapsida. Some people call the earliest groups “mammal-like reptiles”, but this is really misleading, as reptiles are members of an entirely different branch of amniotes, Diapsida. We’ll start with the earliest synapsids, the Pelycosaurs, but first watch this short overview video on the synapsids that preceded true mammals:

Now that you have a basic idea of how true mammals evolved from these early ancestors, let’s dive a little deeper into some of the most important groups and evolutionary transitions.


The first great radiation of Synapsids included several different groups of large lumbering “reptile-like” lineages, including the famous Dimetrodon. Have a look at the model of a Dimetrodon skull chomping down on the ancient amphibian Euryops. Feel free to use your mouse to move around the skulls and explore.

Recall that the distinguishing feature of Synapsids is the single temporal fenestra. In this model, you can see two large openings. The anterior/front hole is the eye socket. The rear hole is that single temporal fenestra. Keep an eye on that as we move forward to look at later lineages. Also note the different lengths of teeth. Yes, they all look sharp and pointed like a reptile’s teeth, but the fact that they differ slightly in size and shape means they could be used for different functions while chewing.

1. How might the longer canine-type (caniform) teeth be used differently than the smaller teeth in the rear of the jaw?

Now have a look at a 3D model of Dimetrodon with its skin on and watch this video about Dimetrodon.

Probably the most recognizable feature of Dimetrodon and many other Pelycosaurs of the time is the large “sail” formed by a row of long spines growing out of the vertebrae of the spinal column. While we still don’t know its exact function, there have been several hypotheses including thermoregulation or sexual signaling.

2. Based on what you learned in the video, explain how the current evidence suggests that its primary function was most likely as a sexual signal, and why the evidence is less supportive of the thermoregulation hypothesis.

By the end of the Permian, the pelycosaurs were gone and replaced by a more advanced group of synapsids, the therapsids.


Therapsids are another wastebasket group of synapsids that include big predators with long, sharp teeth, but also the very first large terrestrial herbivores! One of these groups, Dinocephalia, had bumpy heads with bony projections that they probably used as battering rams. Another group was the Dicynodonts (see Kannemeyeria below), huge herbivores with large canines, a “beak” that lacked teeth, and a bodies that weighed up to 1000kg (2200lbs)!

Artist rendering of the dicynodont Kannemeyeria latifrons. Large green stocky body with a robust head and stumplike canine teeth emerging from the mouth. Creature has a sprawling gait and short tail.
Dicynodont Kannemeyeria latifrons          © Diego David Colmán

But there were still huge predatory hunters like the Gorgonopsians, with large canines, huge skulls with strong muscles for chewing, and bear-like bodies weighing about 300kg. Look at the skull and body of the gorgonopsian Inostrancevia.

3. Inostrancevia has the more advanced Therapsid skull and body adaptations. Looking at the skull, describe the shape and size of the temporal fenestra relative to Dimetrodon. Looking at the full body, what is happening to the position of the limbs?

Most of the therapsids died out in the Permian extinction 252 million years ago when three-quarters of terrestrial species went extinct. This led to the next major synapsid radiation, the cynodonts.


The cynodonts are a wastebasket group of lineages that lived in the Triassic and were very similar to the therapsids that came before them. But they also possessed more mammal-like features than their predecessors. One of the most well-known cynodonts, Thrinaxodon liorhinus, was weasel-like in shape and one of the few carnivores of its time. Look at the skull model and the body image shown below.

Full body artist drawing of Thrinaxodon. Body has brown, short hair, with a somewhat sprawling limb posture, and a short tail. The head has sharp heterodont teeth with sharp canines.
Thrinaxodon © Dinoboy336

4. What new advancements do you see in the skull of Thrinaxodon relative to Inostrancevia?

In addition to changes in the skull, these groups had a muscular diaphragm to assist with breathing, whiskers on the snout, a complete secondary palate that allowed them to chew and breathe at the same time, and a jawbone with only few bones left in it (recall that pelycosaurs have 7 bones in the lower jaw and true mammals only have 1, the dentary bone). The last cynodont groups were even more mammal-like in their features, and it’s difficult to know where to draw the line between them and “true mammals”, but most consider the possession of a single dentary bone in the lower jaw with the jaw articulation between the dentary and squamosal bones to be the best indicator of what defines a true mammal.


The first true mammals are described as mammaliformes because they aren’t part of crown-group Class Mammalia, which branched off a little bit later and includes all of the extant true mammals. These mammaliformes were mostly mouse-like in size and appearance. Critically, they possess the defining synapomorphy of true mammals: a single dentary bone in the jaw articulating with the squamosal bone in the cranium to form the jaw joint. One of the most primitive true mammals was Morganucodon, a shrew-like Morganucodont. Mammaliformes only had one round of tooth replacement (diphyodonty), as opposed to multiple waves of tooth replacement of their ancestors (polyphyodonty). Look at the Morganucodon skull model and body drawing below.

Artist drawing of Morganucodon watsoni. Shrewlike in appearance with pointed rostrum with small eyes and large whiskers. Undersides are white. Body has more upright posture with longer tail.
Morganucodon watsoni © By FunkMonk (Michael B. H.) CC BY-SA 3.0

The Docodonts, another major mammaliform group, were unique in that they had complex, square crowns on the molars (rather than three-cusped patterns of Morganucodon and other early insectivores), suggesting they had a more omnivorous diet. Discovery of full skeletons revealed that this group varied widely in ecology and lifestyle. There were arboreal, squirrel-like species (e.g., Agilodocodon), mole-like burrowers (e.g., Docofossor), and beaver-like swimming diggers (e.g., Castorcauda lutrasimilis).

5. What advancements in the skull do you see in Morganucodon compared to Thrinaxodon and the other skulls before it? Pay special attention to the teeth, zygomatic arch (“cheekbones”), braincase, and jawbone.

Subsequent mammaliformes, members of crown-group Class Mammalia including extant Monotremes and Therians, diversified greatly from these early forms, but most were still quite small as they were living among the dinosaurs. They were probably mostly burrowing or living deep in vegetation to stay safe, and remained in hiding for about 130 million years. The dinosaurs went extinct 65 million years ago, which means that for 2/3 of the age of mammals (~200 million years), mammals were living in hiding from the dinosaurs. It has only been in the last 1/3 that mammals have emerged as the dominant terrestrial animals and have grown in size and diversified into all ecological niches.

Virtual Field Trips

Finally, while you may not be able to see these amazing fossils in person, many museums now have virtual tours that allow you to walk through and see all of their exhibits for free! The American Museum of Natural History in New York City has one of the very best public exhibits of fossil mammals in the world, and today you will get a chance to see it virtually! Begin your walkthrough with the synapsids here to get to the best starting point for the tour.

As you move through the exhibits, look at each area (look for X’s on the floor and arrows guiding you around) and try to zoom in (controls in the bottom left corner) on the displays to read what they say. Below are seven skeletons to find that are labeled clearly enough to identify and bear adaptations that deviate significantly from the earliest small mammals (e.g., Morganucodon).

  • Simosthenurus – an extinct kangaroo
  • Edentates: Glyptodont – the traveling tank
  • Edentates: Giant ground sloth
  • Carnivores: Smilodon
  • Megaloceros – the giant Irish Elk
  • Stenomylus – a small camel
  • Mammut – mastodon

6. Find five of these skeletons, select ONE favorite and take a screenshot. Submit the screenshot to your instructor, and briefly describe TWO clear skeletal features of the skeleton you selected that differ from Morganucodon and what the function of each change might be (e.g., large antlers evolved for sexual combat).

Finally, we’re going to move forward in time to the last Ice Age (50K years ago) and take a tour of the La Brea Tar Pits in Los Angeles. Interestingly, “La Brea” means “the tar”, so you’re really visiting “The The Tar Tar Pits”! The tar pits are amazing treasure troves of fossils big and small, from microfossils of sea life and pollen to megafauna like mammoths, mastodons, dire wolves, and saber-toothed cats. Read the information in their virtual tour, look through the image slides, and watch the short videos.

7. Why did paleontologists reopen Pit 91, and what type of information have they learned?

8. How do the paleontologists use modern bones from outside the tar pit?

9. Why are there far more large carnivores in the tar pits than herbivores?

10. How and why have coyote diets changed from before the extinction of other large carnivores (e.g., sabre-toothed cats and dire wolves) to present day?