Introduction to Physical Anthropology

by Arnie Schoenberg
version: 10/13/19


homologous vertebrate forelimbs from * Anatomy and Physiology of Animals/The Skeleton (CC BY-SA 3.0)

Section 4 Contents

4    paleontology

4.1    paleontology → paleoanthropology → archaeology → history

4.2    macroevolution

4.2.1    Hox genes

4.2.2    allopatric speciation

4.2.3    punctuated equilibrium

4.3    species vs. paleospecies

4.4    interspecific vs. intraspecific variation

4.6    plate tectonics

4.7    adaptive radiation

4.8    analogy vs. homology

4.9    taxonomy

4.10    human taxonomy

4.11    mammals

4.11.1    protomammals

4.11.2    examples of living mammals    monotremes    marsupials    placental mammals

4       paleontology

Paleontology is the study of old life forms. To get a sense of how old we're talking about, review the section on geological time.

Now that we've introduced a few basic concepts in biology, we are going to start mapping our family tree. With genetics we've seen that all life shares DNA, that the origin of life is this molecule and its ability to direct the activities of the individual, to accumulate changes, and to copy itself. With DNA at the base of our tree, we'll continue to trace the branches and connect them to our own family.

4.1     paleontology → paleoanthropology → archaeology → history

The roots "paleo" and "archae" mean old. We saw the word "ontology" already when talking about "the origin of how things became" and the different ontologies that religions and science have. Paleontology looks at life in the past, and the most popular branch is dinosaurs. Closely related human ancestors get their own subfield, paleoanthropology, and the dividing line between paleontology and paleoanthropology is usually when they start walking on two feet. Confirmed human ancestors get another field called archaeology, and the line between paleoanthropology and archaeology is usually set at anatomically modern Homo sapiens. History starts with written records. For this class, we focus on paleoanthropology and use paleontology to give an early context.

Although the line between the paleontology and paleoanthropology, and the line between paleoanthropology and archaeology can be blurry, there is a fairly distinct line between paleontology and archaeology. So, if you ever find yourself passing by an archaeological site, and you stop to chat with the archaeologists, if you want to make yourself seem really stupid, ask them "Have you found any dinosaur bones?"

 Pay special attention to the information and figures about brains and teeth because these are going to be trends of human evolution all the way through to the end of this class.

If you are curious about dating techniques and how fossils form, you could jump forward in the textbook and skim the section on paleoanthropology methods too.

* Skim the Early History of Life on Planet Earth

* Skim a good review of geology and speciation

* Podcast with science historian Dr. Elizabeth Jones on the History of Ancient DNA

Skim  How Old is Old?

Skim Wikipedia's Paleontology

Go to Balboa Park and visit the San Diego Natural History museum, it's free with a resident ID on the first Tuesday of the month.

4.2     macroevolution

Another word for macroevolution is speciation, the production of species, this is the level of evolution that Darwin studied, the kind that occurs over immense periods of time, where small changes accumulate to make life diverge into often drastically different forms. Now that we've introduced Mendel and cellular biology we can explain the two main pieces that Darwin was missing, heredity and variation.

4.2.1     Hox genes

Hox genes are a good example of one mechanism that enables drastic biological changes. Minor variations in the same small set of genes direct a zygote to grow into the shape of a worm, fly, mouse, or a human.

Read  Hox gene intro

Review  Micro and Macro Evolution

Living things share common genes.

*Read about Human Accelerated Regions

*Article on the genes for arms and legs coming from fish

4.2.2     allopatric speciation

"-patric" refers to geography. "allo" is Greek for other. Allopatric speciation happens when two populations are separated geographically; if you can't meet, you can't breed; in the absence of gene flow, variations accumulate through mutation and natural selection effects the two populations differently until they become separate species.

skim species for evolutionary biology

4.2.3     punctuated equilibrium

Darwin saw evolution as the gradual accumulation of changes, but looking closer at the fossil record, especially shellfish, later paleontologists began to question Darwin's ideas of phyletic gradualism, and proposed the theory of punctuated equilibrium, where the equilibrium of stasis or lack of change, is punctuated or broken by rapid evolutionary change. Remember that we are using the word "rapid" in a geological sense, usually it means hundreds of thousands of years.

Figure 74 * More on Punctuated Equilibrium © Copyright 2018 by * The University of California Museum of Paleontology, Berkeley and the Regents of the University of California

* skim this intro to punctuated equilibrium

4.3     species vs. paleospecies

Calling a group of organisms a species is not a fact, it is just a hypothesis, and with paleospecies the hypothesis is even harder to test. The classic definition of a species is something we can demonstrate very clearly: if two individuals can have grandkids, then they're part of the same species. With fossils it's tricky to test this. If you bang two fossils together, they don't make baby fossils. How do we decide whether two individuals from distant time periods are part of the same species, we can't use a time machine to bring a sperm and egg separated by millions of years together to see if that offspring is fertile itself. Our usual species test doesn't work. In the next section on paleoanthropology, we will lump fossils into groups and label them with an official-looking genus and species designation written in Latin and in italics, but it's really important for you to remember that this designation is not a concrete fact, it's just a hypothesis that will continue to be tested (and often contested). Understanding that paleospecies are hypotheses will help you to understand the context for many of the debates in paleontology and especially paleoanthropology.

Does the fact that scientist have debates about specific fossils mean that evolutionary theory has been disproven and women really did come from a rib? No, it justs means that science is self-correcting.


* Lygers, Zonkeys, JaglionsÉ skim examples of hybrids

4.4     interspecific vs. intraspecific variation

When you lump a bunch of fossils together and call them a paleospecies, you are saying that all the differences between the fossils are intraspecific variation, variations within a species. If you split all the different looking fossils into separate species then you are seeing interspecific variation, variation between species; intra- means "among" and inter- means "between"

4.6     plate tectonics

Plate tectonics can cause macroevolution. If a species roams over a continent and that continent splits into two, the evolutionary force of migration is prevented, and the two populations will accumulate variations over time until they eventually become separate species.

4.7     adaptive radiation

When given the opportunity, a group of species will expand and adapt to available ecological niches. A classic example is when around 65 million years ago, mammals took on ecological roles formerly held by dinosaurs after the northwest top of the Yucatán Peninsula was pulverized by a * giant asteroid which left the Chicxulub crater, a rain of fire, mega-tsunamis, and a cloud that cooled the Earth for tens of thousands of years.

Figure 75 the impact of meteors can change the weather by Fredrik and NASA (Public Domain)

Figure 76 150 kilometer wide Chicxulub crater, NASA/JPL-Caltech (Public Domain)

When the dust cleared, the surviving mammal species radiated into the ecological niches formally occupied by dinosaurs. One species' misfortune is another's opportunity.

A good article on * dinosaur paleoecology. Morphospace is from morphology meaning the study of shape and space implies a landscape, or in this case an ecosystem where a particular shape is more or less adaptive.

4.8     analogy vs. homology

When I'm swimming in the ocean and see a vertical fin above the water in the distance, I always freak out and think it's a shark even though it always turns out to be dolphins. Dolphins evolved from a four-legged mammal that might have looked something like a hippo, and the dolphin's fin and the shark's fin are coded for by totally different genes, and have totally different evolutionary pathways. Traits that look the same but evolved separately are called analogies.

Homologies are traits that share a common evolutionary pathway and the same genes that code for them. The range of morphology of vertebrate forelimbs is incredible, but they all have the same genetic source, and thus share most of the same bones.


Figure 77 homologous vertebrate forelimbs from * Anatomy and Physiology of Animals/The Skeleton (CC BY-SA 3.0)

When you see two species with similar traits, the first question to ask is are they similar because they had the same ancestors (parallel) or did they have different ancestors but evolved in the same environment.

Figure 78 Parallel vs. convergent evolution by Oleg Alexandrov (Public Domain)


Figure 79 Convergent evolution for water, ichthyosaur vs dolphin by Sceptic view from Wikimedia Commons (CC BY-SA 4.0)

* example of convergent evolution: echolocation in bats and dolphins

4.9     taxonomy

     The two classic lines of evidence to building phylogenetic (macroevolution) taxonomies have been comparative anatomy and fossils. A genealogical metaphor for comparative anatomy would be to try to draw your family tree by comparing the anthropometrics (measurements the body) of potential living relatives, and comparing fossils is like comparing old family photos; it would be very subjective and open to lots of debate.

Recently, genetics has almost completely taken over comparative anatomy research, because it's like going to the primary source, the gene is what codes for the anatomy. It used to be that using fossils was the only way to get dates, but recently, the differences between the mutations in the mitochondrial DNA (mtDNA) of a species can be used to estimate the time when that species split off from another species with different mtDNA.
The fossil evidence gives us a picture that looks like this:

The Earth is very old—4.5 billion years or more according to scientific estimates. Most of the evidence for an ancient Earth is contained in the rocks that form the Earth's crust. The rock layers themselves—like pages in a long and complicated history—record the events of the past, and buried within them are the remains of life—the plants and animals that evolved from organic structures that existed 3 billion years ago.

Also contained in rocks once molten are radioactive elements whose isotopes provide Earth with an atomic clock. Within these rocks, "parent" isotopes decay at a predictable rate to form "daughter" isotopes. By determining the relative amounts of parent and daughter isotopes, the age of these rocks can be calculated.

Thus, the scientific evidence from rock layers, from fossils, and from the ages of rocks as measured by atomic clocks attests to a very old Earth. [United States Geological Service (USGS) 2008 "The Geologic Time Spiral: A Path to the Past]

Description:  spirialing time line depicting fossil species in different time periods

Figure 80 [click for larger image] "The Geologic Time Spiral: A Path to the Past" by Joseph Graham, William Newman, and John Stacy (USGS) 2008) (Public Domain)

The genetic evidence looks like this:

About this Tree: This tree is from an analysis of small subunit rRNA sequences sampled from about 3,000 species from throughout the Tree of Life. The species were chosen based on their availability, but we attempted to include most of the major groups, sampled very roughly in proportion to the number of known species in each group (although many groups remain over- or under-represented). The number of species represented is approximately the square-root of the number of species thought to exist on Earth (i.e., three thousand out of an estimated nine million species), or about 0.18% of the 1.7 million species that have been formally described and named.

Figure 81 [click for larger image] genealogy of life by genetic distance, "The Tree of Life" by David M. Hillis, Derrick Zwickl, and Robin Gutell, University of Texas © 2003

Both imply the differences between living forms and the time when they branched off from each other. The genetic evidence is more concrete about living forms, the fossil evidence is more concrete about extinct life forms and gives more accurate dates.

Taxonomy is another way to think of your family tree. Biologists use different methods to make taxonomies, such as cladistics (better science) and evolutionary systematics (includes dates of speciation events) but as an anthropologist, I tend to emphasize the "genealogy" of classification – how a particular life form fits into my family tree. I try to figure out what part of my DNA I share with that organism, and probably inherited from a common ancestor. With mitochondrial DNA dating, we can get pretty close to calculating when the common ancestor between two life forms lived and when the split started.

For this class you can use most terminology interchangeably: taxon = clade = branch = phylum = group.

Taxonomies are often presented as definitive answers but try to think of them more as hypotheses or questions about how two species are connected. The whole family tree metaphor has recently come under attack by the evolutionary implications of processes like lateral gene transfer, and fuzzy hybrids, and we are learning more and more that evolution doesn't always follow a nice clean straight line. We have a lot of philosophical baggage that pushes us towards trying to cram complex systems into simple taxonomies (e.g. Porphyrian trees). Linnaeus did it for all life, I did it to introduce how anthropology fits into the branches of knowledge, we do it to represent our family, but none of these taxonomies deals with the exceptions very well.

Figure 82 "Compilation of six Porphyrian and derivated trees" by me! ;)), Wikimedia (Public Domain)

As we saw in the section on lateral gene transfer, there have been examples of two species interchanging DNA without having sex. Also, the concept of a species is not as rigid as we'd like to make it. Every once in awhile the normal sterile hybrid offspring of two different species can be fertile (Horse + Donkey = normally sterile mule).  These events are rare, so it's still worth learning classic evolutionary theory, but we can extrapolate from Charles Lyell's principle of Uniformitarianism that small changes can cause big effects over long periods of time. Call me stubborn, but I'm still not ready to give up on the family tree metaphor. LGT is good evidence that evolution doesn't follow the kind of clean branches that Darwin first sketched, but I think we can still go back to trees to save the metaphor and illustrate how life separates over time into distinct species, but can still occasionally come back together to share genetic material. Have you ever seen how when two separate roots or branches grow right next to each other for a long time that they sometimes fuse and become one root or one branch?

Figure 83 banyan roots grow apart and then together at Wat Mahathat, Ayutthaya, Thailand. "Buddhas Head" by Simon Gurney © AdobeStock #1022942


The theme of separation and reconnection plays an important part in the interpretation of our own recent evolutionary history.

Figure 84 * Reed DL, Smith VS, Hammond SL, Rogers AR, et al. (2004) Genetic Analysis of Lice Supports Direct Contact between Modern and Archaic Humans. PLoS Biol 2(11) (CC BY 4.0)

Figure 85 "Homo lineage 2017 update" based on * Stringer, C. (2012). "What makes a modern human". Nature 485 (7396): 33–35. by Conquistador, Dbachmann via Wikimedia (CC BY 4.0)

Figure 86 Extension to 600 kya (Homo sapiens). 2018 by Dbachmann via Wikimedia (CC BY 4.0)

* another good article about the "tree of life" metaphor

4.9.1 Astrobiology

This class focuses on the planet earth where humans evolved and share ancestry with all known life. But, it's fascinating to think of what life on other planets may be like. There are some serious hypotheses that some evolution may have taken place on other planets and been brought to the earth through meteors

* life in extreme environments.

4.10  human taxonomy

The classic Linnaean taxonomy is a simplified part of your family tree without drawing in all the branches. Linnaeus was great for the 1700s, but can be very misleading today if you try to cram all the different branches of life into arbitrary horizontal categories like: Kingdom, Phylum, Class, Order, Family, etc. All of these categories are arbitrary and the only way to make them work is through lots of "sub-" and "super-". But, it's still useful to ask why the split between two taxa is being made: What do they have in common? How are they different?

So if I want to compare and contrast myself to a frog, I go up the tree to the place where vertebrates split into amphibians and mammals. I will share most of the characteristics of other vertebrates with frogs, and I will be different from frogs in most of the ways mammals are. This helps you determine who is a closer relative, and this is useful in many different ways, e.g., if you want to predict how pollution might effect humans, it is usually better to look at mammals rather than amphibians, if you test a drug on pregnant rhesus monkeys, it might act differently on human mothers because we have a different placenta.

Kingdom: Animalia

Phylum: Chordata

Subphylum: Vertebrata

Class: Mammalia

Subclass: Theria

Infraclass: Eutheria

Order: Primates

Suborder: Anthropoidea

Superfamily: Hominoidea

Family: Hominidae

Genus: Homo

Species: sapiens

(adapted from the Linnean Classification of Humans Dennis O'Neil 2012)

* article on fish with legs, and the evolution of vertebrate limbs.

4.11 mammals

 There are three main branches of mammals alive today, classified mostly on their reproductive system, monotremes lay eggs, marsupials have pouches, and placental mammals keep the kids inside for longer.

Much of what it means to be human is shared with all mammals.

* Humans who can wiggle their ears share the same vestigial auricular muscles with other mamas.

4.11.1 protomammals

Dinosaur-like mammals existed around hundreds of millions of years ago. They evolved into reptiles, mammals, dinosaurs, and birds.

* A new protomammal fossil

* podcast on early mammals from the age of dinosaurs

4.11.2 examples of living mammals

The split between the three groups of mammals living today happened while they were dodging huge dinosaurs in the Triassic period (250-200mya).

The three types of mammals:  monotremes

The monotremes, or protheria, were once a large group of mammals that roamed the world, but today there are only two surviving species: the echidna and the duck-billed platypus. They lay eggs, have poison glands, and have other features we commonly consider reptilian.

Figure 87 Echidnas are sometimes called "Spiny Anteaters" because of their analogous form, but they are only distantly related to their placental anteaters, "Short beaked echidna (Tachyglossus aculeatus) in Ben Boyd National Park" by Sharon Wormleaton, Australia, New South Wales Governement, Office of Heritage & Environment (CC BY 4.0)

Say NO to Progress !

As we discussed in the section on Evolutionary Theory, it's hard not to see ourselves as the end result of evolution, as if the reason for evolution was to make us. For an anthropology class we tend to imply this, but don't get the wrong idea about evolution. Evolution is not directional or progressive, it just means change. To help avoid anthropocentrism, consider that the highest pinnacle of evolution could be the duck-billed platypus. Notice the picture of Charles Darwin as a representative of the "inferior mammals" in the duck-billed platypus family tree:

Figure 88 "Cumbre de la evolución: Ornithorhynchus" by PaleoFreak © 2006 (permission pending)  marsupials

Marsupials, also called metatheria, are animals where newborns must crawl to their mother's pouch to nurse until developed. There are over 300 marsupial species alive today, and two thirds are found in Australian. Here is is a small sample:


Figure 89 Kangaroo with joey in pouch (CC0 1.0)


Notice the opposable digits and claws that allow the koala to grip the branch. How is this different from the human hand?

Figure 90 Female Koala (Phascolarctos cinereus) at Billabong Koala and Aussie Wildlife Park, Port Macquarie, New South Wales, Australiah, by Quartl, Wikimedia Commons (CC BY-SA 3.0)


The opossum is the only marsupial native to North America.

Description: ndiri indiri

Figure 91 Opposum pouch with babies © 2010 The Wildlife Rehabilitation Clinic. (permission pending)

Opossums are great for our ecosystem because they clean up trash, chase away rats, and carry fewer zoonotic diseases. We'll cover zoonosis in more detail in the section on human variation, but looking at the taxonomy of mammals, we see that opossums are very distant relatives to humans, and that distance means different genetic makeup, different proteins, and a different environment for diseases to adapt to, so it's harder for diseases that are adapted to living in opossums to jump to humans.

So be nice to opossums. Drive carefully at night! Opossums are nocturnal, and their defense mechanisms to avoid predation includes moving slowly and playing dead so as not to evoke the chase response from predators. That strategy has evolved for tens of millions of years, but natural selection from automobiles has only been around for a hundred years.

Opossums are nomadic and babies travel with the mother in the pouch or on her back until they are self sufficient. So if you find a single baby opossum with no mother around, it needs help. Put it in a box, keep it warm, do not feed it anything and call a rescue organization. The same goes for finding live baby opossums around a dead mother, but bring the mother too just in case she's "playing 'possum". If you find a dead mother with a pouch full of wriggling babies, if you bring the dead mother and babies to a rescue organization with the babies still in the pouch undisturbed, they will often survive.

In San Diego County, the San Diego Humane Society runs Project Wildlife Phone: (619) 225-9453

More info from the Opossum Society of the United States  placental mammals

Placental mammals, also called eutheria, are known for carrying their fetuses inside a protective placenta until birth.


Figure 92 Group of lemurs by Tambako The Jaguar (CC BY-ND 2.0)

Description: my cousin once removed

Figure 93 Homo sapiens by M © 1994


Figure 94 blue whale by NOAA (CC BY 2.0)


Figure 95 bat fossil (public domain)

Imagination Questions

Does taxonomy make you feel more part of the animal kingdom? Try the exercises below to broaden your family tree.

1) How does the Linnaean taxonomy of humans compare to other life? For every branch in the Linnaean taxonomy of humans, find another species that fits into the categories above ours, but not those below it. For example, for "Order" you might pick cats, which have the same Kingdom, Phylum, Subphylum, Class, and Infraclass as us, but belong to a different Order.

Kingdom: Animalia

Phylum: Chordata

Subphylum: Vertebrata

Class: Mammalia

Subclass: Theria

Infraclass: Eutheria

Order: Carnivora

2) Take the first five to ten letters of your name and pick an animal that starts with each of those letters. Find the most recent common ancestor by looking up the origin of their common groups, and draw a taxonomy that connects all the animals and gives the dates when they split from each other. For example: Aardvark, Rhinoceros beetle, Newt, Ibis, Elephant. Insects first arose about 400 million years ago (mya), amphibians around 300 mya. Mammals split around 260 mya from the reptiles that became dinosaurs and then birds. The oldest fossil ancestors of Elephants and Aardvarks have been found only about 10 million years apart, about 60 mya and 50 mya, which is around when the first primate ancestors were found too, because of the adaptive radiation of mammals after 65mya. So Aardvarks and Elephants are my closest cousins, and Rhinoceros beetles probably don't get invited to many family functions.

3) Draw your family tree back to the Big Bang. Follow your maternal line back, skipping generations in powers of ten. Look up what ancestor was around at times below in the column "years ago" and briefly describe your sample "grandmothers".
I calculated the "years ago" column by multiplying the number of generations by the average generation length. I estimated the average time between generations by taking the average age of fertility, from menarche (first menstruation) to menopause (last menstruation)/death.

power of ten


average age of menarche (first menstruation) average reproductive lifespan or age of menopause

average generation length (years)

years ago

Who was my Great, Great […] Grandma?

Arnie's example:



13 50







17 40




great, great, great, great, great, great, great, great, great, great, grandmother, probably an Irish peasant



? 25




great, [x100], great grandmother, possibly a Celtic peasant



? ?




great, [x1000],great grandmother, an anatomically modern Homo sapiens hunter-gatherer possibly in the Iberian Peninsula with Maternal Haplogroup H3 (I happen to know this because I had my mitochondrial DNA tested)

figure 96 H3 maternal haplogroup © 23andMe, Inc. 2007-2017



? ?







? ?







9 ?














































great, […],great grandmother, an algae-like eukaryote


10, 000,000,000,000





great, […],great grandmother, a cyanobacterium in a stromatolite







great, […],great grandmother, a strand of self- replicating molecules swirling in primordial ooze








Vocabulary 4

convergent evolution
divergent evolution


previous section: 3 osteology

next section: 5 primatology

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problems (mistakes, bad links, etc.)