Link back to the Teacher’s Guide Table of Contents

Contents

  1. Natural and artificial selection; population genetics
  2. Speciation
  3. Evidence for evolution
  4. Phylogeny
  5. Origin of Life

Week 24: Natural and Artificial Selection; Population Genetics (Topics 7.1 to 7.5)

Unit 7: Introductory Thoughts

First, a gripe about the College Board’s name for Unit 7. It’s “Natural Selection.” That’s way too narrow. In fact, one of the major ideas of topics like population genetics and extinction is that not all evolutionary change is selective. There’s a big dose of randomness, which is what genetic drift is all about. There’s also a big dose of contingency in evolutionary history. Who dies in a mass extinction is at least partly about being in the wrong place at the wrong time. The survivors (like our mammalian ancestors who survived that asteroid impact that ended the reign of the dinosaurs 65 million years ago) were often just lucky. Remember to emphasize both ideas to your students.

Topic 7 is a big chunk of our AP Biology course, and the Course and Exam description allots Topic 7 more class periods and a higher AP exam weighting than any other unit. It’s also, to my mind, the apex of our course: it brings together what you’ve previously taught in every other unit, and it sets the stage for ecology. The College Board suggests about 20 – 23 class periods, and I think that’s about right.

However, I make two modifications to the CB sequence that lets me cut this down by a few days. First, I start off the year teaching about natural selection and adaptation. Why? Well, if you agree with Dobzhansky that “nothing in biology makes sense except in the light of evolution,” then you need to teach natural selection and adaptation right at the start of your course. Otherwise, phenomena like the fit between enzymes and substrates don’t make sense. The same is true for the complementary match between receptors and ligands. In addition, teaching just a little bit about natural selection sets you up for teaching about heterozygote advantage when you teach about sickle cell disease in units 5 and 6.  If you didn’t do so this year, consider a day or two about natural selection at the start of next year.

Secondly, I love teaching about the origin of life. But most years, just to save a bit of time, I have my students complete my Origin of Life module over Spring Break or Winter Break. The only prerequisite is that students understand the central dogma. I’ll share more thoughts about the Origin of Life below.

That having been said, let’s look at the objectives for the few first topics in this unit: Natural and Artificial selection, and Population Genetics.

Learning Objectives (with comments): Topics 7.1 to 7.5 (Natural Selection and Population Genetics)

The College Board’s original objectives for these topics are extensive. Here’s a condensed and guided version of what you need to cover.

Topic 7.1: Introduction to Natural Selection

  1. What adaptations are.
  2. How the mutations that lead to adaptation are themselves random. The non-random part of natural selection is the selection part. If it weren’t for mutation, all that selection could do would be to cull the population of less adaptive phenotypes. Mutation is what makes the process of natural selection creative and open-ended.
  3. How natural selection works: The philosopher Daniel Dennett called natural selection “the best idea anybody ever had…It unites the two most disparate features of all of reality. On the one side purposeless matter and motion…on the other side meaning, purpose,and design.”
    If your students can recall and apply what follows, you’ve achieved success:  Inherited variation, followed by selection for beneficial traits and against harmful traits, shifts the average phenotype in a population, leading to adaptation.
  4. Defining evolutionary fitness as reproductive success.

Topics 7.2 and 7.3: Natural Selection and Artificial Selection

  1. How artificial selection works. Though the CED lists natural selection before artificial selection, I teach artificial selection first. It’s concrete and easy to understand. For most students, understanding how selective breeding enabled dog breeders to create various breeds of dogs, or how plant breeders were able to convert wild Brassica oleracea into cultivated varieties like broccoli, cauliflower, cabbage, brussel sprouts, etc., is pretty straightforward. In fact, a great lecture prop (whether in person or online) is to have examples of each of these vegetables to show to your students. But if you can’t you can use this image from my website.
  2. Selection acts on phenotypes. The result of selection (artificial or natural) is a shift in allele frequencies. But what’s being selected are phenotypes. When you use illustrative examples like the peppered moth or the rock pocket mouse, you can talk to your students about how predatory birds (in both cases) are selecting against poorly camouflaged individuals. When the birds eat those individuals, they’re (literally) eating the genes for poor camouflage. Because the genes for good camouflage are left in the bodies of the prey, the paradoxical result is that predation increases the frequency of alleles for good camouflage.
  3. As environments change, so do selective pressures. A great example of this is rapid evolution of beak depth observed in the the Galapagos finches on Daphne Major in the Galapagos Islands, as famously studied by Peter and Rosemary Grant. The Grants were able to track yearly shifts in the mean phenotype of the medium ground finch in response the amount of rainfall on the island, which changed the type of vegetation. This is all covered in HHMI’s video about finch evolution, which you can access at https://www.biointeractive.org/classroom-resources/origin-species-beak-finch. For a summer read, you (or your students) can read The Beak of the Finch, by Jonathan Weiner.

Topics 7.4 and 7.5: Population Genetics and Hardy Weinberg

  1. The key idea here is captured by the enduring understanding “Evolution is characterized by a change in the genetic makeup of a population over time.” This involves a few related ideas:
    1. Gene pools
    2. Allele frequency
  2. It also involves fighting a big point of confusion: The terms “dominant” and “recessive” have nothing to do with “common” and “rare.” If your students are like mine, there are always a few students who will ask something like “If dominant alleles are dominant, then why doesn’t everyone in a population have that allele?” Those students are often my most confident students…and my guess is that most students naively come into a population genetics unit with some version of this incorrect idea in their minds.This is a deeply rooted misconception that I’ve been battling against for years. Overcoming it involves showing students that the meaning of the term “dominant” in “dominant” allele doesn’t make that allele like a dominant army that will conquer all else in its path, and spread like a virus. Ultimately, you want your students to understand that the frequency of an allele has to do with the qualities of the phenotype that it codes for, and whether that phenotype is harmful or beneficial.
  3. Once you’ve taught about gene pools and allele frequency, you can go on to teach how to calculate allele frequencies. You can do that through counting (as in the exercises in this tutorial) and through the Hardy Weinberg equations:
    1. p + q = 1, and
    2. p2 + 2pq +q2 = 1If you’re a gifted math instructor, you can teach students how to manipulate those equations. If (like me) you’re not, you’ll want to consider adopting a trick I learned years ago. Use modified Punnett squares called “cross-multiplication tables.” Here’s what they look like:
       A (0.3)  a (0.7)
       A (0.3)  AA (0.09) Aa (0.21)
       a (0.7)  Aa (0.21) aa (0.49)

      Note how if you know the proportion of recessives  in a population (aa, above), you can take the square root of that to figure out the frequency of the recessive allele. Since p + q = 1, subtracting the frequency of “q” from 1 gives you the frequency of the dominant allele. And from there you can figure everything else out.

      My tutorial on the Hardy-Weinberg equation will walk your students through this step by step.

  4. Once students know how to calculate allele frequencies, you can talk about changes in allele frequencies, which is what evolution is all about. That leads to teaching about the five conditions associated with Hardy Weinberg equilibrium. 
  5. And once that’s secure, you can teach about the conditions that lead to evolutionary change. These are all violations of the various Hardy-Weinberg conditions
    1. Violate large population size, and you have genetic drift, shown either by population bottlenecks, or by the founder effect.
    2. Violate isolation, and you have gene flow.
    3. Violate no net mutation, and you have alleles changing frequency as they mutate from one form to another.
    4. Violate random mating, and you have evolution caused by sexual selection or assortative mating.
    5. Violate no harmful or beneficial alleles, and you have evolution caused by natural selection.

Natural Selection and Population Genetics tutorials on Learn-Biology.com

Here’s a list of tutorials which cover all of the objectives above. You can access the tutorials here.Here’s the associated student learning guide for this unit. 

All of these are pretty short. Your students can probably handle two/night, allowing you to get through them all in a week.

  1. Thinking Like Darwin: Adaptation, Artificial Selection, and Natural Selection

  2. Alleles in Gene Pools

  3. Understanding Allele Frequencies in Gene Pools

  4. The Hardy-Weinberg Equation

  5. The Hardy Weinberg Principle

  6. Natural Selection in Gene Pools

  7. Why Harmful Recessive Alleles Don’t Disappear

  8. Mutation in Gene Pools, and Heterozygote Advantage

  9. Genetic drift (founder effect, bottleneck effect)

  10. Population Genetics Cumulative Quiz

Additional Resources for Natural Selection and Population Genetics.

If  you didn’t start of your year with Natural selection, then please read my notes from Week 1, Days 3 and 4. They’ll point you to two great activities that you’ll be able to use with your students.

A classic population genetics demonstration is to hand out PTC paper and identify the percentage of tasters and non-tasters in your class  population. From there, you can calculate the frequency of the recessive allele (the non-tasting allele) in your class gene pool. To learn more about PTC, read this article at the University of Utah’s Genetic Science Learning Center.

The folks at Flinn have a  POGIL on Hardy Weinberg.

I mentioned above HHMI’s Video about The Galapagos Finches. When I show that video, I also use this student guide (a google doc version of their PDF, with some of their instructor resources thrown in). Here’s the original teacher’s guide (with the answers).

Since mutation is one of the violations of Hardy-Weinberg equilibrium, this unit is a great time to review it. If you need to, you can use Flinn’s POGIL on mutation, or HHMI’s handout about Mutations and M1CR Signalling in the Rock Pocket Mouse. That handout lets you review natural selection, mutation, and cell signaling in one activity. Highly recommended.

HHMI also two additional activities that are excellent for kicking off natural selection and population genetics.

  1. HHMI: Skin Color Evolution. This focuses on the work of Nina Jablonski relating to the evolution of skin color variation in human population. The resources include
    1. Video
    2. Educator and Student Materials
  2. Allele and Phenotype Frequencies in Rock Pocket Mouse Populations. This activity takes what your student previously learned about the evolution of different color phenotypes among rock pocket mice, and grounds it in the Hardy Weinberg equations.

Week 25: Speciation, Phylogeny

Before starting, a note about curriculum sequencing.

The College Board’s course and exam description lists its evolution topics in this order

  1. Natural Selection, Artificial Selection (Topics 7.1 – 7.3)
  2. Population Genetics and Hardy Weinberg (Topics 7.4 and 7.5)
  3. Evidence of Evolution, Common Ancestry, Continuing Evolution (Topics 7.6-7.8)
  4. Phylogeny (Topic 7.9)
  5. Speciation and Extinction, Variations in Populations (Topics 7.10 – 7.12)
  6. Origin of Life (Topic 7.13)

That’s a good start and end, but I think you’ll get better results if you do the following.

  1. Natural Selection, Artificial Selection (Topics 7.1 – 7.3)
  2. Population Genetics and Hardy Weinberg (Topics 7.4 and 7.5)
  3. Speciation and Extinction, Variations in Populations (Topics 7.10 – 7.12)
  4. Phylogeny (Topic 7.9)
  5. Evidence of Evolution, Common Ancestry, Continuing Evolution (Topics 7.6-7.8)
  6. Origin of Life (Topic 7.13)

That’s because Evidence of Evolution is, to a large degree, about homology. Homology only makes sense in the context of ancestral species splitting apart into descendants, which is speciation and phylogeny. And phylogeny only makes sense if you understand speciation.

So, speciation this week, and then phylogeny and evidence for evolution next week.

Teaching notes and objectives for speciation and extinction

Speciation is not, in my experience, a particularly difficult topic for most students. The allopatric model of speciation is very easy to understand. Sympatric speciation that’s not based upon polyploidy (which is extremely common in plants) can be a bit harder for students to visualize (but I provide several examples in my tutorials). And reproductive isolating mechanisms are also straightforward.

What students can have a bit of trouble with is overcoming some naive biology preconceptions. For example, a lot of my students, over the years, don’t know that a taxon like “duck” is a family of species. Similarly, the distinction between a breed or a variety and a species is not an intuitive concept for many students. To help my students with this concept, I do an activity where I hand out copies of Peterson’s Field Guide to Western Birds (I have a half a class set: you can make copies of relevant pages), and I have my students look at the number of duck and songbird species we have in our local area. It’s eye-opening for a lot of students.

The College Board’s Course and Exam Description divides the teaching of speciation and extinction into three topics. Click here to read these in their original wording in my annotated quick guide to the CED (the link takes you to the start of Unit 7: scroll down to get to Topic 7.10).

Here’s my brief outline and sequence for these topics.

  1. The biological species concept (what it is, and what its limits are)
  2. Prezygotic and postzygotic reproductive isolating mechanisms
  3. How speciation occurs
    1. allopatric speciation
    2. sympatric speciation
    3. ring species
    4. adaptive radiation.
  4. Extinction and mass extinction.
    1. background rates of extinction
    2. mass extinctions
    3. Extinction and biodiversity (how adaptive radiations follow mass extinctions).

Please note that there are a few topics that I don’t cover in my tutorials (so be sure, at some point, to teach them to your students)

  1. The pace of evolutionary change
  2. Punctuated equilibrium vs. gradualism.

Note also that we return to to topic of extinction in the last topic in the curriculum, Disruptions to Ecosystems (Topic 8.7).

Teaching Species and Speciation on Learn-Biology.com

Here’s how you can use the five tutorials on Learn-Biology.com to cover the objectives listed above.

Tutorial 1. What is a species?

Covers the biological species concept, its limitations, and reproductive isolating mechanisms.

Tutorial 2. Allopatric speciation

Allopatric speciation

Covers the process of allopatric speciation. If your students can explain a diagram like the one at left, then they’re pretty much set.

Ring Species

I also discuss ring species like the California salamander Ensatina eschscholtzii. 

I use some terminology in my tutorial that’s not part of the CB’s AP curriculum (peripatric, parapatric). They’re useful for distinguishing between different flavors of geographic isolation, but mastery of these terms is not required.

Tutorial 3. Sympatric speciation

Allopolyploidy

Explains how sympatric speciation occurs through polyploidy and allopolyploidy, sexual selection, disruptive selection, and microhabitat differentiation.

Tutorial 4. Adaptive Radiation

How one species can branch into an entire family of descendent species, with a particular focus on how this happens on island chains.

Tutorial 5. Extinction

Covers how species become extinct (the extinction vortex), background rates of extinction, mass extinctions, and the consequences of extinction.

Finally, the module ends with this Speciation and Extinction: Cumulative Quiz

Additional Resources for Teaching Speciation

HHMI has a fantastic activity about speciation (which also introduces phylogeny). It’s called Using DNA to Explore Lizard Phylogeny. This activity goes with the video The Origin of Species: Lizards in an Evolutionary Tree.  It’s a very rich activity, involving speciation, natural selection, sexual selection, convergent evolution, DNA sequencing and phylogeny. It requires a bit of setup (printing out or otherwise making available photos of Anole lizards on various Caribbean Islands), but it’s well worth the effort. Also, the phylogeny program the activity uses can be a bit hit or miss. Use the teacher’s guide to have the output ready to go in case the program hangs up.

You can also use Flinn’s POGILs on Selection and Speciation and Mass Extinction. 

Week 26: Evidence for Evolution & Phylogeny

Teaching Evidence for Evolution: some initial thoughts

Teaching about the evidence for evolution is a key part of our struggle against our common enemy, Biology Confusion. Creationism is widespread throughout the United States. Exactly how widespread is hard to know. It depends a lot on how people are asked about their beliefs. You can read more about that in this article in Scientific American.

Having said that, I need to confess that I have it easy when it comes to teaching about the evidence for evolution. I live and teach in Berkeley, California, a very liberal, pro-science college town. There’s no pushback when I teach this topic. I understand that’s quite different from the situation you might be in.

To support your efforts to teach this topic, our module on evidence for evolution goes into a lot of detail. We offer four tutorials, followed by a comprehensive quiz. Let me walk you through the College Board’s objectives for this topic first, and then I’ll tell you about our tutorials.

A summary of the College Board’s Learning Objectives for Evidence for Evolution

The College Board’s Course and Exam Description divides the teaching of evidence for evolution into three topics. Click here to read these in my annotated quick guide to the CED.

Evidence of evolution (Topic 7.6) looks at

  1. Fossil evidence and radioactive dating of fossils.
  2. Morphological homologies and vestigial structures,
  3. Molecular homologies (homologies based on nucleotide and amino acid sequences)

Common Ancestry (Topic 7.7) looks at

  1. Deep molecular homologies shared by all organisms (DNA, RNA, ribosomes, the genetic code, and shared metabolic pathways)
  2. Cellular and genetic homologies that are shared by all eukaryotes (membrane bound organelles, linear chromosomes, and genes with introns)

Continuing evolution (Topic 7.8) looks at evidence showing how life continues to evolve

  1. Populations continue to evolve
  2. Species continue to evolve, as shown by
    1. genomic changes
    2. changes in the fossil record
    3. evolution of resistance to antibiotics, pesticides, herbicides, etc.
    4. Emerging pathogens

Teaching Evidence for Evolution on Learn-Biology.com

Here’s how you can use the four tutorials on Learn-Biology.com to cover the objectives listed above (and go quite a ways beyond them). Note that the sequence of ideas below is different from what the College Board suggests. As I hope you’ll agree, the sequence below makes more pedagogical and biological sense. In any case, completing our tutorials will ensure that your students will achieve all of the CB objectives…and deepen their biological thinking skills along the way.

Tutorial 1: Evolution: Claims and Historical Observations

Our first tutorial starts by looking at the difference between a hypothesis and a theory. The goal here is to establish the importance of evolution, and to make sure that your students understand that when we say “theory of evolution,” we’re not talking about someone’s idea or opinion, but rather a “comprehensive explanation of some aspect of nature that is supported by a vast body of evidence” (US National Academy of Sciences).

Once that’s established, we look at the two claims that evolutionary theory makes. In other words, if evolution is true, then we should see:

  1. Descent with modification
  2. Change in a population’s genetic structure over time.

Do we see this? The tutorial ends with examples of evolutionary change that have been observed in recent times. The examples include

  1. Evolution of antibiotic and pesticide resistance in bacteria and insects, respectively
  2. Evolution of a new phenotype in the soapberry bug as it adapted to changes in its host species.

Both of these are presented in the context of research studies and data sets, so your students’ ability to interpret and analyze information will deepen as they learn this new content.

Tutorial 2: Homologous and Vestigial structures

This tutorial starts by teaching about adaptive radiation. Why? Because when you think about it, adaptive radiation, on both a small and large scale, is the basis for homologous features. Consider the Galapagos Finches. Their divergent beaks are homologous: derived from a common ancestor, adapted to the different ecological niches into which each descendent species evolved.

On a larger timescale, the same process underlies homologies like these…

…as well as phenomena like the vestigial eyes in cavefish, the human coccyx, and the vestigial muscles that are connected to our ears, (but which most of us are unable to use to reposition our ears (as can many of our mammalian cousins).

Tutorial 3: The Fossil Record and Biogeographical Evidence

This tutorial covers two major areas:

  1. The fossil record
    1. What fossils are and how they form
    2. Relative and absolute dating of fossils
    3. How the fossil record serves as evidence of evolution.
  2. Biogeography and convergent evolution(Side note: Jerry Coyne, in his fabulous book Why Evolution is True, calls biogeography the piece of evidence for evolution that creationists have the most trouble with).This section of the tutorial will leave your students with a solid understanding of
    1. Biogeography and the pattern of life’s distribution on Earth
    2. Parallel evolution
    3. Convergent evolution and analogous traits
    4. The evolution of the unique biology of oceanic islands.

Tutorial 4: Embryological, Molecular, and Genetic Evidence 

This last tutorial covers additional lines of evidence for evolution (mostly covering material in topic 7.7). This includes

  1. Embryological evidence for evolution. Why do early embryonic forms of the animals in the same clade look so similar? Why do features like a post-anal tail arise in the ape clade (our clade) early in embryonic development, only to be reabsorbed later on (before birth)?
  2. What are molecular homologies, and how do they provide evidence of common ancestry and descent with modification?
  3. How can homologous and vestigial features be identified in genes?
  4. What are the deepest homologies that serve as evidence for a common ancestry of all living things?

Finally, the module ends with this cumulative Evidence for Evolution Cumulative Quiz.

Additional Evidence for Evolution Resources

If you’re looking for a worksheet to either preview or consolidate the material in these tutorials, you can use the one on this page. Currently, I’ve only uploaded it in pdf format and Word format. If you’re in a jam and need something that you can modify, email me and I’ll convert it into a google doc for you.

The Youtube Channel “Stated Clearly” has a very solid evidence for evolution video. It’s about 14 minutes long. It might feel a bit elementary, but at the very least it’s a good introduction/summary.

If you have time, then the PBS Evolution series has two great videos, both of which are available on YouTube. The only problem with these videos is that they’re long (2 hours and one hour respectively).

  1. Darwin’s Dangerous Idea simultaneously recreates Darwin’s discovery of natural selection and presents the evidence for evolution.
  2. Great transformations looks at homology, working backwards from whales, to tetrapods, to homeotic genes. Here’s a video guide.

Teaching notes and objectives for Topic 7.9, Phylogeny

Here are the College Board’s objectives related to phylogeny:

  1. EU EVO-3: Life continues to evolve within a changing environment.
  2. LO EVO-3.B: Describe the types of evidence that can be used to infer an evolutionary relationship.
  3. EVO-3.B.1: Phylogenetic trees and cladograms show evolutionary relationships among lineages—
    1. a. Phylogenetic trees and cladograms both show relationships between lineages, but phylogenetic trees show the amount of change over time calibrated by fossils or a molecular clock.
    2. b. Traits that are either gained or lost during evolution can be used to construct phylogenetic trees and cladograms—
      1. i. Shared characters are present in more than one lineage.
      2. ii. Shared, derived characters indicate common ancestry and are informative for the construction of phylogenetic trees and cladograms.
      3. iii. The out-group represents the lineage that is least closely related to the remainder of the organisms in the phylogenetic tree or cladogram.
    3. c. Molecular data typically provide more accurate and reliable evidence than morphological traits in the construction of phylogenetic trees or cladograms.
  4. LO EVO-3.C: Explain how a phylogenetic tree and/or cladogram can be used to infer evolutionary relatedness
    1. EVO-3.C.1: Phylogenetic trees and cladograms can be used to illustrate speciation that has occurred. The nodes on a tree represent the most recent common ancestor of any two groups or lineages.
    2. EVO-3.C.2: Phylogenetic trees and cladograms can be constructed from morphological similarities of living or fossil species and from DNA and protein sequence similarities.
    3. EVO-3.C.3: Phylogenetic trees and cladograms represent hypotheses and are constantly being revised, based on evidence.

To break that down into something a bit more manageable, here’s what to focus on. Students should be able to

  1. Interpret evolutionary relationships based on phylogenetic trees. That includes
    1. being able to determine which clades are most closely related,
    2. being able to determine common ancestors.
  2. Construct phylogenetic trees based on data about shared characteristics.

The most important specialized vocabulary you’ll have to teach in this topic includes:

  1. Phylogenetic tree / cladogram
  2. clade
  3. shared derived character
  4. node
  5. lineage
  6. outgroup
  7. molecular clock

It’s useful if, going into this, your students have familiarity with the difference between homologous and analogous features.

Because I can’t imagine my students leaving my AP Biology course without knowing this, I also teach a bit about traditional classification. That includes binomial nomenclature and the basic classification categories for animals (kingdom, phylum, class, etc.)

Teaching phylogeny on Learn-Biology.com

Much earlier in the year, I introduced the MICE method for interactive learning. It’s a great formula for flipped learning, and I found it to be particularly useful while I was limited to remote teaching during the Pandemic.

MICE stands for

  • Motivation (getting students hooked, arousing curiosity, etc).
  • Interaction (what students do on learn-biology.com)
  • Checking for understanding (what you do with your students during your synchronous learning time).
  • Extension (this includes labs, other interactive activities like HHMI or POGILs, or journal writing).

If you want to motivate your students to learn about phylogeny, take your students to nextstrain.org/sars-cov-2/. SARS-CoV-2, since its emergence, has been evolving in real time. Nextstrain analyzes SARS-CoV-2 sequences from labs around the world, and organizes them into phylogenies. You’ll be able to explore phylogenies like this one


You can show your students a movie showing how this phylogenetic tree grew over time, branching from common ancestors to descendants. And then you can follow that up by having your students consider questions like: how is a phylogenetic tree like this get put together? How does the program know who’s most closely related to whom?

Once you’ve got your students motivated, you can have them go to learn-biology.com. The topic is captured in this one tutorial, which focuses on the following:

Sections 1 and 2. Phylogeny shows life’s branching pattern

This connects phylogenetic trees to the idea of adaptive radiation, using diagrams like this to introduce concepts like clade and node.

Sections 3 and 4: Naming and Classifying species.

Covers binomial nomenclature, and hierarchical classification categories, as shown below. Again, there’s no AP Bio College Board Standard connected to this material…but I hope you agree with me that skipping it is unimaginable.

Section 5. How phylogeny and classification are (or should be) equivalent (but sometimes aren’t)

This introduces some of the complexities of interpreting phylogenetic trees. One goal of this section is communicating how the top to bottom (or left to right) order of clades in a phylogenetic tree might have nothing to do with relatedness. The two trees below, for example, are equivalent, and frogs are no more closely related to gorillas than they are to lizards (because frogs share their most recent common ancestor with both gorillas and lizards at node C).

In other words, this…

is equivalent to this:

I also introduce the idea of monophyletic, polyphyletic, and paraphyletic taxa. These terms don’t appear in the CED, but they’re incredibly useful.

Section 6: Using Character Tables to Create Phylogenetic Trees

Here’s a screenshot of the kind of exercise your students will do in this section as they learn to construct phylogenies.

Section 7: Molecular Clocks

This section covers how molecular clocks can be used to determine dates of common ancestry.

Section 8: How horizontal gene transfer makes the phylogeny of early life very complex.

Why life’s early phylogeny looks like this. It’s all about gene transfer (ongoing) and endosymbiosis.

Additional Resources for teaching Speciation and Phylogeny

HHMI has a great Biointeractive video about the Galapagos finches and adaptive radiation (also mentioned above). If you didn’t use the finches as an example of natural selection, now’s your chance to use them as an example of speciation. When I show that video, I also use this student guide (a google doc version of HHMI’s PDF, with some of their instructor resources thrown in). Here’s the teacher’s guide (with the answers).

If you have access to Jstor you can download Peter Grant’s article about Galapagos Finch evolution in Scientific American. This is the paradigmatic example of adaptive radiation, discovered by none other than Darwin himself (though he famously didn’t understand what he had discovered until years after his discovery). Though written for the public, it’s a complex, detailed article, and it’ll be a great challenge for your students.

Flinn’s POGIL on Phylogenetic Trees is also very good.

Nova’s Evolution lab is excellent, and will really solidify your students’ understanding of phylogeny. However, it takes a lot of time. It’s been several years since I’ve done this activity so be sure to test it out. In addition, if you’re using it, be sure to have your students log in so that the program saves their progress.

Finally, I’d like to pass along an article from the American Biology Teacher by Professor Kristy Halverson about using pipe cleaners to teacher phylogeny. Here’s a link to a worksheet/activity that implements Professor Halverson’s ideas, passed along to me by Kelley Derrick, a Learn-Biology.com using AP Bio teacher from Wasau Wisconsin. Thanks, Kelley!

Week 27: Origin of Life (Topic 7.13)

A note about pacing

Keeping up with the pace of an AP Biology course can be brutal, both for teachers and students. If you’re behind where you want to be, then keep in mind that the Origin of Life module on Learn-Biology.com can be used independently by students with very little teacher support. The only prerequisite is that your students understand the Central Dogma (DNA makes RNA makes protein). So if you’re running behind a bit, assign this over Spring Break (or Presidents Day, or even Winter break). Then, after it’s due, spend a day or two going over key ideas in class.

Teaching the Origin of Life: General Considerations

Teaching about the origin of life can be challenging. A deep dive into the topic requires a lot of biochemistry. On top of that, we’re talking about events that occurred a very long time ago when conditions on Earth were wildly different from the life-sustaining world we live upon today. By its very nature, the topic is more speculative than anything else we teach.

For me, the goal has been to offer students a naturalistic paradigm for approaching the origin of life. What I mean is that even though the topic is difficult and the evidence scanty, we can still approach if from a naturalistic framework. To quote Wikipedia,

Naturalism is the idea or belief that only natural laws and forces (as opposed to supernatural or spiritual ones) operate in the universe. Adherents of naturalism assert that natural laws are the only rules that govern the structure and behavior of the natural world, and that the changing universe is at every stage a product of these laws.

The goal is to avoid what’s shown in this famous Sidney Harris cartoon below:

In other words, we’re playing by the rules of science. If we can’t figure out how something could happen based on the physics of the known universe, we have to go back to the drawing board, think harder, design better experiments, etc. Admittedly, at the high school or introductory college level, this is hard to do…

Origin of Life Learning Objectives

Here are the College Board’s objectives related to the origin of life:

  1. LO SYI-3.E: Describe the scientific evidence that provides support for models of the origin of life on Earth.
    1. SYI-3.E.1: Several hypotheses about the origin of life on Earth are supported with scientific evidence—
      1. a. Geological evidence provides support for models of the origin of life on Earth.
        1. i. Earth formed approximately 4.6 billion years ago (bya). The environment was too hostile for life until 3.9 bya, and the earliest fossil evidence for life dates to 3.5 bya. Taken together, this evidence provides a plausible range of dates when the origin of life could have occurred.
      2. b. There are several models about the origin of life on Earth—
        1. i. Primitive Earth provided inorganic precursors from which organic molecules could have been synthesized because of the presence of available free energy and the absence of a significant quantity of atmospheric oxygen (O2).
        2. ii. Organic molecules could have been transported to Earth by a meteorite or other celestial event.
      3. c. Chemical experiments have shown that it is possible to form complex organic molecules from inorganic molecules in the absence of life—
        1. i. Inorganic molecules/monomers served as building blocks for the formation of more complex molecules, including amino acids and nucleotides.
        2. ii. The joining of these monomers produced polymers with the ability to replicate, store, and transfer information.
    2. SYI-3.E.2: The RNA World Hypothesis proposes that RNA could have been the earliest genetic material.
Here’s my more condensed outline of what to cover.
  1. When did life emerge?
    1. There’s geological evidence that Earth formed about 4.5 bya.
    2. There’s biological and geological evidence that life was well established by 3.5 bya
    3. Based on geological and biological evidence, life probably first emerged on Earth about 3.8 bya.
  2. Where and how did life emerge?
    1. Conditions in a few locations on the early Earth would have made the abiotic formation of biological monomers possible.
    2. A consensus view is emerging that the most likely spot for that to have happened is alkaline hydrothermal vents.
    3. Additional pre-biotic molecules could have come down from space (but this is not nearly as plausible as the hydrothermal vents) 
    4. Formation of monomers would have to be followed by formation of polymers.
    5. Next would be the formation of self-replicating polymers. This, admittedly, is the biggest gap in the story.
    6. At some point, the encapsulation of self-replicating polymers within a lipid bubble led to the formation of cells.
  3. Chemical experiments have validated some of the earliest steps required for the emergence of life
    1. Organic monomers, including nucleotide precursors and amino acids, can be formed under abiotic conditions
    2. The next step —creating complex self replicating polymers — has not yet been achieved, but there are promising approaches.
  4. The RNA world hypothesis promotes the idea that RNA, rather than DNA, served as the first genetic material.

Teaching about the Origin of life on Learn-Biology.com

Our tutorials on Learn-Biology.com cover this material in four tutorials, the main menu for which is on this page. 

  1. Life, LUCA (Last Universal Common Ancestor) and When Life Began

    In this first tutorial, we introduce the evidence for when life began.

  2. Early Earth, Key Steps in the Emergence of Life, Stanley Miller and the Primordial Soup

    This tutorial focuses on the hellish conditions under which life emerged on Earth about 3.8 bya: no atmospheric oxygen, enormous tides, hardly any land, widespread volcanic activity. As we show in tutorial 3, all of this points to the emergence of life not on land, but under the sea

    We also review Stanley Miller’s classic origin-of-life experiment, which is significant in terms of its overall conclusions (abiotic formation of monomers is possible), even though flawed in terms of its underlying set up.

  3. Problems with the Primordial Soup, Alkaline hydrothermal vents

    This tutorial explores some speculation about the possible places where life might have emerged, and then discusses why alkaline hydrothermal vents are now a leading contender for serving as life’s hatchery.

  4. The Origins of Heredity (the RNA World) and The First Cells

    This final tutorial looks at the RNA world in detail. It then goes on to explore some speculations about the the emergence of cells, and the first metabolic systems. If, like me, you thought at some point that glycolysis arose before chemiosmosis and ATP synthase, you might be in for a surprise.

Additional Resources

My tutorials use a fair amount of video. One that I use extensively can be seen at this link on Youtube. There’s also one that has more polished narration and animation that you can watch here.  I’m not sure if either one escapes the “and then a miracle appears” problem, but both of these are worth watching several times and discussing with your students.

I also highly recommend that your students take a deeper look at the RNA world. They can do at Exploring Life’s Origins. The development of this site was guided by Jack Szostak, who won the 2009 Nobel Prize for his discovery of telomeres and telomerase. I’ve developed a worksheet to guide students this material: you can access it here

If you’re looking for more classroom activities, the National Center for Case Study Teaching in Science has two Origin of Life Case studies.

Summative Activities for Unit 7

To pull together Unit 7

  1. Use the AP Bio review materials on Learn-Biology.com. Your students can access these same materials on the Biomania AP Bio app, and results from both are recorded in your teacher dashboard. These review materials include
    1. Unit 7 AP Bio Review Flashcards
    2. Unit 7 AP Bio Review Multiple Choice Questions
    3. Unit 7 AP Bio Review Free Response Questions
  2. The progress check questions on for Unit 7 on AP Classroom.

Links