1. Introduction

Evolution is biology’s central theory. In Topics 7.1 – 7.5 of AP Bio, we looked at two of the mechanisms (natural selection and genetic drift) by which evolution occurs. Now, in Topics 7.6 – 7.8, we’ll look at the evidence upon which this theory is based.

In the United States, while the idea of evolution is accepted by a majority of the population, evolution’s status as a well-supported scientific theory is widely misunderstood^{(Science Daily)}. So let’s start by clarifying the distinction between a theory and a hypothesis.

2. A theory is much more than a hypothesis

In common speech, the word theory is often used in a way that’s synonymous with words like “opinion” or “belief.” For example, you’ve probably heard someone say something like: “That’s your theory. Let me tell you mine.”

That use of the word theory is closer to the scientific idea of a hypothesis. A hypothesis is an idea that requires testing. In science, a theory is an explanation that’s already been tested many times. Unlike a hypothesis, a theory is supported by a significant amount of evidence.

Any science student should be able to quote these definitions for how the words theory and hypothesis are used in a scientific context.

• Theory: An organized explanation of some aspect of the natural world that has been thoroughly tested and is well supported by evidence.
• Hypothesis: A unproven idea or explanation that you can test through study and experimentation. (adapted from Vocabulary.com)

To sharpen your ability to distinguish between a scientific theory and a hypothesis, read the following passages.

A theory explains a phenomenon, accounts for all available data, and is supported by a huge body of evidence. Hypotheses are just guesses that need testing.

Adapted from: Ruth Levy Guyer, Professor of Immunology and Bioethics, Johns Hopkins University and Haverford College.

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A theory is a well-established principle that has been developed to explain some aspect of the natural world…while a hypothesis makes a specific prediction about a specified set of circumstances. A theory has been extensively tested and is generally accepted, while a hypothesis is a speculative guess that has yet to be tested.

Adapted from Kendra Cherry, About.com, Introduction to Research Methods

Work on these flashcards until you can recite the definitions of theory and hypothesis from memory.

3. Theory vs. Hypothesis Flashcards

4. Theory vs. Hypothesis Quiz

Take the quiz below to make sure that this distinction between theory and hypothesis is clear.

5. To prove evolution to be true, we need evidence of descent with modification

Darwin had a three-word phrase that, for him, summed up the process of evolution: descent with modification. 

• Descent means “coming from an ancestor.”
• Modification means “change.”

Descent with modification means that over time, a population might change in ways so that the descendants are different from the ancestors. Or, if you run the clock backward, it means that the current form of a population (or an entire species) might be different from its ancestral form.

So what’s the evidence that descent with modification has occurred? We’ll start below by looking at examples of evolutionary change that have been directly observed during the past century and a half since Darwin published On the Origin of Species. From there, we’ll move on to patterns and features of living things that can only be explained as a consequence of evolutionary changes within a single lineage, or within groups of related species. Along the way, we’ll look at the fossil record, and see how vestiges of past life show how life has changed over time.

6. The Evolution of SARS-CoV-2 Variants

We’ll start with an example of evolutionary change that you’ve observed directly (along with everyone else on the planet). Starting in 2019, the evolution of SARS-CoV-2 variants has been an example of rapid evolutionary change — with disastrous effects on human beings.

The term variant comes from the word vary: it means “different type.” Every time someone is infected with SARS-CoV-2, they produce billions of new viruses. During the replication process, random mutations in SARS-CoV-2’s genes can cause new variants to emerge. Most of those variants result in viruses that don’t work well at infecting cells and moving from one person to the next. However, from time to time, a variant arises that’s more successful than its ancestors at moving from person to person, infecting cells, and replicating while evading the human immune system. Through natural selection, that new variant starts to spread.

For example, the graph on the left shows the rise of the Delta Variant in England between April and mid-June of 2021. The Delta variant is a descendant (with modification) of a previous strain of the virus.

Starting at the end of 2021, the Omicron variant performed the same feat, quickly becoming the dominant strain of the virus in the United States (and the entire world). In the same way as populations of Peppered Moths in Northern England shifted from white to black in response to industrial pollution, populations of SARS-CoV-2 shifted from one variant to another.

How did this change occur? Through mutation followed by natural selection. Each variant has had genotypic and phenotypic differences from its ancestors. For SARS-CoV-2, the genotypic changes have involved changes in its RNA genome. The phenotypic differences have involved changes in the virus’s proteins, particularly its spike protein.

In the case of the Delta variant, a mutation in RNA altered a single amino acid in the SARS-CoV-2’s spike protein that made it much easier for this variant to enter cells.

The Omicron variant has a distinctive combination of more than 50 mutations. These mutations made Omicron far more transmissible than its predecessors.  Thankfully, it also seemed to make the disease caused by an Omicron infection less severe than infection with other strains.

The takeaway: the spread of SARS-CoV-2 variants is a clear case of descent with modification. It’s an example of evolutionary change that occurred, in some cases, in a matter of months.

If you want to learn more about SARS-CoV-2 and COVID-19, you can do so through this tutorial in AP Bio Unit 6 on Learn-Biology.com.

7. Evolution of antibiotic-resistant bacteria and the rise of MRSA

Another example of evolution that’s been observed in recent times has been the emergence of bacterial strains that are resistant to antibiotics.

Let’s start with two key definitions:

• Antibiotics are drugs that kill bacteria.
• A bacterial strain is a subtype of a bacterial species with a unique genetic makeup and phenotype. You can think of “bacterial strain” as roughly equivalent to the viral variants we discussed above, or domesticated varieties of dogs or wild cabbage that we discussed earlier in this course.

Antibiotic-resistant bacterial strains have evolved ways to not be killed by antibiotics. That makes infections with these bacterial strains very dangerous.

Antibiotics were first widely used in the 1940s. One of the first antibiotics is called Penicillin, a substance that was derived from the Penicillium fungus. One of the targets of penicillin was the bacterial species Staphylococcus aureus (often called “Staph aureus,” S. aureus, or “staph“). Normally, S. aureus, along with many other types of bacteria, lives harmlessly on our skin and other parts of our bodies. But there are also forms of S. aureus that can cause skin and sinus infections, along with food poisoning, pneumonia, and wound infections.

When penicillin was first used, it was highly effective at curing staph infections. But by 1950, only ten years after penicillin was first isolated and only 8 years after its first clinical use, 40% of S. aureus studied were penicillin-resistant. By 1960, this had risen to 80%. Now it’s about 98%.

What happened?  It’s all about natural selection.  Here’s an infographic that illustrates the process.

1. Image “A shows the initial population. Most bacterial cells (the gray ones) are susceptible to the antibiotic. But S. aureus populations have genetic variation, and a few cells (shown in red) have differences (mutations) that allow them to survive when exposed to the antibiotic.
2. Application of the antibiotic kills the bacteria that are most easily killed, leaving only those that are resistant.
3. When these resistant bacteria reproduce, their descendants will inherit their genes for antibiotic resistance. Repeat this for a few generations, and the resulting population will be mostly composed of antibiotic-resistant cells.

4. 

   Note that in the case of antibiotic resistance, the genes are often on plasmids. Because of that, the spread of antibiotic resistance genes through reproduction is accompanied by the sharing of genes through conjugation, a type of horizontal gene transfer that we studied in AP Bio Unit 6 (and shown on the right). With both vertical and horizontal gene transfer at work, a bacterial population can evolve antibiotic resistance very quickly.

The widespread use of antibiotics in agriculture has accelerated the evolution of antibiotic-resistant bacterial strains.

In agriculture, antibiotics are used to prevent outbreaks of infection in animals that are kept in close confinement. In 2013, the US Department of Agriculture estimated that 32 million pounds of antibiotics were used in food animal production. That amounts to 80% of the antibiotics used in the United States.

As with humans, the antibiotics fed to animals (A) kill most of the bacteria, but not all of them. The ones that aren’t killed are the ones that have resistance to the antibiotics. Over time, this leads to the selection (B) for antibiotic-resistant strains (C). These can be transferred to people through animal products, through agricultural produce that’s been in contact with animal feces-contaminated soil or water, or during food preparation.

Methicillin is an antibiotic that was introduced in 1959. Within two years of its introduction, methicillin-resistant bacteria had been observed. These methicillin-resistant bacteria have come to be known by the acronym MRSA (methicillin-resistant S.aureus), and they’re much more dangerous than non-MRSA S. aureus. Sometimes, MRSA infections can be controlled by other antibiotics. But the concern is that our arsenal of effective antibiotics is growing increasingly thin, as the bacteria mutate around whatever selective pressure our use of antibiotics creates.

Is this evidence for evolution? Absolutely. With the rise of antibiotic-resistant bacteria, we have a clear example of descent with modification. In this case, the phenotype is resistance to the antibiotic. The genotype is the set of genes that code for the proteins that confer antibiotic resistance.

Study the flashcards below before continuing.

8. Flashcards: SARS-CoV-2 Variants and Antibiotic Resistance

9. Evolution of Pesticide Resistance in Mosquitoes

Malaria is a tropical disease caused by a parasite that infects a person’s red blood cells. Malaria is the number 1 killer of children worldwide. The disease is particularly prevalent in sub-Saharan Africa (source: Forgotten Children Worldwide)

Mosquitoes are the primary way that the parasite that causes malaria spreads from one person to the next.

One approach to controlling malaria has been to suppress mosquito populations with insecticides (insect-killing chemicals). One such pesticide is DDT.

Based on the story of antibiotic resistance in bacteria, you should be able to predict what happened when DDT started to be used to control the mosquitoes that spread malaria.

Here’s a graph showing what happened when scientists studied the survival of mosquitoes to exposure to a DDT solution for one hour, every day, for 18 months.

The X-axis on the graph shows time. The Y axis shows the percentage of mortality. Mortality is the number of deaths in a given period of time. For example, the mortality at point A is over 90%. That means that 90% of the mosquitoes were killed after one hour of exposure to the test solution (4% DDT).

Note how different the mortality rate is at point B (10 months) and point C (16 months)

Based on what we learned about bacterial resistance to antibiotics, you can probably explain what’s happening. Study the graph and answer the questions that follow.

 

Before moving on, it’s important to note that the evolution of resistance is a widely observed phenomenon. Other examples include the emergence of

• Weeds that are resistant to herbicides
• Viruses that are resistant to anti-viral drugs
• Cancer cells that are resistant to chemotherapy drugs that are targeted to kill cancer cells

In every case, the evolutionary dynamic is essentially the same. Pre-existing variations allow some members of the population (which can be organisms, cells, or viruses) to survive whatever has been designed to kill that population. The survivors pass on their genes to their descendants. In short order, the entire population is resistant. The faster the population reproduces, the more quickly resistance can arise.

10. Evolution of new phenotypes in response to host changes in the Soapberry bug

The soapberry bug (Jadera haematoloma) lives in the southeastern United States, with its range stretching from Florida to Oklahoma. It uses a needle-like beak to pierce the outside skin of a fruit, and then pierce the seed coat of seeds within the fruit. Enzymes liquefy the seeds, and the bugs suck up the liquified seed contents.

On the right is a drawing by UC Davis Professor Scott P. Carroll of a soapberry bug feeding on the fruit that’s native to Florida, Cardiospermum corindum. Note the distance between the fruit’s skin and its seed, and the corresponding length of the soapberry bug’s beak.

In historical times (within the last 150 years), several plant species have been introduced from Europe and Asia into the range of the soapberry bug. These introduced species have fruit in which the distance between the outside skin and the seeds inside is different from that of the native species. In Florida, the introduced species (Koelreuteria elegans) had a fruit structure in which the seeds were much closer to the skin of the fruit than in the Florida native, C. corindum.

In the interactive reading below, you can interpret what happened.

11. More Examples of Historically Observed Evolution

There are many other examples of evolutionary change that’s been directly observed.

1. In the previous topic, we learned about the peppered moth, which underwent a change from light coloration to dark coloration and then back to light coloration in response to environmental changes. These changes unfolded in a few decades as industrial pollution changed the environment in England’s forests.
   While the phenomenon of color change in response to pollution — known as industrial melanism — was first identified by naturalists in the 1800s, it wasn’t subject to rigorous experimentation until the 1950s, when B.D. Kettlewell systematically observed bird predation driving selection in moths. Kettlewell’s work was subsequently attacked by creationists and then validated by a series of experiments in the early 2000s by Michael Majerus. You can read more about peppered moth biology on Wikipedia.
2. The three-spine stickleback, which we looked at in the context of gene regulation, has been observed to lose its pelvic spines when adapting to freshwater environments. Recent research indicates that this change can happen in as little as 50 years.
3. John Endler performed a series of natural selection experiments in which the 15 generations of natural and sexual selection could alter the phenotype of guppies. You can read a summary of Endler’s experiments on the UC Berkeley Evolution website. For a much deeper dive, you can read Endler’s paper in Evolution, Volume 34, Issue 1. 

12. Flashcards: Historical Examples of Evolution

13. Cumulative Quiz: Historical Examples of Evolution

What’s next?

Proceed to Topics 7.6 – 7.8, Part 2: Homologous and Vestigial Structures, the next tutorial in AP Bio Unit 7.