Evidence for Evolution Student Learning Guide

1. “Nothing in Biology Makes Sense Except in the Light of Evolution”

The quote above, from a 1973 essay by evolutionary biologist Theodosius Dobzhansky, captures the central importance of evolutionary theory to understanding biology. In what follows, we’ll look at the evidence supporting evolutionary theory. Let’s start by clarifying how the word theory is used in a scientific context.

2. A theory is much more than a hypothesis

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

That use of the word theory is closer to the idea of a hypothesis: A hypothesis is an idea that requires testing. That’s not what we’re talking about when we talk about the theory of evolution. In science, a theory is an explanation supported by a significant evidence. Theories are born as hypotheses — testable ideas — and, as the evidence for these ideas accumulate, a hypothesis graduates to become a theory.

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, 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.

A theory is a well-established principle that has been developed to explain some aspect of the natural world. A theory arises from repeated observation and testing and incorporates facts, laws, predictions, and tested hypotheses that are widely accepted…

While the terms are sometimes used interchangeably in everyday use, the difference between a theory and a hypothesis is important when studying experimental design. Some important distinctions to note include:

    • A theory predicts events in general terms, 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

The formal scientific definition of theory is quite different from the everyday meaning of the word. It refers to a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence. Many scientific theories are so well established that no new evidence is likely to alter them substantially. For example, no new evidence will demonstrate that the Earth does not orbit around the sun (heliocentric theory), or …that matter is not composed of atoms, or that the surface of the Earth is not divided into solid plates that have moved over geological timescales (the theory of plate tectonics)…One of the most useful properties of scientific theories is that they can be used to make predictions about natural events or phenomena that have not yet been observed.

Source: US National Academy of Sciences

So, before we look at the evidence for the theory of evolution, let’s make sure that the distinction between theory and hypothesis is clear.

[qwiz style = “border: 3px solid black; ” qrecord_id=”sciencemusicvideosMeister1961-Evidence for evo: theory v. hypothesis”]

[h]Theory v. Hypothesis


Theory in science

A validated idea

Much more than a hunch

[!] Question 2++++++++++++++[/!]

[q]In the scientific method, the next step after posing an initial question or making an interesting observation is to formulate a testable



[f]Yes. A hypothesis is a testable idea.

[f]No. Theories are MUCH bigger than testable ideas. Theories stand on a solid foundation of accumulated evidence.

[!] Question 3++++++++++++++[/!]

[q]In the 1800s, two German scientists proposed that all living things are composed of cells, and that cells are the fundamental units of life. During the past two hundred years, no living thing has ever been discovered that does not consist of cells. At this point, these ideas about cells are best understood as being a



[f]No. This idea, which applies to all life, is much bigger than a hypothesis.

[f]Yes. This is the cell theory. It has enormous predictive power, and has been confirmed by every living thing ever discovered.

[!] Question 4++++++++++++++[/!]

[q]A specific and testable proposal that attempts to explain a limited set of phenomena is a



[f]Correct: A specific and testable proposal that attempts to explain a limited set of phenomena is a hypothesis.

[f]No. A theory is a well established principle. What’s described above is much too narrow to be a theory.

[!] Question 5++++++++++++++[/!]

[q]Scientists are measuring the effect of a certain hormone on the growth of breast cancer cells. They think that this hormone might increase the growth of tumors. This is an example of a



[f]Yes. A specific, limited prediction such as the one listed above is a perfect example of a hypothesis.

[f]No. This is much to limited an idea to qualify as a theory. Theories are big. They explain a lot of things. Think of gravity or evolution to remind yourself of the enormous scope of a theory.

[!] Question 6++++++++++++++[/!]

[q]A proposed idea about the speed of falling objects was published by a scientist in the 1600s. Over the next centuries, this proposal was supported by a variety of experiments on earth, and by observations of objects in space. No observation refuting this idea has ever been made. At this point, this idea is best classified as a



[f]No. This is much too grand to be a hypothesis. It covers falling objects, and objects in space. A hypothesis would be much more narrow, and not explain such a wide variety of things.

[f]Yes: this is the theory of gravity. It has enormous power to explain, and it’s been repeatedly confirmed for hundreds of years.

[!] Question 7++++++++++++++[/!]

[q]A well-substantiated explanation of some aspect of the natural world, based on a body of facts that have been repeatedly confirmed through observation and experiment.



[f]No. A hypothesis is a tentative prediction that still needs to be confirmed by experiment.

[f]Yes. A well-substantiated explanation of some aspect of the natural world, based on a body of facts that have been repeatedly confirmed through observation and experiment is a beautiful definition of a theory.

[!] Question 8++++++++++++++[/!]

[q]A group of students sets up an experiment to test the idea that tomato plants grown in blue light will produce larger fruit that tomatoes grown in regular sunlight. This idea would best be classified as a



[f]Yes. The narrowness of the idea and its tentative nature classify this as a hypothesis.

[f]No. A theory would have to be much wider in scope, and much more powerful in its ability to explain things.

[!] Question 9++++++++++++++[/!]

[q]The idea that all infectious diseases are caused by germs (bacteria or viruses) has been repeatedly confirmed by hundreds of observations.



[f]No. This is an idea that covers ALL infectious diseases. It’s much too broad to be a hypothesis.

[f]Yes. This is the germ theory of disease, and it’s been repeatedly confirmed for the past 150 years.

[!] Question 10++++++++++++++[/!]

[q]In the scientific literature, there is a strong consensus that global surface temperatures have increased in recent decades and that the trend is caused mainly by human-induced emissions of greenhouse gases. No scientific body of national or international standing opposes this view, though a few organizations hold non-committal positions. At this point, the idea that global warming has been caused by humans should best be considered a



[f]No. Since this idea has been repeatedly confirmed by numerous studies and experiments, it seems to broad and well established to be considered a mere hypothesis.

[f]Yes. The strong consensus, its predictive power, its confirmation though many models of climate, make Global Warming much more like a theory than a hypothesis.


If you want to take this quiz again, click the button below



3. What claims does the theory of evolution make? What needs to be proved?

The theory of evolution makes two claims.

  1. The first claim is descent with modification. That’s the term that Darwin used to describe evolution, and it means that as ancestral populations give rise to descendants, these descendants can change. While that might seem obvious, it contradicts the Biblical notion of unchanging species created by a Creator.
    The idea of descent with modification means that if evolution is occuring,  the current form of a species should be different from its ancestral form. For example, if you could look back 100,000 years, the ancestors of dogs would be different from the dogs you see today. That’s because dogs are the modified descendants of wolves. If you went back 100,000,000 years, there wouldn’t be wolves, but rather an ancient, earlier mammalian species that was in the line that, millions of years later, led to wolves. That claim applies to every other species alive today, including humans.
  2. The second claim is that as evolution occurs, there should be an underlying change in a population’s genetic makeup. The description of descent with modification in # 1 above would have been familiar to Darwin and Wallace, who formulated the modern theory of evolution in the 1800s. That’s because it focuses on appearance, or phenotype. But during the 20th century an increasingly gene-centered view of evolution has emerged. This view of evolution sees populations changing not just in terms of average phenotype, but in terms of its gene pool.
From Darwin’s First Notebook on Transmutation of Species. A, B, C and D are descendants of species 1. A and B are distant relatives, while B and C are closer.

If we look at life, both present and past, descent with modification (and the genetic changes that underlie it), will unfold in two ways. We can track these in the image to the left, a sketch by Darwin in one of his notebooks. He  made this sketch in 1837  (twenty two years before his publication of The Origin of Species). 

The first way that evolution unfolds is change in a lineage, over time. If “1” at left represents a species, then A, B, C, and D are all descendant species. If you follow the line from 1 to any of its descendants, you should be able to observe descent with modification along the way. Biologists call this anagenesis: evolution within a single lineage over time.

The second way that evolution unfolds is shown by the diagram’s branching pattern. Since species 1 is the ancestral species that gave rise to A, B, C, and D, then all of these descendant species should have shared features that result from their common ancestry. If this diagram were of a family, then A, B, C and D would be cousins. You’d could predict that B and C would be more alike (both genetically and phenotypically) than B and A, because, in Darwin’s representation, B and C are more closely related than A and B are.

Flipping the logic gives us a way to find evidence of evolution. Pretend this is a family tree. If you didn’t know that B and C were related, but you did a DNA test and and found that they shared a certain percentage of their genes, you would have to conclude that they were related: siblings, cousins, etc. And while it’s less direct, if you found certain shared inherited phenotypes, that would lead you to the same conclusion. With species, you can do the same thing. Shared DNA sequences can serve as evidence of common descent. So can shared inherited phenotypes. After all, if these species weren’t the descendants of a common ancestor, why would they share DNA sequences, or other inherited traits?

So, two evolutionary propositions have to be proved. What’s the evidence for

  1. Descent with modification
  2. Genetic change in a population’s genetic structure

And how will we see evidence of either in life’s branching pattern?

4. Observations of Evolution in Recent Times

Darwin was a gradualist: he saw change in the natural world as occurring through the gradual accumulation of small changes which, over time, would add up to significant change. Hence, his view of evolution was one in which changes would be imperceptibly slow, over thousands or millions of years, and only discernible in hindsight.

However, a variety of studies during the late 19th, 20th, and 21st century have shown that evolution can proceed rapidly. In other words, scientists have observed both descent with modification, and changes in a population’s genetic structure. Here are a few examples.

4a. Evolution of Antibiotic resistant bacteria and the rise of MRSA.

Staphylococcus aureus is a bacterium. It’s one of many bacterial species that harmlessly live on our skin and other parts of our bodies, but there are also pathogenic forms that can cause skin and sinus infections, along with food poisoning, pneumonia, and wound infections. Up to 50,000 deaths/year are associated with S. aureus infections, and about 500,000 hospital patients become infected with S. aureus each year.

Bacterial infections by S. aureus can be treated with antibiotics: substances that kill bacteria or inhibit bacterial growth. However, widespread use of antibiotics has created selective pressure for S. aureus (and other infectious bacteria) to evolve antibiotic resistance, making antibiotics increasingly ineffective. The first widely used antibiotic, penicillin, was introduced in 1943. But by the 1950s, penicillin-resistant strains of S. aureus were common.

Natural selection was at work. S. aureus populations have genetic variation. Most bacterial cells can’t reproduce when exposed to to penicillin, a molecule that inhibits cell wall formation. But some bacterial cells produce an enzyme called penicillinase, which cleaves apart penicillin, making it ineffective. These individual bacterial cells were able to survive the doses of penicillin that killed off the rest of the population. When the survivors reproduced, they passed along their genes for resistance. By 1950, only seven years after penicillin was introduced, 40% of S. aureus studied were penicillin-resistant. By 1960, this had risen to 80%. Now it’s about 98%.

Some other features of bacterial reproduction have enhanced the spread of resistance. Bacteria don’t only pass their genes on to their descendants. Through tiny, transferrable circles of DNA called plasmids, bacteria can also pass genes to other members of their population. This is called horizontal gene transfer. Transfer of antibiotic resistance genes through plasmids has further increased antibiotic resistance.

Here’s an infographic that illustrates the process.

  1. Image “A shows the initial population. Most bacterial cells (the gray ones) are killed by the antibiotic. A small percentage are antibiotic-resistant. Note that the resistance is a pre-adaptation. It didn’t arise in response to the selective pressure, but was part of the population’s pre-existing genetic variation.
  2. Application of the antibiotic kills all the bacteria that are susceptible, leaving only those that are resistant.
  3. As the bacteria reproduce, the new population will be mostly composed of antibiotic-resistant cells.
  4. Horizontal gene transfer of genes for antibiotic resistance increases the proportion of antibiotic resistant individuals in the population.

Widespread use of antibiotics in agriculture has made the problem worse.

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 (80% of the antibiotics used in the United States). As with humans, the antibiotics feed to animals (A) kills only the susceptible bacteria, selecting antibiotic resistant strains (B and C). These can be transferred to people through animal products, through 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. Like penicillin, methicillin inhibits bacterial cell wall formation, but through a different mechanism than penicillin did. However, within two years of its introduction, methicillin-resistant bacteria had been observed. In this case, the resistant bacteria were able to use an enzyme to synthesize their cell walls through a mechanism that wasn’t inhibited by methicillin. 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. Often, MRSA infections can be controlled by other antibiotics, such as vancomycin. 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.

4b. Evolution of Pesticide Resistance in Mosquitoes

The Anopheles mosquito is a prime carrier of the parasite that causes malaria

Mosquitoes are the primary vector for the Plasmodium parasite that causes malaria. Malaria is the number 1 killer of children worldwide, and killed 445,000 people in 2016, over half of whom were under the age of 5. The disease is particularly prevalent in sub-Saharan Africa (source: Forgotten Children Worldwide)


One approach to controlling malaria has been to suppress mosquito populations with insecticides (insect-killing chemicals). One such pesticide is DDT (dichlorophenyl trichloroethane). It was developed in the 1940s, and works by opening sodium channels in the membranes of insect neurons, causing these neurons to misfire, leading to spasms and death.

Based on the story of antibiotic resistance in bacteria, you should be able to predict what happened.

Here’s a graph showing what happened when scientists measured the resistance of mosquitoes to exposure of 4% DDT solution for one hour. Measurements were done under controlled conditions, over a period of 18 months. Study the graph and answer the questions that follow.

[qwiz qrecord_id=”sciencemusicvideosMeister1961-Evidence for evo: DDT”]

[h] DDT Resistance In Mosquitoes

[q] At which time period (A, B, or C) did the vast majority of the mosquitoes have pesticide resistance?

[textentry single_char=”true”]

[c*] C

[f] Excellent. At point “C,” only 20% of the mosquitoes are dying after 1 hour of exposure to the solution. If they’re not dying, they must be resistant.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Find the point in time when the mortality (the amount of death) is very low. That’s when most of the population is resistant.

[q] At which time period (A, B, or C) were the majority of the mosquitoes susceptible to DDT?

[textentry single_char=”true”]

[c*] A

[f] Excellent. At point “A,” the mortality is almost 100%. That means that at this point in time, the mosquitoes are susceptible to the mosquitoes.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Find the point in time when the mortality (the amount of death) is very high. That’s when most of the population is still susceptible to DDT.

[q] At point “C” in the graph below, most of the mosquitoes were [hangman] to DDT.

[c] resistant

[f] Good!

[q multiple_choice=”true”] True or false: In response to DDT, mosquitoes developed a mutation that made them resistant.

[c] true

[f] No. Natural selection is not about populations producing mutations that help them survive environmental challenges. It’s about the environment selecting variant phenotypes that make the individuals who have them more suited to surviving and reproducing. The mutation precedes the challenge.

[c*] false

[f] Excellent. Natural selection is not about populations producing mutations that help them survive environmental challenges. It’s about the environment selecting variant phenotypes that make the individuals who have them more suited to surviving and reproducing. The mutation precedes the challenge.

[q multiple_choice=”true”] At which point in the graph below are there individuals with mutations that enable them to survive exposure to DDT?

[c] A

[f] No. It’s true that some individuals in A must have had a mutation that enabled them to survive exposure to DDT. But there’s a better answer.

[c] B

[f] No. It’s true that about 50% of the individuals in B must have had a mutation that enabled them to survive exposure to DDT. But there’s a better answer.

[c] C

[f] No. It’s true that most individuals in C must have had a mutation that enabled them to survive exposure to DDT. But there’s a better answer.

[c*] A, B, and C

[f] Yes. All of these populations must have possessed individuals with mutant phenotypes that allowed them to survive exposure to DDT.


4c. Evolution of new phenotypes in response to host changes in the Soapberry bug

Soapberry bug (source: wikipedia)

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 fruit, and then pierce the seed coat of seeds within the fruit. Enzymes liquify the seeds, and the bugs suck up the liquified seed contents.

Source: Evolution, 46 (4), 1992, pp 1052 -1069. Permission granted by S.P. Carroll.

Here’s a drawing by UC Davis Professor Scott P Carroll of the 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 Eurasia 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.

[qwiz qrecord_id=”sciencemusicvideosMeister1961-Evidence for evo: soapberry bug”]

[h]Phenotype shifts in response to introduced host species in the soapberry bug

[i]Note that in this graph, the values above and below the 0 line are positive.

[q labels = “top”]The graph below shows how there’s a correlation between the distance between the wall of the fruit and the surface of the ________, and the length of the soapberry bug’s __________. The population with the __________ beaks are those which feed on the __________ fruit, in which there’s a greater distance between the fruit wall and the seed.


[fx] No, that’s not correct. Please try again.

[f*] Great!


[fx] No, that’s not correct. Please try again.

[f*] Great!


[fx] No. Please try again.

[f*] Correct!


[fx] No. Please try again.

[f*] Great!


[q labels = “top”]The table below shows what happened in Florida in soapberry bug populations that started feeding on the introduced species. In the table, match the average beak length of the soapberry bugs with the plants they feed upon.


Average Soapberry bug beak length on native and introduced host plants
Host Plant Origin Average distance from fruit wall to seed (mm) Average beak length (mm)
Balloon Vine (C. corindum) Native 11.92 _______
Goldenrain tree (K. elegans) Introduced 2.82 _______


[fx] No. Please try again.

[f*] Great!


[fx] No. Please try again.

[f*] Excellent!

[q labels = “top”]Let’s interpret these results.


Soapberry beak length on native and introduced host plants (Carroll and Boyd, Evolution, 1992)
Host Plant Origin Average distance from fruit wall to seed (mm) Average beak length
Balloon Vine (C. corindum) Native 11.92 9.32
Goldenrain tree (K. elegans) Introduced 2.82 6.93

When soapberry bug populations colonized the introduced host (the Goldenrain tree), these populations ___________ to their host’s fruit structure. What’s notable is the ___________ with which this shift occurred: a few dozen ___________. Additionally, when eggs from one host were transplanted to the other, the offspring’s beaks maintained the length of the population from which the eggs were harvested. This shows that the shift in ____________ was based in an underlying __________ change.  (source: Campbell, Biology, 11th edition, page 475).


[fx] No. Please try again.

[f*] Great!


[fx] No. Please try again.

[f*] Good!


[fx] No. Please try again.

[f*] Great!


[fx] No. Please try again.

[f*] Good!


[fx] No, that’s not correct. Please try again.

[f*] Excellent!

[q]To summarize. In the introduced fruit K. elegans the distance between the fruit wall and the seed is much [hangman] than in it is in the native fruit, C. corindum. In those populations of the soapberry bug that began to exploit the fruit of this new host, there was less [hangman] pressure for extremely long beaks. Bugs with [hangman] beaks experienced no loss of evolutionary [hangman] (and might have increased their fitness, since less energy was required to build a very long [hangman]. Within a few dozen generations, populations exploiting K. elegans had significantly shorter beaks than populations on the native fruit, making this a documented example of [hangman] with [hangman].









5. Cumulative Quiz: Historical Examples of Evolution

There are numerous examples of rapid evolutionary change that’s been observed by biologists. To learn more, use any of the following links

  1. This article in Discover Magazine has several examples.
  2. The evolution of the Peppered Moth. This is an example of industrial melanism first identified in the 1800s, confirmed by B.D. Kettlewell in the 1950s, subsequently attacked by creationists, then validated by experiments at the start of the 21st century by Michael Majerus). You can read about the scientific history and biology on Wikipedia
  3. Species formation (also based on host shifts and introduced species) in the apple maggot fly.

[qwiz qrecord_id=”sciencemusicvideosMeister1961-Evidence for Evo: historical examples”]

[h] Historical Examples of Evolutionary Change


[q] Because of the large body of evidence supporting evolution, it should be thought of as a [hangman], rather than a [hangman].

[c] theory

[f] Great!

[c] hypothesis

[f] Great!

[q] If evolution is true, then one should be able to provide evidence for descent with [hangman] in any specific lineage. For example, fossils would show that a currently existing species’ [hangman] are different from the current form of that species.

[c] modification

[f] Great!

[c] ancestors

[f] Great!

[q] If evolution is true, then a population’s [hangman] makeup should be changing over time.

[c] genetic

[f] Correct!

[q] The diagram below represents a situation in which species 1 through 9 all evolved from a common ancestor. If evolution is true, then the species 1 through 9 should share some shared traits. At the same time, in each lineage these traits might be [hangman] in different ways.

[c] modified

[f] Correct!

[q] Darwin thought that evolutionary change had to happen slowly. That makes him a [hangman]. However, observations of evolutionary change in the 19th, 20th, and 21st centuries indicate that evolutionary change can happen [hangman]: in a few decades.

[c] gradualist

[f] Excellent!

[c] quickly

[f] Great!

[q] Because of our overuse of antibiotics, many bacterial strains have become antibiotic [hangman].

[c] resistant

[f] Great!

[q] In the diagram below, images A and B show how antibiotic resistance was pre-[hangman], and then [hangman] for by overuse of antibiotics.

[c] existing

[f] Great!

[c] selected

[f] Correct!

[q] In the diagram below, image D shows how antibiotic [hangman] in bacteria can spread through [hangman] gene transfer.

[c] resistance

[f] Excellent!

[c] horizontal

[f] Great!

[q] The difficult-to-treat strain of Staphylococcus aureus bacteria that has evolved in recent decades is known by the acronym [hangman].

[c] MRSA

[f] Great!

[q]Since its introduction in the 1940s, DDT has become increasingly ineffective due to the evolution of pesticide [hangman] in mosquitoes that carry the Plasmodium parasite which causes [hangman].



[q multiple_choice=”true”] True or false: In response to DDT, mosquitoes developed a mutation that made them resistant.

[c] true

[f] No. Natural selection is not about populations producing mutations that help them survive environmental challenges. It’s about the environment selecting variant phenotypes that make the individuals who have them more suited to surviving and reproducing. The mutation precedes the challenge.

[c*] false

[f] Excellent. Natural selection is not about populations producing mutations that help them survive environmental challenges. It’s about the environment selecting variant phenotypes that make the individuals who have them more suited to surviving and reproducing. The mutation precedes the challenge.

[q]Like the mosquito, the soapberry bug is an example of an insect that [hangman] quickly in response to selective [hangman]. In the case of the soapberry bug, populations that exploited a new food resource quickly changed their [hangman]. Specifically, the [hangman] length of soapberry bug populations became significantly [hangman] in a few decades.









  1. Homologous and Vestigial Structures (the next tutorial in this module)
  2. Evidence for Evolution Menu