Lab 4 pre-lab.

To begin our unit on evolution, we will explore the various types of evidence for evolution and further your understanding of the important principles and concepts that comprise the single, greatest, unifying theory in all of biology. We will also explore systematics and taxonomy in this unit. Both use evolutionary concepts to help us order the natural world for study and analysis, and to better understand and describe the relatedness of Earth's organisms.

• Introduction
• Do you know enough?
• What we will do in lab?
• LABridge

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What does the theory of evolution entail?

The theory of evolution comprises two simple tenants:

1. Species change over time.
2. Species are related by decent from a common ancestor.

Change over time is straightforward; over the incredible expanse of time since the formation of Earth, approximately 4.56 billion years ago, the diversity of organisms on this planet has changed. You can compare it to a "null" version that would state that species are immutable and never-changing; that every species we see now has existed in the same form since the beginning of geological time.
​The processes of evolution show how decent from a common ancestor occurs. Evolution usually occurs through a combination of two different processes: via natural selection (a deterministic process), or randomness (a processed guided only by chance). Evolution can occur exclusively via natural selection, or exclusively through randomness, when the process is mixed, we refer to it as stochastic. 
Let us use the extinction of the dinosaurs, the K–T extinction (i.e., Cretaceous–Tertiary extinction) as an example. A 10km asteroid hit Chicxlub, Mexico approximately 66 million years ago, killing off 75% of all life in existence. Among the few animal-survivors were small mammals, who could regulate their own body temperature and had lower energetic needs, unlike the dominant reptiles of the time. Again, the asteroid impact was random, but the evolution (and subsequent radiation and speciation) of mammals across the planet, filling the now empty niches, occurred via natural selection. Remember the term for for this type of rapid speciation is adaptive radiation, as we explored with cichlids in Lab 3.
​Evolution via natural selection was first described by Darwin (see the sidebar) as "descent with modification" as organisms that descend from an ancestor are modified over time by their environments. It is often characterized by "survival of the fittest," meaning that individuals that are best fit to their environment are more likely to survive, reproduce, and pass on their traits. If these traits increase survivability and reproductive success, we characterize them as adaptive traits. Evolutionary fitness, therefore, can come as a result of physiological, morphological, and/or behavioral characteristics, if those characteristics are adaptive. Speciation, the evolution of new species, arises as organisms collect enough new adaptive traits, that they begin to separate from their original ancestral populations. The subsequent development of reproductive barriers places them on their own evolutionarily trajectories. 
As natural selection is a deterministic process (i.e., it occurs due to cause vs. chance alone), therefore, it allows for significant explanatory power and predictive ability. As an example, Darwin and Wallace independently considered a strange orchid from Madagascar with an incredibly long "nectar spur" which housed nectar at the very bottom. Independently, they both proposed that due to natural selection, a moth must also exist in Madagascar with an equally long proboscis to reach the nectar. It was not until twenty years later that naturalists finally discovered a giant hawkmoth with a footlong proboscis that could feed on the flower's nectar. This phenomenon, when two species influence each other's evolution, is know as co-evolution.

Charles Darwin published his book "On the Origin of Species" in 1859. Because of this, he is often credited as the founder of natural selection. However, Alfred Wallace (right), a contemporary and scientific competitor, also reached the same conclusions independently.

The star orchid and the co-evolved hawk moth (photographed by Robert Clark).

Click for link to article.

Be sure you understand the two primary tenants of evolution.

Know the bold-faced terms on this page and review the images and captions.

Read the short article on Darwin and Wallace's hawkmoth.

DO you know enough about the evidence for evolution?

Evidence for evolution can be biogeographical, structural, or genetic.​ The overwhelming evidence in support of evolution comes from many scientific subdisciplines, including paleontology, biogeography, comparative anatomy, comparative embryology, and molecular biology. Each has hypotheses, based on testable, objective data, supported by evolutionary evidence, and each provides testable and objective evidence in support of evolutionary hypotheses. Recall from Lab 2, that testing a single hypothesis, even with repetition, cannot lead to a theory; it can, however, add to theoretical development. Although it was first proposed by Darwin and Wallace, it is the hypotheses tested and supported by these subdisciplines that have built the theory of evolution as we know it today. Each, in its own way, contributes to ideas of change over time and common ancestry. Review the three examples below. We will explore others in lab.

Biogeographical

How and when species arise provides evidence for change over time.

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The study of the distribution of plants, animals, and ecosystems across the Earth, and the causes of variation in their distribution, is called biogeography; think, "where" and "why." Island biogeography has provided some of the strongest evidence for evolution as seen with Darwin's finches across the Galapagos Islands. Other examples include lizards in the Canary Islands and the unique flora and fauna of Madagascar.

Darwin's finches: The different environments on various Galapagos Islands exerted different evolutionary pressures leading to different adaptive traits in the finches that occupied them, eventually leading to new species of finches on each. This is also an example of adaptive radiation, similar to the cichlids in Lake Malawi.

Structural

Shared structural forms provide evidence of shared ancestry.

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Many sub-disciplines use structural similarities as evidence for evolution. Comparative embryology is a branch of biology that is related to the formation, growth, and development of embryo. It has bolstered evolutionary theory by showing all vertebrates develop similarly and therefore have a common ancestor. Understand that natural selection can only operate on what already exists, it does not re-start from scratch. 

Human embryos develop gill slits and post-anal tails. The million year old genetic "instruction manual" that we share with all vertebrates, having evolved from fish (the first), programs all vertebrate embryos in the same way. However, since these features are not needed for our survival after birth, they are lost during later stages of development.

MoleculAr

Shared genetics structures provides evidence of descent from a common ancestor.

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Our understanding of the molecular evidence for evolution has exploded in recent decades as techniques have been refined. As we understand the complete genomes of more and more taxa, it is clear that all life is related. Comparative genomics compares genomic features (DNA sequence, genes, gene order, regulatory sequences, etc.) across taxa and provides a lot of evidence for shared evolutionary relationships.

The genetic similarity of other taxa compared to humans is above (click to enlarge). Each living thing on this planet is comprised of the same nucleotides and amino acids. This provides strong evidence for a shared common ancestor. Genomics is getting us closer to defining LUCA, the Last Universal Common Ancestor.

Review the three categories of evidence for evolution and the examples provided.

Watch the short YouTube videos under biogeography (on finches) and structure (on embryos).

The last YouTube video on LUCA is posted for you to watch if you are interested.

What will we do in lab & how will we do iT?

Lab 4 contains three exercises. Each one provides more more structural support for the theory of evolution from paleontology and comparative anatomy.

1. You will explore the fossil record by categorizing and ordering fossilized specimens.
2. You will investigate homologous and analogous vertebrate forelimbs as evidence for divergent and convergent evolution.
3. You will examine and measure skulls of humans and close human relatives to produce a phylogeny.
4. You will look for vestigial structures in the literature and construct a scientific argument.

Review "it's just a theory"

*Please come to class with an open-mind. Evolution need not be a controversial or touchy subject. Evolution and faith are not mutually exclusive; they operate in entirely different areas of human experience and answer different questions.

If you feel confident with this material, click the bridge icon below and navigate to Blackboard to take the LABridge for this week. Be ready to be tested on this material before you go to the quiz, and make sure you have your Lab Notebook Guide ready to submit as well.

Click here to get to WKU's blackboard to take your LABridge for this week.

Lab 4 Protocol

Following this lab you should be able to...

• Learn the geologic timeline
• Become familiar with the overwhelming evidence in support of evolution
• Observe fossil, embryological, and skeletal evidence for evolution
• Analyze hominid skulls for anatomical differences/similarities supporting human evolution

Overview. In today's lab you will investigate various types of evidence for evolution.

1. ​Exercise I. What does the fossil evidence tell us?
2. Exercise II. What can we learn from homologous and analogous structures?
3. Exercise III. What evidence exists of the path of human evolution?
4. Exercise IV. Do Vestigial Structures Exist?

• Exercise I
• Exercise II
• Exercise III
• Exercise IV

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Exercise I. What does the fossil evidence tell us?

Fossils (remnants of ancient species that have been preserved underground) can provide biogeographical, structural, and even molecular evidence of evolution. They give us a window into the past. Through the fossil record, we know what types of life were abundant when, and when large extinction events (like the K-T event) occurred. Critically, fossils help us better understand geologic time, the expansive time scale since the creation of Earth (see the image in the sidebar).
There are many different types of fossils. 

• Some fossils are imprints of what used to be a living organism.
• Other fossils are shapes where a 3-dimentional object used to be buried. The object was degraded and the space filled with minerals. These are called cast fossils.
• Other types of fossils include: molds, trace fossils (e.g., tracks), petrified fossils, body fossils, etc.

The fossil record is a detailed library of all the fossils available today. Of course, with the passage of billions of years, and billions upon billions of grains of sand and dirt to sift through, a complete fossil record is impossible, though new fossils are discovered every day. These new fossils shed light on our understanding of how organisms transition from one environment to another and from one species to another (known as transitional species). In short, they help us understand the evolution of life as we know it. 
​The oldest known fossils are 3.4 billion years old. Scientists date fossils by dating the fossil layer via radiometric dating, or by dating the layers surrounding the fossil and bracketing the potential time range. 

• Radiometric dating. Scientists can analyze the rocks and minerals in a fossil to determine which types are present and in what quantities. Because these elements decay at a constant rate, scientists can back-calculate the age of the rock by knowing how much of the element is left.
  • Scientists date igneous rock using elements that are slow to decay (e.g., uranium and potassium). 
  • Sedimentary rocks can be dated using radioactive carbon, but because carbon decays relatively quickly, this only works for rocks <50 thousand years.
• Bracketing: If scientists cannot use the fossil itself to determine the age, they use bracketing. By dating the surrounding layers, they can determine the potential "youngest" and "oldest" age for the fossil, providing an estimated age range. The oldest known fossils are 3.4 billion years old.

Geologic timeline. Click to enlarge.

Types of fossils. Click to enlarge.

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Procedure.​

1. Download your Lab Notebook Guide.
2. Examine the geologic timeline in the sidebar and observe the evolutionary history of life.
3. Answer the questions regarding the geologic timeline in your Lab Notebook Guide.
4. Examine the fossils provided.
5. Some are labeled with their age as "X millions of years" or with the period or epoch.
6. Select 10 fossils to examine and complete the table in your Lab Notebook Guide.
7. You will be asked to describe them, identify their age (as best as possible), likely fossil type, and to put them in order of geological time. 

Click to download.

Exercise II. How do homologous structures provide evidence of evolution?

Morphological character traits also provide solid structural and biogeographical evidence for evolution (like the beaks on Darwin's finches). In fact, depending on the trait, morphology can highlight two important types of evolution. 

​Divergent evolution occurs when two related taxa, with similar morphological characters, begin to split, or diverge, from one another. Similarities in the morphology of these taxa exist because they were shared in a recent common ancestor. These taxa have a similar appearance because they are closely related. ​

• Humans are a great example of divergent evolution. Our hominid lineage split from our most related extant lineage, the great apes, approximately 4 to 6 million years ago. 
• Divergent evolution is supported by homologous structures. These structures are derived from the same feature but have been modified by natural selection to perform differently for different animals. We used these structures to group related taxa on our phylogenetic trees.

​Convergent evolution occurs when two lesser related taxa evolve similar morphologies due to similar environments and evolutionary pressure, but NOT because of close shared ancestry. These taxa have a similar appearance but are not closely related. 

• Birds, bats, and pterosaurs* all have wings. Having wings is required for flight and birds, mammals, and reptiles all have examples of species that can/could fly. These three taxa evolved winged flight independent of each other.​
• Convergent evolution is supported by analogous structures. These structures are not derived from a similar ancestor. We had to violate parsimony to include these more than one time on our phylogenies because the traits evolved independently in different lineages. 

Vertebrate forelimbs present a clear example of homologous structures in support of divergent evolution and of analogous structures in support of convergent evolution.
Our upper limbs, like those of all other vertebrates, are descended from the pectoral fins of fishes, our oldest vertebrate ancestors, just as our hind limbs, or legs, are descended from the pelvic fins of ancient fishes. This is true for all animals with backbones. As such, you can observe the similarities between the forelimbs and/or hindlimbs of all vertebrates alive today, as well as those that went extinct. This is best done by observing examples of forelimbs with different functions, and looking for anatomical similarities.
​You can also observe differences amongst these structures as a clear example of analogous structures in support of convergent evolution. This is best done by observing examples of forelimbs with the same function, and looking for anatomical differences.
We will discuss and use homologous and analogous structures to create our phylogenies next week as well!

Full image reference: Cornell, B. 2016. Cladistics/structural-evidence [online]. 

Homologous vs. analogous traits. Click to enlarge.

Phylogeny showing divergent vs. convergent evolution. Click to enlarge (credit: Cornell, 2016)

Homologous vs. analogous structures across vertebrate forelimbs. Click to enlarge (credit: Cornell, 2016).

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Materials. You will be provided with many skeletal examples of vertebrate forelimbs (courtesy of Dr. Huskey).

Procedure.

1. These skeletons are fragile. Please look but do not touch. If you need assistance, ask your TA. 
2. Examine the forelimbs of the species provided.
3. Refer to the anatomy diagram in the sidebar for terminology.
4. Determine which bones, digits, nails, etc. are homologous with the other species.
5. Draw and label the limbs using the proper anatomical terms, on a separate sheet of paper.
6. Complete the table and questions in your Lab Notebook Guide. 
7. You will be asked to suggest a way in which each limb functions based on its morphology, and determine with whom the forelimb is analogous and homologous. 

Vertebrate forelimb anatomical terms. Click to enlarge (credit: Christopher AuYeung).

Exercise iii. What was the pathway of human evolution?

Humans (Homo sapiens) are in the Primate order and the family Hominidae, referred to as hominids. This group includes all the extant and extinct members of the great apes. This taxonomic grouping leads to one of the biggest misconceptions about the theory of evolution; that "humans descended from chimpanzees." While it is true that the chimpanzee (Pan troglodytes) is our closest living relative, we diverged from a shared evolutionary path 4 to 6 million years ago. In this exercise you will learn where we fit in terms of our extant hominid relatives. We will focus on the evolutionary path of our early human ancestors as we split from them and forged our own evolutionary journey. The figure below illustrates these relationships and misconceptions.

Hominid Phylogeny. Extant taxa from the family Hominidae (referred to as hominids). Time is shown in "millions of years ago" on the y-axis. Items in red explain common misconceptions. The blue box highlights our own evolutionary pathway.

Human taxonomy and classification table.

​The path of human evolution is long, complicated, and incomplete; we are constantly filling in branches and gaps with new evidence. The more we learn, the more obvious it is that there were many species of human-like primate over time, many of which coexisted. Some of the best structural evidence for our own evolutionary path comes from examination of the skulls of these recent ancestors in comparison with our own. For example, cranial capacity (cc) increased through time, peaked with Homo neanderthalensis, and decreased slightly among extant humans. Today we will build a table of characteristics across extant and extinct members of the Hominidae family, using skull analysis and other research sources. You will then use your table of characters to fill in some blanks on a simplified phylogeny. A phylogeny is simply an illustration of evolutionary relationships, like an evolutionary family tree. We will explore this concept further in our next lab. 

Materials.

Procedure.

1. Click on the figure above of the simplified hominid phylogeny. Discuss it with your group and address any misconceptions or questions. Most of our work today will involve the relationships among our most recent human ancestor in the blue box.
2. Watch the video: Seven Million Years of Human Evolution. It is only 6 minutes long and will be extremely helpful for this activity. 
3. Go to Exercise III. in your Lab Notebook Guide. Locate the table of characteristics. Review the taxa that we will include and the various traits you will document. Some have been provided. Others you will need to record on your own, or measure for yourselves.
4. Skull Measurements: You will need to complete some skull measurements. Use the figures in the sidebar for directions on these measurements and how to calculate the index.
5. Skull Characteristics: You will be asked to subjectively rate some skull characteristics on a scale from 1 (most like the common ancestor all hominids) to 5 (most like us). You will be rating across eight taxa so you will need to use some numbers more than once.  
6. Abilities: Some characteristics detail what these taxa were capable of doing. These answers are available in the video.
7. As you complete the table think about these traits. Almost all of them are related to a move from the trees to the ground, bipedalism, and a change in diet. Together, many biologists hypothesize, these characters eventually led to our larger brains and increased intelligence.  
8. After completing the table, move on to part 2. You are provided with a partially completed evolutionary tree (sometimes called a phylogeny or cladogram) of hominids. Your task is to use the information gathered in part 1, to complete this phylogeny.
9. If you are struggling with a particular species, look them up here at the Smithsonian Natural History Museum site called, What does it mean to be human?
10. Please note that this is only a partial tree and missing several species and unresolved taxa. As an example: There is an awesome documentary on Netflix right now about a recently discover hominid, the Naledi. Here's a quick trailer for Unknown: Cave of Bones. Most scientists believe the Naledi were a sister species to H. erectus (our direct ancestor). 
11. Complete the questions in your Lab Notebook Guide and move on the Exercise IV, which is to be completed at home.
12. Be sure to get approval as a group to check-out.

Skull diagrams including common terminology. Click to enlarge.

Additional skull diagrams. Click to enlarge.

Measurement directions and index formulas. Click to enlarge.

Sources: American Museum of Natural History, and The Tangled Bank by Carl Zimmer.

Exercsie IV. DO Vestigial StrucTures Exist?

Vestigial structures are another type of structural evidence for evolution. These are structures that persist in extant taxa but have lost their original function. Such structures may have a new derived function, but are still considered vestiges (e.g., remnant eyes in blind salamanders and the pelvic bones of marine mammals). These structure tell us, for example, that blind salamanders diverged from a linage that had sight, and marine mammals evolved from a terrestrial lineage where the pelvis was required to support their weight on land. They are like evolutionary "Easter eggs."​

Please read the excerpt in the sidebar from Vestigial Biological Structures (Senter et al., 2015). In it, the authors provide some examples of well-known vestigial traits and describe a counter-argument offered by anti-evolutionists, that these structures are not actually found in the scientific literature and that in fact, they all still function as "intended." You are going to test the idea that vestigial structures are absent from the scientific literature.​​

Procedure. Read the claim below. Follow the directions and complete your Lab Notebook Guide.​

CLAIM: Scientists have lost confidence in the existence of vestigial structures and can no longer identify any verifiable ones. ​No truly vestigial biological structures exist. Rather, in each case, the structure is functional but its function was unknown when it was labeled as vestigial. ​All structures previously identified as vestigial are actually misidentified as such (Senter et al., 2015).

1. Read the claim above carefully. Think critically about the propositions set forth. You can read the excerpt in the sidebar for more context.
2. Search the literature for examples that support or refute this claim. Decide which position you will support.
3. Use terms like “vestigial” and “vestige," to search online databases for examples of articles in which biological structures are explicitly identified as vestigial.
4. Record each of your sources in the Google Sheet in the side bar along with the requested details.​
5. Collect enough sources to build a good scientific argument (five minimum). Review the figure in the sidebar about Scientific Arguments. 
6. After collecting evidence, construct a scientific argument based on your evidence. Such arguments have three primary parts: a claim, evidence, and reasoning.
7. Complete your Lab Notebook Guide.

Vestigial Structures Excerpt

Vestigial structures database. Click for link to Google Sheet.

Image from Sampson, Grooms, and Walker (2010). Click for link to article.

Faculty Spotlight: Steve Huskey

Dr. Huskey also co-authored this lab manual and has provided all the real skeletons on display for analysis.

Dr. Huskey examines the link between functional design and ecological utility in vertebrates. He uses dissected carcasses, articulated skeletons, and animal behavior to better understand how evolution has shaped organismal design and performance. In the laboratory, he uses high-speed video cameras and pressure sensors to understand the feeding mechanisms of fishes. In the field, he uses SCUBA, rebreathers, portable high-speed video systems, and still-cameras to tease out the intricacies of specialized feeding performance in everything from pelagic to reef species. He and his lab use biomechanics, gross dissection, dermestid beetles, and behavioral observations to draw conclusions about what makes predators successful at doing what they do best -- catching and killing their prey. If you are interested in evolution or functional ecology, send him an email @ [email protected]​.
Recent Publications:
Extreme Morphology, Functional Trade-offs, and Evolutionary Dynamics in a Clade of Open-Ocean Fishes (Perciformes: Bramidae)... 
The Skeleton Revealed: An Illustrated Tour of the Vertebrates [BOOK]