Putman’s Biol 160 Lab 11: Evolution’s Evidence

Lab 11: Evolution’s Evidence Introduction The Principle of Evolution states that populations of organisms evolved, and are still evolving, from a common ancestor through changes over time. These changes resulted from variations exhibited among individuals that allowed them to survive and reproduce in a changing environment. Evolution has remained the best scientific explanation for the origins and diversity of life since it was proposed by Charles Darwin in 1859. The characteristics of organisms come from the characteristics of their ancestors, with little to profound changes added each generation. A group of people with blue eyes, light skin and freckles have these characteristics because their ancestors had these characteristics. Another group of people may have brown eyes, dark skin and no freckles, these characteristics coming from their ancestors. Both groups share the common characteristics that all humans share, derived from a common human ancestry, yet we can differentiate between these two groups because of the high number of similar characteristics. We can identify children from each family by their similar characteristics, and we can determine how closely people are related by the relative number of similar and dissimilar characteristics. People who are most closely related have the most characteristics in common, and people who are most distantly related have the least characteristics in common. This is the basic principle we use to determine relatedness among all organisms, including people. There are four lines of evidence seen in nature that clearly suggest the evolutionary origins of the diversity of life: 1) Fossils, 2) Comparative Anatomy, 3) Comparative Embryology and 4) Comparative Molecular Sequences. Evidence from Fossils Perhaps the hardest evidence that organisms have changed over time comes from fossils. In the fossil record are the traces of organisms that no longer exist, and evidence of organisms that are clearly related to those living today, only with features presently unseen. From the fossil record we can clearly see the great age of the earth, the overall progression from simple to more complex forms of life, the extinction of species and entire groups, the replacement of those groups with newly-evolved species, and in some lines, the very clear evolution from one species to completely different and new species—and more evidence consistent with evolution is being collected with each new study. Problems with the fossil record arise from the imperfect nature of the fossilization process. In order for an organism to be fossilized, it must fall into, or be covered by, some airtight agent such as mud, tar, or amber. The most common entombing agent is mud, suggesting that the most common fossilized organisms are aquatic, especially marine (which, of course, is great for marine paleontologists!). This type of entombing agent forms sedimentary rock. Further, common organisms would be fossilized more often than rare organisms, and organisms with hard parts such as shells or bones fossilize much more readily than organisms that are soft and squishy.

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Putman’s Biol 160 Lab 11: Evolution’s Evidence Table 11.1. The geological time scale annotated with major origins and extinctions. ERA

PERIOD

EPOCH

Cenozoic

Quaternary

Recent Pleistocene Pliocene Miocene Oligocene Eocene Paleocene

Tertiary

Mesozoic

Paleozoic

Cretaceous Jurassic Triassic Permian Carboniferous Devonian Silurian Ordovician Cambrian

Proterozoic

MILLIONS OF YEARS AGO 0.01 1.8 6 24 38 57 65 140 200 240 285 350 400 435 500 570

3500

OCCURRENCES

Evolution of humans Evolution of pinnipeds Evolution of cetaceans Extinction of 50% of all species Evolution of flowering plants Evolution of mammals & dinosaurs Extinction of 90% of all species Evolution of reptiles Evolution of sharks & amphibians Evolution of land plants & land arthropods Evolution of vertebrates Massive diversification of invertebrates Evolution of seaweeds & invertebrates First known fossils (marine)

The age of fossils can be determined both directly and indirectly. As mountains wear down, they deposit sediments. Volcanoes erupt, covering the sediments with ash and lava. In time, more sediments are deposited on top of the volcanic rock, and so forth. This creates geological lines or strata, one on top of another, with the youngest deposited on top, the oldest on the bottom. Fossils found within more recently-deposited rock can be assumed to be younger than fossils found within more anciently-deposited rock strata. Table 11.2. Half-lives of several radioactive substances. It takes the indicated amount of time for half the weight of a particular isotope to decompose. By measuring the amount of the radioactive material remaining and the amount of the decomposition product, the age of the material can be determined. Original isotope uranium-238 potassium-40 uranium-235 carbon-14

Decomposition product lead-206 argon-40 lead-207 carbon-12

Half-life 4.5 billion years 1.5 billion years 713.0 million years 5730 years

Volcanic material contains radioactive substances, which decompose at known rates. We can thus measure the amount of radioactive isotope remaining, the amount of its decomposition product present, and determine the age of the rock by knowing the half-life, or time it takes onehalf of the radioactive isotope to decompose. If we do this for strata above and below a particular

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Putman’s Biol 160 Lab 11: Evolution’s Evidence fossil-bearing rock layer, we can estimate the age of the fossils. If fossils were embedded with volcanic ash, then a direct measurement of the age of the fossil is possible. Certain fossils occur only during specific geological times; these fossils are called index fossils because, once they have been dated using the above techniques, they can be used to date other fossils found with them in other places. Since nature breaks up and folds rocks, nature breaks up and folds the fossil record, creating gaps, and even inversions where geological strata will reverse itself, going from young to old rocks on top, adding a measure of difficulty in reading the fossil record. These geological tricks of nature are, however, rather easy to uncover with appropriate field work. Evidence from Comparative Anatomy If you look at a collection of organisms, it is natural to focus on characteristics that appear similar and to group the organisms based on these characteristics. In evolutionary biology, we focus on shared characteristics that we assume were present in the ancestral species. These characteristics we term primitive or plesiomorphic characteristics. Characteristics found only within a particular group, or clade, are termed derived or apomorphic characteristics. It is important to note at this point that not all characteristics that appear to be similar are homologous--derived from common ancestors. Some are simply the product of similar natural selection pressures and are said to be analogous. Analogous structures are those that may look superficially similar, have similar functions, but are structurally different hence, not derived from common ancestors. For instance, birds, bats and butterflies have wings, fish and whales have fins, and octopuses and jellyfish have tentacles—yet none of these appendages suggest evolutionary relationships because their underlying structures are completely different. Now, let’s say we’re studying the evolutionary relationships between salamanders, alligators, monkeys and gorillas. Note that all members of the group are tetrapods--four legged. Because of this, this characteristic is said to be primitive or plesiomorphic. As all members of the group are tetrapods, we assume their common ancestor was a tetrapod. Note that alligators, monkeys and gorillas are have an amnion—a membrane that encloses their embryos—whereas salamanders do not. Since this characteristic is found only in this subgroup, it is a derived or apomorphic characteristic.

perch salamander alligator monkey gorilla

fur amnion four legs

Figure 11.1. Cladogram of the tetrapods.

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Putman’s Biol 160 Lab 11: Evolution’s Evidence For the clade consisting of salamanders, alligators, monkeys and gorillas (the tetrapods, Fig. 11.1), the tetrapod condition is plesiomorphic and the unique characteristics that differentiate them are apomorphic characteristics. So, the determination of whether or not a characteristic is plesiomorphic or apomorphic depends on the clade in question. To represent evolutionary relationships, biologists construct cladograms. Using our group of organisms, the simplest cladogram can be constructed, noting the apomorphic characteristics at the internodes (between the branches) of the tree. Note that I’ve included an additional species, a perch. The perch in this cladogram is what is called an outgroup, an organism that is not part of the study to which the organisms of the study can be compared. Every cladogram must have an outgroup. The first step in the construction of a cladogram is to determine the apomorphic characteristics. We then construct a data matrix: Character perch salamander alligator monkey gorilla

1 0 1 1 1 1

2 0 0 1 1 1

3 0 0 0 1 1

1. Four legs? No (0), Yes (1) 2. Amnion? No (0), Yes (1) 3. Fur? No (0), Yes (1)

The next step is to construct a similarity matrix, adding the number of characteristics in common between each species: perch perch salamander alligator monkey gorilla

salamander 0

alligator 0 1

monkey 0 1 2

gorilla 0 1 2 3

Link together the two species that are the most similar: monkey gorilla

Now, considering the monkey/gorilla clade (M/G) as a single unit, make a new similarity matrix, comparing M/G to the rest of the species: perch perch salamander alligator M/G

salamander 0

alligator 0 1

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M/G 0 2 4

Putman’s Biol 160 Lab 11: Evolution’s Evidence From our matrix, it is clear that the alligator is the next that should branch off: alligator monk ey gorilla

We continue in this fashion until all of our species are accounted for, including our outgroup. Various other formal procedures are also used to construct cladograms, and there are computer programs to assist us. Judgment, experience and common sense are also used. Cladistics is the branch of biology that specializes in cladistic analysis and the construction of cladograms. Evidence from Comparative Embryology

Figure 11.2. Comparative embryology of vertebrates.

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Putman’s Biol 160 Lab 11: Evolution’s Evidence Just as adult anatomy of closely-related species is more similar than adult anatomy of more distantly-related species, the developmental stages of closely-related species are quite similar. Further, developmental stages exhibit characteristics of the organisms from which they evolved, characteristics that then may develop in the adult into completely different structures, both functionally and structurally. As examples of this, all embryonic vertebrates have tails and gill slits. Tails may be reabsorbed into the body in some vertebrates (apes, including humans) or may develop into structures helping the animal to swim (fish, amphibians, whales), hang onto tree limbs (opossums, monkeys) or help with balance (lizards, kangaroos). Gill slits and associated structures are functional in “lower” vertebrates (fish, amphibians), but develop into components of the jaw and ear in “higher” vertebrates (amphibians, “reptiles,” birds and mammals). Again, since all organisms are products of their past, and are made of structures they inherit from their ancestors, it should be no surprise that they bear witness to past evolutionary history!

Fig. 11.3. Chick embryo, 72-hr. Ex. www.developmentalbiology.net

Evidence from Comparative Molecular Sequences As species evolve over evolutionary time, the structure of their molecules changes. Species that are closely related have fewer differences in the structure of their molecules than species that are distantly related. This is because the molecules of closely-related species have had less time to change than more distantly-related species. The most obvious molecule in which we see evolutionary changes is DNA. The DNA sequence of a species is different enough from other species to make it a species. Not surprisingly, closely-related species have DNA sequences that are more similar than distantlyrelated species. Besides DNA, RNA sequences are also widely studied and provide us with huge amounts of data consistent with the principle of evolution.

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Putman’s Biol 160 Lab 11: Evolution’s Evidence One of the most widely-studied molecular sequences is that of cytochrome c. Hopefully, you remember cytochrome c as being one of the electron carriers in the electron transport chain of cellular respiration. Since all cells, from bacteria to plants to humans undergo cellular respiration, they all have cytochrome c. Cytochrome c is said to be a highly conserved molecule, meaning that it hasn’t changed much over evolutionary time. But the few changes it has undergone are important in helping us determine the relationships of higher taxa such as the relationships between domains, kingdoms, phyla and classes. Specifically, we study and compare the amino acid sequences of cytochrome c, although we could just as well study the DNA sequences of the genes that code for the molecule. The purpose of this lab is to introduce you to the four general areas of evidence seen in nature in where we observe evolution’s evidence.

Laboratory Objectives After mastery of this laboratory, including doing the assigned readings and required laboratory work, the student should be able to: 1. Discuss how fossils, comparative anatomy, comparative embryology and comparative molecular sequences provide evidence for evolution.

Materials and Methods Evidence from Fossils 1. At the demo table will be a series of fossils labeled with their names and dates, as determined using index fossils. Do not handle the fossils unless your instructor gives you permission! For at least ten fossils on display, record its name and age in the results portion of this lab write-up. Using Table 11.1, determine the era, period and epoch (if given) for each specimen, and record this information as well. 2. Also for the fossil organisms you examine, try to determine if the organisms were aquatic (lived in the water) or were terrestrial (lived on land). Record evidence you observe or infer from your observations! 3. On the display in the lab will be a representative “missing link” fossil. Do not handle or touch the missing link fossil! In your lab report, answer the following question about the fossil: a. Identity of “missing link” fossil. b. Age. c. Era, period and epoch (if given). d. What two groups of organisms this “missing link” connects. e. Characteristics of each group supporting that this is a “missing link” fossil!

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Putman’s Biol 160 Lab 11: Evolution’s Evidence Evidence from Comparative Anatomy 1. Select five specimens from the demo table. Examine the specimens carefully. Determine at least five apomorphic characters for your group. Construct a data matrix and a similarity matrix. Then, based on your similarity matrix, and your judgment, construct a cladogram for your group of specimens. If you need help, ask your instructor! 2. Your instructor will give you a handout comparing the upper limb of vertebrates with that of the ancestral vertebrate. Compare the indicated bones with that of the ancestral limb and determine which are most primitive (have changed the least from the ancestral condition) and which are most advanced (have changed the most from the ancestral condition). For two of the most modified bones, suggest what special function these bones allow in the animal(s) that possess these bones! Evidence from Comparative Embryology 1. From the demo table, obtain commercially-prepared slides showing the embryological development of a chick and a pig (or any two vertebrate species). Observe the two embryos and list five similarities, using Fig. 11.3 to help you identify structures. Evidence from Comparative Molecular Sequences 1. You will be provided with a selection of actual cytochrome c amino acid sequences from various organisms. Using the procedures already learned in this lab, construct a similarity matrix for your organisms and then construct a cladogram. When you are finished, ask your instructor for the identity of each of the organisms to see if your cladogram makes sense!

Make sure you cleanup your work station, clean all equipment you used and put it back, and help in general to keep the lab clean and in order!

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Putman’s Biol 160 Lab 11: Evolution’s Evidence

Biol 160 Lab 11: Evolution Prelab (5 points)

Name: ___________________________________ Date: ________________ Lab Section: ________

~Complete this prelab before coming to lab; it is due at the beginning of lab! Evidence from Fossils 1. Why is the fossil record imperfect; that is to say, why does the fossil record contain mostly aquatic species or species that once lived by water, rather than a perfect record of every organism that once lived?

2. What must happen in order for something to be fossilized?

3. Why are shells and bones the most common type of fossil?

Evidence from Comparative Anatomy 4. What is a plesiomorphic characteristic? Give an example!

5. What is an apomorphic characteristic? Give an example!

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Putman’s Biol 160 Lab 11: Evolution’s Evidence 6. What do we mean when we say then wing of a bat is a structure homologous to the flipper of a whale, yet the wing of a butterfly is not homologous but is analogous to the wing of a bat?

Evidence from Comparative Embryology 7. Human embryos have a tail, flipper-like limb buds and gill slits. Why?

Evidence from Comparative Molecular Sequences 8. Whales and humans have cytochrome c sequences that are more similar than fish and whales. Why?

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Putman’s Biol 160 Lab 11: Evolution’s Evidence

Biol 160 Lab 11: Evolution Lab Report (20 points)

Name: ___________________________________ Date: ________________ Lab Section: ________

Results Evidence from Fossils 1. Identity, age, era, period, epoch and habitat of ten different fossil organisms. Habitat Identity

Age

Era

Period

Epoch

Marine or Terrestrial Evidence?

2. “Missing link” fossil: a. Identity of “missing link” fossil: ____________________________________ b. Age: ____________________________ c. Era: ___________________ Period: ___________________ Epoch: _______________

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Putman’s Biol 160 Lab 11: Evolution’s Evidence d. The two groups this organism connects + characteristics of each:

Group 1: Characteristics:

Group 2: Characteristics:

1.

1.

2.

2.

3.

3.

Evidence from Comparative Anatomy 1. Five apomorphic characters for specimens/species examined: Character 1: Character 2: Character 3: Character 4: Character 5: 2. Data matrix for specimens/species examined: Specimen/Species

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1

Characters 2 3 4 5

Putman’s Biol 160 Lab 11: Evolution’s Evidence 3. Similarity matrix for specimens/species examined: Specimen/ Species

1

2

3

1 2 3 4 5 6

4. Cladogram based on similarity matrix:

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4

5

6

Putman’s Biol 160 Lab 11: Evolution’s Evidence 5. Comparison of the bones of the upper limbs of representative vertebrates: Name of Animal

Most Primitive Bones

Most Advanced Bones

6. Two of the most modified bones and the special function these bones allow in the animal(s) that possess these bones: a. Bone: ____________________ Special Function:

b. Bone: ____________________ Special Function:

Evidence from Comparative Embryology 1. Two embryos examined: _______________________ and _______________________ 2. Five structures similar in the embryo: a. ______________________________________________________________________ b. ______________________________________________________________________ c. ______________________________________________________________________ d. ______________________________________________________________________ e. ______________________________________________________________________

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Putman’s Biol 160 Lab 11: Evolution’s Evidence

Evidence from Comparative Molecular Sequences 1. Similarity matrix of cytochrome c sequences: Species

A

B

C

A B C D E

2. Cladogram based on similarity matrix: Hint: Some possible cladograms might include these:

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D

E

Putman’s Biol 160 Lab 11: Evolution’s Evidence Discussion 1. What five things does the fossil record tell us?

2. Why do we suspect that a fossil found 10 meters from the surface in sedimentary rock is older than a fossil found 1 meter deep in the same type of rock?

3. A particular fossil is found in sedimentary rock strata immediately beneath igneous strata containing rocks with the composition ½ U-235 and ½ Pb-207. What can be inferred about the age of the fossil?

4. What are index fossils and how can they be used to date other fossils?

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Putman’s Biol 160 Lab 11: Evolution’s Evidence 5. What kinds of organisms were most common during the Paleozoic?

6. What kinds of organisms were most common during the Mesozoic?

7. What kinds of organisms were most common during the Cenozoic?

8. Consider a group of molluscs: an octopus, a clam, a snail, a slug and a chiton. All molluscs have a mantle, which in most is capable of producing a shell, and a rasping organ used in feeding called the radula. At the beginning of their evolution, clams lost the radula in favor of filter-feeding. We think mollusks evolved from flatworms, which have a ladder-like nervous system, very similar to the most primitive mollusks. Name at least one plesiomorphic characteristic of this group. Name at least two apomorphic characteristics of this group. Name an organism that could be used as an outgroup.

9. Are the most common organisms always represented in the fossil record? Why or why not?

10. Besides the protein cytochrome c, what other types of molecules could we compare the sequences of in order to determine evolutionary relationships?

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