Lab 2 Evolution

LAB 2 EVOLUTION I Objectives By the end of this lab, the student should be able to: 1. Identify the main components of DNA. 2. Describe the flow of information from DNA to Protein. 3. Transcribe DNA to RNA and translate RNA to an amino acid sequence. 4. Explain the importance of mutation in the creation of genetic variation and how point mutations can affect the amino acid sequence. 5. Describe how Gene Flow, Genetic Drift and Natural Selection affect the allele frequencies of populations. 6. Explain how various lines of evidence support the theory of evolution. 7. Describe the function of phylogenetic trees. 8. Explain what the nodes and branches on a phylogenetic tree represent. 9. Determine the relationships between different extant groups on a phylogenetic tree. II 1Introduction It is widely believed that all life on Earth is descended from a single ancestral life-form, and the enormous diversity now seen is the result of evolution. Evolution is the process by which organisms accumulate changes in their DNA that lead to new forms and new species over time. In this lab, we will be looking at some of the principles and processes behind the development of the diversity of life on the planet. III DNA, RNA and Proteins All organisms carry within their cells a complete set of instructions: the plans for the construction and operation of the entire organism. These instructions are in the form of deoxyribonucleic acid , or DNA . DNA is composed of a double string of nucleic acids , bound together by a backbone of phosphate and deoxyribose, a sugar. DNA is structured like a spiral staircase. Each step is made up of a pair of nucleotide bases . In DNA, there are four types of nucleotide bases: adenine (A), guanine (G), cytosine (C) and thymine (T) . Adenine is always paired with thymine, and guanine is always paired with cytosine. This sequence of bases forms the genetic code. Take a look at Figure 2-1 below, and 2-1

EVOLUTION, cont'd. circle and label (or highlight in different colours): the bases, the hydrogen bonds, the deoxyribose sugar, and the phosphate group. Figure 2-1: Basic structure of a DNA molecule showing nucleotide bases. Examine the DNA model(s) on the side bench. Identify the basic components of DNA: nucleotide base(s), deoxyribose sugar, and phosphate and try to “read” a few of the base pairs on the model. You can “read’ the DNA model by knowing that A always pairs with T with two hydrogen bonds and C always pairs with G by three hydrogen bonds. Once you have identified the pair of bases you are looking at, you can tell which specific base each is by knowing that T and C have a single carbon ring, while A and G have a double carbon ring. Ask your instructor for help if you are confused. Transcription and Translation DNA is housed in the nucleus of the cell. When the information is needed to make a particular protein, the double helix uncoils, and a single strand (known as the sense strand ) is read in a process called transcription that produces a single stranded messenger RNA (mRNA) molecule. 2-2

EVOLUTION, cont'd. Table 2-1: Amino acid codon equivalents. First Base Second Base Third Base U C A G U Phenylalanine (Phe) Phenylalanine Leucine Leucine Serine (Ser) Serine Serine Serine Tyrosine (Tyr) Tyrosine Stop Stop Cysteine (Cys) Cysteine Stop Tryptophan (Trp) U C A G C Leucine (Leu) Leucine Leucine Leucine Proline (Pro) Proline Proline Proline Histadine (His) Histadine Glutamine (Gln) Glutamine Arginine (Arg) Arginine Arginine Arginine U C A G A Isoleucine (Ile) Isoleucine Isoleucine Methionine/Start (Met) Threonine (Thr) Threonine Threonine Threonine Asparagine (Asn) Asparagine Lysine (Lys) Lysine Serine Serine Arginine Arginine U C A G G Valine (Val) Valine Valine Valine Alanine (Ala) Alanine Alanine Alanine Aspartate (Asp) Aspartate Glutamate (Glu) Glutamate Glycine (Gly) Glycine Glycine Glycine U C A G To start translating a sequence of mRNA, the ribosome must first identify the start codon, which is Methionine. What is the codon for Methionine/Start? ___________________ Translation ends when the ribosome identifies the stop codon for that sequence. What are the codons for stop? _______________________ Using your knowledge of translation, translate the following RNA sequence: mRNA AAC UCA GAU UGC CUU Amino acid sequence: _____ ______ ______ ______ ______ Once an amino acid sequence has been created and modified, it is called a peptide . Peptides are then folded, often along with other peptides, into three dimensional macromolecules called proteins . Proteins have many functions. They are used by living organisms to act as building materials. Actin and Myosin are proteins that make up the contracting muscle cells and Tubulin is the main component of the internal structure of cells. Proteins are used as enzymes to catalyze reactions. Pepsin and Lipase are examples of enzymes that break down food molecules in your digestive tract. Hemoglobin is a transport protein whose function is to carry oxygen in your blood. Antibodies (part of your immune system) that protect you from viruses, bacteria and other foreign invaders are also made of proteins. 2-4

EVOLUTION, cont'd. Exercise 3: Mutations New cells arise from cell division. Before a cell divides, it must make a copy of its DNA, so that the new cells have the same information as the original cell. This copying is called DNA replication . What happens if a mistake is made during DNA replication, and the new DNA copy is different than the original? This is called mutation . Mutation, then, is an error made in the replication of DNA, and is the source of all genetic variation. Mutation can take many forms. The simplest is a point mutation , which only affects a single base in the sequence. A base could be deleted (removed), a different one could be substituted, or an extra one could be inserted (added) into a strand of replicating DNA. Substitution Mutation: Taking the previous example, imagine that the sixth base in the sense strand (Thymine) is substituted with a Guanine. DNA sense strand: TTG AG G CTA ACG GAA RNA: AAC _____ _____ _____ ______ Amino acid sequence: ______ ______ ______ ______ ______ How is the amino acid sequence different from the original protein produced? ______________ ____________________________________________________________________________ Looking at Table 2-1, we can see that the codon with the first two bases of U and C, can have any base at the third position and still code for the amino acid Serine. However, if a substitution is made in the first two positions of the codon, it will change the amino acid for which it codes. An example where a substitution mutation of a single base has had significant impacts on human health is the one that results in the hemoglobin molecule (the protein that carries oxygen in our red blood cells) found in individuals with Sickle-cell Anemia . This single substitution has resulted in hemoglobin that does not carry oxygen as well as the normal variant and has significant impacts on the health of the individuals who carry this mutation. We will watch a video on Natural Selection in relation to the sickle-cell mutation later in this lab. Deletion Mutation: This time, instead of a substitution, we have deleted the sixth base. Notice that the Cytosine base from the next codon moves into the position of the deleted base. The _ at the end of the sequence is just to indicate that we do not KNOW which base will fill that spot. 2-5

EVOLUTION, cont'd. IV Mechanisms of Evolution How does this genetic variation distribute itself through a population, and lead to the formation of new species? There are several mechanisms by which variation spread within a population. The most common are gene flow , genetic drift , and natural selection . A population is any group of individuals which only breed with other members of that group. A population could be isolated from another population by distance, by some barrier like a lake, a desert or a mountain range; or by any factor that makes the individuals of one population unable or unwilling to breed with individuals of another population. A population, because its individuals interbreed, is often referred to as having a gene pool (the sum total of all the genetic information within a population). A gene is the code that results in a particular characteristic, such as eye colour. An allele , is a variant of a gene. Using the same example, there is a blue eyes allele, and a brown eyes allele. Most variation can be expressed in terms of alleles. A Gene Flow Individuals from one population might migrate to another area, and thereby introduce their genes into the local population. Thus their genes are said to flow from one population to the next. Take for example, a species of salmon. Salmon typically return to the stream in which they hatched to spawn. Each spawning stream would have an isolated population of salmon. Occasionally a salmon enters the wrong stream, and introduces its genes into another population of salmon. This would be an example of gene flow. B Genetic Drift When a new allele arises in a population, over time, it may become fixed in the population. A fixed allele means that all individuals in the population will carry that allele. It is also possible that an allele may disappear from a gene pool. An allele's frequency changes over time. When a small segment of a genetically diverse population forms a separate population, then some alleles, especially ones which were not all that abundant to begin with, may be lost at random. Thus the genetic makeup of a small isolated population can be thought of as having drifted away from that of the parent population. Exercise 4: Genetic Drift The genetic drift jars model what happens to alleles in a small sample of a larger population. Each jar represents a population of 100 organisms, (beads) which carries the colour gene in the form of two alleles: red and white. These beads are an isolated population. Imagine they inhabit an isolated island. Take all the jars and line them up in order. Start with the 50:50 jar. Imagine you are a natural disaster (such as a storm or a landslide), which does not care what colour the survivors are. 2-7

EVOLUTION, cont'd. Every generation or so, you wipe out 90% of the population. Shake the jar to randomize the contents. Close your eyes and randomly select 10 beads. These are the survivors of the disaster. Observe the ratio of red to white beads, and replace them in the jar you got them from. Record the % of red beads on the graph on the following page. Now, after a time, the ten survivors have repopulated the island. Take the jar with the same ratio as the survivors (for example, if 6 of your survivors are red and 4 survivors are white, use the 60:40 jar next). This is the new population. A disaster hits again, wiping out 90% of the new population – randomly select 10 survivors. Note the ratio of the ten survivors, and plot the proportion of red beads on the graph. Repeat this procedure for fifteen generations, or until one allele becomes fixed and the other one extinct. Plot your results on the chart on the side bench. At the end of the lab, before you leave, look at the class results and answer the following questions: What does the trend tell you? Was one allele preferred over the other? What determined the direction of change? ____________________________________________________________________________ Repeat the experiment with only five survivors. Was there any difference in the number of generations required to fix an allele? What factor affects the rate of genetic drift? ____________________________________________________________________________ 2-8 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 0 10 20 30 40 50 60 70 80 90 100 10 Survivors Generation # % Red Beads

EVOLUTION, cont'd. Where were HIGH frequencies of people with sickle-cell anemia found? ___________________ ____________________________________________________________________________ Where were LOW frequencies of people with sickle-cell anemia found? ___________________ ____________________________________________________________________________ What insect was found where there were high frequencies of sickle-cell anemia? ____________ What disease does this insect carry? _______________ When the researcher viewed samples of blood from around East Africa, he tested for two things. What were they? 1. _________________________________________________________________________ 2. _________________________________________________________________________ What correlation did he find? ____________________________________________________ ____________________________________________________________________________ Genes are carried on chromosomes and everyone has a pair of each chromosome. Genes can have different versions called alleles. If you have two of the SAME alleles, it is called: ______________________________ If you have two DIFFERENT alleles, it is called: ___________________________________ If two parents are heterozygous for the sickle-cell trait, there are three possible combinations for the offspring with the following odds: _________ odds of being homozygous for the sickle-cell gene _________ odds of being heterozygous _________ odds of being homozygous for the normal gene Why are those offspring homozygous for the sickle-cell gene at a disadvantage? ___________ ____________________________________________________________________________ In a malarial environment, why are those individuals who are homozygous for the normal gene at a disadvantage? ____________________________________________________________ ____________________________________________________________________________ 2-10

EVOLUTION, cont'd. What is the advantage of being heterozygous for sickle-cell in a malarial environment? ____________________________________________________________________________ ____________________________________________________________________________ What was the genetic change that causes Sickle-cell anemia? __________________________ ____________________________________________________________________________ How does the sickle-cell mutation protect the carrier from Malaria? _______________________ ____________________________________________________________________________ V Evidence of Evolution Evidence in support of evolution must show that organisms have changed over the time but the most closely related must still have many features in common. In the next part of the lab, you will examine two lines of evidence in support of evolution: A Fossil Record B Comparative Anatomy A Fossil Record Fossils are the remains or traces of organisms from earlier geological periods. Very few organisms form fossils, and of those that do, many fossils are destroyed by natural geological processes. Of existing fossils, only a few are exposed at the surface of the earth where they are available for examination. Thus, known fossils represent only a tiny sample of the organisms that have lived on earth. Organisms can be found as fossils in many different forms: a) Unaltered Remains - these are a very rare occurrence. Examples of these types of fossils include frozen mammoths found in Siberia, insects embedded in amber and the “Iceman of the Similaun” found in 1991. Recently, 20 million year old magnolia leaves were discovered in Oregon, and although partially altered, they were green when found and have yielded DNA sequences. b) Hard Fossils - more commonly, the hard parts of an organism are fossilized , or preserved in a form different from when they were alive . Carbon Films - plant leaves and flowers are commonly preserved as thin imprints or films of carbon on the bedding planes of rocks. Permineralization - plant trunks and roots are converted to coal or replaced by minerals like quartz or opal. This results in “petrified” fossils. Usually the replacement only retains the 2-11

EVOLUTION, cont'd. Note some differences found in the vertebrates shown: Frog:________________________________________________________________________ ____________________________________________________________________________ Bat: ________________________________________________________________________ ____________________________________________________________________________ Chicken: _____________________________________________________________________ ____________________________________________________________________________ VI Phylogenetic Trees Phylogenetic trees , also known as phylogenies , evolutionary trees , or cladograms , are visual representations of the historical branching pattern of evolution. Since speciation events typically result in the formation of two species from one, this evolutionary pattern can be depicted as a repeatedly forking road moving through time, with some branches going extinct and other branches forking again and again. The terminal twigs that reach the present day represent extant (i.e. still living) species or other taxa (E.g. phyla, classes, families). Figure 2-2 below shows a simple phylogenetic tree. 2-13 Each fork on the tree represents a hypothesized speciation event Present day Time : amount of time depicted depends on scale: is tree depicting closely related sub-species or distantly related phyla? Past Fig. 2-2: A phylogenetic tree depicting the evolutionary pattern that results from a series of speciation events

EVOLUTION, cont'd. As we are unable to go back in time and directly verify the exact branching pattern, all phylogenetic trees are hypotheses about how evolution may have unfolded on Earth. As new data are gathered, phylogenetic trees are being continually re-worked so that the depicted hypotheses fit the best available data. a) On the tree in Figure 2-2, circle the extinction events. b) Explain why all phylogenetic trees considered hypotheses. ________________________________________________________________________ ________________________________________________________________________ 1) LUCA: Back to the Beginning Life on Earth shares a common ancestor and all modern organisms, be they bacteria, plant, fish, insect, or primate, can trace their origins back approximately 3.5 billion years to an early group of organisms that probably shared similarities with modern bacteria (Fig. 2-3). This molecularly soupy group of prokaryotes, which forms the basal node on the tree of life, is collectively referred to as L.U.C.A ., the Last Universal Common Ancestor . Some fundamental cellular components such as DNA, ribosomes, and plasma membranes, which are still universally shared by all life forms, were undoubtedly already in place in the LUCA. These components are so molecularly complex—ribosomes for instance are comprised of 50+ proteins and RNA molecules thousands of nucleotides long—that it is unlikely that they would be so similar if they evolved independently. a) What are three fundamental cellular components that all living organisms share? ______________________________________________________________________ 2-14 Fig. 2-3: A phylogenetic tree depicting LUCA and the three domains Time (3.5 billion years approx.) Ba ct eri a Eu ka ry a Ar ch ae a L.U.C.A.

EVOLUTION, cont'd. from Bacteria to Human is not the correct way to visualize evolution (Fig. 2-4). The adjacent branching tree, which is a more appropriate way to view evolution, indicates that while humans and chimps share a common ancestor, humans do not descend from chimps. The chimp-human common ancestor was neither a chimp nor human, but rather an ancestor to both species. Both modern chimps and humans have continued to evolve, morphologically and genetically, for six million years since splitting from that common ancestor. The same argument can be said for every node—e.g. the ancestor of humans and amoebas was neither an amoeba nor human but rather a common ancestor to both, and both branches have continued to evolve since their split ~700 million years ago. On a related note, students often envision time is being depicted as moving from left to right, from primitive groups to more modern ones. On the tree in Figure 2-5 below, it is incorrect to think of sponges as a “primitive” group and humans as “modern”, and thus see time moving from left to right. Rather, extant sponges and humans are both the product 3.5 billion years of evolution, and primitive is a term better used to describe characteristics found in common ancestors, characteristics which may be retained in modern groups. Taxa that appear on the right-hand side of an upright phylogeny (i.e. humans on the tree below) are not more advanced; indeed the tree could be rotated at the nodes to put any branch in the right-most position. The most recent common ancestor (MRCA) of this group occurred approximately 600mya and all branches that make it to the top of the tree are modern extant groups, and thus time moves from bottom to top on this tree. Again, branches that do not reach the top of the tree typically represent groups that went extinct (e.g. dinosaurs). 2-16 Human Chimp Mouse Monkey Chicken Fish Amoeba Bacteria This node is not a chicken ! H u m a n M o u se C hi m p C hi c k e n Fi s h M o n k e y A m o e b a B a c t e ri a Fig. 2-4: The linear progression (above left) from Bacteria to Human is not the correct way to visualize evolution; the branching tree-like analogy (above right) is a more apt. Nodes do not represent any modern species but rather an ancestor to all of its descendants.

EVOLUTION, cont'd. Students can also have difficulties determining which groups are closest relatives. Looking at the tree above, answer this question: Are humans or earthworms closer relatives to sponges? Explain your answer. _________________________________________________________________________ ___________________________________________________________________________ Most students, and many biologists for that matter, observe that earthworms are positioned closer on the tree to sponges, and they also have observed sponges and earthworms and believe them to share similar invertebrate morphology. So they incorrectly answer that earthworms and sponges are closer relatives than humans and sponges. But proximity of the tips on a phylogenetic tree is not always an indicator of relatedness. The correct answer is that earthworms and humans are equally related to sponges because they share a common ancestor prior to joining with the sponge lineage. On the tree, sponges are the “outgroup”, and the other groups form a monophyletic clade (Clade Bilateria) that share a common ancestor (and a bilateral body plan) approximately 540 million years ago. This ancestor then joined with the sponge ancestor approximately 650 million years ago. 2-17 Spo nge s E ar th w or m s H u m an s Do gs Time Din osa urs Present Day Time 650 mya 540 mya Fig. 2-5: In this phylogeny, sponges are not primitive and humans more modern; time does not move from left to right.