Fundamentals of Biology Organisms to Ecosystems

1. Which of the following statements is FALSE? None of the above; All are true. 2. Look at the 5 phylogenetic hypotheses (A-E) shown above. How many DIFFERENT phylogenies are shown? 4 3. How many different phylogenies are shown here? 1 4. Using the information in the data matrix and the phylogeny in the figure above what is the tree length? 8 5. What is the tree length and consistency index for the hypothesis shown above? TL = 10, CI = 0.6 6. Use the figure above to evaluate whether the following statement is True or False: The letters d, e, and f indicate the location of common ancestors. True 7. Use the figure above to evaluate whether the following statement is True or False: The most recent common ancestor of taxa F and D is located at 4. False 8. Use the information above to evaluate whether the following statement is True or False: The consistency index of this phylogeny is 4/7 False 9. The most parsimonious phylogeny will have the highest Consistency Index. True 10. Use the figure above to evaluate whether the following statement is True or False: The phylogeny above includes 6 speciation events True 11. The number of possible phylogenetic hypotheses for a set of taxa is determined by__________ The number of taxa 12. Use the data table above to calculate the tree length and consistency index for this hypothesis (phylogeny Z). None of the above 13. Use the data table above to calculate the consistency index and tree length for this hypothesis (phylogeny R; not shown) CI = 10/15, treelength = 15 14. Given the following tree lengths and consistency instances which phylogeny is the most parsimonious? Tree length = 9, CI = 1.00 15. Use the figure above to evaluate whether the following statement is True or False: When “reading” the tree, one begins at location f True 16. Use the figure above to evaluate whether the following statement is True or False: Taxa C, D, E, and F and their most recent common ancestor form a monophyletic group False 17. Use the figure above to evaluate whether the following statement is True or False: Taxa B, C, D, E and their most recent common ancestor form a monophyletic group False 18. Use the information above to evaluate whether the following statement is True or False: Dividing the treelength by the actual number of state changes will provide the consistency index False 19. The number of phylogenies for a set of taxa is determined by the minimum number of character state changes False 20. Which process contributes to the origination and continuation of new traits on a phylogeny? All of the above contribute 21. Use the data matrix and phylogeny shown above. How many character state changes occur for the character wings on this phylogeny? 2 22. Which of the following statements is TRUE regarding the tree above? Node X represents the most recent common ancestor of hippos and horses 23. Use the figure above to evaluate whether the following statement is True or False: True or False: In the phylogeny shown above, taxa A, B, C, D, E, F, and G form the ingroup. False 24. A group of six closely related plants varies in leaf type. Two of the taxa have rounded leaves, three of the taxa have pointed leaves, and one of the taxa has oval shaped leaves. The minimum number of character state changes for the character leaf type in a phylogeny of these taxa could range from 1 to 4 depending on the phylogeny. False 25. Use the figure above to evaluate whether the following statement is True or False: Taxon A is most closely related to taxon B. True 26. Use the figure above to evaluate whether the following statement is True or False: The phylogeny above includes 7 speciation events. False 27. What is the consistency index of the phylogenetic tree above? 0.83 28. If a biologist performs a phylogenetic analysis of 25 taxa, which of the following variables will determine the number of possible phylogenetic hypotheses for these taxa? The number of taxa 29. How many speciation events are depicted in this phylogenetic tree? 4 30. Use the information above to evaluate whether the following statement is True or False: For the phylogeny shown above, the actual number of character state changes for the character # petals is 3. False 31. Use the figure above to evaluate whether the following statement is True or False: In the phylogeny shown above, G is the outgroup. True 32. A character state is a version of a character. True 33. How many phylogenetic different hypotheses are shown in the figure above? How many different phylogenetic hypotheses are shown above? 3 34. Use the figure above to evaluate whether the following statement is True or False: The most recent common ancestor of taxa A and F is located at 5. True 35. Phylogeny M and its associated data matrix are shown above. What is the consistency index for phylogeny M? 5/7 LECTURES 3-6 1. Look at the map of Africa (A) and Madagascar (M) shown above, and 4 different phylogenies for a group of 6 viruses. Virus strains from mainland Africa are shown using an A and viruses strains from Madagascar are shown using an M. A biologist has proposed that all the virus strains from Africa (A) originated from Madagascan (M) ancestors. Which hypothesis would best support her claim? 2 2. Look at the phylogeny, proposed groups (dashed boxes), and group names (A-G) to the right. Which group names (A-G) have been accurately (i.e. without error) assigned using phylogenetic principles? Groups B, F, and G 3. Look at the phylogeny and fossil record shown above. What would be the most likely location for the MRCA (most recent common ancestor) of Taxa B and D? Layer 9 4. Look at the 4 phylogenies above G = Guam (an Island) and M = Mainland Asia. Which hypothesis supports the claim that all of the Guam taxa (G) are a monophyletic group derived from taxa from Mainland Asia (M)? C 5. When building phylogenies, biologists try to find the best hypothesis by doing what? All of the above 6. What type(s) of data can be used for testing the hypothesis of a phylogenetic tree? All of the above 7. Which hypothesis is best supported by evidence regarding the evolution of feathers, wings, and flight? C 8. Phylogenies are used to test whether the scientific names that taxa have been given reflect the similarity of their physical features. False 9. The fossil record cannot preserve detailed information about the ecological interactions of species from millions of years ago because behaviors cannot be fossilized. False 10. The types of sediments found in sedimentary rocks containing fossils can inform scientists about the type of environment in which the organism originally lived. True 11. Which of the four phylogenies most closely match the fossil record? 3 12. You discover a fossil fern in a rock. Which of the following statements about the plant fossil is TRUE? None of the above 13. Phylogenies cannot be used to determine which evolutionary processes caused the evolutionary relationships among a group of taxa. True 14. Together, phylogenies and information about the rate of mutation can be used to predict the timing of a taxon’s origination. True 15. Which of the following statements about phylogenies is FALSE? Phylogenies can be used to identify which processes caused evolutionary change. PRACTICE TEST 1. Which of the following statements is TRUE? None of the above. 2. Which of the following statements is TRUE? The fossil record contains many intermediates between dinosaurs and modern birds. 3. Look at the phylogeny shown above. Which statement is TRUE? None of the above statements is true. 4. Use the phylogeny and data matrix shown above. What is the tree length for Phylogeny Q? 7 5. Look at the diagram above showing four taxa (1,2,3,4) each containing individual organisms.Which of the following would be good characters and character states to use in a phylogenetic analysis of these taxa? None of the above 6. Use the phylogeny and data matrix shown above. How many character state changes occur for the character Gene 3 on phylogeny Q? 3 7. Using the data matrix shown above, what is the minimum number of character state changes for this set of taxa? 6 8. Given the following treelengths and CIs, which phylogeny is most parsimonious (best supported)? Treelength 9, CI 1.0 9. Use the figure above to evaluate whether the following statement is True or False: In the phylogeny shown above, A is the outgroup. False 10. Use the information above to evaluate whether the following statement is True or False: According to parsimony, the common ancestor of the entire phylogeny had character state 1 for bark. True 11. Use the information above to evaluate whether the following statement is True or False: For the phylogeny shown above, the actual number of character state changes for the character bark is 2. False 12. Use the figure above to evaluate whether the following statement is True or False: Taxa B, C, D, E and their most recent common ancestor form a monophyletic group. False 13. Use the figure above to evaluate whether the following statement is True or False: Taxa D, E, F, and G and their most recent common ancestor form a monophyletic group. False MY ANSWER (If the hypothesis with the higher consistency index does not match the fossil record for these taxa, the biologists would have to revise their investigation. A high consistency index of 1.0 represents the best possible hypothesis. If this high consistency index does not match the fossil record, then it is possible that the most parsimonious hypothesis is not the most accurate. They would have to revise their hypotheses.) CORRECT ANSWER: (1) Do taxa have a good fossil record? If not, then it may not be a problem. (2) check with geographic distribution--does it match fossil record or phylogeny? (3) add different types of characters MY ANSWER (If both phylogenetic hypotheses have the same consistency index, then that means that both hypotheses had the same minimum number of possible changes. This also likely means they are both equally parsimonious. Scientists should try testing other hypotheses to find a consistency index of 1.0.) CORRECT ANSWER: (1) Add more data--additional characters+states and re-analyze; (2) check match with fossil record and choose best match, (3) check with geographic distribution and choose best match. 1. Phylogeny M and its associated data matrix are shown above. How many character state changes occur for the character eyes on phylogeny M? 2 2. Use the data matrix shown above to determine the minimum number of character state changes for these taxa. 5 3. Use the data table above to calculate the consistency index and tree length for this hypothesis (phylogeny R; not shown). CI = 10/15, treelength = 15 4. Use the information above to evaluate whether the following statement is True or False: Dividing the treelength by the actual number of state changes will provide the consistency index. False PHYLOGENY HW What is a phylogeny? Phylogeny. A phylogeny is a hierarchical branching diagram that displays the evolutionary relationships of a group of taxa. Character state data are used to determine the most probable pattern of ancestry, using the principle of parsimony. (We will delve more into characters and parsimony later.) Each vertical line is a branch that represents either a single taxon lineage or a common ancestor lineage. The top branches are the individual taxa in our study while the internal branches are the common ancestors of those taxa. In phylogenetics, what are the units of study? Taxa. “Taxa,” plural form of the word “taxon,” are categories of organisms. Taxa can be referred to as biological units, taxonomic groupings of organisms such as species, genus and family. Phylogenies compare different taxa at various levels. Some phylogenies use taxonomic species whereas other phylogenies use higher level groupings such as taxonomic families. Taxa in a study. Ideally we would study every single species within a higher level taxon such as all species of butterflies and moths (Order: Lepidoptera). In that case, our phylogenetic analysis would not be biased. However, scientists cannot feasibly study all members of a taxon, even if we discovered every species. As such researchers carefully choose a subset of known taxa to study. Taxa on a phylogeny. Phylogenies are typically made up of taxa at a single taxonomic level. For example, one phylogeny may depict patterns of ancestry of five genera in the Felidae family while another may display eight species of the Felis genus (below). **question 6 Which of the following set of taxa would we typically use on a single phylogeny? 10 families Common Ancestors. Common ancestry is the basis of evolutionary relationships. The branching pattern on a phylogeny describes how different taxa are related to each other. A phylogeny consists of both terminal branches and internal branches. Below we see a phylogeny showing both types of branches. The different letters represent lineages that are derived from those shown below them. These terminal branches are the taxa we would be studying in this tree. The different numbers represent lineages that are the ancestors of derived taxa. These internal branches are the taxa that are important due to their relation with the taxa on the terminal branches. Note: Terminal taxa are often (yet not always) living species (but may be fossil taxa, too). The taxa representing common ancestors, however, are no longer living. We must infer their character states from information we have about the terminal taxa on a phylogeny. Where is the evolutionary starting point on a phylogeny? Root. The root is the earliest common ancestor displayed. All of the taxa in the phylogeny are descendants of this common ancestor. In fact, another name for the root is “last common ancestor.” (The last common ancestor is our earliest common ancestor.) Thus, it is the "root" of all of the other lineages. This root is our starting point for looking at evolutionary change and ancestry on a phylogeny. On the phylogeny below, the branch (lineage) highlighted in yellow (1) represents the "root.” What are the ingroup and outgroup? Ingroup. The ingroup includes the taxa whose evolutionary relationships (to each other) we wish to determine. You may think of the ingroup as the study group. Taxa are more closely related to each other within the ingroup than between ingroup and outgroup. The outgroup includes one or more taxa that are not in our study group but are hypothesized to be somewhat closely related to them Sister taxa are equally related to the other taxa on a phylogeny. ● The ingroup includes the taxa whose evolutionary relationships (to each other) we wish to determine. ● ● You may think of the ingroup as the study group. Taxa are more closely related to each other within the ingroup than between ingroup and outgroup. ● The outgroup includes one or more taxa that are not in our study group but are hypothesized to be somewhat closely related to them. Outgroup. The outgroup consists of one or more taxa that are not in our ingroup but are related to the taxa in our ingroup. The outgroup serves as a reference point that allows us to determine the direction of character evolution. In terms of character states, the outgroup is our evolutionary starting point. The true starting point is the root of a phylogeny, since this is our bottom branch. However, the common ancestor at the root and our taxon at the outgroup have the same character states. Thus the outgroup is the closest taxon to the root of a phylogeny. What is a character? Characters. Characters are the data that we will use to perform phylogenetic analyses. A character is any observable feature (trait or part) of an organism shared across a taxon. Morphology, gene sequences, protein types, protein structures, behavioral features, and ecological attributes are all observable features of organisms that can be used as characters. For example, scales among various fish genera or ecological role of several species of frog are both valid characters. What is a character state? Character States. A character state is a variation that we observe in a character. “Beak shape” may be our character, whereas “curved” and “straight” could be our character states. “Number of body segments” may be our character, and “5”, “6”, and “7” our character states. “Shell” may be our character, and “present” and “absent” our character states. Can any feature be a character? Characters in a population. A character must be shared by nearly all members of a taxon. If only one individual in a population of bird species has a third eye and every other individual has two eyes, it is not very useful to use “number of eyes” as a character for these birds. However, if all but a few individuals of bird species 1 has a large beak and if all but a few individuals of bird species 2 has a small beak, then "beak size" may be a useful character. On a phylogeny that compares bird species 1 and bird species 2, "beak size" can be used since there are at least two character state variations useful for comparing these taxa. Thus, a character is considered at the level of a population, not at the level of individual members. We only use characters for which nearly all of the members of a taxon share the same character state. A character is a feature or trait of organisms shared across a taxon, not a character of just one individual. (In parallel, evolution is considered at the level of a population, as well. Individuals do not evolve, populations do. Although individuals change, in biology this is called development, not evolution.) A character state is a variant of a feature or trait of organisms shared across a taxonomic category, not the "state of character" of just one individual. What makes a character good for use in phylogenetics? Good Characters. A good character to use by biologists in a study creates an identity for one group and differentiates it from other groups. This means that (1) a good character is shared by all members of a taxon and (2) a good character is not shared with too many other taxa. A good character… (a). shows greater variation among the taxa you are interested in than within each taxon. (b). and has variation that is heritable and independent of other characters. Parsimony. A common motif in all of science is the principle of parsimony. The idea is that the simplest explanation that fits your data is the best one. Parsimony favors omission or elimination of unnecessary steps. Methodological parsimony involves identifying which solution requires the fewest number of changes. Below are three possible sequences for change in shading for four circles with two different character states, the same as in the last question. Since n = 2 and the most parsimonious solution possible = 1 change, minimum number of changes in character state = n - 1. Phylogenetic Parsimony: Arrangement of Terminal Taxa. The principle of parsimony we have been reviewing using simple examples with circles can be applied to phylogenies, as well. The concept is exactly the same. The most parsimonious solution removes unnecessary steps to minimize the number of changes used to explain a pattern. Which of the following is false? The phylogeny on the right is less parsimonious because the terminal taxa are arranged differently. Which of the following is true? It is possible to have multiple equally valid hypotheses. Comparison The number of changes is the same for both hypotheses. However, the hypotheses are different in that the locations of hypothesized evolutionary change differ between the two. Hypothesis 1 hypothesizes that the two most recent common ancestors were blue whereas Hypothesis 2 hypothesizes that the two most recent common ancestors were white. Both hypotheses are actually equally valid. We don't know whether those two common ancestors were white or blue, but we don't need to know. These two hypotheses depict only a very slight shift in the meaning of the phylogeny. Implication The pattern of branching on a phylogeny, which depicts hypothesized patterns of ancestry and thus also evolutionary relationships, is what gives a phylogeny most of its meaning. If arrangement of terminal taxa is the same and the pattern of branching is the same, then the number of character state changes on that phylogeny would also be the same, due to our use of the principle of parsimony. Data Matrix. A data matrix is a table we use to distribute character state data across our taxa. Number of Character States. The number of character states is symbolized by the variable n. Number of Character State Changes (Minimum). For each character, the minimum possible number of state changes is n-1. This value is a theoretical minimum, meaning an actual phylogeny will probably show a higher number of changes. Since we have all of the values of n, we can easily compute n-1. Tree length. Tree length is a “statistic” that describes how many times a character state change has occurred on our phylogeny. It is the number of evolutionary “steps” that occurred. For example, if a bird’s plumage evolves from yellow to red (Y→R) only once in our phylogeny, this represents one character state change. If four different species independently evolved red plumage, then this change occurred four times in our phylogeny (Y→R, Y→R, Y→R, Y→R), and we therefore have four character state changes. If we add up all the changes in all the character states in our phylogeny (determined above) we will come up with the tree length. Parsimony using Tree Length. Given the same character state data for your characters, changes in tree topology typically cause changes in tree length. The higher your tree length the more evolutionary steps that were involved in changes of character state. The more evolutionary steps involved in explaining a pattern of evolutionary change, the less parsimonious your phylogenetic hypothesis. Consistency index (CI). Consistency Index, or CI, is a phylogeny statistic that depends on tree length and minimum number of changes Consistency Index (CI): Convergent Evolution. The CI quantifies the magnitude of convergent evolution in our phylogeny. A phylogeny where no convergent evolution has occurred will have a CI of 1.0. On the other hand, a phylogeny where the same trait arose multiple times would have a CI between 0 and 1. Parsimony using Consistency Index. When comparing phylogenetic hypotheses for a defined set of taxa, the minimum number of evolutionary steps will always be the same. This means that the top number for your consistency index division will also be the same when calculating consistency index for different hypothetical arrangements of the same taxa on a phylogeny. Holding this number constant means that increasing the bottom number, tree length, will decrease the consistency index. This is because dividing by a larger number gives you a smaller number. For example, while 4 is larger than 2, the fraction ¼ is smaller than ½. Thus, CI value is inversely proportional to tree length. Consistency indices range only from 0 to 1. Which of the following is false? Species Subset A has the same outgroup as the outgroup for all seven species Fossil data. The fossil remains of living things provide a rich source of information that may be used to test whether a phylogenetic hypothesis is well supported or not. For example, the order of appearance of fossils in rocks may be used to infer when species evolved. Species that occur earlier in the fossil record are likely to have originated (evolved) before species that occur only later (more recently) in the fossil record. The species that evolved earlier tend to be species that are the ancestors to those that are more recent. Similarly, the species that evolved later tend to be species that are derived from those that came before them. Did S. fossilus evolve into the other species of Squirmidae? No, because S. fossilus is in the outgroup, and an outgroup taxon is a related taxon outside the taxa being studied (the ingroup) 1. Use the information above to evaluate whether the following statement is True or False: According to parsimony, the common ancestor of the entire phylogeny had character state 0 for roots. False 2. The SARS virus was identified using what methodology? Phylogenetic analysis