The exam has 200 points

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1 Bio 312, Spring 2018 Exam 4 ( 1 ) Name: 1. HUMAN EVOLUTION Please write the first letter of your last name in the box; 5 points will be deducted if your name is hard to read or the box does not contain the correct letter. (a, 3 pts). Diagram the spread of modern Homo sapiens. Clearly label the site of origination of Clearly label the site of modern Homo sapiens and use arrows to indicate the movements of populations from there to the rest of the world. (b, 2 pts) Approximately how long ago did modern humans leave their area of origination and begin their spread to the rest of the world? years ago The exam has 200 points (c, 3 pts) Draw the phylogeny for the 4 species of great apes and an appropriate outgroup in the box below. (d, 3 pts). Many of the inferences about early human evolution are based upon fragmentary fossils, quite often only skulls or partial skulls. Despite this we can infer the shift from quadrupedal walking (like gorillas, using all four limbs) to bipedal walking with only fossil skulls. What trait in fossil skulls provides evidence about the walking style employed by the individual and what is the trend seen in that trait that allow us to infer the shift from quadrupedal to bipedal walking?

2 Bio 312, Spring 2018 Exam 4 ( 2 ) Name: 2. PHYLOGENETIC CONCEPTS. (a, 4 pts) Consider eight taxa (A, B, C, D, E, F, G, H). In the box to the right, draw a phylogenetic tree that represents the following relationships between the taxa. - Taxa D and H are sister taxa. - Taxon F is basal to all the taxa except B - Taxon B is the outgroup. - Taxa D, G, and H define a monophyletic group. - Taxa C, D, E, G, and H define a monophyletic group. - Taxa C, D, G, and H define a paraphyletic group. The remaining questions on this page refer to the four phylogenies indicated below. The ancestral phenotypic state is white, with current taxa (labeled A through J) having either a white or black phenotype. (b, 3 pts) If evolutionary transitions in which the trait can change from white to black are typically more common than changes from black to white which phylogeny is most likely the correct one? (circle one) Tree A Tree B Tree C Tree D most likely most likely most likely most likely (c, 3 pts) Consider a scenario in which white coloration is always associated with iteroparous reproduction and black coloration associated with semelparous reproduction. Which two of these phylogenies would provide the strongest support for a causal relationship between coloration and reproductive strategy? Phylogenies and provide stronger support than phylogenies and

3 Bio 312, Spring 2018 Exam 4 ( 3 ) Name: 3. PHYLOGENETIC APPLICATIONS. Use the phylogeny on the last page showing the relationships for the families within the mammalian order carnivora (Eizirik et al. Molecular Phylogenetics and Evolution 56(1): ). The figure on the final phylogeny they obtained and the list shows the common names for the taxa listed. Use your knowledge of phylogenetics and the information on the phylogeny to answer the following questions. (a, 2 pts) What is the common name for the outgroup used in this study pictured to the right? (b, 3 pts) In this article the authors proposed the placement of the supercute genus Ailurus within a new family named Ailuridae. Previously Ailurus had been contained within the family procyonidae. Why did the authors propose that the classification of Ailurus be changed from the original naming system in which Ailurus was a member of the procyonidae family? (c, 3 pts) It turns out that Ailurus was first placed in the procyonidae family in 1825 by Georges Cuvier. We discussed this scientist's contributions to the history of science and the development of the theory of evolutionearlier this semester. What was the major idea about the history of life on earth that Cuvier promoted? (d, 3 pts) As we can see from the phylogeny, red pandas (Ailurus) aren't like panda bears at all. If we defined a group of taxa as the group including all "pandas", but not their ancestor, what would be the scientific term for such a group? (e, 3 pts) Which of the following taxa is most closely related to the linsang pictured to the right? Spotted hyena Weasel Leopard Ferret Otter Red panda (f, 3 pts) About when did the most recent common ancestor of skunks, weasels and racoons live? 13.1 MYA 30.0 MYA 20.0 MYA 32.0 MYA 20.7 MYA 40.5 MYA 27.4 MYA 42.6 MYA

4 Bio 312, Spring 2018 Exam 4 ( 4 ) Name: 4. PHYLOGENETIC RELATIONSHIPS. For each of the three sets of taxa listed below, draw the correct phylogeny in the box provided. (a, 3 pts) Annelida, arthropoda, chondrichthyes, ctenophora, mollusca, nematoda. (b, 3 pts) Archaea, chiroptera, echinodermata, eubacteria, ornithischia, porifera. (c, 3 pts) Elephants, humans, lions, kangaroos, pigs, rats, whales

5 Bio 312, Spring 2018 Exam 4 ( 5 ) Name: 5. RESPONSE TO SELECTION, ALLELE FREQUENCIES. Consider a situation in which a population of 6,000 individuals is homozygous for a wildtype allele and a new mutation arises which creates an advantageous co-dominant allele. The new allele provides a 3% fitness advantage over the wildtype in heterozygotes and a 6% advantage in homozygotes. (a, 2 pts) What is the probability that this mutant allele will increase in frequency and fix in the population? (provide answer to nearest 0.001) Prob (fix) = For the rest of these questions consider an allele that does eventually fix in the population (b, 4 pts) If the allele does fix in the population, it was novel mutation that generated a temporary in the population which eventually resulted in a at the locus. (c, 2 pts) When the frequency of the advantageous allele was 20%, what was p? (provide answer to nearest ) (d, 2 pts) When the frequency of the advantageous allele was 50%, what was p? (provide answer to nearest ) (e, 2 pts) When the frequency of the advantageous allele was 80%, what was p? (provide answer to nearest ) p = p = p = (f, 2 pts) What is the name of the concept that this pattern of p values demonstrates? This demonstrates the 6. RESPONSE TO SELECTION, PHENOTYPE VALUES. Consider a situation in which a population of 6,000 individuals has a range of values for a quantitative trait like mass. (a, 3 pts) Consider a scenario in which the mean of the overall population is 240 Kg and a subset with a mean mass of 255 Kg is chosen for mating, if they produce an offspring generation with a mean mass of 248 Kg, what is the narrow sense heritability of the population? (provide answer to nearest 0.001) (b, 3 pts) Now consider a scenario in which we choose a subset on individuals with a mean mass of 256 Kg from the offspring generation and mate them, what is the expected mean mass of the third generation? (provide answer to nearest 0.001) h 2 = Mean = (c, 2 pts) What is the name of the equation that you used to answer these questions? This equation is the

6 Bio 312, Spring 2018 Exam 4 ( 6 ) Name: 7. POPULATION GENETICS. Consider a population of 10,000 individuals at Hardy-Weinberg equilibrium with three polymorphic loci that each have two alleles as follows. - One locus controls pelage (fur) pattern and the population possesses two alleles: a dominant allele "S" that confers a solid pattern and a recessive one "s" that confers a striped pattern. - One locus controls pelage (fur) coloration and the population possesses two alleles: a dominant allele "D" that confers a dark color and a recessive one "d" that confers a pale color. - One locus controls the presence or absence of a tail and the population possesses two alleles: a dominant allele "T" that confers a tail and a recessive one "t" that results in no tail. Assume that the three loci are in linkage equilibrium and the number of individuals are as follows: Solid dark pelage with a tail = 4608 Solid dark pelage without a tail = 2592 Solid pale pelage with a tail = 1536 Solid pale pelage without a tail = 864 Striped dark pelage with a tail = 192 Striped dark pelage without a tail = 108 Striped pale pelage with a tail = 64 Striped pale pelage without a tail = 36 (a, 2 pts each) What are the frequencies of each of the alleles? (provide answers to nearest 0.001) F(S) = F(D) = F(T) = F(s) = F(d) = F(t) = (b, 2 pts each) What are the frequencies of triple heterozygotes (i.e., individuals heterozygous at all loci) and triple homozygotes (i.e., individuals homozygous at all loci) in the population? (provide answers to nearest 0.001) Freq. of het/het = Freq. of homo/homo = 8. MUTATION:SELECTION BALANCE. Genetic diseases arise from the segregation of deleterious alleles. These are usually recessive, but in rare cases they are co-dominant or dominant. Consider a hypothetical genetic variant, "a", which researchers find is associated with reduced reproduction compared to individuals with the wildtype "A" allele. Studies show that individuals who are homozygous for this allele have 50% as many children as wildtype individuals do. Assume for the questions below that the population of the USA is approximately 350,000,000. (a, 3 pts) If the deleterious allele is recessive, and the number of affected individuals in the US is 1,400 what is the best estimate for the mutation rate from the wildtype allele to the mutant allele? (Provide answer to 3 significant figures) (b, 3 pts) For the deleterious allele in part (a), what is the expected number of "carriers" for this disorder (i.e., heterozygotes) in the USA?(round to the nearest integer) (c, 3 pts) If the deleterious allele is dominant, and the number of affected individuals in the US is 350 what is the best estimate for the mutation rate from the wildtype allele to the mutant allele? (Provide answer to 3 significant figures) = # carriers = =

7 Bio 312, Spring 2018 Exam 4 ( 7 ) Name: 9. HISTORY OF SCIENCE AND EVOLUTIONARY BIOLOGY Match the names of the biologists/philosophers below with their contributions to the field of biology or evolution as listed. For each question you may only select one of the correct responses (answers with more than one letter are automatically marked wrong). You may not choose the same letter more than once. There are more choices than blanks, you will leave unused choices. (1 pt each) Aristotle Cuvier, Baron Georges Darwin, Charles Fisher, Ronald Lamarck, Jean-Baptiste Linnaeus, Carl Lyell, Sir Charles Mendel, Gregor Plato A. A founder of molecular evolution, invented the idea of a molecular clock B. Argued for "catastrophism" in which sudden changes ruled the fossil record C. Argued for "uniformitarianism" whereby gradual changes ruled the fossil record D. Conceived of a "scale of Nature", an ordered listing of all living things E. Conceived of a theory of evolution via the inheritance of acquired characters F. Developed the philosophical idea of "types", "ideals" or molds. G. Developed the theory of "punctuated equilibrium" to describe changes in the fossil record H. Discovered particulate inheritance I. Invented modern species nomenclature and founded the field of biological classification. J. Mathematician who led the modern synthesis of the early 20th century K. Proposed natural selection as the mechanism of evolution in a famous 1859 book. 10. HISTORY OF LIFE ON EARTH Order the events listed below from most recent (#1) to most ancient (#10) (6 pts) 10 MYA 400 MYA Cambrian explosion Extinction of dinosaurs First mammals Cretaceous period Most recent common ancestor of humans and Chimpanzee Origin of ediacaran fauna Origin of life You taking this exam

8 Bio 312, Spring 2018 Exam 4 ( 8 ) Name: 11. SPECIES CONCEPTS. In class we considered a number of different species concepts and their relative merits and drawbacks - which species concepts are most appropriate and useful varies from field to field. Paleontologists study the history of life by examining fossils of past organisms and determining the nature and properties of past environments. Many researchers identify species in the fossil record and describe the properties of these species as they change over time and branch into multiple descendant species. (a, 3 pts) Consider a species concept that is useful for paleontologists. Name this species concept, describe the criteria used for defining species, and explain why this is useful for paleontology. (b, 3 pts) Consider a species concept that is NOT useful for paleontologists. Name this species concept, describe the criteria used for defining species, and explain why this is NOT useful for paleontology. Microbiologists study single celled prokaryotic and eukaryotic organisms, most of which reproduce by fission and clone themselves. Many researchers seek to identify species present in the environment and describe properties that differentiate the species that are found in different locations. (c, 3 pts) Consider a species concept that is useful for microbiologists. Name this species concept, describe the criteria used for defining species, and explain why this is useful for microbiology. (d, 3 pts) Consider a species concept that is NOT useful for microbiologists. Name this species concept, describe the criteria used for defining species, and explain why this is NOT useful for microbiology.

9 Bio 312, Spring 2018 Exam 4 ( 9 ) Name: FOR THE REMAINING QUESTIONS USE YOUR SCANTRON FORM, MULTIPLE CHOICE: (3 pts each). W bb Bb BB For the next two questions consider a population that is segregating two alleles at each of two loci. The figure to the right shows the fitness values of the nine different genotypes. AA Aa aa (1) Which of the following best describes the "A" and "a" alleles? (A) Allele "A" is advantageous and dominant, while "a" is deleterious and recessive. (B) Allele "A" is advantageous and recessive, while "a" is deleterious and dominant. (C) Allele "A" is deleterious and dominant, while "a" is advantageous and recessive. (D) Allele "A" is deleterious and recessive, while "a" is advantageous and dominant. (E) Allele "A" is deleterious and co-dominant, while "a" is advantageous and co-dominant. (2) Which of the following best describes the "B" and "b" alleles? (A) Allele "B" is advantageous and dominant, while "b" is deleterious and recessive. (B) Allele "B" is advantageous and recessive, while "b" is deleterious and dominant. (C) Allele "B" is deleterious and dominant, while "b" is advantageous and recessive. (D) Allele "B" is deleterious and recessive, while "b" is advantageous and dominant. (E) Allele "B" is deleterious and co-dominant, while "b" is advantageous and co-dominant. (3) The fossil skull shown to the right is from an organism that lived million years ago in central Africa (current day Kenya). This is the first species described in class that shows evidence of making and modifying stone tools. It is either one of our ancestors or a very close relative of this ancestor. Which species is this? (A) Ardipithecus ramidus. (D) Pan paniscus. (B) Australopithecus anamensis. (E) Sahelanthropus tchadensis. (C) Homo rudolphensis. (4) The fossil skull shown to the right is from an organism that lived 6-7 million years ago in central Africa (current day Chad). It is either one of our ancestors or a very close relative of this ancestor. Which species is this? (A) Ardipithecus ramidus. (D) Pan paniscus. (B) Australopithecus anamensis. (E) Sahelanthropus tchadensis. (C) Homo rudolphensis. (5) Consider the fossil skeletons shown to the right (they have been scaled to the same height). Which of the sequences below is the correct one that names the species, from left to right? (A) Chimpanzee... Gorilla... Orangutan... Human (B) Chimpanzee... Orangutan... Gorilla... Human (C) Gorilla... Orangutan... Chimpanzee... Human (D) Orangutan... Chimpanzee... Gorilla... Human (E) Orangutan... Gorilla... Chimpanzee... Human

10 Bio 312, Spring 2018 Exam 4 ( 10 ) Name: (6) Axial patterning in vertebrates is largely regulated by which of the following set of genes? (A) Axon genes (C) HOX genes (E) QTL genes (B) Exon genes (D) Knockout genes (7) In the discussion of humans and our relationship to nature, which of the following was described as a likely explanation for the greater acceptance of a continuum between humans and apes in Asia than in Europe? (A) Christian religious texts specifically state that apes are animals unlike many Asian texts. (B) Darker coloration of primates than Northern Europeans makes them seem very different. (C) Higher rates of marijuana use in Asia than in Europe. (D) Native primates in Asia makes their similarity obvious whereas Europe lacks primates. (E) Religious teachings in the East focusing on a young Earth and reincarnation. (8) The study with the infants that used the rabbit and dog stuffed animals provided evidence to support which evolutionary psychology hypothesis? (A) Altruism is presnet at very early ages and disappears as people get older. (B) Babies are unable to distinguish between real and artificial animals. (C) Babies can instinctually recognize that animals like dogs are more dangerous than rabbits. (D) In-group and out-group bias is inherent and not learned. (E) Male and female babies have different reactions to similar stimuli. (9) Which of the following describes the smoke detector principle? (A) Alarm calls should be high in pitch to allow them to be heard over large distances. (B) Fire is an inate fear that most animals have evolved to possess. (C) It is better, overall, to be overly brave than overly cautious. (D) It is better, overall, to be overly cautious than overly brave. (E) It is better to overperceive sexual interest than to underperceive it. (10) When an organism's developmental process proceeds at the normal rate, but is stopped early, the type of developmental change is termed which of the following? (A) Acceleration (D) Paedomorphosis (B) Hypermorphosis (E) Progenesis (C) Neoteny (11) When an organism's developmental process proceeds at the normal rate, but is stopped early, this type of developmental change results in a final adult phenotype termed which of the following? (A) Acceleration (D) Paedomorphosis (B) Hypermorphosis (E) Progenesis (C) Neoteny (12) The study of fossil formation is termed which of the following? (A) Declension (D) Taxonomy (B) Fossilectomy (E) Vesuvial studies (C) Taphonomy

11 Bio 312, Spring 2018 Exam 4 ( 11 ) Name: (13) Which of the following was NOT one of the four distinct model of female choice described in class? (A) Contests. (D) Handicap principle. (B) Direct benefit. (E) Hybridization avoidance. (C) Good genes. (14) Vestigial traits can include traits that arise temprarily during development without becoming a part of the final organisms. Which trait was discussed in class as an example of this type of vestigial trait? (A) Archaeopteryx wings. (D) Newt lungs. (B) Chicken digits. (E) Snake limbs. (C) Mouse ears. (15) The game theory scenario modeling the behavior of pairs of individuals was called. (A) Axles and wheels. (D) Prisoner's dilemma. (B) Bluff/raise strategy. (E) Tragedy of the commons. (C) Deception point. (16) The field of evo-devo that uses mathematical techniques to study how structures change during the ontogenetic trajectory was called which of the following? (A) Allometry (D) Neoteny (B) Comparative embryology (E) Population genetics (C) Irish elk studies (17) Which of the following correctly depicts the chronological sequence from earliest to most recent? (A) Archaen, Cenozoic, Mesozoic, Paleozoic, Proterozoic. (B) Archaen, Proterozoic, Paleozoic, Mesozoic, Cenozoic. (C) Paleozoic, Proterozoic, Archaen, Mesozoic, Cenozoic. (D) Proterozoic, Paleozoic, Archaen, Mesozoic, Cenozoic. (E) Proterozoic, Paleozoic, Archaen, Cenozoic, Mesozoic. (18) Which of the following correctly depicts the chronological sequence from earliest to most recent? (A) Cambrian, Cretaceous, Jurassic, Triassic, Tertiary. (B) Cambrian, Triassic, Jurassic, Cretaceous, Tertiary. (C) Cretaceous, Jurassic, Triassic, Cambrian, Tertiary. (D) Cretaceous, Triassic, Jurassic, Cambrian, Tertiary. (E) Jurassic, Triassic, Cretaceous, Cambrian, Tertiary. (19) Novel mutations that involve nucleotide changes, but not amino acid changes, are termed which of the following? (A) Major (C) Nonsynonymous (E) Conservative (B) Minor (D) Synonymous (20) Novel mutations that involve a thymine changing to an adenine would be classified as which of the following? (A) Conservative (C) Transition (E) Neutral (B) Radical (D) Transversion

12 Bio 312, Spring 2018 Exam 4 ( 12 ) Name: The following 3 questions are about the website you were asked to read through for this exam. (21) From the 1930s to the 1970s the Salton Sea was mainly used for what purpose? (A) An Air Force bombing range. (D) Recreation and tourism. (B) Commercial fishing. (E) Uranium mining. (C) Naval weapons testing. (22) Today the anvironment of the Salton Sea is not great for many species, but there is one group that thrives here (relatively) and for which this region is an important breeding ground. Which group is this? (A) Amphibeans. (D) Mammals. (B) Birds. (E) Reptiles. (C) Fish. (23) Which of the following is NOT one of the proposed solutions to the problems facing the Salton Sea? (A) Adding plants to the area to create marshland and cover the toxic soil. (B) Bring saltwater from the Sea of Cortez via pipelines. (C) Desalination of the seawater itself. (D) Divert water from the Colorado via a new series of aquaducts. (E) Dividing the Salton Sea into sections (e.g., hypersaline pools, perimeter sea) that can be more easily managed. The following 3 questions are about the video you were asked to watch for this exam. (24) The host of this video is best described as which of the following? (A) A Caucasian male wearing a checkered shirt. (B) A Hispanic female wearing a blue blouse. (C) A Native American female wearing a white blouse. (D) An African American male wearing a striped shirt. (E) An Asian male wearing a blue shirt. (25) The host describes several flaws about the figure. Which of the following is NOT one of the flaws he talked about? (A) Neanderthals are shown as our ancestors, which is incorrect. (B) Only males are shown, not females. (C) Species that are not recognized as close relatives of humans are shown. (D) The figure makes evolution look like a linear process. (E) Too many non-african species are shown. (26) At the end the host states that rather than as a linear march of species leading from left to right, a better depiction of human evolution would be...? (A) a circle leading back to the beginning. (B) a starburst with branches out from a center. (C) a procession from lower to higher. (D) a procession from right to left. (E) a tree or a fractal.

13 Bio 312, Spring 2018 Exam 4 ( 13 ) Name: Sci. Name Common name Acinonyx Cheetahs Ailuropoda Panda bears Ailurus Red panda Arctocephalus Fur seals Bassaricyon Olingos Bassariscus Ringtailed cat Canis Dogs Civettictis African civets Conepatus Skunks Crocuta Spotted hyena Cryptoprocta Fossa Eira Tayra Enhydra Sea otter Felis Small cats Fossa Fossa Galidia Mongooses Genetta Genets Helogale Mongooses Herpestes Mongooses Hyaena Hyenas Ichneumia Mongooses Ictonyx Polecats Leopardus Ocelot, kodkod Lontra American otters Lynx Lynx Manis Pangolins Martes Martens Meles Badgers Mephitis Skunks Mirounga Elephant seals Mustela Weasels Mydaus Stink badgers Nandinia Palm civets Nasua Coati Nyctereutes Raccoon dogs Odobenus Walrus Panthera Lions, tigers Paradoxurus Palm civets Parahyaena Brown hyenas Phoca Common seals Potos Kinkajous Prionodon Linsangs Procyon Raccoons Proteles Aardwolves Rhynchogale Mongooses Spilogale Spotted skunks Suricata Meerkats Taxidea Badgers Urocyon Foxes Ursus Bears Zalophus Sea lion Fig. 2. Timescale of carnivoran diversification, based on the Thorne/Kishino relaxed molecular clock method, incorporating 21 fossil calibrations (similar results were obtained with BEAST see Fig. 3, Table 6 and Supplementary Information). The tree is a cladogram with node depths (branch lengths) drawn proportional to time, with a timescale shown at the bottom, including the paleontological epochs of the Cenozoic Era (Paleoc. = Paleocene; Pi = Pliocene; Pe = Pleistocene). Family names are indicated on the right, as are the major suborders Feliformia and Caniformia. Numbers above nodes are divergence ages in MYA (millions of years ago); only nodes defining families or higher clades are labeled (the only exception is the New World sub-clade of the Mephitidae, mentioned in the main text); see Table 6 for point estimates and credibility intervals for node ages estimated with Divtime and BEAST.

14 Bio 312, Spring 2018 Exam 4 ( 14 ) Name: