Evolutionary Biology Fall 2012

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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%207.%20Systematics.%20F%2012.pdf}}Study Guide 7. Systematics. F 12.pdf
 
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%208%20Clocks%2C%20Life%20F%2012.docx}}Study Guide 8 Clocks, Life F 12.docx

Revision as of 15:51, 28 October 2012

EEB 2245: Evolutionary Biology


Meeting Time: Tuesdays and Thursdays, 12:30-1:45 in UTEB 150

Instructor: Chris Simon, Professor EEB, Office: Biopharm 305D, phone 6-4640, Lab: Biopharm 323 & 325, phone 6-3947;
e-mail: chris.simon@uconn.edu [e-mail is the best place to leave messages.]

Office hours: Flexible except in the morning before our class. See me after class or send me an e-mail to arrange a meeting. I encourage quick questions by electronic mail. With longer questions or many questions, please come to see me or your TA, Colin Carlson. Don’t wait until the day before an exam!

Teaching Assistant: Colin Carlson, e-mail: colin.carlson@uconn.edu

Class Website: http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Category:EEB_Courses

Grade: The goal of this class is to teach you the basic principles of evolution and to give you an appreciation for the science. It is important to me that you learn the material. I hate to assign grades but they are required. Therefore I am trying an experiment this semester to try to lessen the pressure on the midterm and enhance your learning experience. Each Friday I will post a Study Guide. Each Wednesday, TA Colin Carlson will host a study guide review session. Each Thursday at the end of class, as a quiz, I will ask you a few questions from that study guide. We’ll grade the quizzes and return them to you by the following Thursday. Hopefully these quizzes will serve to prepare you for the first midterm and to ensure that your grade is not based on your performance on only the midterm and the final.

EEB 245: There will be a series of ten quizzes (as described above) and two one-hour exams covering each half of the course (listed on the syllabus) and a comprehensive one-hour synthetic final exam. The second one-hour exam will be given in the same two-hour time block as the synthetic final. The quizzes will count 10% of your total grade, the first exam 40% and the second hour exam plus the final will count 25% each.

EEB 245W: If you are registered for EEB 245W, 75% of the final course grade will be determined by your lecture exams (as above) and 25% by your term paper. As required by University regulations, an F in the W part of the course will result in an F for the entire course. At least two drafts of your writing assignment must be successfully completed to pass the course. A detailed set of instructions will be provided and W students will be assigned a W instructor during the first week of class.

Text: Futuyma, D. J. 2009. Evolution. Second Edition. Sinauer Publications, Sunderland, Mass. http://www.sinauer.com/detail.php?id=2238. The UCONN coop should have lots of used copies. Please read assigned chapters prior to the class for which they are scheduled. Additional supplementary readings may be assigned during the semester. See also new value options from Sinauer: http://www.sinauer.com/detail.php?id=2238#tions


Syllabus: Download the PDF. The syllabus always evolves. I will periodically send updated versions which track our true progress and introduce late breaking topics.

Pdficon small.gifSyllabus EEB 2245 F 2012 27 Oct 12.rtf


Quiz Keys:

Pdficon small.gifQuiz 1. History, Creationism. Key.docx
Pdficon small.gifQuiz 2, Fall 12 Key.docx
Pdficon small.gifEEB 2245. Quiz 3 F 12 key rev.docx
Pdficon small.gifQuiz 4. Load, Levels of Selection, Plasticity key.docx
Pdficon small.gifQuiz 5, F12 EEB 2245 key.docx


Midterm Answer Key:

Matching. First three questions: fill in the blanks below with one of the following answers:

   a) drift, b) gene flow, c) selection

1) ___b__ It could be described as the rate of immigration of alleles.

2) ___a__ It’s influence is related to population size.

3) __ c__ It is defined as differential survival of different genotypes.


Matching: Use the following list to answer questions 4-6 a) reporter for the Baltimore Sun; b) Attorney for the defense; c) Attorney for the prosecution; d) Rhea County resident who contacted the ACLU; e) young teacher who volunteered to stand trial.

c 4) What was the role of William Jennings Bryan in the “scopes monkey trial”?

c 5) What was the role of Clarence Darrow in the “scopes monkey trial”?

d 6) What was the role of George Rappalyea in the “scopes monkey trial”?

a 7) In 1987, a US Supreme Court decision banned the teaching of the biblical story of creation in public schools. Answer either: a) true or b) false.

a 8) In 2005, the Dover Area School District sought to teach creationism in the guise of “Intelligent Design.” They were challenged by the Kitzmiller family in court. The conservative judge ruled that Intelligent Design was not science, was not different from creationism, and should not be taught in public schools. Answer either: a) true or b) false.

Matching: Fill in the blanks in questions 9-13 with the letters a-e indicating one of the following names:

                   a. Weismann;   b. Lamarck;   c. Lyell;   d. Malthus;   e. Mendel.

9) _a___ Performed experiments where he cut the tails off mice and showed that the offspring remained long-tailed; argued for inheritance of germ cells versus somatic cells.

10) _d___ Was influential in Darwin’s thinking; he wrote an economics text which talked about exponential population growth followed by a struggle between classes.

11) _e___ A contemporary of Darwin who conducted genetics experiments and understood inheritance better than any known person of his day. He was not influential in Darwin’s thinking.

12) _b___ Was a strong advocate of evolution (which he called transmutation); believed in spontaneous generation. Believed that species descriptions are man made. Believed in the inheritance of aquired characteristics.

13) _c___ An influential geologists whose work was studied by and instructive to Darwin; he did not believe in Evolution.

e 14) Which of the following is not an assumption of the Hardy Weinberg equation: a) mating is random, b) natural selection is not operating, c) there are no migration of alleles at the locus of interest, d) there are no new mutations, e) allele frequencies will change from one generation to the next.

d 15) Which of the following statements about genetic drift is incorrect (assume no selection; no gene flow; random mating; no new mutations): a) the probability that an allele will become fixed equals the initial frequency of that allele b) allele frequencies fluctuate at random but eventually one allele will become fixed c) different populations may become fixed for different alleles d) the larger the population, the faster the rate of genetic drift of any given allele. e) genetic drift can preserve genetic variability in species if the species consists of a series of small isolated populations

c 16) Which answer best describes the disease “Cystic Fibrosis.” a) Malaria selects in favor of this disease; Caused by mutations in a gene encoding a sodium channel protein; up to 500 different recorded mutations are thought to cause the disease, rare in Finland; maintained by balancing selection. b) Associated with G6PDH (glucose 6 phosphate dehydrogenase) deficiency; Missing transmembrane conductance regulator; Caused by a parasite carried by an insect; rare in Finland; maintained by directional selection c) High incidence in areas formerly decimated by typhoid fever; Missing transmembrane conductance regulator; rare in Finland; caused by mutations in a gene encoding a sodium channel protein; up to 500 different recorded mutations are thought to cause the disease; maintained by balancing selection d) Caused by a parasite carried by an insect; Malaria selects in favor of this disease; Missing transmembrane conductance regulator; common in Finland; maintained by disruptive selection.

a 17) How will a short bottle neck affect heterozygosity? a) little effect, b) strong effect, c) no effect

b 18) How will a long bottle neck affect heterozygosity in a population? a) little effect, b) strong effect, c) no effect

b 19) How will a short bottle neck affect number of alleles in a population? a) little effect, b) strong effect, c) no effect

a 20) Two genes located on the same chromosome are called “linked.” Answer either: a) true or b) false.

b 21) Two genes located on the same chromosome will never assort independently. Answer either: a) true or b) false.

c 22) The classical view of variation in natural populations before Lewontin and Hubby was that mutations at any given locus were: a) common and deleterious; b) common and advantageous; c) rare and deleterious; d) rare and advantageous.

d 23) Dolph Schluter’s stickleback fish were found naturally occurring as three morphs: bottom feeders, top feeders, and generalists. An experimental pond containing bottom feeders and generalists eventually evolved to contain:

          a) only generalists,                    b) only top feeders 
          c) only bottom feeders              d) a mixture of top feeders and bottom feeders 

b 24) Which of the following is true about Lee and Vacquier’s (1992) study of sperm-binding protein lysin in abalones. They compared the lysin DNA sequences of seven species (all pairwise comparisons). a) they found more differences among species at first positions of codons than at third positions. b) they found more differences among species at second positions of codons than at third positions. c) they found more differences among species at third positions of codons than at second positions. d) they found more differences among species at third positions of codons than at first positions. e) They concluded that natural selection had no effect on the lysin protein.

c 25) Templeton defined species via the cohesion species concept as, the most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms. Which of the following is not an intrinsic cohesion mechanism:

           a) gene flow;              b) shared evolutionary history           c) disruptive selection  
           d) shared ecology     e) reproductive isolation from other species

c 26) The farther apart two populations of a species, the less likely they are to exchange genes due to isolation by distance. The more isolated two populations, the greater the genetic differentiation. Gradual accumulation of genetic differences due to selection and drift (and not counteracted by sufficient gene flow) can lead to reproductive isolation. Rare cases exist where populations at either end of a continuum of gene flow (isolation by distance model) come into secondary contact but are reproductively isolated. These species are called:

                    a) sister species,                     b) cryptic species,           c) ring species,   
                    d) isolation speices,                 e) sibling speices.

e 27) Founder events encourage speciation because:

     a)  Formation of new co-adapted allele complexes; 
     b)  Genetic drift is likely to occur (assuming the population remains small for a substantial period of time) resulting in a reduction in heterozygosity compared to the source population; 
     c)  A large reduction in the number of alleles compared to the source population changes the genetic environment of the colonizers; 
     d)  Predators and competitors are likely to be absent changing selection pressures compared to the source population; 
     e)  All of the above 

e 28) How does small population size and low mobility increase the chance of chromosomal speciation in organisms like gophers, naked mole rats and wingless grasshoppers. a) gene flow is reduced so each population evolves in isolation, b) rare deleterious chromosomal variants are more likely to be fixed by chance due to genetic drift, c) natural selection will favor rare variants, d) all of the above, e) all of the above except c

d 29) The development of new coadapted allele complexes are thought to explain why… a) Peter and Rosemary grant noticed that over time hybrid Galapagos finches increased in fitness over generations and seemed to be breeding more often with other hybrids. They suggested that these hybrids were becoming a new species. b) Loren Rieseberg noticed that the in crosses between Helianthus annuus and H. petiolaris, pollen viability of the hybrid offspring changed over time from 10% to 90% (in just five generations). c) Megan Higgie and coworkers found that undisplaced Drosophila birchii from the northern extreme of the range when placed in mating cages with D. serrata developed reproductive character displacement in just nine generations. d) The answer is a and b but not c. e) The answer is a and c but not b.

d 30) Which of the following is not a finding of Coyne and Orr’s review of 60 years worth of Drosophila mating studies: a) Strength of pre-zygotic isolation increases over time. b) Time required for reproductive isolation is variable (usually between 1 & 3 million years) c) Prezygotic isolation evolves first (stronger among sympatric taxa) d) Postzygotic isolation evolves more rapidly in the homogametic sex. e) Strength of post-zygotic isolation increases over time.

e 31) Which of the following is not a problem with barcoding: a) Using only mtDNA to recognize species (because mitochondria can be passed across species boundaries). b) Polyploids would not be recognized as different species from diploid progenitor. c) Nuclear copies of mtDNA could be sequenced in some populations while true mitochondrial copies were sequenced in other populations. If they were different enough they would seem to be two different species. d) Using a designated (2-3%) percent pairwise sequence divergence between species as a species boundary. e) Using barcoding as a first pass to recognize potential new species.

d 32) In periodical cicadas, life cycle switching resulted in speciation by what mechanism:

      a) allopatric speciation,      b) chromosomal speciation,    c) founder effect speciation, 
      d) allochronic speciation    e)  host-race speciation

c 33) In periodical cicadas reproductive character displacement was seen by John Cooley and David Marshall in what character: a) abdomen color, b) mitochondrial DNA sequence, c) male song pitch, d) Male mating dance, e) wing color.

Written answers:

34) List four possible consequences of secondary contact between two formerly isolated populations (2 points):

a) populations meet but don’t mate (full reproductive isolation)

b) populations meet and mate randomly and fuse together (no isolation)

c) populations meet, mate but hybrids less fit (Bonus: possible selection for reproductive character displacement, genes may or may not introgress into parent populations depending on selection).

d) populations meet, mate but hybrids more fit in hybrid zones (stable hybrid zone)

Written Answers continued: The tree frog Hyla versicolor is believed to have evolved from Hyla chrysoscelis multiple times in multiple locations by doubling its chromosomes (polyploidy). A phylogenetic tree for your reference is presented on the next page. Answer the questions below after studying the phylogenetic tree.

35) Would a biologist who believes in the biological species concept be willing to call each population of Hyla versicolor a different species? Circle: Yes or No. Explain your answer in one to three sentences:

Yes or No. No, because if brought into the lab individuals from any population of H. versicolor can still mate with individuals of any other population and not mate with other species. Yes, if you consider geographic isolation to constitute reproductive isolation such that they are not potentially interbreeding.

36) Would a biologist who believes in the biological species concept be willing to call all populations of Hyla versicolor a single species? Circle: Yes or No. Explain your answer in one to three sentences:

Yes, because individuals from all populations have the same mating song, same morphology and can breed freely if brought together in the laboratory and they cannot mate with individuals outside of their own species. They may some day become separate species but are not yet different in any way.

37) Would a biologist who believes in the phylogenetic species concept be willing to call each population of Hyla versicolor a different species? Circle: Yes or No Explain your answer in one to three sentences:

Yes, because each population has an independent evolutionary origin on the tree and they are diagnosable by their DNA. They are on different evolutionary trajectories. However, someone who believes in psc would be bothered by the fact that the southwestern Hv do not form a monophyletic clade on the tree but are instead indistinguishable from eastern Hc.

38) Would a biologist who believes in the phylogenetic species concept be willing to call all populations of Hyla versicolor a single species? Circle: Yes or No Explain your answer in one to three sentences:

No, because they are not a single clade; they have independent evolutionary origins. They are diagnosably distinct based on their DNA. Species are not supposed to be polyphyletic.

39) Would a biologists who believes in the biological species concept treat all Hyla chrysocelis as a single species?

Yes, because they all share the same mating call and they could all potentially interbreed, (unless you consider geographic isolation to prevent potential interbreeding). In addition there are no morphological behavioral or chromosomal differences and they do not reproduce with individuals outside of their speices.

40) Would a biologist who believes in the phylogenetic species concept treat all Hyla chrysocelis as a single species?

Yes or No. No, because Hyla versicolor is nested within them and excluding Hv would bother some psc people. They might want to name each clade of Hc and Hv as separate species diagnosable by their DNA. Yes, if a broad-minded Psc person would allow for multiple origins of a polyploid within an existing species. All Hc do share one common ancestor (even though if you remove Hv they are not technically “monophyletic”).


Study Guides, Handouts:

Pdficon small.gifStudy Guide I EEB 2245 F 12 .doc
Pdficon small.gifDarwin Chronology and Pubs (handout)
Pdficon small.gifArchitects of the Modern Synthesis (Handout)
Pdficon small.gifStudy Guide 2. EEB 2245 Fall 12Hardy Weinberg.rtf
Pdficon small.gifStudy Guide 3. EEB 2245 Fall 12 Bottlenecks, Founders, Selection.rtf
Pdficon small.gifNatural Selection Review Table.pdf
Pdficon small.gifStudy Guide 4. F12 Selection II rev.doc
Pdficon small.gifStudy Guide 5. F12 variation isolation speciation.doc
Pdficon small.gifStudy Guide 6 Hybridization.docx
Pdficon small.gifLect 16. Handout Constructing Evolutionary Trees 2012.pdf
Pdficon small.gifStudy Guide 7. Systematics. F 12.pdf
Pdficon small.gifStudy Guide 7 answers systematics F 12.rtf
Pdficon small.gifStudy Guide 8 Clocks, Life F 12.docx


Lecture notes:

Pdficon small.gifEEB 2245 Lect. 1 Intro (four per page) 2012.pdf
Pdficon small.gifEEB 2245 Lect. 1 Intro 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lec. 2 Evidence 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 3 History 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect 3. History (6 per page) EEB2245.pdf
Pdficon small.gif EEB 2245 Lect. 4. Population Biology, HW (4 per page).pdf
Pdficon small.gifEEB 2245 Lect. 4 Population Biology 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 5. Deviations from HW F12.pdf
Pdficon small.gifEEB 2245 Lect 6. H-W selection, Inbreeding & Drift Geneflow.pdf
Pdficon small.gifEEB 2245 Lecture 5 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 6 (with lines).pdf
Pdficon small.gifEEB 2245 Lect 7. Inbreeding, gene flow, selection.pdf
Pdficon small.gifEEB 2245 Lect. 7 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 8. Selection I revised F12.pdf
Pdficon small.gifEEB 2245 Lect. 9. Natural Selection II plasticity coevolution F12.pdf
Pdficon small.gifEEB 2245 Lect. 9. (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 10. Load, Geographic Variation.pdf
Pdficon small.gifLecture 10 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 11 Geog. Var. (cont) Factors reducing geneflow.pdf
Pdficon small.gifLecture 11 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 12 Isolation, species concepts.pdf
Pdficon small.gifLecture 12 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 13. Speciation Mechanisms.pdf
Pdficon small.gifLecture 13 (with lines).pdf
Pdficon small.gifEEB 2245 Lect 14. Hybridization.pdf
Pdficon small.gifLecture 14 (with lines).pdf
Pdficon small.gifLect. 15. Systematics EEB 2245 F 2012.pdf
Pdficon small.gifLect. 16 F12 Building Trees 23Oct12.pdf
Pdficon small.gifLecture 16 (with lines).pdf
Pdficon small.gifLect. 17 F12 Building Trees Morph. Molec. Evolution Rev F12.pdf


Evolution in the News, Scientific Literature, and You Tube

Watch your back mate! Courtship of peacock spider Maratus volans from Australia- 23 Mar 2011

African mouse sheds patches of skin and hair to escape predators- 26 Sep 2012

Cool Looking Monkey New to Science Found in Congo- 14 Sep 12

Peppered moths vindicated! - 28 February 2012
Darwin's long-lost fossils - 17 January 2012

H1N1- A case of suspended animation- 29 Aug 2012

Tool use evolution

Tool Use Evolution- Sept 2002

“Tool-use is commonly attributed to humans and other primates. However, several bird species are also known to use tools habitually. Egyptian vultures (Neophron percnopterus) are famous for dropping stones on ostrich eggs (Van Lawick-Goodall & Van Lawick-Goodall 1966), green-backed herons (Butroides striatus) use bait to catch fish (Walsh et al. 1985), satin bower birds (Ptilonorhynchus violaecus) use bark-wads to paint their bower (Chaffer 1945), and New Caledonian crows (Corvus moneduloides) make and use two forms of tools to capture prey (Hunt 1996). The woodpecker finch (Cactospiza pallida), one of 15 species of Darwin's Finches, is perhaps the most famous example of a tool-using bird. It uses twigs or cactus spines to pry arthropods from tree-holes and crevices (Eibl-Eibesfeldt 1961; Eibl-Eibesfeldt & Sielman 1962)…. social learning is not an important mechanism in the acquisition of tool-use in the woodpecker finch (Tebbich et al. 2001).”





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