BIO 111 Chapter Notes - Chapter 16: Maximum Likelihood Estimation, Convergent Evolution, Notochord

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silverbee937

6 Feb 2017

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University of Rochester

Department

Biology

Course

BIO 111

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Minckley

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16. 2 phylogeny can be reconstructed from traits of organisms. In group the group of organisms that are of primary interest. Out group the group of organisms that are related to the in group, but are known to be in a different phylogeny (i. e. the root is between the in group and the out group) Parsimony provides the simplest explanation for phylogenetic data: the parsimony principle the preferred explanation of observed data is the simplest explanation. The one that requires the least homoplasies: o(cid:272)(cid:272)a(cid:373)"s razor the best explanation is the one that best fits the data while making the fewest assumptions. Phylogenies are reconstructed from many sources of data: any trait that is genetically determined (heritable) can be used in a phylogenetic analysis, morphology. Morphology the presence, size, shape, and other attributes of body parts. Is still the most used way of distinguishing and classifying species. Few morphological traits can be compared across taxa (distantly related organisms)

Related Questions

12. What is the primary aim of the scientific method? A. To formulate a hypothesis B. To introduce new variables into an ExperimentC. To include control groups in an experiment D. To modify an Experiment E. To discard the results if they do not support the hypothesis.

13. Supporters of spontaneous generation believe in the theory of biogenesis. True or false14. Louise pastors experiments discounted the theory of abiogenesis true or false

15. Hey Siri is a? E. Collection of statements, for positions, or concepts that explain or accounts for a natural event B. Prediction C. Process of experimentation D. Tentative explanation to account for what has been observed or measured 16. Joseph Listerâs concept of a sepsis in the medical setting consisted of what procedure? A. The practice of the handwashing B. The use of an autoclave C. Do use of antibiotics D. Do use of gloves 17. Which of the following is the largest in size? A.Escherichia coli(bacteria)B. Amoeba proteus (protozoa)C.Poliovirus (virus) D. Mycobacterium tuberculosis/Tuberculosis E.Bacillus anthacis/Anthrax

19. The smallest and most specific of the levels of classification is species. What level of classification is directly above species A.period domainB.familyC. Genus D. Phylum20. What time refers to the degree of evolutionary relatednessBetween living organisms? A. Morphology B. Physiology C. Hierarchy . Phylogeny

21. Which of the following statements regarding evolution is correct? A. Change is that favor survival or lost B.Living things change rapidly through millions of yearsC. Evolution results and structural and functional changes in organisms D. Changes that are not beneficial are preserved 22. Who is fox used what cell component in the classification of organisms into three domains? A.mRNA B.Protiens C.rRNA D.none of the above

23. Micro organisms can be found in all natural habitats. This defines micro organisms as being? A. Microscopic B. Eukaryotic C. Parasitic D. ubiquitous

24. The prokaryotic cell structure includes A. Nucleus, mitochondria B. Ribosomes, cell membranes C. All of the above D. None of the above

25.Regarding the involvement of micro organisms and energy and nutrient flow

A. Bacteria and fungi are important and decomposition

B. Algae are characterized as photosynthetic

C. All of the above are correct

D. None of the above is correct

26. The terms parasite, hots, pathogen, biofilms, and epidemiology are associated with:

A. The role of microorganisms in defomposition

B. The role of microorganisms in bio-remediation

C. The role of viruses in the infectious disease process

D. The role of microorganisms in the infectious disease process

E. None if the above

27. The scientific method can be summarized as:

A. A process

B. Observation, hypothesis, experiment, assessment of data, conclusion

C. All the above

28.in the development of medical microbiology;

A.ferdinand Cohn discovered heat-resistant bacterial spores

B. Robert Koch linked specific organism to specific diseases

C.louis pasteur and Roberts clutch advance the germ theory of disease D. All of the above are correct E. None of the above is correct number

29 the formal system of organizing classifying and naming organisms is called A. Morphology B. Physiology C. Here Archie D. Phylogeny E. None of the above number

30. The horse fox system of classification containâs a. The domains you Eukarya, archaea, bacteria

B. The kingdoms plants, fungi, animals, protists, Monerans, C. All of the above D. None of the above

Chapter No. 2

31. The simplest form of matter not the visible into simpler substances is? 32. Positively charged subatomic particles are? 33. Neutral subatomic particles are? 34. Negatively charged subatomic particles? 35. A pure substances with a chair at the rustic number of protons, Neutrons, and electrons? 36. The atomic number? 37. The number of protons and neutrons is the? 38. Verriant forms of the same element that differ in the number of neutrons are? 39. The space surrounding the atomic nucleus where electrons are likely to be found? 40. A chemical substance that results from the combination of two or more Adams? 41. Chemical? Are formed when two or more atoms share, donate, or except electrons to form molecules. 42. Chemical bonding where electrons are shared among Adams are? 43. Chemical bonding where electrons are transferred to one Adam forming positively charged cations and negatively charged and ions? 44. Chemical bonding that is described as weak bonds between hydrogen and other Adams?

45. Regarding covalent, ionic, and hydrogen bonds, the following is true a period is covalent bonds electrons are shared among Adams be. In ionic bonds, electrons are transferred to one Adam forming (+) cations and (-) anions C. Hydrogen bonds are weak bonds between hydrogen and other Adams D. All of the above are correct E. None of the above are correct 46. Reactants also called substrates are molecules that start a reaction and products are substances left by a reaction. True or false 47. The pH scale express is the concentration of H plus ions, and it ranges from A.0 to 7 B. 1 to 14 C. 0 to 14 D. None of the above 48. Organic chemicals are compounds containing carbon bonded to nitrogen Adams. True or false 49. Carbon see is the fundamental element of life and eight. Contains four Adams and itâs our orbital be. Can form single, double, or triple covalent bonds see. Can form linear, branched, Or ringed moleculesD. All of the above are correct E. None of the above are correct 50. Biochemicals are organic compounds produced by living things and include A Carbohydrates B. Lipids C. Proteins D. Nucleic acidâs E. All of the above are correct letter F. None of the above are correct51. In Marco molecules large are compounds assembled from smaller subunits. A monomer is a subunit and a polymer is a chain of monomers. true or false

52. Proteins pre-dominant molecules and cells,There monomers are the 20 amino acids, and there are polymers are peptides, polypeptides, proteins. There are some units are linked by peptide bonds. Which of the following protein characteristics are true A proteins fold into very specific 3-D shapes B proteins function as support, enzymes, transport, defense, movement C all of the above are correct D none of the above are correct 53. DNA the deoxyribonucleic acid. DNA is formed by two long poly nucleotide strands linked by hydrogen bonds, the following is also threw a. A, C, C, GR nitrogen bases B. The DNA molecule is a double helix C. DNA functions as hereditary material

D. All of the above are correct E. None of the above are correct chapter 4. 54. Peptidoglycans, dipicolinic acid, and mycolic acid are chemicals. They are: Letter a. Associated with cell Walls and their function is protection B. Associated with the cell membranes and their function is protection C. All of the above are correct D. None of the above are correct 55. Steroids are chemicals found in pleomorphic Mycoplasma plasma. They are: E. Associated with cell walls and their function is protection B. Associated with the cell membrane and their function is protection C. All of the above are correct D. None of the above are correct 56. The cell membrane cytoplasmic membrane A. Has a phospholipid Byler B. Has it embedded proteins C. Is the conceptualized in the fluid Mosaic model D. All of the above

57. Which of the following is incorrect regarding the bacterial cell wall? Hey. Is it a target of certain antibiotics B. It determines the shape of the bacterium C. It prevents a bacterium from bursting due to changes in osmotic pressure D. Itâs comeposition where is among the major bacterial groups E. It is composed of repeating framework of lipids 58. Which of the following is incorrect regarding plasmids? E. They are extra chromosomal B. They Can become integrated into the bacterial chromosome C. They can come for protective traits D. They are essential for bacterial growth and survival E. They are important in genetic engineering techniques 59. Identification of bacteria requires a study of all but which of the following? A. Microscopic and macroscopic morphologyB. Bacterial physiology C. Quantitive analysis D. Serological analysis E. Genetic and molecular analysis

60. What is the structure of each of these functions

60. Adhesion 61. Proteins Synthesis 62. Selective permeability 63. Protective, pathogenicity 64. Site of mini bio chemical reactions 70 to 80% water 65. Iocomotion, chemotaxis 66. Nutrient storage (glycogen,PHB)

67. Conjunction 68. Protection from dehydration 69. Heat resistance(linked to calcium and dipicolinic acid) 70. Play a role infected catheters ,IUDs, artificial hip joints

Here are the key Structures for Questions 60 to 70

KEY:Flagella, endospores, so membrane, inclusion body, cytoplasmic matrix, ribosomes, cell-capsule, fimbriae, slime layer, Pilus, biofilms

Chapter No. 5

What are the eukaryotic structure of each of these functions

71. Generation of energy ATP 72. Site of ribosomes in you create excels 73. Locomotion 74. Location of chromosomes and nucleolus75. Convert sunlight energy into chemical energy such as algae and plants 76. Synthesis of nine proteins such as lipids 77. And enzyme found in tears saliva 78. Contains a verity of enzymes79. Collects and packages proteins

Here are the key for question 71 through 79

KEY:Lysosome, mitochondria, nucleus, lysozyme, Goldi-apparatus , flagella, cilia,pseudopia, PER, SER, chloroplasts, nucleus

80. Helminthes include: A. Roundworms(Nematodes) B. Tapeworms (cestodes)C. Flukes(Trematodes) D. all of the above E. None of the above

81. The cell walls of fungi are composed of what? A. Peptide Dougla can be. Chitin or cellulose C. All of the above D. None of the above

82. Where does RNA synthesis in Eukaryotes occur?

83. Asexual reproduction in fungi occurs by what process? A. Binary fission B. Meiosis C. Nuclear fusion D. Mitosis

84. Which of the following defines a lysosome? A. The Sicle that originates from the gold Golgi apparatus and contains a veriety of enzymesB a membrane bound sack contains fluids or solid particles to be digested see. A buck you all that contains reserve nutrients D. A vac you are that regulates osmotic pressure 85. Which of the following is correct regarding chloroplasts? K. They are the primary producers of organic nutrients B. They are found In LG and plant cells letter C. Oxygen gas is produced as a byproduct of their activities D. They convert the energy of sunlight into chemical energy through photosynthesis E. All of the above are correct.

89. All fungi utilize what as a nutritional substrate? A. Organic nutrients be. Carbon dioxide C. Inorganic ions D. Hydrant sulfide

86. What is formed when hyphae of two opposite fungi strains fuse in form diploidy spores?Sporangium, ConidiaB. Basidiospores, zygospores, Ascospores

C.All of the above are correct 87. What statement regarding the fungi is incorrect? E. Many species are pathogenic to field crops B. Fungi decomposed organic matter in return essential minerals to the soil C. They can be used to produce large quantities of antibiotics, alcohol, anod vitamins D. All of the above are correct E. All of the above are incorrect

ceruleansnake435

Random, chance events that change allele frequencies are knownas:

A. Gene flow

B. Genetic drift

C. Natural selection

D. Balancing selection

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Question 21 pts

What type of selection acts to maintain the two extremephenotypic variants in a population?

A. Disruptive selection

B. Directional selection

C. Positive selection

D. Artificial selection

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Question 31 pts

Approximately, how much of our DNA is shared with our closestrelatives, chimpanzees?

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Question 41 pts

The large canines of male baboons are likely the result of________, while the fact that some male baboons are very colorfulis probably the result of _______.

A. Mutation; balancing selection

B. Gene flow; sexual dimorphism

C. Male competition; female choice

D. Mate choice; genetic drift

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Question 51 pts

Negative assortative mating results in an increased frequency ofhomozygous genotypes within a population.

True

False

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Question 61 pts

Genetic evidence suggests that humans and Neandertals neverinterbred.

True

False

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Question 71 pts

The specific variant of the FOXP2 gene associated with languageacquisition in humans is found in both humans and Neandertals.

True

False

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Question 81 pts

Industrial melanism describes the change in moth color from paleto dark after pollution from factories resulted in coating treetrunks with a layer of dark soot. Which statement is trueconcerning industrial melanism?

A. After pollution levels increased, all moths became darkercolored because soot got on their wings

B. The dark moths survived better after pollution levelsincreased because they were not poisoned by the pollutants

C. Individual moths changed their color in response to thepollution

D. Dark moths were present in the population before pollutionlevels increased

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Question 91 pts

Patterns of evolution can be seen above the species level

True

False

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Question 101 pts

Inbreeding is problematic because it increases the probabilitythat offspring inherit two copies of a recessive mutation thatcauses disease.

True

False

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Question 111 pts

As a species, cheetahs seem to have a high risk of extinctionbecause:

A. Gene flow has caused a proliferation of unnecessarygenes.

B. The species' genetic diversity is very low due to a previouspopulation bottleneck event.

C. The species has undergone extreme sexual selection in orderfor males to achieve faster running speeds.

D. Gene flow has been stifled due to an increase in demand forcaptive cheetahs.

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Question 121 pts

A strand of DNA undergoes mutation. Which mutation occurred?

Original DNA- GGA CTC TTA CCC CAC GGA

Mutated DNA- GGG CTC TTA CCC CAC GGA

A. point mutation

B. insertion mutation

C. deletion mutation

D. inversion mutation

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Question 131 pts

A change from one nucleotide to another nucleotide is known as awhat?

A. Point mutation

B. Insertion mutation

C. Deletion mutation

D. Inversion mutation

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Question 141 pts

A change from one nucleotide to another nucleotide is known as awhat?

A. point mutation

B. insertion mutation

C. deletion mutation

D. inversion mutation

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Question 151 pts

According to the Typological Species Concept, species are:

A. An interbreeding group of organisms

B. Static entities endowed with fixed properties

C. A local population of organisms that have similargenes, interbreed, and produce offspring

D. An exclusive community of gene exchange

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Question 161 pts

Recognizing reproductive isolation is key to defining speciesunder the Biological Species Concept.

True

False

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Question 171 pts

The binomial system of classification was developed by:

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Question 181 pts

A derived trait, unique to a particular taxon within a givencladogram is called:

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Question 191 pts

Analogy, and not homology, is useful for reconstructingevolutionary history.

True

False

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Question 201 pts

A phylogeny is which of the following:

A. A depiction of an organism's complete genome

B. A depiction of evolutionary relationships betweenorganisms

C. The gradual evolution of one species intoanother

D. The Latin name of an organism including its genus andspecies designation

coffeegoat763

1.. Polymorphisms for a given trait are relatively common in most species. Discuss the possible advantages or polymorphisms in terms of evolutionary fitness. Be sure to relate your discussion to a specific example. It is also possible that organisms showing more heterozygosity may actually be less fit. Describe one such possible scenario.

2. In the peppered moth (Biston betularia), black individuals may be either homozygous (A1A1) or heterozygous(A1A2), whereas the pale gray moths are homozygous (A2A2). Suppose that in a sample of 250 moths from one locality, 108 are black, and 142 are gray.

3. Retrace the history of primate evolution from early primates to monkeys, apes and hominins. When did some ofthe significant divergences occur (such as between the prosimians and the monkeys or between the chimps and hominins)? What was happening with the continents and the major climatic conditions during these times?What are the major species (including the extinct species) along the human lineage after the split with the chimps and bonobos? Where did many of these events occur on the globe and when?

4. Spencer Wells described his study how the genetic markers in humans are being used to infer the historical geographical distribution of humans and the dispersal of our ancestors. Explain how the genetic markers on our DNA (from blood samples) helps us understand that history. What are the techniques he is using? What is the nature of the evidence? What are the major conclusions about the journey of our ancestors out of Africa?What were the major migrations of humans to all the other continents? Approximately when did each migration occur and what were the major paths? How does the evidence support these conclusions? What Supporting evidence besides the DNA evidence is being used to support these conclusions?

5. Provide an adaptive and a non adaptive hypothesis for the evolutionary loss of useless organs, such as eyes in many cave-dwelling animals. How might these hypotheses be tested?

6. Directional selection is one of the models of natural selection. Describe this type of selection in terms of the frequencies of advantageous alleles over time. What is the trend over time? What is the eventual outcome for this allele as long as no other evolutionary factors intervene? Describe at least one good example of directional selection.

7. Consider the first copy of an allele for insecticide resistance that arises by mutation in a population of insects exposed to an insecticide. Is this mutation an adaptation? If, after some generations, we find that most of the population is resistant, is the resistance an adaptation? If we discover genetic variation for insecticide resistance in a population that has had no experience of insecticides, is that variation an adaptation? If an insect population is polymorphic for two alleles, each of which confers resistance against one of two pesticides that are alternately applied, is that variation an adaptation? Or is each of the two resistance traits an adaptation?Explain your reasoning thoroughly.

8. Suppose that a mutation in a species of annual plant increases allocation to chemical defenses against herbivores, but decreases production of flowers and seeds (i.e., there is an allocation trade-off). What would you have to measure in a field study in order to predict whether or not the frequency of the mutation will increase?

9. In many socially monogamous species of parrots and other birds, both sexes are brilliantly colored or highly ornamented. Is sexual selection likely to be responsible for the coloration and ornaments of both sexes? How can there be sexual selection in pair-bonding species with a 1:1 sex ratio, since every individual presumably obtains a mate? Which of the models of sexual selection described in the book might account for these species characteristics?

10. Kin selection explains why organisms may provide benefits to relatives. Is there a conflict between the principle of kin selection and the evolution of siblicide and abortion?

11.Many species of albatrosses and other seabirds nest in colonies on islands. The adult search for food at sea,sometimes over great distances. Some ecologists who study seabirds turn to their favorite topic of discussion in a bar one evening, and one says, âI can imagine an albatross genotype that destroys the eggs of nestlings of its colony mates when the parents are away foraging, and leaves them dead without eating them. Do you think such a behavior would evolve?â One of his companions says, âYes, because it would make more food available for the albatross and its offspring.â Another says, âNo, because it would threaten the survival of the population.â The fourth says, âYouâre both wrong. I have a different explanation for why albatrosses donât kill othersâ chicks.â What is the fourth ecologistâs explanation, and why does she think her companions are wrong?

12. The concept of a species is fundamental to understanding biology, yet there may not be one definition that fits all âtypesâ of organisms (e.g. animals, plants, fungi, bacteria, slime mold, lichens, etc.). Discuss several of the definitions of a species as presented in class and present your own definition for a species. Compare the strengths and weaknesses of each definition. Ernst Mayr is strong proponent of the biological species concept.How does he justify his position? Do you agree or disagree? If we employ the biological species concept, when did species first exist? What were organisms before then, if not species? What might the consequences of the emergence of species be for processes of adaptation and diversification? Be sure to explain your reasoning thoroughly.

13. The process of speciation ultimately involves the development of reproductive isolation between two related populations of organisms. Describe the various types of both prezygotic and postzygotic reproductive isolation and give an example of each.

14. Respond to the following quote from the character named Mr. Spock in âStar Trekâ:âA truly successful parasite is commensal, living in amity with its host, or even giving it positive advantages, as for instance, the protozoans who live in the digestive system of your termites and digest for them the wood they eat. A parasite that regularly and inevitably kills its host cannot survive long, in the evolutionary sense, unless it multiplies with tremendous rapidity ... it is not pro-survival.âFrom what you have learned in this course, do you agree or disagree with Spock? How can you apply your reasoning to the relative âfitnessâ of HIV which causes AIDS, the Ebola virus which causes hemorrhagic fever,fleas which suck blood from dogs, or the prokaryotic ancestors of mitochondria and chloroplasts?

15. In many species of birds and mammals, clutch size is larger in populations at high latitudes than in population sat low latitudes. Species of lizards and snakes at high latitudes often have smaller clutches, however, and are more frequently viviparous (bear live young rather than laying eggs), than low-latitude species. What selective factors might be responsible for these patterns? Explain your reasoning.

16. The popular media often presents evolution as being a predictable process with a definite goal. For instance, in one âStar Trek: Voyagerâ episode, the captain instructs the shipâs computer to extrapolate the âprobable courseâ of evolution of hadrosaurs (a bipedal dinosaur), if hadrosaurs had been removed from Earth before the Cretaceous-Tertiary (K-T) Extinction and allowed to evolve on another planet. What information about the hadrosaursâ new environment would have been useful in developing the best possible prediction? Given what you know on genetic drift and selective agents, is it possible to accurately predict the long-term course of evolution?

17. Young children often develop strong food preferences that sometimes seem bizarre to their parents --- such as wanting to eat only a certain food prepared in a familiar way, or being reluctant to each new foods or foods with strong or bitter tastes (like coffee and some vegetables). Develop an evolutionary explanation for such preferences. What evidence would you gather to investigate your hypothesis and rule out alternative explanations?

18. Many organisms, such as mammals, only reproduce by sexual means. Other organisms are exclusively asexual,such as many of the bacteria and fungi. And still others have ways of propagating by both sexual and asexualmeans. Discuss the relative advantages and disadvantages of each mode of reproduction. Why arenât all organisms sexual critters? Why are many asexual organisms still very successful as evidenced by the pure abundance and diversity? What is the adaptive significance of having different genders (e.g. male and female)?In other words, why sex?

19. How might differential expression and regulation by Hox genes contribute to mosaic evolution in which different segments of an animal body plan evolve different morphology?

20. Development of a morphological structure involves many different types of gene products, including transcription factors, signaling proteins, and âeffectorâ genes such as enzymes. When a morphological change occurs in a single mutational step, which of these types might be more or less likely to be involved? Within a gene, would such single-step events be more likely to involve coding or non-coding sequences, and what characteristics of the geneâs function might affect this likelihood?

21. Since 2001, the complete DNA sequences of the genomes of many people have been determined. If humans,along with other forms of life, have evolved from a common ancestor, what evidence of this would be expected in the human genome? In what ways might the history and processes of evolution help us interpret and make sense of the human genome sequence data?

22. Paleontologists and some biologists commonly infer function, and even behavior, from anatomical details.Skeletal features, for example, are often used to infer that an extinct mammal (such as an early hominid) was highly, somewhat, or not at all arboreal. This inference assumes a good fit of form to function (i.e., optimal form). Can this assumption be justified?

23. Stephen Jay Gould (1989) and others have argued that the evolution of self-conscious, intelligent species (i.e.humans) was historically contingent: it would not have occurred had any of a great many historical events been different. The philosopher Daniel Dennett (1995) and others have disagreed, arguing that convergent evolution is so common that if humans had not evolved, some other lineage would probably have given rise to a species with similar mental abilities. What do you think, and why? If Gouldâs position is right, what are its philosophical implications, if any?

24. Explain how Intelligent Design was determined as a religious view rather than a scientific view in the court casein Dover, PA. Should a scientific explanation of evolution be included in a science curriculum in K-12 schools?How is science and religion different in how they seek answers to questions? How is term "theory" used differently in science than in everyday English use? What is biological evolution? What evidence is used to support the scientific explanation of evolution? Is it possible to accept scientific explanations without rejecting religious faith?

25. Discuss how a creationist versus an evolutionary biologist might explain some human characteristics and the implications of their differences. Sample characteristics: eyes; wisdom teeth; individually unique friction ridges(fingerprints); five digits rather than some other number; susceptibility to infections; fever when infected;variation in sexual orientation; limited life span.

BIO 111 Chapter Notes - Chapter 16: Maximum Likelihood Estimation, Convergent Evolution, Notochord

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